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@incollection{citeulike:13626283,  abstract = {{Bacterial conjugation is a cell-cell communication by which neighbor cells transmit circular DNA strands called plasmids. The transmission of these plasmids has been traditionally modeled using differential equations. Recently agent-based systems with spatial resolution have emerged as a promising tool that we use in this work to assess three different schemes for modeling the bacterial conjugation. The three schemes differ basically in which point of cell cycle the conjugation is most prone to happen. One alternative is to allow a conjugative event occurs as soon a suitable recipient is found, the second alternative is to make conjugation equally like to happen throughout the cell cycle and finally, the third one technique to assume that conjugation is more likely to occur in a specific point late in the cell cycle.}},  author = {Prestes Garc\'{\i}a, Antonio and Rodr\'{\i}guez-Pat\'{o}n, Alfonso},  booktitle = {9th International Conference on Practical Applications of Computational Biology and Bioinformatics},  citeulike-article-id = {13626283},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-319-19776-0\_1},  citeulike-linkout-1 = {http://link.springer.com/chapter/10.1007/978-3-319-19776-0\_1},  doi = {10.1007/978-3-319-19776-0\_1},  editor = {Overbeek, Ross and Rocha, Miguel P. and Fdez-Riverola, Florentino and De Paz, Juan F.},  pages = {1--9},  posted-at = {2015-05-24 17:33:57},  priority = {2},  publisher = {Springer International Publishing},  series = {Advances in Intelligent Systems and Computing},  title = {{A Preliminary Assessment of Three Strategies for the Agent-Based Modeling of Bacterial Conjugation}},  url = {http://dx.doi.org/10.1007/978-3-319-19776-0\_1},  volume = {375},  year = {2015}  }  @article{doi:10.1080/00031305.1973.10479042,  author = {Good, I. J.},  citeulike-article-id = {13557773},  citeulike-linkout-0 = {http://dx.doi.org/10.1080/00031305.1973.10479042},  citeulike-linkout-1 = {http://amstat.tandfonline.com/doi/abs/10.1080/00031305.1973.10479042},  doi = {10.1080/00031305.1973.10479042},  eprint = {http://amstat.tandfonline.com/doi/pdf/10.1080/00031305.1973.10479042},  journal = {The American Statistician},  keywords = {degrees-of-freedom},  number = {5},  pages = {227--228},  posted-at = {2015-03-22 07:21:51},  priority = {2},  title = {{What are Degrees of Freedom?}},  url = {http://amstat.tandfonline.com/doi/abs/10.1080/00031305.1973.10479042},  volume = {27},  year = {1973}  }  @article{citeulike:901103,  abstract = {{The F sex factor of Escherichia coli is a paradigm for bacterial conjugation and its transfer (tra) region represents a subset of the type IV secretion system (T4SS) family. The F tra region encodes eight of the 10 highly conserved (core) gene products of T4SS including TraAF (pilin), the TraBF, -KF (secretin-like), -VF (lipoprotein) and TraCF (NTPase), -EF, -LF and TraGF (N-terminal region) which correspond to TrbCP, -IP, -GP, -HP, -EP, -JP, DP and TrbLP, respectively, of the P-type T4SS exemplified by the IncP plasmid RP4. F lacks homologs of TrbBP (NTPase) and TrbFP but contains a cluster of genes encoding proteins essential for F conjugation (TraFF, -HF, -UF, -WF, the C-terminal region of TraGF, and TrbCF) that are hallmarks of F-like T4SS. These extra genes have been implicated in phenotypes that are characteristic of F-like systems including pilus retraction and mating pair stabilization. F-like T4SS systems have been found on many conjugative plasmids and in genetic islands on bacterial chromosomes. Although few systems have been studied in detail, F-like T4SS appear to be involved in the transfer of DNA only whereas P- and I-type systems appear to transport protein or nucleoprotein complexes. This review examines the similarities and differences among the T4SS, especially F- and P-like systems, and summarizes the properties of the F transfer region gene products.}},  address = {Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9.},  author = {Lawley, T. D. and Klimke, W. A. and Gubbins, M. J. and Frost, L. S.},  citeulike-article-id = {901103},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/12855161},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=12855161},  day = {15},  issn = {0378-1097},  journal = {FEMS microbiology letters},  keywords = {bacterial-biology},  month = jul,  number = {1},  pages = {1--15},  pmid = {12855161},  posted-at = {2015-02-17 10:31:05},  priority = {2},  title = {{F factor conjugation is a true type IV secretion system.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/12855161},  volume = {224},  year = {2003}  }  @article{citeulike:13515388,  abstract = {{Success in synthetic biology depends on the efficient construction of robust genetic circuitry. However, even the direct engineering of the simplest genetic elements (switches, logic gates) is a challenge and involves intense lab work. As the complexity of biological circuits grows, it becomes more complicated and less fruitful to rely on the rational design paradigm, because it demands many time-consuming trial-and-error cycles. One of the reasons is the context-dependent behavior of small assembly parts (like BioBricks), which in a complex environment often interact in an unpredictable way. Therefore, the idea of evolutionary engineering (artificial directed in vivo evolution) based on screening and selection of randomized combinatorial genetic circuit libraries became popular. In this article we build on the so-called dual selection technique. We propose a plasmid-based framework using toxin-antitoxin pairs together with the relaxase conjugative protein, enabling an efficient autonomous in vivo evolutionary selection of simple Boolean circuits in bacteria (E. coli was chosen for demonstration). Unlike previously reported protocols, both on and off selection steps can run simultaneously in various cells in the same environment without human intervention; and good circuits not only survive the selection process but are also horizontally transferred by conjugation to the neighbor cells to accelerate the convergence rate of the selection process. Our directed evolution strategy combines a new dual selection method with fluorescence-based screening to increase the robustness of the technique against mutations. As there are more orthogonal toxin-antitoxin pairs in E. coli, the approach is likely to be scalable to more complex functions. In silico experiments based on empirical data confirm the high search and selection capability of the protocol.}},  author = {Bene\v{s}, David and Sos\'{\i}k, Petr and Rodr\'{\i}guez-Pat\'{o}n, Alfonso},  citeulike-article-id = {13515388},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/25622012},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=25622012},  day = {26},  issn = {1064-5462},  journal = {Artificial life},  month = jan,  pages = {1--14},  pmid = {25622012},  posted-at = {2015-02-12 19:12:41},  priority = {2},  title = {{An Autonomous In Vivo Dual Selection Protocol for Boolean Genetic Circuits.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/25622012},  year = {2015}  }  @article{citeulike:13500899,  author = {Arutyunov, Denis and Frost, Laura S.},  citeulike-article-id = {13500899},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2013.03.010},  doi = {10.1016/j.plasmid.2013.03.010},  issn = {0147619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = jul,  number = {1},  pages = {18--32},  posted-at = {2015-01-25 19:13:04},  priority = {0},  title = {{F conjugation: Back to the beginning}},  url = {http://dx.doi.org/10.1016/j.plasmid.2013.03.010},  volume = {70},  year = {2013}  }  @article{citeulike:13398149,  author = {Millan, A. San and Pe\~{n}a-Miller, R. and Toll-Riera, M. and Halbert, Z. V. and McLean, A. R. and Cooper, B. S. and MacLean, R. C.},  citeulike-article-id = {13398149},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/ncomms6208},  day = {10},  doi = {10.1038/ncomms6208},  issn = {2041-1723},  journal = {Nature Communications},  keywords = {plasmid},  month = oct,  pages = {5208+},  posted-at = {2014-11-27 08:56:33},  priority = {2},  title = {{Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids}},  url = {http://dx.doi.org/10.1038/ncomms6208},  volume = {5},  year = {2014}  }  @article{citeulike:13095534,  abstract = {{Purpose This paper is to describe development of the features and functions of Repast Simphony, the widely used, free, and open source agent-based modeling environment that builds on the Repast 3 library. Repast Simphony was designed from the ground up with a focus on well-factored abstractions. The resulting code has a modular architecture that allows individual components such as networks, logging, and time scheduling to be replaced as needed. The Repast family of agent-based modeling software has collectively been under continuous development for more than 10 years. Method Includes reviewing other free and open-source modeling libraries and environments as well as describing the architecture of Repast Simphony. The architectural description includes a discussion of the Simphony application framework, the core module, ReLogo, data collection, the geographical information system, visualization, freeze drying, and third party application integration. Results Include a review of several Repast Simphony applications and brief tutorial on how to use Repast Simphony to model a simple complex adaptive system. Conclusions We discuss opportunities for future work, including plans to provide support for increasingly large-scale modeling efforts.}},  author = {North, MichaelJ and Collier, NicholsonT and Ozik, Jonathan and Tatara, EricR and Macal, CharlesM and Bragen, Mark and Sydelko, Pam},  booktitle = {Complex Adaptive Systems Modeling},  citeulike-article-id = {13095534},  citeulike-linkout-0 = {http://dx.doi.org/10.1186/2194-3206-1-3},  citeulike-linkout-1 = {http://link.springer.com/article/10.1186/2194-3206-1-3},  doi = {10.1186/2194-3206-1-3},  issn = {2194-3206},  journal = {Complex Adaptive Systems Modeling},  keywords = {simulation-and-modeling},  number = {1},  pages = {1--26},  posted-at = {2014-11-23 19:10:02},  priority = {2},  publisher = {Springer-Verlag},  title = {{Complex adaptive systems modeling with Repast Simphony}},  url = {http://dx.doi.org/10.1186/2194-3206-1-3},  volume = {1},  year = {2013}  }  @article{citeulike:13422987,  abstract = {{Macromolecular transport by bacterial type IV secretion systems involves regulated uptake of (nucleo)protein complexes by the cell envelope-spanning transport channel. A coupling protein receptor is believed to recognize the specific proteins destined for transfer, but the steps initiating their translocation remain unknown. Here, we investigate the contribution of a complex of transfer initiation proteins, the relaxosome, of plasmid R1 to translocation of competing transferable substrates from mobilizable plasmids ColE1 and CloDF13 or the bacteriophage R17. We found that not only does the R1 translocation machinery engage the R1 relaxosome during conjugative self-transfer and during infection by R17 phage but it is also activated by its cognate relaxosome to mediate the export of an alternative plasmid. Transporter activity was optimized by the R1 relaxosome even when this complex itself could not be transferred, i.e., when the N-terminal activation domain (amino acids 1 to 992 [N1-992]) of TraI was present without the C-terminal conjugative helicase domain. We propose that the functional dependence of the transfer machinery on the R1 relaxosome for initiating translocation ensures that dissemination of heterologous plasmids does not occur at the expense of self-transfer.}},  author = {Lang, Silvia and Gruber, Christian J. and Raffl, Sandra and Reisner, Andreas and Zechner, Ellen L.},  citeulike-article-id = {13422987},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/24682328},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=24682328},  issn = {1098-5530},  journal = {Journal of bacteriology},  month = jun,  number = {11},  pages = {2108--2121},  pmid = {24682328},  posted-at = {2014-11-08 17:07:38},  priority = {2},  title = {{Common requirement for the relaxosome of plasmid R1 in multiple activities of the conjugative type IV secretion system.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/24682328},  volume = {196},  year = {2014}  }  @article{citeulike:13059905,  abstract = {{  We investigate host-pathogen dynamics and conditions for coexistence in two models incorporating frequency-dependent horizontal transmission in conjunction with vertical transmission. The first model combines frequency-dependent and uniparental vertical transmission, while the second addresses parasites transmitted vertically via both parents. For the first model, we ask how the addition of vertical transmission changes the coexistence criteria for parasites transmitted by a frequency-dependent horizontal route, and show that vertical transmission significantly broadens the conditions for parasite invasion. Host-parasite coexistence is further affected by the form of density-dependent host regulation. Numerical analyses demonstrate that within a host population, a parasite strain with horizontal frequency-dependent transmission can be driven to extinction by a parasite strain that is additionally transmitted vertically for a wide range of parameters. Although models of asexual host populations predict that vertical transmission alone cannot maintain a parasite over time, analysis of our second model shows that vertical transmission via both male and female parents can maintain a parasite at a stable equilibrium. These results correspond with the frequent co-occurrence of vertical with sexual transmission in nature and suggest that these transmission modes can lead to host-pathogen coexistence for a wide range of systems involving hosts with high reproductive rates.  }},  author = {Altizer, S. M. and Augustine, D. J.},  citeulike-article-id = {13059905},  citeulike-linkout-0 = {http://dx.doi.org/10.1098/rspb.1997.0113},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1688434/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/9265188},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=9265188},  day = {22},  doi = {10.1098/rspb.1997.0113},  issn = {0962-8452},  journal = {Proceedings. Biological sciences / The Royal Society},  keywords = {epidemiology},  month = jun,  number = {1383},  pages = {807--814},  pmcid = {PMC1688434},  pmid = {9265188},  posted-at = {2014-02-25 04:24:07},  priority = {2},  title = {{Interactions between frequency-dependent and vertical transmission in host-parasite systems.}},  url = {http://dx.doi.org/10.1098/rspb.1997.0113},  volume = {264},  year = {1997}  }  @article{citeulike:13059904,  abstract = {{  A number of pathogens may be transmitted from parent to child at or before birth (vertically) or from one individual to another by contact (horizontally). A natural deterministic and non-spatial model, introduced by Lipsitch et al. [Proc. Roy. Soc. London Ser. B 260 (1995) 3211 shows that an epidemic is possible if the vertical transmission or the horizontal transmission is high enough. In contrast, we introduce a stochastic spatial model that shows that, on a particular graph, if the vertical transmission is not high enough, then the infected individuals disappear even for very high horizontal transmission. This illustrates the fact that introducing space may greatly change the qualitative behavior of a model.  }},  author = {Schinazi, R. B.},  citeulike-article-id = {13059904},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/11121817},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=11121817},  issn = {0025-5564},  journal = {Mathematical biosciences},  keywords = {epidemiology},  month = nov,  number = {1},  pages = {1--8},  pmid = {11121817},  posted-at = {2014-02-25 04:23:18},  priority = {2},  title = {{Horizontal versus vertical transmission of parasites in a stochastic spatial model.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/11121817},  volume = {168},  year = {2000}  }  @article{citeulike:10157337,  abstract = {{  Sex-ratio distorting parasites are of interest due to their effects upon host population dynamics and their potential to influence the evolution of host sex determination systems. In theory, the ability to distort host sex-ratios allows a parasite with efficient vertical (hereditary) transmission to dispense completely with horizontal (infectious) transmission. However, recent empirical studies indicate that some sex-ratio distorting parasites have retained the capability for horizontal transmission.  Numerical simulations using biologically realistic parameters suggest that a feminising parasite is only likely to lose the capability for horizontal transmission if its host occurs at low density and/or has a male-biased primary sex ratio. It is also demonstrated that even a small amount of horizontal transmission can allow multiple feminising parasites to coexist within a single host population. Finally it is shown that, by boosting its host's rate of population growth, a feminising parasite can increase its own horizontal transmission and allow the invasion of other, more virulent parasites.  The prediction that sex-ratio distorting parasites are likely to retain a degree of horizontal transmission has important implications for the epidemiology and host-parasite interactions of these organisms. It may also explain the frequent co-occurrence of several sex-ratio distorting parasite species in nature.  }},  author = {Ironside, Joseph E. and Smith, Judith E. and Hatcher, Melanie J. and Dunn, Alison M.},  citeulike-article-id = {10157337},  citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2148-11-370},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268771/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/22188680},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=22188680},  day = {21},  doi = {10.1186/1471-2148-11-370},  issn = {1471-2148},  journal = {BMC evolutionary biology},  keywords = {epidemiology},  month = dec,  pages = {370+},  pmcid = {PMC3268771},  pmid = {22188680},  posted-at = {2014-02-25 04:01:53},  priority = {2},  title = {{Should sex-ratio distorting parasites abandon horizontal transmission?}},  url = {http://dx.doi.org/10.1186/1471-2148-11-370},  volume = {11},  year = {2011}  }  @article{citeulike:13059895,  abstract = {{  We analyse a model of the transmission dynamics of a parasite transmitted both vertically and horizontally. The basic reproductive ratio (R0) of the parasite is shown to be a sum of horizontal and vertical components. We derive expressions for the equilibrium prevalence of infection for a mixture of horizontal and vertical transmission; prevalence can reach 100\% if transmission is sufficiently high. At the endemic equilibrium, if prevalence is high, most transmission will in general be vertical, but horizontal transmission rates must be high to reach and stably maintain such an equilibrium. Surprisingly, for such parasites the highest equilibrium rates of vertical transmission are observed when horizontal transmission is very effective. We discuss the implications for assessing the importance of horizontal v. vertical transmission from field data, and we suggest some implications for the evolution of virulence.  }},  author = {Lipsitch, M. and Nowak, M. A. and Ebert, D. and May, R. M.},  citeulike-article-id = {13059895},  citeulike-linkout-0 = {http://dx.doi.org/10.1098/rspb.1995.0099},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/7630898},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=7630898},  day = {22},  doi = {10.1098/rspb.1995.0099},  issn = {0962-8452},  journal = {Proceedings. Biological sciences / The Royal Society},  keywords = {epidemiology},  month = jun,  number = {1359},  pages = {321--327},  pmid = {7630898},  posted-at = {2014-02-25 03:58:48},  priority = {2},  title = {{The population dynamics of vertically and horizontally transmitted parasites.}},  url = {http://dx.doi.org/10.1098/rspb.1995.0099},  volume = {260},  year = {1995}  }  @article{citeulike:13059893,  abstract = {{  The question as to how the ratio of horizontal to vertical transmission depends on the coefficient of horizontal transmission is investigated in host-parasite models with one or two parasite strains. In an apparent paradox, this ratio decreases as the coefficient is increased provided that the ratio is taken at the equilibrium at which both host and parasite persist. Moreover, a completely vertically transmitted parasite strain that would go extinct on its own can coexist with a more harmful horizontally transmitted strain by protecting the host against it.  }},  author = {Faeth, Stanley H. and Hadeler, Karl P. and Thieme, Horst R.},  citeulike-article-id = {13059893},  citeulike-linkout-0 = {http://dx.doi.org/10.1080/17513750601040367},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/22880612},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=22880612},  doi = {10.1080/17513750601040367},  issn = {1751-3766},  journal = {Journal of biological dynamics},  keywords = {epidemiology},  month = jan,  number = {1},  pages = {45--62},  pmid = {22880612},  posted-at = {2014-02-25 03:51:26},  priority = {0},  title = {{An apparent paradox of horizontal and vertical disease transmission.}},  url = {http://dx.doi.org/10.1080/17513750601040367},  volume = {1},  year = {2007}  }  @article{citeulike:12080754,  abstract = {{Synthetic biology employs traditional engineering concepts in the construction of cells and organisms. One of the most fundamental concepts is feedback, where the activity of a system is influenced by its output. Feedback can imbue the system with a range of desirable properties such as reducing the rise time or exhibiting an ultrasensitive response. Feedback is also commonly found in nature, further supporting the incorporation of feedback into synthetic biological systems. In this review, we discuss the common attributes of negative and positive feedback loops in gene regulatory networks, whether alone or in combination, and describe recent applications of feedback in metabolic engineering, population control, and the development of advanced biosensors. The examples principally come from synthetic systems in the bacterium Escherichia coli and in the budding yeast Saccharomyces cerevisiae, the two major workhorses of synthetic biology. Through this review, we argue that biological feedback represents a powerful yet underutilized tool that can advance the construction of biological systems. \^{a}–º There are important distinctions between feedback in process control and in biology. \^{a}–º Negative, positive, and combined feedback exhibit unique properties. \^{a}–º Feedback can be readily applied to advance the construction of biological systems.}},  author = {Afroz, Taliman and Beisel, Chase L.},  citeulike-article-id = {12080754},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ces.2013.02.017},  doi = {10.1016/j.ces.2013.02.017},  issn = {00092509},  journal = {Chemical Engineering Science},  keywords = {synbio-dna},  month = nov,  pages = {79--90},  posted-at = {2014-01-12 11:44:12},  priority = {2},  title = {{Understanding and exploiting feedback in synthetic biology}},  url = {http://dx.doi.org/10.1016/j.ces.2013.02.017},  volume = {103},  year = {2013}  }  @article{citeulike:12729383,  abstract = {{BACKGROUND:It is not yet known whether DNA methylation levels can be used to accurately predict age across a broad spectrum of human tissues and cell types, nor whether the resulting age prediction is a biologically meaningful measure.RESULTS:I developed a multi-tissue predictor of age that allows one to estimate the DNA methylation age of most tissues and cell types. The predictor, which is freely available, was developed using 8,000 samples from 82 Illumina DNA methylation array datasets, encompassing 51 healthy tissues and cell types. I found that DNA methylation age has the following properties: first, it is close to zero for embryonic and induced pluripotent stem cells; second, it correlates with cell passage number; third, it gives rise to a highly heritable measure of age acceleration; and, fourth, it is applicable to chimpanzee tissues. Analysis of 6,000 cancer samples from 32 datasets showed that all of the considered 20 cancer types exhibit significant age acceleration, with an average of 36 years. Low age-acceleration of cancer tissue is associated with a high number of somatic mutations and TP53 mutations, while mutations in steroid receptors greatly accelerate DNA methylation age in breast cancer. Finally, I characterize the 353 CpG sites that together form an aging clock in terms of chromatin states and tissue variance.CONCLUSIONS:I propose that DNA methylation age measures the cumulative effect of an epigenetic maintenance system. This novel epigenetic clock can be used to address a host of questions in developmental biology, cancer and aging research.}},  author = {Horvath, Steve},  citeulike-article-id = {12729383},  citeulike-linkout-0 = {http://dx.doi.org/10.1186/gb-2013-14-10-r115},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/24138928},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=24138928},  day = {21},  doi = {10.1186/gb-2013-14-10-r115},  issn = {1465-6906},  journal = {Genome Biology},  keywords = {bioinformatic},  month = oct,  number = {10},  pages = {R115+},  pmid = {24138928},  posted-at = {2013-10-22 18:01:52},  priority = {2},  title = {{DNA methylation age of human tissues and cell types}},  url = {http://dx.doi.org/10.1186/gb-2013-14-10-r115},  volume = {14},  year = {2013}  }  @book{citeulike:12060394,  author = {Cormen, Thomas H. and Leiserson, Charles E. and Rivest, Ronald L.},  citeulike-article-id = {12060394},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0262530910},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0262530910},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0262530910},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0262530910},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0262530910/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0262530910},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0262530910},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0262530910},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0262530910\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0262530910},  day = {25},  howpublished = {Paperback},  isbn = {0262530910},  keywords = {books},  month = jun,  posted-at = {2013-02-23 11:00:36},  priority = {2},  publisher = {The MIT Press},  title = {{Introduction to Algorithms (MIT Electrical Engineering and Computer Science)}},  url = {http://www.worldcat.org/isbn/0262530910},  year = {1990}  }  @article{citeulike:9348039,  abstract = {{The conjugative plasmid R388 and a number of other plasmids carry an operon, stbABC, adjacent to the origin of conjugative transfer. We investigated the role of the stbA, stbB, and stbC genes. Deletion of stbA affected both conjugation and stability. It led to a 50-fold increase in R388 transfer frequency, as well as to high plasmid loss. In contrast, deletion of stbB abolished conjugation but provoked no change in plasmid stability. Deletion of stbC showed no effect, neither in conjugation nor in stability. Deletion of the entire stb operon had no effect on conjugation, which remained as in the wild-type plasmid, but led to a plasmid loss phenotype similar to that of the R388ΔstbA mutant. We concluded that StbA is required for plasmid stability and that StbA and StbB control conjugation. We next observed the intracellular positioning of R388 DNA molecules and showed that they localize as discrete foci evenly distributed in live Escherichia coli cells. Plasmid instability of the R388ΔΔstbA mutant correlated with aberrant localization of the plasmid DNA molecules as clusters, either at one cell pole, at both poles, or at the cell center. In contrast, plasmid molecules in the R388ΔΔstbB mutant were mostly excluded from the cell poles. Thus, results indicate that defects in both plasmid maintenance and transfer are a consequence of variations in the intracellular positioning of plasmid DNA. We propose that StbA and StbB constitute an atypical plasmid stabilization system that reconciles two modes of plasmid R388 physiology: a maintenance mode (replication and segregation) and a propagation mode (conjugation). The consequences of this novel concept in plasmid physiology will be discussed. The ability of bacteria to evolve and adapt to new environments most often results from the acquisition of new genes by horizontal transfer. Plasmids have a preponderant role in gene exchanges through their ability to transfer DNA by conjugation, a process that transports DNA between bacteria. Besides, plasmids are autonomous DNA molecules that are faithfully transmitted to cell progeny during vegetative cell multiplication. In this study, we report a system composed of two proteins, StbA and StbB, which act to balance plasmid R388 physiology between two modes: a maintenance mode (vertical transmission) and a propagation mode (horizontal transmission). We demonstrate that StbA is essential to ensure faithful assortment of plasmid copies to daughter cells. In turn, StbB is required for plasmid R388 adequate localization for conjugation. This is the first report of a system which reconciles plasmid segregation and conjugation. Furthermore, R388 belongs to the IncW family of conjugative plasmids, which are of particular interest due to their exceptionally broad host range. We show that the StbAB system is conserved among a wide variety of conjugative plasmids, mainly broad host range plasmids. Thus, the Stb system could constitute an interesting therapeutic target to prevent the spread of adaptive genes.}},  author = {Guynet, Catherine and Cuevas, Ana and Moncali\'{a}n, Gabriel and de la Cruz, Fernando},  citeulike-article-id = {9348039},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pgen.1002073},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098194/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21625564},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21625564},  day = {19},  doi = {10.1371/journal.pgen.1002073},  issn = {1553-7404},  journal = {PLoS Genet},  keywords = {plasmid},  month = may,  number = {5},  pages = {e1002073+},  pmcid = {PMC3098194},  pmid = {21625564},  posted-at = {2013-02-08 07:50:47},  priority = {2},  publisher = {Public Library of Science},  title = {{The stb Operon Balances the Requirements for Vegetative Stability and Conjugative Transfer of Plasmid R388}},  url = {http://dx.doi.org/10.1371/journal.pgen.1002073},  volume = {7},  year = {2011}  }  @book{citeulike:8426210,  author = {Banks, Jerry and Carson, John S. and Nelson, Barry L. and Nicol, David M.},  citeulike-article-id = {8426210},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0136062121},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0136062121},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0136062121},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0136062121},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0136062121/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0136062121},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0136062121},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0136062121},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0136062121\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0136062121},  day = {06},  edition = {5},  howpublished = {Paperback},  isbn = {0136062121},  keywords = {books},  month = jul,  posted-at = {2013-01-23 17:57:53},  priority = {0},  publisher = {Prentice Hall},  title = {{Discrete-Event System Simulation (5th Edition)}},  url = {http://www.worldcat.org/isbn/0136062121},  year = {2009}  }  @book{citeulike:201641,  abstract = {{There's a "Frank \& Ernest" comic strip showing a chick breaking out of its shell, looking around, and saying, "Oh, wow! Paradigm shift!" Blame the late Thomas Kuhn. Few indeed are the philosophers or historians influential enough to make it into the funny papers, but Kuhn is one.

The Structure of Scientific Revolutions is indeed a paradigmatic work in the history of science. Kuhn's use of terms such as "paradigm shift" and "normal science," his ideas of how scientists move from disdain through doubt to acceptance of a new theory, his stress on social and psychological factors in science--all have had profound effects on historians, scientists, philosophers, critics, writers, business gurus, and even the cartoonist in the street.

Some scientists (such as Steven Weinberg and Ernst Mayr) are profoundly irritated by Kuhn, especially by the doubts he casts--or the way his work has been used to cast doubt--on the idea of scientific progress. Yet it has been said that the acceptance of plate tectonics in the 1960s, for instance, was sped by geologists' reluctance to be on the downside of a paradigm shift. Even Weinberg has said that "Structure has had a wider influence than any other book on the history of science." As one of Kuhn's obituaries noted, "We all live in a post-Kuhnian age." --Mary Ellen Curtin }},  author = {Kuhn, Thomas S.},  citeulike-article-id = {201641},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0226458083},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0226458083},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0226458083},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0226458083},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0226458083/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0226458083},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0226458083},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0226458083},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0226458083\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0226458083},  day = {15},  edition = {3rd},  howpublished = {Paperback},  isbn = {0226458083},  keywords = {books},  month = dec,  posted-at = {2012-12-01 12:29:56},  priority = {2},  publisher = {The University of Chicago Press},  title = {{The Structure of Scientific Revolutions, 3rd Edition}},  url = {http://www.worldcat.org/isbn/0226458083},  year = {1996}  }  @book{citeulike:2574898,  abstract = {{The high-level language of R is recognized as one of the most powerful and flexible statistical software environments, and is rapidly becoming the standard setting for quantitative analysis, statistics and graphics. R provides free access to unrivalled coverage and cutting-edge applications, enabling the user to apply numerous statistical methods ranging from simple regression to time series or multivariate analysis.

Building on the success of the author's bestselling Statistics: An Introduction using R, The R Book is packed with worked examples, providing an all inclusive guide to R, ideal for novice and more accomplished users alike. The book assumes no background in statistics or computing and introduces the advantages of the R environment, detailing its applications in a wide range of disciplines.

  • Provides the first comprehensive reference manual for the R language, including practical guidance and full coverage of the graphics facilities.
  • Introduces all the statistical models covered by R, beginning with simple classical tests such as chi-square and t-test.
  • Proceeds to examine more advance methods, from regression and analysis of variance, through to generalized linear models, generalized mixed models, time series, spatial statistics, multivariate statistics and much more.

The R Book is aimed at undergraduates, postgraduates and professionals in science, engineering and medicine. It is also ideal for students and professionals in statistics, economics, geography and the social sciences.}},  author = {Crawley, Michael J.},  citeulike-article-id = {2574898},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0470510242},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0470510242},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0470510242},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0470510242},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0470510242/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0470510242},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0470510242},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0470510242},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0470510242\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0470510242},  day = {19},  edition = {1},  howpublished = {Hardcover},  isbn = {0470510242},  keywords = {books},  month = jun,  posted-at = {2012-11-25 11:12:50},  priority = {2},  publisher = {Wiley},  title = {{The R Book}},  url = {http://www.worldcat.org/isbn/0470510242},  year = {2007}  }  @article{citeulike:11671699,  abstract = {{  The finP gene of plasmid R1 is located between the genes traM and traJ, partially overlapping the first few nucleotides of the latter. It codes for a repressor of the conjugation system. The product of this gene is a small RNA of 72 nucleotides and, because it is transcribed from the opposite DNA strand, it is complementary to the 5' non-translated sequences, the ribosome-binding site, and the first two codons of traJ mRNA. The finP transcript is present in much higher concentrations in R1 than in R1-19 containing cells, the latter being a derepressed mutant of the former. A synthetic finP gene expressed from a synthetic lambda PL promoter markedly reduced the conjugation frequency of pDB12, a multicopy derivative of R1-19. Mutagenesis of finP showed that only finP loop II mutants have lost the ability to repress conjugation of R1-19 in trans. They are also the only ones which derepress conjugal DNA transfer of R1, probably by competing for the finO product, a molecule needed as corepressor for maximal activity. Mutations interrupting potential open reading frames of finP do not abolish finP repressor activity. Hence finP acts as an antisense RNA blocking the expression of the traJ gene by interacting with traJ mRNA through loop II.  }},  author = {Koraimann, G. and Koraimann, C. and Koronakis, V. and Schlager, S. and H\"{o}genauer, G.},  citeulike-article-id = {11671699},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/1707476},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=1707476},  issn = {0950-382X},  journal = {Molecular microbiology},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {77--87},  pmid = {1707476},  posted-at = {2012-11-12 08:29:16},  priority = {2},  title = {{Repression and derepression of conjugation of plasmid R1 by wild-type and mutated finP antisense RNA.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/1707476},  volume = {5},  year = {1991}  }  @article{citeulike:11152159,  abstract = {{  Conjugative plasmids are involved in the dissemination of important traits such as antibiotic resistance, virulence determinants and metabolic pathways involved in adapting to environmental niches, a process termed horizontal or lateral gene transfer. Conjugation is the process of transferring DNA from a donor to a recipient cell with the establishment of the incoming DNA and its cargo of genetic traits within the transconjugant. Conjugation is mediated by self-transmissible plasmids as well as phage-like sequences that have been integrated into the bacterial chromosome, such as integrative and conjugative elements (ICEs) that now include conjugative transposons. Both conjugative plasmids and ICEs can mediate the transfer of mobilizable elements by sharing their conjugative machinery. Conjugation can either be induced, usually by small molecules or peptides or by excision of the ICE from the host chromosome, or it can be tightly regulated by plasmid- and host-encoded factors. The transfer potential of these transfer regions depends on the integration of many signals in response to environmental and physiological cues. This review will focus on the mechanisms that influence transfer potential in these systems, particularly those of the IncF incompatibility group.  }},  author = {Frost, Laura S. and Koraimann, G\"{u}nther},  citeulike-article-id = {11152159},  citeulike-linkout-0 = {http://dx.doi.org/10.2217/fmb.10.70},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20632805},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20632805},  doi = {10.2217/fmb.10.70},  issn = {1746-0921},  journal = {Future microbiology},  keywords = {bacterial-biology},  month = jul,  number = {7},  pages = {1057--1071},  pmid = {20632805},  posted-at = {2012-11-12 08:28:27},  priority = {2},  title = {{Regulation of bacterial conjugation: balancing opportunity with adversity.}},  url = {http://dx.doi.org/10.2217/fmb.10.70},  volume = {5},  year = {2010}  }  @article{citeulike:10239892,  abstract = {{  Most natural conjugative IncF plasmids encode a fertility inhibition system that represses transfer gene expression in the majority of plasmid-carrying cells. The successful spread of these plasmids in clinically relevant bacteria has been suggested to be supported by a transitory derepression of transfer gene expression in newly formed transconjugants. In this study, we aimed to monitor the extent of transitory derepression during agar surface matings in situ by comparing plasmid spread of the IncF plasmid R1 and its derepressed mutant R1drd19 at low initial cell densities. A zygotic induction strategy was used to visualize the spatial distribution of fluorescent transconjugants within the heterogeneous environment. Epifluorescence and confocal microscopy revealed different transfer patterns for both plasmids, however, spread beyond the first five recipient cell layers adjacent to the donor cells was not observed. Similar results were observed for other prototypical conjugative plasmids. These results cannot rule out that transitory derepression contributes to the limited R1 plasmid invasion, but other factors like nutrient availability or spatial structure seem to limit plasmid spread.  Copyright {\copyright} 2012 Elsevier Inc. All rights reserved.  }},  author = {Reisner, Andreas and Wolinski, Heimo and Zechner, Ellen L.},  citeulike-article-id = {10239892},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2012.01.001},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338210/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/22248925},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=22248925},  doi = {10.1016/j.plasmid.2012.01.001},  issn = {1095-9890},  journal = {Plasmid},  keywords = {bacterial-biology},  month = mar,  number = {2},  pages = {155--161},  pmcid = {PMC3338210},  pmid = {22248925},  posted-at = {2012-11-11 21:30:47},  priority = {2},  title = {{In situ monitoring of IncF plasmid transfer on semi-solid agar surfaces reveals a limited invasion of plasmids in recipient colonies.}},  url = {http://dx.doi.org/10.1016/j.plasmid.2012.01.001},  volume = {67},  year = {2012}  }  @article{citeulike:11624837,  abstract = {{  Horizontal transfer of genes between species is an important mechanism for bacterial genome evolution. In Escherichia coli, conjugation is the transfer from a donor (F(+)) to a recipient (F(-)) cell through cell-to-cell contact. We demonstrate what we believe to be a novel qPCR method for quantifying the transfer kinetics of the F plasmid in a population by enumerating the relative abundance of genetic loci unique to the plasmid and the chromosome. This approach allows us to query the plasmid transfer rate without the need for selective culturing with unprecedented single locus resolution. We fit the results to a mass action model where the rate of plasmid growth includes the lag time of newly formed F(+) transconjugants and the recovery time between successive conjugation events of the F(+) donors. By assaying defined mixtures of genotypically identical donor and recipient cells at constant inoculation densities, we extract an F plasmid transfer rate of 5 × 10(-10) (cells/mL · min)(-1). We confirm a plasmid/chromosome ratio of 1:1 in homogenous F(+) populations throughout batch growth. Surprisingly, in some mixture experiments we observe an excess of F plasmid in the early saturation phase that equilibrates to a final ratio of one plasmid per chromosome.  Copyright {\copyright} 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.  }},  author = {Wan, Zhenmao and Varshavsky, Joseph and Teegala, Sushma and McLawrence, Jamille and Goddard, Noel L.},  citeulike-article-id = {11624837},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.bpj.2011.04.054},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3127179/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21723834},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21723834},  day = {6},  doi = {10.1016/j.bpj.2011.04.054},  issn = {1542-0086},  journal = {Biophysical journal},  keywords = {bacterial-biology},  month = jul,  number = {1},  pages = {237--244},  pmcid = {PMC3127179},  pmid = {21723834},  posted-at = {2012-11-06 22:45:07},  priority = {2},  title = {{Measuring the rate of conjugal plasmid transfer in a bacterial population using quantitative PCR.}},  url = {http://dx.doi.org/10.1016/j.bpj.2011.04.054},  volume = {101},  year = {2011}  }  @article{citeulike:11560962,  abstract = {{  The aggregation-mediated conjugation system of Bacillus thuringiensis subsp. israelensis, encoded by the 200-kb plasmid pXO16, is highly potent in transferring itself and efficient in mobilizing other nonconjugative plasmids. The present study reveals some salient features of this conjugation system. Our observations can be summarized as follows: (i) The conjugative transfer takes about 3(1/2) to 4 min. For a 200-kb plasmid this corresponds to about 1 kb per second. (ii) The ability to transfer the plasmid seems to be evenly distributed among the donors. (iii) Functionally, the mating complex was found to consist of one donor and one recipient cell, even though aggregates comprising thousands of interconnected cells are formed. (iv) Having donated the plasmid, the donor needs a "period of recovery" of about 10 min before it can redonate the plasmid. (v) Secondary transfer, i.e., transfer from newly formed transconjugants, is delayed about 40 min. This maturation time exceeds the generation time, and it may indicate that to display donor activity, a surface protein (the aggregation substance) has to be uniformly incorporated into the cell wall. Lastly, we found that when the experiments were sufficiently short and when the recipient cells were in excess compared with the donors, the process of conjugation could be reasonably described by a kinetic model analogous to the Michaelis-Menten model for enzyme catalysis. This allowed us to estimate (vi) the maximal conjugation rate to be about 0.05 transconjugant per donor per minute, and (vii) the Km value, i.e., the concentration of recipient that results in half of the maximal conjugation rate, to be about 4 x 10(6) recipients/ml.  Copyright 1998 Academic Press.  }},  author = {Andrup, L. and Smidt, L. and Andersen, K. and Boe, L.},  citeulike-article-id = {11560962},  citeulike-linkout-0 = {http://dx.doi.org/10.1006/plas.1998.1346},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/9657931},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=9657931},  doi = {10.1006/plas.1998.1346},  issn = {0147-619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = jul,  number = {1},  pages = {30--43},  pmid = {9657931},  posted-at = {2012-10-27 10:30:00},  priority = {0},  title = {{Kinetics of conjugative transfer: a study of the plasmid pXO16 from Bacillus thuringiensis subsp. israelensis.}},  url = {http://dx.doi.org/10.1006/plas.1998.1346},  volume = {40},  year = {1998}  }  @article{moon12,  abstract = {{Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits, and they have been used in various cellular engineering applications, including the implementation of process control in metabolic networks and the coordination of spatial differentiation in artificial tissues. A key limitation is that the circuits are based on biochemical interactions occurring in the confined volume of the cell, so the size of programs has been limited to a few circuits. Here we apply part mining and directed evolution to build a set of transcriptional AND gates in Escherichia coli. Each AND gate integrates two promoter inputs and controls one promoter output. This allows the gates to be layered by having the output promoter of an upstream circuit serve as the input promoter for a downstream circuit. Each gate consists of a transcription factor that requires a second chaperone protein to activate the output promoter. Multiple activator-chaperone pairs are identified from type III secretion pathways in different strains of bacteria. Directed evolution is applied to increase the dynamic range and orthogonality of the circuits. These gates are connected in different permutations to form programs, the largest of which is a 4-input AND gate that consists of 3 circuits that integrate 4 inducible systems, thus requiring 11 regulatory proteins. Measuring the performance of individual gates is sufficient to capture the behaviour of the complete program. Errors in the output due to delays (faults), a common problem for layered circuits, are not observed. This work demonstrates the successful layering of orthogonal logic gates, a design strategy that could enable the construction of large, integrated circuits in single cells.}},  author = {Moon, Tae Seok S. and Lou, Chunbo and Tamsir, Alvin and Stanton, Brynne C. and Voigt, Christopher A.},  citeulike-article-id = {11418907},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature11516},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature11516},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/23041931},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=23041931},  day = {8},  doi = {10.1038/nature11516},  issn = {1476-4687},  journal = {Nature},  keywords = {synbio-dna},  month = nov,  number = {7423},  pages = {249--253},  pmid = {23041931},  posted-at = {2012-10-11 20:44:49},  priority = {2},  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},  title = {{Genetic programs constructed from layered logic gates in single cells.}},  url = {http://dx.doi.org/10.1038/nature11516},  volume = {491},  year = {2012}  }  @article{haurwitz12,  author = {Qi, Lei and Haurwitz, Rachel E. and Shao, Wenjun and Doudna, Jennifer A. and Arkin, Adam P.},  citeulike-article-id = {11266160},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt.2355},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt.2355},  day = {16},  doi = {10.1038/nbt.2355},  issn = {1087-0156},  journal = {Nat Biotech},  keywords = {synbio-dna},  month = oct,  number = {10},  pages = {1002--1006},  posted-at = {2012-10-11 20:43:43},  priority = {2},  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},  title = {{RNA processing enables predictable programming of gene expression}},  url = {http://dx.doi.org/10.1038/nbt.2355},  volume = {30},  year = {2012}  }  @article{citeulike:1760768,  abstract = {{We demonstrate the measurement of mass, density, and size of cells and nanoparticles using suspended microchannel resonators. The masses of individual particles are quantified as transient frequency shifts, while the particles transit a microfluidic channel embedded in the resonating cantilever. Mass histograms resulting from these data reveal the distribution of a population of heterogeneously sized particles. Particle density is inferred from measurements made in different carrier fluids since the frequency shift for a particle is proportional to the mass difference relative to the displaced solution. We have characterized the density of polystyrene particles, Escherichia coli, and human red blood cells with a resolution down to}},  author = {Godin, Michel and Bryan, Andrea K. and Burg, Thomas P. and Babcock, Ken and Manalis, Scott R.},  citeulike-article-id = {1760768},  citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=APPLAB000091000012123121000001\&idtype=cvips\&gifs=yes},  citeulike-linkout-1 = {http://link.aip.org/link/?APL/91/123121},  citeulike-linkout-2 = {http://dx.doi.org/10.1063/1.2789694},  citeulike-linkout-3 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=4828874},  doi = {10.1063/1.2789694},  institution = {Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA},  issn = {0003-6951},  journal = {Applied Physics Letters},  keywords = {system-biology},  month = sep,  number = {12},  pages = {123121--123121-3},  posted-at = {2012-10-06 20:15:06},  priority = {2},  publisher = {AIP},  title = {{Measuring the mass, density, and size of particles and cells using a suspended microchannel resonator}},  url = {http://dx.doi.org/10.1063/1.2789694},  volume = {91},  year = {2007}  }  @book{citeulike:11329941,  author = {Kim, Byung H. and Gadd, Geoffrey M.},  citeulike-article-id = {11329941},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0521712300},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0521712300},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0521712300},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0521712300},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0521712300/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0521712300},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0521712300},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0521712300},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0521712300\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0521712300},  day = {03},  edition = {1},  howpublished = {Paperback},  isbn = {0521712300},  keywords = {books},  month = mar,  posted-at = {2012-09-27 06:55:23},  priority = {2},  publisher = {Cambridge University Press},  title = {{Bacterial Physiology and Metabolism}},  url = {http://www.worldcat.org/isbn/0521712300},  year = {2008}  }  @article{citeulike:3484224,  abstract = {{A fundamental but unanswered biological question asks how much energy, on average, Earth's different life forms spend per unit mass per unit time to remain alive. Here, using the largest database to date, for 3,006 species that includes most of the range of biological diversity on the planet—from bacteria to elephants, and algae to sapling trees—we show that metabolism displays a striking degree of homeostasis across all of life. We demonstrate that, despite the enormous biochemical, physiological, and ecological differences between the surveyed species that vary over 1020-fold in body mass, mean metabolic rates of major taxonomic groups displayed at physiological rest converge on a narrow range from 0.3 to 9 W kg−1. This 30-fold variation among life's disparate forms represents a remarkably small range compared with the 4,000- to 65,000-fold difference between the mean metabolic rates of the smallest and largest organisms that would be observed if life as a whole conformed to universal quarter-power or third-power allometric scaling laws. The observed broad convergence on a narrow range of basal metabolic rates suggests that organismal designs that fit in this physiological window have been favored by natural selection across all of life's major kingdoms, and that this range might therefore be considered as optimal for living matter as a whole.}},  author = {Makarieva, Anastassia M. and Gorshkov, Victor G. and Li, Bai-Lian and Chown, Steven L. and Reich, Peter B. and Gavrilov, Valery M.},  citeulike-article-id = {3484224},  citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0802148105},  citeulike-linkout-1 = {http://www.pnas.org/content/105/44/16994.abstract},  citeulike-linkout-2 = {http://www.pnas.org/content/105/44/16994.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18952839},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18952839},  day = {04},  doi = {10.1073/pnas.0802148105},  issn = {1091-6490},  journal = {Proceedings of the National Academy of Sciences},  keywords = {bacterial-biology},  month = nov,  number = {44},  pages = {16994--16999},  pmid = {18952839},  posted-at = {2012-09-25 21:48:31},  priority = {2},  publisher = {National Academy of Sciences},  title = {{Mean mass-specific metabolic rates are strikingly similar across life's major domains: Evidence for life's metabolic optimum}},  url = {http://dx.doi.org/10.1073/pnas.0802148105},  volume = {105},  year = {2008}  }  @article{citeulike:11319330,  abstract = {{Power laws describing the dependence of metabolic rate on body mass have been established for many taxa, but not for prokaryotes, despite the ecological dominance of the smallest living beings. Our analysis of 80 prokaryote species with cell volumes ranging more than 1 000 000-fold revealed no significant relationship between mass-specific metabolic rate q and cell mass. By absolute values, mean endogenous mass-specific metabolic rates of non-growing bacteria are similar to basal rates of eukaryote unicells, terrestrial arthropods and mammals. Maximum mass-specific metabolic rates displayed by growing bacteria are close to the record tissue-specific metabolic rates of insects, amphibia, birds and mammals. Minimum mass-specific metabolic rates of prokaryotes coincide with those of larger organisms in various energy-saving regimes: sit-and-wait strategists in arthropods, poikilotherms surviving anoxia, hibernating mammals. These observations suggest a size-independent value around which the mass-specific metabolic rates vary bounded by universal upper and lower limits in all body size intervals.}},  author = {Makarieva, Anastassia M. and Gorshkov, Victor G. and Li, Bai-Lian},  citeulike-article-id = {11319330},  citeulike-linkout-0 = {http://dx.doi.org/10.1098/rspb.2005.3225},  citeulike-linkout-1 = {http://rspb.royalsocietypublishing.org/content/272/1577/2219.abstract},  citeulike-linkout-2 = {http://rspb.royalsocietypublishing.org/content/272/1577/2219.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/16191633},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=16191633},  day = {22},  doi = {10.1098/rspb.2005.3225},  issn = {1471-2954},  journal = {Proceedings of the Royal Society B: Biological Sciences},  keywords = {bacterial-biology},  month = oct,  number = {1577},  pages = {2219--2224},  pmid = {16191633},  posted-at = {2012-09-25 21:48:04},  priority = {2},  publisher = {The Royal Society},  title = {{Energetics of the smallest: do bacteria breathe at the same rate as whales?}},  url = {http://dx.doi.org/10.1098/rspb.2005.3225},  volume = {272},  year = {2005}  }  @book{citeulike:11288097,  author = {Snyder, Larry and Champness, Wendy},  citeulike-article-id = {11288097},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/1555813992},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/1555813992},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/1555813992},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/1555813992},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/1555813992/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/1555813992},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/1555813992},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN1555813992},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=1555813992\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/1555813992},  day = {31},  edition = {3},  howpublished = {Hardcover},  isbn = {1555813992},  keywords = {books},  month = may,  posted-at = {2012-09-21 17:27:00},  priority = {2},  publisher = {ASM Press},  title = {{Molecular Genetics of Bacteria, Third Edition (Snyder, Molecular Genetics of Bacteria)}},  url = {http://www.worldcat.org/isbn/1555813992},  year = {2007}  }  @article{citeulike:11283443,  author = {Mendelson, N. H.},  citeulike-article-id = {11283443},  citeulike-linkout-0 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC281548/},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/6182451},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=6182451},  issn = {0146-0749},  journal = {Microbiological reviews},  keywords = {bacterial-biology},  month = sep,  number = {3},  pages = {341--375},  pmcid = {PMC281548},  pmid = {6182451},  posted-at = {2012-09-20 17:16:34},  priority = {0},  title = {{Bacterial growth and division: genes, structures, forces, and clocks.}},  url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC281548/},  volume = {46},  year = {1982}  }  @book{citeulike:106700,  abstract = {{Santiago Ramon y Cajal was a mythic figure in science. Hailed as the father of modern anatomy and neurobiology, he was largely responsible for the modern conception of the brain. His groundbreaking works were New Ideas on the Structure of the Nervous System and Histology of the Nervous System in Man and Vertebrates. In addition to leaving a legacy of unparalleled scientific research, Cajal sought to educate the novice scientist about how science was done and how he thought it should be done. This recently rediscovered classic, first published in 1897, is an anecdotal guide for the perplexed new investigator as well as a refreshing resource for the old pro.

Cajal was a pragmatist, aware of the pitfalls of being too idealistic -- and he had a sense of humor, particularly evident in his diagnoses of various stereotypes of eccentric scientists. The book covers everything from valuable personality traits for an investigator to social factors conducive to scientific work.}},  author = {Santiago Ram\'{o}n},  citeulike-article-id = {106700},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0262681501},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0262681501},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0262681501},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0262681501},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0262681501/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0262681501},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0262681501},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0262681501},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0262681501\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0262681501},  day = {27},  edition = {1},  howpublished = {Paperback},  isbn = {0262681501},  keywords = {books},  month = feb,  posted-at = {2012-09-19 16:20:28},  priority = {0},  publisher = {A Bradford Book},  title = {{Advice for a Young Investigator (Bradford Books)}},  url = {http://www.worldcat.org/isbn/0262681501},  year = {2004}  }  @article{aksnes1991theoretical,  author = {Aksnes, D. L. and Egge, J. K.},  citeulike-article-id = {11227658},  journal = {Marine ecology progress series. Oldendorf},  keywords = {simulation-and-modeling},  number = {1},  posted-at = {2012-09-11 21:29:11},  priority = {0},  title = {{A theoretical model for nutrient uptake in phytoplankton.}},  volume = {70},  year = {1991}  }  @article{citeulike:2706275,  abstract = {{A fundamental characteristic of cells is the ability to divide. To date, most parameters of bacterial cultures, including cell division, have been measured as cell population averages, assuming that all bacteria divide at a uniform rate. We monitored the division of individual cells in Escherichia coli cultures during different growth phases. Our experiments are based on the dilution of green fluorescent protein (GFP) upon cell division, monitored by flow cytometry. The results show that the vast majority of E. coli cells in exponentially growing cultures divided uniformly. In cultures that had been in stationary phase up to four days, no cell division was observed. However, upon dilution of stationary phase culture into fresh medium, two subpopulations of cells emerged: one that started dividing and another that did not. These populations were detectable by GFP dilution and displayed different side scatter parameters in flow cytometry. Further analysis showed that bacteria in the non-growing subpopulation were not dead, neither was the difference in growth capacity reducible to differences in stationary phase-specific gene expression since we observed uniform expression of several stress-related promoters. The presence of non-growing persisters, temporarily dormant bacteria that are tolerant to antibiotics, has previously been described within growing bacterial populations. Using the GFP dilution method combined with cell sorting, we showed that ampicillin lyses growing bacteria while non-growing bacteria retain viability and that some of them restart growth after the ampicillin is removed. Thus, our method enables persisters to be monitored even in liquid cultures of wild type strains in which persister formation has low frequency. In principle, the approaches developed here could be used to detect differences in cell division in response to different environmental conditions and in cultures of unicellular organisms other than E. coli.}},  author = {Roostalu, Johanna and J\~{o}ers, Arvi and Luidalepp, Hannes and Kaldalu, Niilo and Tenson, Tanel},  citeulike-article-id = {2706275},  citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2180-8-68},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377270/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18430255},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18430255},  day = {23},  doi = {10.1186/1471-2180-8-68},  issn = {1471-2180},  journal = {BMC microbiology},  keywords = {bacterial-biology},  month = apr,  number = {1},  pages = {68+},  pmcid = {PMC2377270},  pmid = {18430255},  posted-at = {2012-08-30 09:44:30},  priority = {2},  title = {{Cell division in Escherichia coli cultures monitored at single cell resolution.}},  url = {http://dx.doi.org/10.1186/1471-2180-8-68},  volume = {8},  year = {2008}  }  @article{citeulike:7155221,  abstract = {{The bacteria cell envelope is a complex multilayered structure that serves to protect these organisms from their unpredictable and often hostile environment. The cell envelopes of most bacteria fall into one of two major groups. Gram-negative bacteria are surrounded by a thin peptidoglycan cell wall, which itself is surrounded by an outer membrane containing lipopolysaccharide. Gram-positive bacteria lack an outer membrane but are surrounded by layers of peptidoglycan many times thicker than is found in the Gram-negatives. Threading through these layers of peptidoglycan are long anionic polymers, called teichoic acids. The composition and organization of these envelope layers and recent insights into the mechanisms of cell envelope assembly are discussed.}},  author = {Silhavy, Thomas J. and Kahne, Daniel and Walker, Suzanne},  citeulike-article-id = {7155221},  citeulike-linkout-0 = {http://dx.doi.org/10.1101/cshperspect.a000414},  citeulike-linkout-1 = {http://cshperspectives.cshlp.org/cgi/content/abstract/2/5/a000414},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2857177/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/20452953},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=20452953},  day = {1},  doi = {10.1101/cshperspect.a000414},  issn = {1943-0264},  journal = {Cold Spring Harbor Perspectives in Biology},  keywords = {bacterial-biology},  month = may,  number = {5},  pmcid = {PMC2857177},  pmid = {20452953},  posted-at = {2012-08-28 21:33:13},  priority = {2},  title = {{The Bacterial Cell Envelope}},  url = {http://dx.doi.org/10.1101/cshperspect.a000414},  volume = {2},  year = {2010}  }  @article{citeulike:11137172,  abstract = {{Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI) recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.}},  author = {Gorochowski, Thomas E. and Matyjaszkiewicz, Antoni and Todd, Thomas and Oak, Neeraj and Kowalska, Kira and Reid, Stephen and Tsaneva-Atanasova, Krasimira T. and Savery, Nigel J. and Grierson, Claire S. and di Bernardo, Mario},  citeulike-article-id = {11137172},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0042790},  day = {24},  doi = {10.1371/journal.pone.0042790},  journal = {PLoS ONE},  keywords = {synbio-bacterial},  month = aug,  number = {8},  pages = {e42790+},  posted-at = {2012-08-26 19:39:45},  priority = {2},  publisher = {Public Library of Science},  title = {{BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology}},  url = {http://dx.doi.org/10.1371/journal.pone.0042790},  volume = {7},  year = {2012}  }  @article{citeulike:11137152,  abstract = {{Pasciak and Gavis were first to propose a model of nutrient uptake that includes both physical transport by diffusion and active biological transport across the cell membrane. While the Pasciak–Gavis model is not complicated mathematically (it can be expressed in closed form as a quadratic equation), its parameters are not so easily interpretable biologically as are the parameters of the Michaelis–Menten uptake model; this lack of transparency is probably the main reason the Pasciak–Gavis model has not been adopted by ecologically oriented modelers. Here I derive a Michaelis-like approximation to the Pasciak–Gavis model, and show how the parameters of the latter map to those of the Michaelis-like model. The derived approximation differs from a pure Michaelis–Menten model in a subtle but potentially critical way: in a pure Michaelis–Menten model, the half-saturation constant for nutrient uptake is independent of the density of transporter (or †porterâ€) proteins on the cell surface, while in the Pasciak–Gavis model and its Michaelis-like approximation, the half-saturation constant does depend on the density of porter proteins. The Pasciak–Gavis model predicts a unique relationship between cell size, nutrient concentration in the medium, the half-saturation constant of porter-limited nutrient uptake, and the resulting rate of uptake; the Michaelis-like approximation preserves the most important feature of that relationship, the size at which porter limitation gives way to diffusion limitation. Finally I discuss the implications for community structure that are implied by the Pasciak–Gavis model and its Michaelis-like approximation.}},  author = {Armstrong, Robert A.},  citeulike-article-id = {11137152},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.dsr.2008.05.004},  doi = {10.1016/j.dsr.2008.05.004},  issn = {09670637},  journal = {Deep Sea Research Part I: Oceanographic Research Papers},  keywords = {system-biology},  month = oct,  number = {10},  pages = {1311--1317},  posted-at = {2012-08-26 18:58:18},  priority = {2},  title = {{Nutrient uptake rate as a function of cell size and surface transporter density: A Michaelis-like approximation to the model of Pasciak and Gavis}},  url = {http://dx.doi.org/10.1016/j.dsr.2008.05.004},  volume = {55},  year = {2008}  }  @article{citeulike:11134919,  author = {Aksnes, D. L. and Cao, F. J.},  citeulike-article-id = {11134919},  citeulike-linkout-0 = {http://www.int-res.com/abstracts/meps/v440/p41-51/},  comment = {10.3354/meps09355  },  journal = {Mar Ecol Prog Ser},  keywords = {simulation-and-modeling},  pages = {41--51},  posted-at = {2012-08-25 22:44:55},  priority = {0},  title = {{Inherent and apparent traits in microbial nutrient uptake}},  url = {http://www.int-res.com/abstracts/meps/v440/p41-51/},  volume = {440},  year = {2011}  }  @article{citeulike:11069571,  abstract = {{It has been proposed that bacterial plasmids cannot be maintained by infectious transfer alone and that their persistence requires positive selection for plasmid-borne genes. To test this hypothesis, the population dynamics of two laboratory and five naturally occurring conjugative plasmids were examined in chemostat cultures of E. coli K-12. Both laboratory plasmids and three of the five wild plasmids failed to increase in frequency when introduced at low frequencies. However, two of the naturally occurring plasmids rapidly increased in frequency, and bacteria carrying them achieved dominance in the absence of selection for known plasmid-borne genes. Three hypotheses for the invasion and persistence of these two plasmids were examined. It is concluded that although these two extrachromsomal genetic elements are repressed for conjugative pili synthesis, as a consequence of high rates of transfer during periods of transitory derepression in newly formed transconjugants, they become established and are maintained by infectious transfer alone. The implications of these observations to the theory of plasmid maintenance and the evolution of repressible conjugative pili synthesis are discussed.}},  author = {Lundquist, Peter D. and Levin, Bruce R.},  citeulike-article-id = {11069571},  citeulike-linkout-0 = {http://www.genetics.org/content/113/3/483.abstract},  citeulike-linkout-1 = {http://www.genetics.org/content/113/3/483.full.pdf},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/3015715},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=3015715},  day = {01},  issn = {1943-2631},  journal = {Genetics},  keywords = {bacterial-biology},  month = jul,  number = {3},  pages = {483--497},  pmid = {3015715},  posted-at = {2012-08-15 17:20:21},  priority = {2},  publisher = {Genetics Society of America},  title = {TRANSITORY DEREPRESSION AND THE MAINTENANCE OF CONJUGATIVE PLASMIDS},  url = {http://www.genetics.org/content/113/3/483.abstract},  volume = {113},  year = {1986}  }  @article{citeulike:11069565,  abstract = {{A closed-loop control system drives progression of the coupled stalked and swarmer cell cycles of the bacterium Caulobacter crescentus in a near-mechanical step-like fashion. The cell-cycle control has a cyclical genetic circuit composed of four regulatory proteins with tight coupling to processive chromosome replication and cell division subsystems. We report a hybrid simulation of the coupled cell-cycle control system, including asymmetric cell division and responses to external starvation signals, that replicates mRNA and protein concentration patterns and is consistent with observed mutant phenotypes. An asynchronous sequential digital circuit model equivalent to the validated simulation model was created. Formal model-checking analysis of the digital circuit showed that the cell-cycle control is robust to intrinsic stochastic variations in reaction rates and nutrient supply, and that it reliably stops and restarts to accommodate nutrient starvation. Model checking also showed that mechanisms involving methylation-state changes in regulatory promoter regions during DNA replication increase the robustness of the cell-cycle control. The hybrid cell-cycle simulation implementation is inherently extensible and provides a promising approach for development of whole-cell behavioral models that can replicate the observed functionality of the cell and its responses to changing environmental conditions.}},  author = {Shen, Xiling and Collier, Justine and Dill, David and Shapiro, Lucy and Horowitz, Mark and McAdams, Harley H.},  citeulike-article-id = {11069565},  citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0805258105},  citeulike-linkout-1 = {http://www.pnas.org/content/105/32/11340.abstract},  citeulike-linkout-2 = {http://www.pnas.org/content/105/32/11340.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18685108},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18685108},  day = {12},  doi = {10.1073/pnas.0805258105},  issn = {1091-6490},  journal = {Proceedings of the National Academy of Sciences},  keywords = {bacterial-biology},  month = aug,  number = {32},  pages = {11340--11345},  pmid = {18685108},  posted-at = {2012-08-15 17:10:09},  priority = {2},  publisher = {National Academy of Sciences},  title = {{Architecture and inherent robustness of a bacterial cell-cycle control system}},  url = {http://dx.doi.org/10.1073/pnas.0805258105},  volume = {105},  year = {2008}  }  @article{citeulike:11069564,  abstract = {{This paper is the second in a series of two, and studies microbial lag in cell number and/or biomass measurements caused by temperature changes with an individual-based modeling approach. For this purpose, the theory of cell division, as discussed in the first part of this series of research papers, was implemented in the individual-based modeling framework BacSim. Simulations of this model are compared with experimental data of Escherichia coli, growing in an aerated, glucose-rich medium and subjected to sudden temperature shifts. The premise of a constant cell volume under changing temperature conditions predicts no lag in cell numbers after the shift, in contrast to the experimental observations. Based on literature research, two biological mechanisms that could be responsible for the observed lag phenomena are proposed. The first assumes that the average cell volume depends on temperature while the second assumes that a lag in biomass growth occurs after the temperature shift. For a lag in cell number caused by an increased average cell volume, the cell biomass always increases at the maximal rate. Therefore, cells are evidently not stressed and do not have to adapt to the new conditions, as opposed to a lag in biomass growth. Implementation and simulation of both mechanisms are found to describe the experimental observations equally well. Therefore, further research is needed to distinguish between the two mechanisms. This can be done by observing, in addition to cell numbers, a measure for the average cell volumes. In conclusion, the individual-based modeling approach is a good methodology to investigate and test biological theories and assumptions. Also, based on the simulations, suggestions for further experimental observations can be made.}},  author = {Dens, E. J. and Bernaerts, K. and Standaert, A. R. and Kreft, J. U. and Van Impe, J. F.},  citeulike-article-id = {11069564},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ijfoodmicro.2004.11.017},  doi = {10.1016/j.ijfoodmicro.2004.11.017},  issn = {01681605},  journal = {International Journal of Food Microbiology},  keywords = {bacterial-biology},  month = jun,  number = {3},  pages = {319--332},  posted-at = {2012-08-15 17:07:54},  priority = {2},  title = {{Cell division theory and individual-based modeling of microbial lag}},  url = {http://dx.doi.org/10.1016/j.ijfoodmicro.2004.11.017},  volume = {101},  year = {2005}  }  @article{citeulike:5970580,  abstract = {{Adaptation to fluctuations in nutrient availability is a fact of life for single-celled organisms in the 'wild'. A decade ago our understanding of how bacteria adjust cell cycle parameters to accommodate changes in nutrient availability stemmed almost entirely from elegant physiological studies completed in the 1960s. In this Opinion article we summarize recent groundbreaking work in this area and discuss potential mechanisms by which nutrient availability and metabolic status are coordinated with cell growth, chromosome replication and cell division.}},  author = {Wang, Jue D. and Levin, Petra A.},  citeulike-article-id = {5970580},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrmicro2202},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrmicro2202},  day = {06},  doi = {10.1038/nrmicro2202},  issn = {1740-1526},  journal = {Nat Rev Micro},  keywords = {bacterial-biology},  month = nov,  number = {11},  pages = {822--827},  posted-at = {2012-08-15 16:53:42},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Metabolism, cell growth and the bacterial cell cycle}},  url = {http://dx.doi.org/10.1038/nrmicro2202},  volume = {7},  year = {2009}  }  @article{citeulike:11069556,  abstract = {{This series of two papers deals with the theory of cell division and its implementation in an individual-based modeling framework. In this first part, the theory of cell division is studied on an individual-based level in order to learn more about the mechanistic principles behind microbial lag phenomena. While some important literature on cell division theory dates from 30 to 40 years ago, until now it has hardly been introduced in the field of predictive microbiology. Yet, it provides a large amount of information on how cells likely respond to changing environmental conditions. On the basis of this theory, a general theory on microbial lag behavior caused by a combination of medium and/or temperature changes has been developed in this paper. The proposed theory then forms the basis for a critical evaluation of existing modeling concepts for microbial lag in predictive microbiology. First of all, a more thorough definition can be formulated to define the lag time \^{I}» and the previously only vaguely defined physiological state of the cells in terms of mechanistically defined parameters like cell mass, RNA or protein content, specific growth rate and time to perform DNA replication and cell division. On the other hand, existing predictive models are evaluated with respect to the newly developed theory. For the model of [Hills, B., Wright, K.A., 1994. New model for bacterial growth in heterogeneous systems. J. Theor. Biol. 168, 31–41], a certain fitting parameter can also be related to physically meaningful parameters while for the model of Augustin et al. (2000) [Augustin, J.-C., Rosso, L., Carlier, V.A. 2000. A model describing the effect of temperature history on lag time for Listeria monocytogenes. Int. J. Food Microbiol. 57, 169–181] a new, mechanistically based, model structure is proposed. A restriction of the proposed theory is that it is only valid for situations where biomass growth responds instantly to an environment change. The authors are aware of the fact that this assumption is not generally acceptable. Lag in biomass can be caused, for example, by a delayed synthesis of some essential growth factor (e.g., enzymes). In the second part of this series of papers [Dens, E.J., Bernaerts, K., Standaert, A.R., Kreft, J.-U., VanImpe, J.F., 2005. Cell division theory and individual-based modeling of microbial lag: Part II. modeling lag phenomena induced by temperature shifts. Int. J. Food Microbiol.], the theory of cell division is implemented in an individual-based simulation program and extended to account for lags in biomass growth. In conclusion, the cell division theory applied to microbial populations in dynamic medium and/or temperature conditions provides a useful framework to analyze microbial lag behavior.}},  author = {Dens, E. J. and Bernaerts, K. and Standaert, A. R. and Van Impe, J. F.},  citeulike-article-id = {11069556},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ijfoodmicro.2004.11.016},  doi = {10.1016/j.ijfoodmicro.2004.11.016},  issn = {01681605},  journal = {International Journal of Food Microbiology},  keywords = {individual-based-modeling},  month = jun,  number = {3},  pages = {303--318},  posted-at = {2012-08-15 16:47:45},  priority = {2},  title = {{Cell division theory and individual-based modeling of microbial lag}},  url = {http://dx.doi.org/10.1016/j.ijfoodmicro.2004.11.016},  volume = {101},  year = {2005}  }  @article{citeulike:10082694,  abstract = {{The relationship between events during the bacterial cell cycle has been the subject of frequent debate. While early models proposed a relatively rigid view in which DNA replication was inextricably coupled to attainment of a specific cell mass, and cell division was triggered by the completion of chromosome replication, more recent data suggest these models were oversimplified. Instead, an intricate set of intersecting, and at times opposing, forces coordinate DNA replication, cell division, and cell growth with one another, thereby ensuring the precise spatial and temporal control of cell cycle events.}},  author = {Haeusser, Daniel P. and Levin, Petra A.},  citeulike-article-id = {10082694},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.mib.2008.02.008},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397022/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18396093},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18396093},  doi = {10.1016/j.mib.2008.02.008},  issn = {13695274},  journal = {Current Opinion in Microbiology},  keywords = {bacterial-biology},  month = apr,  number = {2},  pages = {94--99},  pmcid = {PMC2397022},  pmid = {18396093},  posted-at = {2012-08-15 16:46:12},  priority = {2},  title = {{The great divide: coordinating cell cycle events during bacterial growth and division}},  url = {http://dx.doi.org/10.1016/j.mib.2008.02.008},  volume = {11},  year = {2008}  }  @article{citeulike:11054594,  author = {Harold, F. M.},  citeulike-article-id = {11054594},  citeulike-linkout-0 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC408323/},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/4261111},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=4261111},  issn = {0005-3678},  journal = {Bacteriological reviews},  keywords = {bacterial-biology},  month = jun,  number = {2},  pages = {172--230},  pmcid = {PMC408323},  pmid = {4261111},  posted-at = {2012-08-12 18:37:48},  priority = {2},  title = {{Conservation and transformation of energy by bacterial membranes.}},  url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC408323/},  volume = {36},  year = {1972}  }  @article{citeulike:711968,  abstract = {{TransportDB (http://www.membranetransport.org) is a relational database designed for describing the predicted cellular membrane transport proteins in organisms whose complete genome sequences are available. For each organism, the complete set of membrane transport systems was identified and classified into different types and families according to putative membrane topology, protein family, bioenergetics and substrate specificities. Web pages were created to provide userâ€friendly interfaces to easily access, query and download the data. Additional features, such as a BLAST search tool against known transporter protein sequences, comparison of transport systems from different organisms and phylogenetic trees of individual transporter families are also provided. TransportDB will be regularly updated with data obtained from newly sequenced genomes.}},  address = {The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.},  author = {Ren, Qinghu and Kang, Katherine H. and Paulsen, Ian T.},  citeulike-article-id = {711968},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkh016},  citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/32/suppl\_1/D284.abstract},  citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/32/suppl\_1/D284.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/14681414},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=14681414},  day = {01},  doi = {10.1093/nar/gkh016},  issn = {1362-4962},  journal = {Nucleic Acids Research},  keywords = {bacterial-biology},  month = jan,  number = {suppl 1},  pages = {D284--D288},  pmid = {14681414},  posted-at = {2012-08-12 18:37:15},  priority = {2},  publisher = {Oxford University Press},  title = {{TransportDB: a relational database of cellular membrane transport systems}},  url = {http://dx.doi.org/10.1093/nar/gkh016},  volume = {32},  year = {2004}  }  @article{citeulike:10649634,  abstract = {{  Like eukaryotes, bacteria must coordinate division with growth to ensure cells are the appropriate size for a given environmental condition or developmental fate. As single-celled organisms, nutrient availability is one of the strongest influences on bacterial cell size. Classic physiological experiments conducted over four decades ago first demonstrated that cell size is directly correlated with nutrient source and growth rate in the Gram-negative bacterium Salmonella typhimurium. This observation subsequently served as the basis for studies revealing a role for cell size in cell cycle progression in a closely related organism, Escherichia coli. More recently, the development of powerful genetic, molecular, and imaging tools has allowed us to identify and characterize the nutrient-dependent pathway responsible for coordinating cell division and cell size with growth rate in the Gram-positive model organism Bacillus subtilis. Here, we discuss the role of cell size in bacterial growth and development and propose a broadly applicable model for cell size control in this important and highly divergent domain of life.  Copyright {\copyright} 2012 Elsevier Ltd. All rights reserved.  }},  author = {Chien, An-Chun and Hill, Norbert S. and Levin, Petra A.},  citeulike-article-id = {10649634},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.cub.2012.02.032},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350639/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/22575476},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=22575476},  day = {8},  doi = {10.1016/j.cub.2012.02.032},  issn = {09609822},  journal = {Current Biology},  keywords = {system-biology},  month = may,  number = {9},  pages = {R340--R349},  pmcid = {PMC3350639},  pmid = {22575476},  posted-at = {2012-08-02 18:47:47},  priority = {2},  title = {{Cell Size Control in Bacteria}},  url = {http://dx.doi.org/10.1016/j.cub.2012.02.032},  volume = {22},  year = {2012}  }  @article{citeulike:10904155,  abstract = {{Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. Our whole-cell model accounts for all annotated gene functions and was validated against a broad range of data. The model provides insights into many previously unobserved cellular behaviors, including in vivo rates of protein-DNA association and an inverse relationship between the durations of DNA replication initiation and replication. In addition, experimental analysis directed by model predictions identified previously undetected kinetic parameters and biological functions. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery. Copyright {\copyright} 2012 Elsevier Inc. All rights reserved.}},  author = {Karr, Jonathan R. and Sanghvi, Jayodita C. and Macklin, Derek N. and Gutschow, Miriam V. and Jacobs, Jared M. and Bolival, Benjamin and Assad-Garcia, Nacyra and Glass, John I. and Covert, Markus W.},  citeulike-article-id = {10904155},  citeulike-linkout-0 = {http://www.cell.com//abstract/S0092-8674(12)00776-3},  citeulike-linkout-1 = {http://dx.doi.org/10.1016/j.cell.2012.05.044},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413483/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/22817898},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=22817898},  day = {20},  doi = {10.1016/j.cell.2012.05.044},  issn = {00928674},  journal = {Cell},  keywords = {system-biology},  month = jul,  number = {2},  pages = {389--401},  pmcid = {PMC3413483},  pmid = {22817898},  posted-at = {2012-07-24 08:27:05},  priority = {2},  publisher = {Cell Press},  title = {{A Whole-Cell Computational Model Predicts Phenotype from Genotype}},  url = {http://dx.doi.org/10.1016/j.cell.2012.05.044},  volume = {150},  year = {2012}  }  @article{citeulike:10887724,  abstract = {{We applied transmission electron microscopy and densitometric image analysis to measure the cell volume (V) and dry weight (DW) of single bacterial cells. The system was applied to measure the DW ofEscherichia coli DSM 613 at different growth phases and of natural bacterial assemblages of two lakes, Piburger See and Gossenk\"{o}llesee. We found a functional allometric relationship between DW (in femtograms) and V (in cubic micrometers) of bacteria (DW = 435 · V 0.86); i.e., smaller bacteria had a higher ratio of DW to V than larger cells. The measured DW of E. coli cells ranged from 83 to 1,172 fg, and V ranged from 0.1 to 3.5 μm3(n = 678). Bacterial cells from Piburger See and Gossenk\"{o}llesee (n = 465) had DWs from 3 fg (V = 0.003 μm3) to 1,177 fg (V = 3.5 μm3). Between 40 and 50\% of the cells had a DW of less than 20 fg. By assuming that carbon comprises 50\% of the DW, the ratio of carbon content to Vof individual cells varied from 466 fg of C μm−3 forVs of 0.001 to 0.01 μm3 to 397 fg of C μm−3 (0.01 to 0.1 μm3) and 288 fg of C μm−3 (0.1 to 1 μm3). Exponentially growing and stationary cells of E. coli DSM 613 showed conversion factors of 254 fg of C μm−3 (0.1 to 1 μm3) and 211 fg of C μm−3 (1 to 4 μm3), respectively. Our data suggest that bacterial biomass in aquatic environments is higher and more variable than previously assumed from volume-based measurements.}},  author = {Loferer-Kr\"{o}{\ss}bacher, M. and Klima, J. and Psenner, R.},  citeulike-article-id = {10887724},  citeulike-linkout-0 = {http://aem.asm.org/content/64/2/688.abstract},  citeulike-linkout-1 = {http://aem.asm.org/content/64/2/688.full.pdf},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/9464409},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=9464409},  day = {01},  issn = {1098-5336},  journal = {Applied and Environmental Microbiology},  keywords = {individual-based-modeling},  month = feb,  number = {2},  pages = {688--694},  pmid = {9464409},  posted-at = {2012-07-16 16:54:17},  priority = {2},  publisher = {American Society for Microbiology},  title = {{Determination of Bacterial Cell Dry Mass by Transmission Electron Microscopy and Densitometric Image Analysis}},  url = {http://aem.asm.org/content/64/2/688.abstract},  volume = {64},  year = {1998}  }  @book{citeulike:606459,  abstract = {{The much-discussed book that explores how cooperation can emerge in a world of  self-seeking egoists--whether superpowers, businesses, or individuals--when  there is no central authority to police their actions.}},  author = {Axelrod, Robert},  citeulike-article-id = {606459},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0465021212},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0465021212},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0465021212},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0465021212},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0465021212/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0465021212},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0465021212},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0465021212},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0465021212\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0465021212},  day = {01},  howpublished = {Paperback},  isbn = {0465021212},  keywords = {books},  month = oct,  posted-at = {2012-07-15 20:33:33},  priority = {2},  publisher = {Basic Books},  title = {{The Evolution of Cooperation}},  url = {http://www.worldcat.org/isbn/0465021212},  year = {1985}  }  @article{citeulike:10886138,  abstract = {{Microbial biofilms are complex, self-organized communities of bacteria, which employ physiological cooperation and spatial organization to increase both their metabolic efficiency and their resistance to changes in their local environment. These properties make biofilms an attractive target for engineering, particularly for the production of chemicals such as pharmaceutical ingredients or biofuels, with the potential to significantly improve yields and lower maintenance costs. Biofilms are also a major cause of persistent infection, and a better understanding of their organization could lead to new strategies for their disruption. Despite this potential, the design of synthetic biofilms remains a major challenge, due to the complex interplay between transcriptional regulation, intercellular signaling, and cell biophysics. Computational modeling could help to address this challenge by predicting the behavior of synthetic biofilms prior to their construction; however, multiscale modeling has so far not been achieved for realistic cell numbers. This paper presents a computational method for modeling synthetic microbial biofilms, which combines three-dimensional biophysical models of individual cells with models of genetic regulation and intercellular signaling. The method is implemented as a software tool (CellModeller), which uses parallel Graphics Processing Unit architectures to scale to more than 30,000 cells, typical of a 100 ?m diameter colony, in 30 min of computation time.}},  author = {Rudge, Timothy J. and Steiner, Paul J. and Phillips, Andrew and Haseloff, Jim},  booktitle = {ACS Synthetic Biology},  citeulike-article-id = {10886138},  citeulike-linkout-0 = {http://dx.doi.org/10.1021/sb300031n},  citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/sb300031n},  day = {11},  doi = {10.1021/sb300031n},  journal = {ACS Synth. Biol.},  keywords = {system-biology},  month = jul,  number = {8},  pages = {345--352},  posted-at = {2012-07-15 18:51:45},  priority = {2},  publisher = {American Chemical Society},  title = {{Computational Modeling of Synthetic Microbial Biofilms}},  url = {http://dx.doi.org/10.1021/sb300031n},  volume = {1},  year = {2012}  }  @article{citeulike:8220094,  abstract = {{A Complex Adaptive System is a collection of autonomous, heterogeneous agents, whose behavior is defined with a limited number of rules. A Game Theory is a mathematical construct that assumes a small number of rational players who have a limited number of actions or strategies available to them. The CAS method has the potential to alleviate some of the shortcomings of GT. On the other hand, CAS researchers are always looking for a realistic way to define interactions among agents. GT offers an attractive option for defining the rules of such interactions in a way that is both potentially consistent with observed real-world behavior and subject to mathematical interpretation. This article reports on the results of an effort to build a CAS system that utilizes GT for determining the actions of individual agents. {\copyright} 2009 Wiley Periodicals, Inc. Complexity, 16,24–42, 2010}},  author = {Hadzikadic, Mirsad and Carmichael, Ted and Curtin, Charles},  citeulike-article-id = {8220094},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/cplx.20316},  doi = {10.1002/cplx.20316},  journal = {Complexity},  keywords = {game-theory},  number = {1},  pages = {34--42},  posted-at = {2012-07-12 12:12:42},  priority = {2},  publisher = {Wiley Subscription Services, Inc., A Wiley Company},  title = {{Complex adaptive systems and game theory: An unlikely union}},  url = {http://dx.doi.org/10.1002/cplx.20316},  volume = {16},  year = {2010}  }  @book{citeulike:10870407,  author = {Harte, John},  citeulike-article-id = {10870407},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0199593426},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0199593426},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0199593426},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0199593426},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0199593426/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0199593426},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0199593426},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0199593426},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0199593426\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0199593426},  day = {01},  howpublished = {Paperback},  isbn = {0199593426},  keywords = {books},  month = sep,  posted-at = {2012-07-09 18:38:15},  priority = {2},  publisher = {Oxford University Press, USA},  title = {{Maximum Entropy and Ecology: A Theory of Abundance, Distribution, and Energetics (Oxford Series in Ecology and Evolution)}},  url = {http://www.worldcat.org/isbn/0199593426},  year = {2011}  }  @article{citeulike:10312133,  abstract = {{A cytometric method for the estimation of end-point conjugation rates is developed and adapted to surface conjugation. This method improves the through-put of conjugation assays based on replica-plating and results in less noisy experimental data. Although conjugation on solid surfaces deviates from ideal conditions in which cells are continuously mixed, results show that, within the limits of high initial population densities and short mating times, end-point estimates of the conjugation rates are robust measurements. They are independent of the donor/recipient ratios and, to some extent, of the sampling time. Remixing the mating population in the course of a conjugation experiment results in a boost in the frequency of transconjugants. \^{a}–º A cytometric method to determine surface conjugation rates. \^{a}–º End-point estimation of conjugation rates adapted to this method. \^{a}–º Experimental data on transfer rates of plasmid R388 oriT.}},  author = {del Campo, Irene and Ruiz, Ra\'{u}l and Cuevas, Ana and Revilla, Carlos and Vielva, Luis and de la Cruz, Fernando},  citeulike-article-id = {10312133},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2012.01.008},  doi = {10.1016/j.plasmid.2012.01.008},  issn = {0147619X},  journal = {Plasmid},  keywords = {system-biology},  month = mar,  number = {2},  pages = {174--182},  posted-at = {2012-07-07 12:09:33},  priority = {2},  title = {{Determination of conjugation rates on solid surfaces}},  url = {http://dx.doi.org/10.1016/j.plasmid.2012.01.008},  volume = {67},  year = {2012}  }  @article{citeulike:1433130,  abstract = {{This feature explores how the laws of thermodynamics can explain natural selection and life itself.}},  address = {London, United Kingdom. ja\[email protected]},  author = {Whitfield, John},  citeulike-article-id = {1433130},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pbio.0050142},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17503967},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17503967},  day = {15},  doi = {10.1371/journal.pbio.0050142},  issn = {1545-7885},  journal = {PLoS Biol},  keywords = {systems-ecology},  month = may,  number = {5},  pages = {e142+},  pmid = {17503967},  posted-at = {2012-07-03 20:10:01},  priority = {2},  publisher = {Public Library of Science},  title = {{Survival of the Likeliest?}},  url = {http://dx.doi.org/10.1371/journal.pbio.0050142},  volume = {5},  year = {2007}  }  @article{citeulike:10831402,  abstract = {{  Most research in biology is empirical, yet empirical studies rely fundamentally on theoretical work for generating testable predictions and interpreting observations. Despite this interdependence, many empirical studies build largely on other empirical studies with little direct reference to relevant theory, suggesting a failure of communication that may hinder scientific progress. To investigate the extent of this problem, we analyzed how the use of mathematical equations affects the scientific impact of studies in ecology and evolution. The density of equations in an article has a significant negative impact on citation rates, with papers receiving 28\% fewer citations overall for each additional equation per page in the main text. Long, equation-dense papers tend to be more frequently cited by other theoretical papers, but this increase is outweighed by a sharp drop in citations from nontheoretical papers (35\% fewer citations for each additional equation per page in the main text). In contrast, equations presented in an accompanying appendix do not lessen a paper's impact. Our analysis suggests possible strategies for enhancing the presentation of mathematical models to facilitate progress in disciplines that rely on the tight integration of theoretical and empirical work.  }},  author = {Fawcett, Tim W. and Higginson, Andrew D.},  citeulike-article-id = {10831402},  citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.1205259109},  citeulike-linkout-1 = {http://www.pnas.org/content/early/2012/06/22/1205259109.abstract},  citeulike-linkout-2 = {http://www.pnas.org/content/early/2012/06/22/1205259109.full.pdf},  citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/109/29/11735},  citeulike-linkout-4 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406806/},  citeulike-linkout-5 = {http://view.ncbi.nlm.nih.gov/pubmed/22733777},  citeulike-linkout-6 = {http://www.hubmed.org/display.cgi?uids=22733777},  day = {17},  doi = {10.1073/pnas.1205259109},  issn = {1091-6490},  journal = {Proceedings of the National Academy of Sciences of the United States of America},  keywords = {transversal},  month = jul,  number = {29},  pages = {11735--11739},  pmcid = {PMC3406806},  pmid = {22733777},  posted-at = {2012-07-02 15:29:00},  priority = {2},  publisher = {National Academy of Sciences},  title = {{Heavy use of equations impedes communication among biologists.}},  url = {http://dx.doi.org/10.1073/pnas.1205259109},  volume = {109},  year = {2012}  }  @article{citeulike:10841271,  author = {Rajapakse, Indika and Groudine, Mark and Mesbahi, Mehran},  citeulike-article-id = {10841271},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1002543},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386158/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/22761554},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=22761554},  day = {28},  doi = {10.1371/journal.pcbi.1002543},  issn = {1553-7358},  journal = {PLoS Comput Biol},  keywords = {network-dynamics},  month = jun,  number = {6},  pages = {e1002543+},  pmcid = {PMC3386158},  pmid = {22761554},  posted-at = {2012-07-02 15:27:34},  priority = {2},  publisher = {Public Library of Science},  title = {{What Can Systems Theory of Networks Offer to Biology?}},  url = {http://dx.doi.org/10.1371/journal.pcbi.1002543},  volume = {8},  year = {2012}  }  @article{citeulike:10802678,  abstract = {{An overarching goal of synthetic and systems biology is to engineer and understand complex biochemical systems by rationally designing and analyzing their basic component interactions. Practically, the extent to which such reductionist approaches can be applied is unclear especially as the complexity of the system increases. Toward gradually increasing the complexity of systematically engineered systems, programmable synthetic circuits operating in cell-free in vitroenvironments offer a valuable testing ground for principles for the design, characterization, and analysis of complex biochemical systems. Here we illustrate this approach using in vitro transcriptional circuits (?genelets?) while developing an activatable transcriptional switch motif and configuring it as a bistable autoregulatory circuit, using just four synthetic DNA strands and three essential enzymes, bacteriophage T7 RNA polymerase, Escherichia coli ribonuclease H, and ribonuclease R. Fulfilling the promise of predictable system design, the thermodynamic and kinetic constraints prescribed at the sequence level were enough to experimentally demonstrate intended bistable dynamics for the synthetic autoregulatory switch. A simple mathematical model was constructed based on the mechanistic understanding of elementary reactions, and a Monte Carlo Bayesian inference approach was employed to find parameter sets compatible with a training set of experimental results; this ensemble of parameter sets was then used to predict a test set of additional experiments with reasonable agreement and to provide a rigorous basis for confidence in the mechanistic model. Our work demonstrates that programmable in vitro biochemical circuits can serve as a testing ground for evaluating methods for the design and analysis of more complex biochemical systems such as living cells.}},  author = {Subsoontorn, Pakpoom and Kim, Jongmin and Winfree, Erik},  booktitle = {ACS Synthetic Biology},  citeulike-article-id = {10802678},  citeulike-linkout-0 = {http://dx.doi.org/10.1021/sb300018h},  citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/sb300018h},  day = {13},  doi = {10.1021/sb300018h},  journal = {ACS Synth. Biol.},  keywords = {synbio-dna},  month = jun,  posted-at = {2012-06-19 18:38:08},  priority = {2},  publisher = {American Chemical Society},  title = {{Ensemble Bayesian Analysis of Bistability in a Synthetic Transcriptional Switch}},  url = {http://dx.doi.org/10.1021/sb300018h},  year = {2012}  }  @article{citeulike:10216868,  abstract = {{Despite substantial progress in synthetic biology, we still lack the ability to engineer anything as complex as Nature has. One of the many reasons is that we lack the requisite tools for independently controlling the expression of multiple genes in parallel. While our toolbox is still spare, the situation is rapidly changing. This opinion discusses some recent approaches and open challenges in designing orthogonal regulators of gene expression in bacteria. View high quality image (70K) \^{a}–º Our ability to engineering orthogonal transcription factors in bacteria is limited. \^{a}–º RNA-based regulators are particularly promising. \^{a}–º Engineered two-component systems offer a new powerful tool.}},  author = {Rao, Christopher V.},  citeulike-article-id = {10216868},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.copbio.2011.12.015},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/22237017},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=22237017},  day = {9},  doi = {10.1016/j.copbio.2011.12.015},  issn = {09581669},  journal = {Current Opinion in Biotechnology},  keywords = {synbio-bacterial},  month = jan,  pmid = {22237017},  posted-at = {2012-06-03 18:13:12},  priority = {2},  title = {{Expanding the synthetic biology toolbox: engineering orthogonal regulators of gene expression}},  url = {http://dx.doi.org/10.1016/j.copbio.2011.12.015},  year = {2012}  }  @article{citeulike:8167869,  abstract = {{Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR) abound in the genomes of almost all archaebacteria and nearly half the eubacteria sequenced. Through a genetic interference mechanism, bacteria with CRISPR regions carrying copies of the DNA of previously encountered phage and plasmids abort the replication of phage and plasmids with these sequences. Thus it would seem that protection against infecting phage and plasmids is the selection pressure responsible for establishing and maintaining CRISPR in bacterial populations. But is it? To address this question and provide a framework and hypotheses for the experimental study of the ecology and evolution of CRISPR, I use mathematical models of the population dynamics of CRISPR-encoding bacteria with lytic phage and conjugative plasmids. The results of the numerical (computer simulation) analysis of the properties of these models with parameters in the ranges estimated for Escherichia coli and its phage and conjugative plasmids indicate: (1) In the presence of lytic phage there are broad conditions where bacteria with CRISPR-mediated immunity will have an advantage in competition with non-CRISPR bacteria with otherwise higher Malthusian fitness. (2) These conditions for the existence of CRISPR are narrower when there is envelope resistance to the phage. (3) While there are situations where CRISPR-mediated immunity can provide bacteria an advantage in competition with higher Malthusian fitness bacteria bearing deleterious conjugative plasmids, the conditions for this to obtain are relatively narrow and the intensity of selection favoring CRISPR weak. The parameters of these models can be independently estimated, the assumption behind their construction validated, and the hypotheses generated from the analysis of their properties tested in experimental populations of bacteria with lytic phage and conjugative plasmids. I suggest protocols for estimating these parameters and outline the design of experiments to evaluate the validity of these models and test these hypotheses. CRISPR is the acronym for the adaptive immune system that has been found in almost all archaebacteria and nearly half the eubacteria examined. Unlike the other defenses bacteria have for protection from phage and other deleterious DNAs, CRISPR has the virtues of specificity, memory, and the capacity to abort infections with a virtually indefinite diversity of deleterious DNAs. In this report, mathematical models of the population dynamics of bacteria, phage, and plasmids are used to determine the conditions under which CRISPR can become established and will be maintained in bacterial populations and the contribution of this adaptive immune system to the ecology and (co)evolution of bacteria and bacteriophage. The models predict realistic and broad conditions under which bacteria bearing CRISPR regions can invade and be maintained in populations of higher fitness bacteria confronted with bacteriophage and narrower conditions when the confrontation is with competitors carrying conjugative plasmids. The models predict that CRISPR can facilitate long-term co-evolutionary arms races between phage and bacteria and between phage- rather than resource-limited bacterial communities. The parameters of these models can be independently estimated, the assumptions behind their construction validated, and the hypotheses generated from the analysis of their properties tested with experimental populations of bacteria.}},  author = {Levin, Bruce R.},  citeulike-article-id = {8167869},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pgen.1001171},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/21060859},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=21060859},  day = {28},  doi = {10.1371/journal.pgen.1001171},  issn = {1553-7404},  journal = {PLoS Genet},  keywords = {system-biology},  month = oct,  number = {10},  pages = {e1001171+},  pmid = {21060859},  posted-at = {2012-06-01 15:52:16},  priority = {2},  publisher = {Public Library of Science},  title = {{Nasty Viruses, Costly Plasmids, Population Dynamics, and the Conditions for Establishing and Maintaining CRISPR-Mediated Adaptive Immunity in Bacteria}},  url = {http://dx.doi.org/10.1371/journal.pgen.1001171},  volume = {6},  year = {2010}  }  @article{citeulike:10684862,  abstract = {{Synthetic gene circuits are designed to program new biological behaviour, dynamics and logic control. For all but the simplest synthetic phenotypes, this requires a structured approach to map the desired functionality to available molecular and cellular parts and processes. In other engineering disciplines, a formalized design process has greatly enhanced the scope and rate of success of projects. When engineering biological systems, a desired function must be achieved in a context that is incompletely known, is influenced by stochastic fluctuations and is capable of rich nonlinear interactions with the engineered circuitry. Here, we review progress in the provision and engineering of libraries of parts and devices, their composition into large systems and the emergence of a formal design process for synthetic biology.}},  author = {Slusarczyk, Adrian L. and Lin, Allen and Weiss, Ron},  citeulike-article-id = {10684862},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrg3227},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrg3227},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/22596318},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=22596318},  day = {18},  doi = {10.1038/nrg3227},  issn = {1471-0056},  journal = {Nat Rev Genet},  keywords = {synbio-dna},  month = jun,  number = {6},  pages = {406--420},  pmid = {22596318},  posted-at = {2012-05-20 17:06:00},  priority = {2},  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},  title = {{Foundations for the design and implementation of synthetic genetic circuits}},  url = {http://dx.doi.org/10.1038/nrg3227},  volume = {13},  year = {2012}  }  @article{citeulike:6413442,  abstract = {{The aim of this paper is to introduce a method of verification of individual-based modeling through a relevant example. We build two individual-based models for the movement of elvers in the French river 'Adour'. We rigorously obtain a set of stochastic differential equations and a partial differential equation for the elvers' density, both of which describe the same phenomenon. We solve the partial differential equation numerically and compare statistically the results of both methods, concluding that they are equivalent. This approach constitutes a verification and a protocol of analysis of our individual-based models.}},  author = {G\'{o}mez-Mourelo, Pablo},  citeulike-article-id = {6413442},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ecolmodel.2005.05.014},  day = {25},  doi = {10.1016/j.ecolmodel.2005.05.014},  issn = {03043800},  journal = {Ecological Modelling},  keywords = {individual-based-modeling},  month = oct,  number = {1},  pages = {93--111},  posted-at = {2012-04-19 20:04:31},  priority = {2},  title = {{From individual-based models to partial differential equations}},  url = {http://dx.doi.org/10.1016/j.ecolmodel.2005.05.014},  volume = {188},  year = {2005}  }  @article{citeulike:4819382,  abstract = {{Individual-based modelling approaches are being used to simulate larger complex spatial systems in ecology and in other fields of research. Several novel model development issues now face researchers: in particular how to simulate large numbers of individuals with high levels of complexity, given finite computing resources. A case study of a spatially-explicit simulation of aphid population dynamics was used to assess two strategies for coping with a large number of individuals: the use of 'super-individuals' and parallel computing. Parallelisation of the model maintained the model structure and thus the simulation results were comparable to the original model. However, the super-individual implementation of the model caused significant changes to the model dynamics, both spatially and temporally. When super-individuals represented more than around 10 individuals it became evident that aggregate statistics generated from a super-individual model can hide more detailed deviations from an individual-level model. Improvements in memory use and model speed were perceived with both approaches. For the parallel approach, significant speed-up was only achieved when more than five processors were used and memory availability was only increased once five or more processors were used. The super-individual approach has potential to improve model speed and memory use dramatically, however this paper cautions the use of this approach for a density-dependent spatially-explicit model, unless individual variability is better taken into account.}},  author = {Parry, Hazel R. and Evans, Andrew J.},  citeulike-article-id = {4819382},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ecolmodel.2008.02.002},  day = {24},  doi = {10.1016/j.ecolmodel.2008.02.002},  issn = {03043800},  journal = {Ecological Modelling},  keywords = {individual-based-modeling},  month = jun,  number = {2-4},  pages = {141--152},  posted-at = {2012-04-19 18:42:26},  priority = {2},  title = {{A comparative analysis of parallel processing and super-individual methods for improving the computational performance of a large individual-based model}},  url = {http://dx.doi.org/10.1016/j.ecolmodel.2008.02.002},  volume = {214},  year = {2008}  }  @inproceedings{citeulike:10560743,  abstract = {{One of the processes by which microorganisms are able to rapidly adapt to changing conditions is horizontal gene transfer, whereby an organism incorporates additional genetic material from sources other than its parent. These genetic elements may encode a wide variety of beneficial traits. Under certain conditions, many computational models capture the evolutionary dynamics of adaptive behaviors such as toxin production, quorum sensing, and biofilm formation, and have even provided new insights into otherwise unknown or misunderstood phenomena. However, such models rarely incorporate horizontal gene transfer, so they may be incapable of fully representing the vast repertoire of behaviors exhibited by natural populations. Although models of horizontal gene transfer exist, they rarely account for the spatial structure of populations, which is often critical to adaptive behaviors. In this work we develop a spatial model to examine how conjugation, one mechanism of horizontal gene transfer, can be maintained in populations. We investigate how both the costs of transfer and the benefits conferred affect evolutionary outcomes. Further, we examine how rates of transmission evolve, allowing this system to adapt to different environments. Through spatial models such as these, we can gain a greater understanding of the conditions under which horizontally-acquired behaviors are evolved and are maintained.}},  address = {New York, NY, USA},  author = {Connelly, Brian D. and Zaman, Luis and McKinley, Philip K. and Ofria, Charles},  booktitle = {Proceedings of the 13th annual conference on Genetic and evolutionary computation},  citeulike-article-id = {10560743},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=2001608},  citeulike-linkout-1 = {http://dx.doi.org/10.1145/2001576.2001608},  doi = {10.1145/2001576.2001608},  isbn = {978-1-4503-0557-0},  keywords = {systems-ecology},  location = {Dublin, Ireland},  pages = {227--234},  posted-at = {2012-04-12 22:42:41},  priority = {2},  publisher = {ACM},  series = {GECCO '11},  title = {{Modeling the evolutionary dynamics of plasmids in spatial populations}},  url = {http://dx.doi.org/10.1145/2001576.2001608},  year = {2011}  }  @book{citeulike:5687173,  citeulike-article-id = {5687173},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0521642949},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0521642949},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0521642949},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0521642949},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0521642949/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0521642949},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0521642949},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0521642949},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0521642949\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0521642949},  day = {03},  edition = {1},  howpublished = {Hardcover},  isbn = {0521642949},  keywords = {books},  month = jul,  posted-at = {2012-04-01 17:40:07},  priority = {2},  publisher = {Cambridge University Press},  title = {{The Geometry of Ecological Interactions: Simplifying Spatial Complexity (Cambridge Studies in Adaptive Dynamics)}},  url = {http://www.worldcat.org/isbn/0521642949},  year = {2000}  }  @book{citeulike:606462,  abstract = {{This book explores the process of modeling complex systems in the widest sense of that term, drawing on examples from such diverse fields as ecology, epidemiology, sociology, seismology, as well as economics. It also provides the mathematical tools for studying the dynamics of these systems. Boccara takes a carefully inductive approach in defining what it means for a system to be "complex" (and at the same time addresses the equally elusive concept of emergent properties). This is the first text on the subject to draw comprehensive conclusions from such a wide range of analogous phenomena.}},  author = {Boccara, Nino},  citeulike-article-id = {606462},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0387404627},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0387404627},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0387404627},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0387404627},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0387404627/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0387404627},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0387404627},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0387404627},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0387404627\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0387404627},  day = {18},  edition = {1},  howpublished = {Hardcover},  isbn = {0387404627},  keywords = {books},  month = nov,  posted-at = {2012-04-01 17:39:20},  priority = {2},  publisher = {Springer},  title = {{Modeling Complex Systems (Graduate Texts in Contemporary Physics)}},  url = {http://www.worldcat.org/isbn/0387404627},  year = {2003}  }  @article{citeulike:10511624,  abstract = {{Bacteria growing in a suitable medium increase in number by having each cell increase in size, and then each cell divides to produce two daughter cells. The increase in cell number in a culture is therefore a result of the activity of the cell during the division cycle, between the period of birth by division and the subsequent division.}},  author = {Cooper, Stephen},  booktitle = {eLS},  citeulike-article-id = {10511624},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/npg.els.0001419},  doi = {10.1038/npg.els.0001419},  keywords = {bacterial-biology},  posted-at = {2012-03-29 12:37:31},  priority = {2},  publisher = {John Wiley \& Sons, Ltd},  title = {{Bacterial Reproduction and Growth}},  url = {http://dx.doi.org/10.1038/npg.els.0001419},  year = {2001}  }  @book{citeulike:6430524,  author = {Schmidt-Nielsen, Knut},  citeulike-article-id = {6430524},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0521319870},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0521319870},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0521319870},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0521319870},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0521319870/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0521319870},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0521319870},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0521319870},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0521319870\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0521319870},  day = {27},  edition = {1},  howpublished = {Paperback},  isbn = {0521319870},  keywords = {transversal},  month = jul,  posted-at = {2012-03-23 17:55:19},  priority = {2},  publisher = {Cambridge University Press},  title = {{Scaling: Why is Animal Size so Important?}},  url = {http://www.worldcat.org/isbn/0521319870},  year = {1984}  }  @article{citeulike:10372358,  abstract = {{Many real networks are not isolated from each other but form networks of  networks, often interrelated in non trivial ways. Here, we analyze an epidemic  spreading process taking place on top of two interconnected complex networks.  We develop a heterogeneous mean field approach that allows us to calculate the  conditions for the emergence of an endemic state. Interestingly, a global  endemic state may arise in the coupled system even though the epidemics is not  able to propagate on each network separately, and even when the number of  coupling connections is small. Our analytic results are successfully confronted  against large-scale numerical simulations.}},  archivePrefix = {arXiv},  author = {Saumell-Mendiola, Anna and Serrano, M. \'{A}ngeles and Bogu\~{n}\'{a}, Mari\'{a}n},  citeulike-article-id = {10372358},  citeulike-linkout-0 = {http://arxiv.org/abs/1202.4087},  citeulike-linkout-1 = {http://arxiv.org/pdf/1202.4087},  day = {18},  eprint = {1202.4087},  keywords = {network-science},  month = feb,  posted-at = {2012-03-23 17:53:19},  priority = {2},  title = {{Epidemic spreading on interconnected networks}},  url = {http://arxiv.org/abs/1202.4087},  year = {2012}  }  @article{citeulike:101,  abstract = {{Complex networks are studied across many fields of science. To uncover their structural design principles, we defined †network motifs,†patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks. We found such motifs in networks from biochemistry, neurobiology, ecology, and engineering. The motifs shared by ecological food webs were distinct from the motifs shared by the genetic networks of Escherichia coli and Saccharomyces cerevisiae or from those found in the World Wide Web. Similar motifs were found in networks that perform information processing, even though they describe elements as different as biomolecules within a cell and synaptic connections between neurons in Caenorhabditis elegans. Motifs may thus define universal classes of networks. This approach may uncover the basic building blocks of most networks.}},  address = {Departments of Physics of Complex Systems and Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100.},  author = {Milo, R. and Shen-Orr, S. and Itzkovitz, S. and Kashtan, N. and Chklovskii, D. and Alon, U.},  citeulike-article-id = {101},  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.298.5594.824},  citeulike-linkout-1 = {http://www.sciencemag.org/content/298/5594/824.abstract},  citeulike-linkout-2 = {http://www.sciencemag.org/content/298/5594/824.full.pdf},  citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/298/5594/824},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/12399590},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=12399590},  citeulike-linkout-6 = {http://www.sciencemag.org/cgi/content/full/298/5594/824},  day = {25},  doi = {10.1126/science.298.5594.824},  issn = {1095-9203},  journal = {Science},  keywords = {network-science},  month = oct,  number = {5594},  pages = {824--827},  pmid = {12399590},  posted-at = {2012-03-20 17:17:45},  priority = {2},  publisher = {American Association for the Advancement of Science},  title = {{Network Motifs: Simple Building Blocks of Complex Networks}},  url = {http://dx.doi.org/10.1126/science.298.5594.824},  volume = {298},  year = {2002}  }  @article{citeulike:10476610,  abstract = {{  The variability of (i) the B period between birth and initiation of chromosome replication, (ii) the U period between initiation of chromosome replication and initiation of cell constriction, and (iii) the interdivision period (tau) have been estimated for slowly growing Escherichia coli B/r F. Cultures synchronized by the membrane elution technique were pulse-labeled with [3H]thymidine or continuously labeled with [3H]thymine. After fixation, the pattern of deoxyribonucleic acid replication was analyzed by electron microscopic radioautography. Cell length was found to increase exponentially with age at two different slow growth rates. The coefficient of variation of the B period was estimated to be 60\%, that of the U period was 29\%, and that of the interdivision period was 12\%. From these values and the coefficient of variation of length at different cell cycle events were calculated a negative correlation between the B and U period (r = -0.9) and a positive correlation between length at birth and cell separation (r = 0.6). Initiation of chromosome replication and cell constriction were strictly correlated both with respect to age (r = 0.7) and length (r = 0.8). On the other hand, length at initiation of chromosome replication was distantly correlated with age (r = 0.1) or length at birth (r = 0.3). This low correlation excludes a model in which chromosome initiation is controlled by a random event in the B period. It favors a model in which chromosome initiation occurs at a particular distributed size independent of cell division.  }},  author = {Koppes, L. J. and Meyer, M. and Oonk, H. B. and de Jong, M. A. and Nanninga, N.},  citeulike-article-id = {10476610},  citeulike-linkout-0 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC294487/},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/6997267},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=6997267},  issn = {0021-9193},  journal = {Journal of bacteriology},  keywords = {bacterial-biology},  month = sep,  number = {3},  pages = {1241--1252},  pmcid = {PMC294487},  pmid = {6997267},  posted-at = {2012-03-19 17:05:28},  priority = {2},  title = {{Correlation between size and age at different events in the cell division cycle of Escherichia coli.}},  url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC294487/},  volume = {143},  year = {1980}  }  @article{citeulike:44,  abstract = {{The study of networks pervades all of science, from neurobiology to statistical physics. The most basic issues are structural: how does one characterize the wiring diagram of a food web or the Internet or the metabolic network of the bacterium Escherichia coli? Are there any unifying principles underlying their topology? From the perspective of nonlinear dynamics, we would also like to understand how an enormous network of interacting dynamical systems — be they neurons, power stations or lasers — will behave collectively, given their individual dynamics and coupling architecture. Researchers are only now beginning to unravel the structure and dynamics of complex networks.}},  address = {Department of Theoretical and Applied Mechanics and Center for Applied Mathematics, Cornell University, Ithaca, New York 14853-1503, USA. [email protected]},  author = {Strogatz, Steven H.},  citeulike-article-id = {44},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/35065725},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/410268a0},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/11258382},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=11258382},  day = {08},  doi = {10.1038/35065725},  issn = {0028-0836},  journal = {Nature},  keywords = {network-science},  month = mar,  number = {6825},  pages = {268--276},  pmid = {11258382},  posted-at = {2012-03-18 20:17:09},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Exploring complex networks}},  url = {http://dx.doi.org/10.1038/35065725},  volume = {410},  year = {2001}  }  @article{citeulike:7651748,  abstract = {{In the present article we emphasize the importance of modeling time in the  context of agent-based models. To this end, we present a (selective) survey of  the Cellular Automata-literature on updating and draw parallels to the issue of  agent activation in agent-based models. By means of two simple models,  Schelling's segregation model and Epstein's demographic prisoner's dilemma we  investigate the influence of choosing different regimes of agent activation.  Our experiments indicate that timing is not a critical issue for very simple  models but bears huge influence on model behavior and results as soon as the  degree of complexity increases only so slightly. After a brief review of the  way commonly used ABM simulation environments handle the issue of timing, we  draw some tentative conclusions about the importance of timing and the need for  more research towards that direction, similar to the concerted effort on  updating in cellular automata.}},  archivePrefix = {arXiv},  author = {Radax, Wolfgang and Rengs, Bernhard},  citeulike-article-id = {7651748},  citeulike-linkout-0 = {http://arxiv.org/abs/1008.0941},  citeulike-linkout-1 = {http://arxiv.org/pdf/1008.0941},  day = {5},  eprint = {1008.0941},  keywords = {individual-based-modeling},  month = aug,  posted-at = {2012-03-18 16:49:38},  priority = {2},  title = {{Timing matters: Lessons From The CA Literature On Updating}},  url = {http://arxiv.org/abs/1008.0941},  year = {2010}  }  @article{citeulike:10471975,  abstract = {{Modelling populations on an individual-by-individual basis has proven to be a fruitful approach. Many complex patterns that are observed on the population level have been shown to arise from simple interactions between individuals. However, a major problem with these models is that the typically large number of individuals needed requires impractically large computation times. The common solution, reduction of the number of individuals in the model, can lead to loss of variation, irregular dynamics, and large sensitivity to the value of random generator seeds. As a solution to these problems, we propose to add an extra variable feature to each model individual, namely the number of real individuals it actually represents. This approach allows zooming from a real individual-by-individual model to a cohort representation or ultimately an all-animals-are-equal view without changing the model formulation. Therefore, the super-individual concept offers easy possibilities to check whether the observed behaviour is an artifact of following a limited number of individuals or of lumping individuals, and also to verify whether individual variability is indeed an essential ingredient for the observed behaviour. In addition the approach offers arbitrarily large computational advantages. As an example the super-individual approach is applied to a generic model of the dynamics of a size-distributed consumer cohort as well as to an elaborate applied simulation model of the recruitment of striped bass.}},  author = {Scheffer, M. and Baveco, J. M. and DeAngelis, D. L. and Rose, K. A. and van Nes, E. H.},  citeulike-article-id = {10471975},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/0304-3800(94)00055-m},  doi = {10.1016/0304-3800(94)00055-m},  issn = {03043800},  journal = {Ecological Modelling},  keywords = {individual-based-modeling},  month = jul,  number = {2-3},  pages = {161--170},  posted-at = {2012-03-18 16:45:58},  priority = {2},  title = {{Super-individuals a simple solution for modelling large populations on an individual basis}},  url = {http://dx.doi.org/10.1016/0304-3800(94)00055-m},  volume = {80},  year = {1995}  }  @article{citeulike:5785993,  abstract = {{  Prokaryotes come in a wide variety of shapes, determined largely by natural selection, physical constraints, and patterns of cell growth and division. Because of their relative simplicity, bacterial cells are excellent models for how genes and proteins can directly determine morphology. Recent advances in cytological methods for bacteria have shown that distinct cytoskeletal filaments composed of actin and tubulin homologs are important for guiding growth patterns of the cell wall in bacteria, and that the glycan strands that constitute the wall are generally perpendicular to the direction of growth. This cytoskeleton-directed cell wall patterning is strikingly reminiscent of how plant cell wall growth is regulated by microtubules. In rod-shaped bacilli, helical cables of actin-like MreB protein stretch along the cell length and orchestrate elongation of the cell wall, whereas the tubulin-like FtsZ protein directs formation of the division septum and the resulting cell poles. The overlap and interplay between these two systems and the peptidoglycan-synthesizing enzymes they recruit are the major driving forces of cylindrical shapes. Round cocci, on the other hand, have lost their MreB cables and instead must grow mainly via their division septum, giving them their characteristic round or ovoid shapes. Other bacteria that lack MreB homologs or even cell walls use distinct cytoskeletal systems to maintain their distinct shapes. Here I review what is known about the mechanisms that determine the shape of prokaryotic cells.  }},  author = {Margolin, William},  citeulike-article-id = {5785993},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.cub.2009.06.033},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19906583},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19906583},  day = {15},  doi = {10.1016/j.cub.2009.06.033},  issn = {1879-0445},  journal = {Current biology : CB},  keywords = {system-biology},  month = sep,  number = {17},  pages = {R812--R822},  pmid = {19906583},  posted-at = {2012-02-14 17:36:47},  priority = {2},  title = {{Sculpting the bacterial cell.}},  url = {http://dx.doi.org/10.1016/j.cub.2009.06.033},  volume = {19},  year = {2009}  }  @article{citeulike:10328527,  abstract = {{  A major goal of biological research is to provide a mechanistic understanding of diverse biological processes. To this end, synthetic biology offers a powerful approach, whereby biological questions can be addressed in a well-defined framework. By constructing simple gene circuits, such studies have generated new insights into the design principles of gene regulatory networks. Recently, this strategy has been applied to analyze ecological and evolutionary questions, where population-level interactions are critical. Here, we highlight recent development of such systems and discuss how they were used to address problems in ecology and evolutionary biology. As illustrated by these examples, synthetic ecosystems provide a unique platform to study ecological and evolutionary phenomena that are challenging to study in their natural contexts.  Copyright {\copyright} 2012. Published by Elsevier Ltd.  }},  author = {Tanouchi, Yu and Smith, Robert P. and You, Lingchong},  citeulike-article-id = {10328527},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.copbio.2012.01.006},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/22310174},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=22310174},  day = {4},  doi = {10.1016/j.copbio.2012.01.006},  issn = {1879-0429},  journal = {Current opinion in biotechnology},  keywords = {system-biology},  month = feb,  pmid = {22310174},  posted-at = {2012-02-11 09:55:12},  priority = {0},  title = {{Engineering microbial systems to explore ecological and evolutionary dynamics.}},  url = {http://dx.doi.org/10.1016/j.copbio.2012.01.006},  year = {2012}  }  @article{citeulike:453514,  abstract = {{Understanding the emergence of the complex organization of biofilms from the interactions of its parts, individual cells and their environment, is the aim of the individual-based modelling (IbM) approach. This IbM is version 2 of BacSim, a model of Escherichia coli colony growth, which was developed into a two-dimensional multi-substrate, multi-species model of nitrifying biofilms. It was compared with the established biomass-based model (BbM) of Picioreanu and others. Both models assume that biofilm growth is due to the processes of diffusion, reaction and growth (including biomass growth, division and spreading). In the IbM, each bacterium was a spherical cell in continuous space and had variable growth parameters. Spreading of biomass occurred by shoving of cells to minimize overlap between cells. In the BbM, biomass was distributed in a discrete grid and each species had uniform growth parameters. Spreading of biomass occurred by cellular automata rules. In the IbM, the effect of random variation of growth parameters of individual bacteria was negligible in contrast to the E. coli colony model, because the heterogeneity of substrate concentrations in the biofilm was more important. The growth of a single cell into a clone, and therefore also the growth of the less abundant species, depended on the randomly chosen site of attachment, owing to the heterogeneity of substrate concentrations in the biofilm. The IbM agreed with the BbM regarding the overall growth of the biofilm, due to the same diffusion-reaction processes. However, the biofilm shape was different due to the different biomass spreading mechanisms. The IbM biofilm was more confluent and rounded due to the steady, deterministic and directionally unconstrained spreading of the bacteria. Since the biofilm shape is influenced by the spreading mechanism, it is partially independent of growth, which is driven by diffusion-reaction. Chance in initial attachment events modifies the biofilm shape and the growth of single cells because of the high heterogeneity of substrate concentrations in the biofilm, which again results from the interaction of diffusion-reaction with spreading. This stresses the primary importance of spreading and chance in addition to diffusion-reaction in the emergence of the complexity of the biofilm community.}},  address = {Cardiff School of Biosciences, Cardiff University, PO Box 915, Cardiff CF10 3TL, UK. [email protected]},  author = {Kreft, Jan-Ulrich and Picioreanu, Cristian and Wimpenny, Julian W. T. and van Loosdrecht, Mark C. M.},  citeulike-article-id = {453514},  citeulike-linkout-0 = {http://mic.sgmjournals.org/content/147/11/2897.abstract},  citeulike-linkout-1 = {http://mic.sgmjournals.org/content/147/11/2897.full.pdf},  citeulike-linkout-2 = {http://mic.sgmjournals.org/cgi/content/abstract/147/11/2897},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/11700341},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=11700341},  day = {01},  issn = {1465-2080},  journal = {Microbiology},  keywords = {individual-based-modeling},  month = nov,  number = {11},  pages = {2897--2912},  pmid = {11700341},  posted-at = {2012-02-06 19:34:43},  priority = {0},  publisher = {Society for General Microbiology},  title = {{Individual-based modelling of biofilms}},  url = {http://mic.sgmjournals.org/content/147/11/2897.abstract},  volume = {147},  year = {2001}  }  @article{citeulike:10314292,  abstract = {{Many bacteria exhibit multicellular behaviour, with individuals within a colony coordinating their actions for communal benefit. One example of complex multicellular phenotypes is myxobacterial fruiting body formation, where thousands of cells aggregate into large three-dimensional structures, within which sporulation occurs. Here we describe a novel theoretical model, which uses Monte Carlo dynamics to simulate and explain multicellular development. The model captures multiple behaviours observed during fruiting, including the spontaneous formation of aggregation centres and the formation and dissolution of fruiting bodies. We show that a small number of physical properties in the model is sufficient to explain the most frequently documented population-level behaviours observed during development in Myxococcus xanthus. Understanding how relatively simple, single cell bacteria can communicate and coordinate their actions is important for explaining how complex multicellular behaviour can emerge without a central controller. Myxobacteria are particularly interesting in this respect because cells undergo multiple phases of coordinated behaviour during their life-cycle. One of the most fascinating and complex phases is the formation of fruiting bodies—large multicellular aggregates of cells formed in response to starvation. In this article we use evidence from the latest experimental data to construct a computational model explaining how cells can form fruiting bodies. Both in our model and in nature, cells move together in dense swarms, which collide to form aggregation centres. In particular, we show that it is possible for aggregates to form spontaneously where previous models require artificially induced aggregates to start the fruiting process.}},  author = {Holmes, Antony B. and Kalvala, Sara and Whitworth, David E.},  citeulike-article-id = {10314292},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000686},  day = {26},  doi = {10.1371/journal.pcbi.1000686},  journal = {PLoS Comput Biol},  keywords = {simulation-and-modeling},  month = feb,  number = {2},  pages = {e1000686+},  posted-at = {2012-02-04 18:32:02},  priority = {2},  publisher = {Public Library of Science},  title = {{Spatial Simulations of Myxobacterial Development}},  url = {http://dx.doi.org/10.1371/journal.pcbi.1000686},  volume = {6},  year = {2010}  }  @article{citeulike:10293307,  author = {Gubbins, Michael J. and Lau, Isabella and Will, William R. and Manchak, Janet M. and Raivio, Tracy L. and Frost, Laura S.},  citeulike-article-id = {10293307},  citeulike-linkout-0 = {http://dx.doi.org/10.1128/jb.184.20.5781-5788.2002},  citeulike-linkout-1 = {http://jb.asm.org/content/184/20/5781.abstract},  citeulike-linkout-2 = {http://jb.asm.org/content/184/20/5781.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/12270837},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=12270837},  day = {15},  doi = {10.1128/jb.184.20.5781-5788.2002},  issn = {1098-5530},  journal = {Journal of Bacteriology},  keywords = {bacterial-biology},  month = oct,  number = {20},  pages = {5781--5788},  pmid = {12270837},  posted-at = {2012-02-01 21:59:31},  priority = {0},  publisher = {American Society for Microbiology},  title = {{The Positive Regulator, TraJ, of the Escherichia coli F Plasmid Is Unstable in a cpxA* Background}},  url = {http://dx.doi.org/10.1128/jb.184.20.5781-5788.2002},  volume = {184},  year = {2002}  }  @article{citeulike:3420502,  abstract = {{The structure of bacterial populations is governed by the interplay of many physical and biological factors, ranging from properties of surrounding aqueous media and substrates to cell–cell communication and gene expression in individual cells. The biomechanical interactions arising from the growth and division of individual cells in confined environments are ubiquitous, yet little work has focused on this fundamental aspect of colony formation. We analyze the spatial organization of Escherichia coli growing in a microfluidic chemostat. We find that growth and expansion of a dense colony of cells leads to a dynamical transition from an isotropic disordered phase to a nematic phase characterized by orientational alignment of rod-like cells. We develop a continuum model of collective cell dynamics based on equations for local cell density, velocity, and the tensor order parameter. We use this model and discrete element simulations to elucidate the mechanism of cell ordering and quantify the relationship between the dynamics of cell proliferation and the spatial structure of the population.}},  author = {Volfson, Dmitri and Cookson, Scott and Hasty, Jeff and Tsimring, Lev S.},  citeulike-article-id = {3420502},  citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0706805105},  citeulike-linkout-1 = {http://www.pnas.org/content/105/40/15346.abstract},  citeulike-linkout-2 = {http://www.pnas.org/content/105/40/15346.full.pdf},  citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/105/40/15346},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/18832176},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=18832176},  day = {07},  doi = {10.1073/pnas.0706805105},  issn = {1091-6490},  journal = {Proceedings of the National Academy of Sciences},  keywords = {simulation-and-modeling},  month = oct,  number = {40},  pages = {15346--15351},  pmid = {18832176},  posted-at = {2012-01-31 19:31:51},  priority = {0},  publisher = {National Academy of Sciences},  title = {{Biomechanical ordering of dense cell populations}},  url = {http://dx.doi.org/10.1073/pnas.0706805105},  volume = {105},  year = {2008}  }  @article{citeulike:10289515,  abstract = {{  A model is formulated to examine the possibility of (co)existence of plasmids of the same incompatibility and surface exclusion group in a bacterial population living under a feast-and-famine regime. The condition is given under which a growth rate decreasing plasmid can invade a bacterial population. It appears that in case only one plasmid type is present, the frequency of plasmid bearers will tend to a stable equilibrium if the food supply at each growth site gets exhausted and if both plasmid-free and plasmid-bearing bacteria need an equal quantity of food per cell division. If these two conditions are not satisfied, the frequency of plasmid-bearers might oscillate. Two plasmids will sometimes be able to coexist, but only if they follow different survival strategies; one with a high conjugational transfer rate and a lower fitness of its host, and the other with a low transfer rate and a higher host fitness. Coexistence of three plasmids of the same surface exclusion group is impossible.  }},  author = {Van der Hoeven, N.},  citeulike-article-id = {10289515},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/3531375},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=3531375},  issn = {0303-6812},  journal = {Journal of mathematical biology},  keywords = {simulation-and-modeling},  number = {3},  pages = {313--325},  pmid = {3531375},  posted-at = {2012-01-31 19:31:30},  priority = {0},  title = {{Coexistence of incompatible plasmids in a bacterial population living under a feast and famine regime.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/3531375},  volume = {24},  year = {1986}  }  @article{citeulike:10289514,  abstract = {{  A model is formulated to examine the possibility of coexistence of two or more plasmids of the same surface exclusion group in a bacterial chemostat culture. It appears that two plasmids are able to coexist. If two plasmids can coexist they will follow different survival strategies, one with a high conjugational transfer rate and a low fitness of its host, and other with a low transfer rate and a high host fitness. Coexistence of three plasmids of the same surface exclusion group is impossible.  }},  author = {van der Hoeven, N.},  citeulike-article-id = {10289514},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/6503308},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=6503308},  day = {5},  issn = {0022-5193},  journal = {Journal of theoretical biology},  keywords = {simulation-and-modeling},  month = oct,  number = {3},  pages = {411--423},  pmid = {6503308},  posted-at = {2012-01-31 19:30:55},  priority = {0},  title = {{A mathematical model for the co-existence of incompatible, conjugative plasmids in individual bacteria of a bacterial population.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/6503308},  volume = {110},  year = {1984}  }  @article{citeulike:8629705,  abstract = {{The percolation paradigm is widely used in spatially explicit epidemic models where disease spreads between neighbouring hosts. It has been successful in identifying epidemic thresholds for invasion, separating non-invasive regimes, where the disease never invades the system, from invasive regimes where the probability of invasion is positive. However, its power is mainly limited to homogeneous systems. When heterogeneity (environmental stochasticity) is introduced, the value of the epidemic threshold is, in general, not predictable without numerical simulations. Here, we analyse the role of heterogeneity in a stochastic susceptible–infected–removed epidemic model on a two-dimensional lattice. In the homogeneous case, equivalent to bond percolation, the probability of invasion is controlled by a single parameter, the transmissibility of the pathogen between neighbouring hosts. In the heterogeneous model, the transmissibility becomes a random variable drawn from a probability distribution. We investigate how heterogeneity in transmissibility influences the value of the invasion threshold, and find that the resilience of the system to invasion can be suitably described by two control parameters, the mean and variance of the transmissibility. We analyse a two-dimensional phase diagram, where the threshold is represented by a phase boundary separating an invasive regime in the high-mean, low-variance region from a non-invasive regime in the low-mean, high-variance region of the parameter space. We thus show that the percolation paradigm can be extended to the heterogeneous case. Our results have practical implications for the analysis of disease control strategies in realistic heterogeneous epidemic systems.}},  author = {Neri, Franco M. and P\'{e}rez-Reche, Francisco J. and Taraskin, Sergei N. and Gilligan, Christopher A.},  citeulike-article-id = {8629705},  citeulike-linkout-0 = {http://dx.doi.org/10.1098/rsif.2010.0325},  citeulike-linkout-1 = {http://rsif.royalsocietypublishing.org/content/8/55/201.abstract},  citeulike-linkout-2 = {http://rsif.royalsocietypublishing.org/content/8/55/201.full.pdf},  citeulike-linkout-3 = {http://rsif.royalsocietypublishing.org/cgi/content/abstract/8/55/201},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/20630880},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=20630880},  day = {06},  doi = {10.1098/rsif.2010.0325},  issn = {1742-5662},  journal = {Journal of The Royal Society Interface},  keywords = {epidemiology},  month = feb,  number = {55},  pages = {201--209},  pmid = {20630880},  posted-at = {2012-01-31 06:37:51},  priority = {0},  publisher = {The Royal Society},  title = {{Heterogeneity in susceptible–infected–removed (SIR) epidemics on lattices}},  url = {http://dx.doi.org/10.1098/rsif.2010.0325},  volume = {8},  year = {2011}  }  @article{citeulike:10283930,  abstract = {{Plasmid invasion in biofilms is often surprisingly limited in spite of the close contact of cells in a biofilm. We hypothesized that this poor plasmid spread into deeper biofilm layers is caused by a dependence of conjugation on the growth rate (relative to the maximum growth rate) of the donor. By extending an individual-based model of microbial growth and interactions to include the dynamics of plasmid carriage and transfer by individual cells, we were able to conduct in silico tests of this and other hypotheses on the dynamics of conjugal plasmid transfer in biofilms. For a generic model plasmid, we find that invasion of a resident biofilm is indeed limited when plasmid transfer depends on growth, but not so in the absence of growth dependence. Using sensitivity analysis we also find that parameters related to timing (i.e. a lag before the transconjugant can transfer, transfer proficiency and scan speed) and spatial reach (EPS yield, conjugal pilus length) are more important for successful plasmid invasion than the recipients' growth rate or the probability of segregational loss. While this study identifies one factor that can limit plasmid invasion in biofilms, the new individual-based framework introduced in this work is a powerful tool that enables one to test additional hypotheses on the spread and role of plasmids in microbial biofilms.}},  author = {Merkey, Brian V. and Lardon, Laurent A. and Seoane, Jose M. and Kreft, Jan-Ulrich and Smets, Barth F.},  citeulike-article-id = {10283930},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1462-2920.2011.02535.x},  doi = {10.1111/j.1462-2920.2011.02535.x},  journal = {Environmental Microbiology},  keywords = {individual-based-modeling},  number = {9},  pages = {2435--2452},  posted-at = {2012-01-29 22:09:40},  priority = {0},  publisher = {Blackwell Publishing Ltd},  title = {{Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual-based modelling study}},  url = {http://dx.doi.org/10.1111/j.1462-2920.2011.02535.x},  volume = {13},  year = {2011}  }  @article{citeulike:7251185,  abstract = {{BACKGROUND:Modeling a dynamical biological system is often a difficult task since the a priori unknown parameters of such models are not always directly given by the experiments. Despite the lack of experimental quantitative knowledge, one can see a dynamical biological system as (i) the combined evolution tendencies (increase or decrease) of the biological compound concentrations, and: (ii) the temporal features, such as delays between two concentration peaks (i.e. the times when one of the components completes an increase (resp. decrease) phase and starts a decrease (resp. increase) phase).RESULTS:We propose herein a new hybrid modeling framework that follows such biological assumptions. This hybrid approach deals with both a qualitative structure of the system and a quantitative structure. From a theoretical viewpoint, temporal specifications are expressed as equality or inequality constraints between delay parameters, while the qualitative specifications are expressed as an ordered pattern of the concentrations peaks of the components. Using this new hybrid framework, the temporal specifications of a biological system can be obtained from incomplete experimental data. The model may be processed by a hybrid model-checker (e.g. Phaver) which is able to give some new constraints on the delay parameters (e.g. the delay for a given transition is exactly 5 hours after the later peak of a gene product concentration). Furthermore, by using a constraint solver on the previous results, it becomes possible to get the set of parameters settings which are consistent with given specifications. Such a modeling approach is particularly accurate for modeling oscillatory biological behaviors like those observed in the Drosophila circadian cycles. The achieved results concerning the parameters of this oscillatory system formally confirm the several previous studies made by numerical simulations. Moreover, our analysis makes it possible to propose an automatic investigation of the respective impact of per and tim on the circadian cycle.CONCLUSIONS:A new hybrid technique for an automatic formal analysis of biological systems is developed with a special emphasis on their oscillatory behaviors. It allows the use of incomplete and empirical biological data.}},  author = {Fromentin, Jonathan and Eveillard, Damien and Roux, Olivier},  citeulike-article-id = {7251185},  citeulike-linkout-0 = {http://dx.doi.org/10.1186/1752-0509-4-79},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20525331},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20525331},  doi = {10.1186/1752-0509-4-79},  issn = {1752-0509},  journal = {BMC Systems Biology},  keywords = {system-biology},  number = {1},  pages = {79+},  pmid = {20525331},  posted-at = {2012-01-26 19:54:11},  priority = {2},  title = {{Hybrid modeling of biological networks: mixing temporal and qualitative biological properties}},  url = {http://dx.doi.org/10.1186/1752-0509-4-79},  volume = {4},  year = {2010}  }  @book{citeulike:191333,  author = {Zeigler, Bernard P. and Praehofer, Herbert and Kim, Tag G.},  citeulike-article-id = {191333},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0127784551},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0127784551},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0127784551},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0127784551},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0127784551/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0127784551},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0127784551},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0127784551},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0127784551\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0127784551},  day = {24},  edition = {2},  howpublished = {Hardcover},  isbn = {0127784551},  keywords = {books},  month = jan,  posted-at = {2011-12-12 18:47:25},  priority = {0},  publisher = {Academic Press},  title = {{Theory of Modeling and Simulation, Second Edition}},  url = {http://www.worldcat.org/isbn/0127784551},  year = {2000}  }  @article{citeulike:10019410,  abstract = {{Conjugative plasmid transfer is key to the ability of bacteria to rapidly adapt to new environments, but there is no agreement on a single quantitative measure of the rate of plasmid transfer. Some studies derive estimates of transfer rates from mass-action differential equation models of plasmid population biology. The often-used 'endpoint method' is such an example. Others report measures of plasmid transfer efficiency that simply represent ratios of plasmid-bearing and plasmid-free cell densities and do not correspond to parameters in any mathematical model. Unfortunately, these quantities do not measure the same thing – sometimes differing by orders of magnitude – and their use is often clouded by a lack of specificity. Moreover, they do not distinguish between bulk transfer rates that are only relevant in well-mixed populations and the 'intrinsic' rates between individual cells. This leads to problems for surface-associated populations, which are not well-mixed but spatially structured. We used simulations of a spatially explicit mathematical model to evaluate the effectiveness of these various plasmid transfer efficiency measures when they are applied to surface-associated populations. The simulation results, supported by some experimental findings, showed that these measures can be affected by initial cell densities, donor-to-recipient ratios and initial cell cluster size, and are therefore flawed as universal measures of plasmid transfer efficiency. The simulations also allowed us to formulate some guiding principles on when these estimates are appropriate for spatially structured populations and how to interpret the results. While we focus on plasmid transfer, the general lessons of this study should apply to any measures of horizontal spread (e.g., infection rates in epidemiology) that are based on simple mass-action models (e.g., SIR models in epidemiology) but applied to spatial settings.}},  author = {Zhong, Xue and Droesch, Jason and Fox, Randal and Top, Eva M. and Krone, Stephen M.},  citeulike-article-id = {10019410},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jtbi.2011.10.034},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/22085738},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=22085738},  day = {9},  doi = {10.1016/j.jtbi.2011.10.034},  issn = {00225193},  journal = {Journal of Theoretical Biology},  keywords = {individual-based-modeling},  month = feb,  pages = {144--152},  pmid = {22085738},  posted-at = {2011-11-25 21:02:05},  priority = {2},  title = {{On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations}},  url = {http://dx.doi.org/10.1016/j.jtbi.2011.10.034},  volume = {294},  year = {2012}  }  @book{citeulike:7745379,  author = {Saltelli, A. and Tarantola, Stefano and Campolongo, Francesca and Ratto, Marco},  citeulike-article-id = {7745379},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0470870931},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0470870931},  citeulike-linkout-10 = {http://www.worldcat.org/oclc/53138568},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0470870931},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0470870931},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0470870931/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0470870931},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0470870931},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0470870931},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0470870931\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0470870931},  day = {02},  edition = {1},  howpublished = {Hardcover},  isbn = {0470870931},  keywords = {books},  month = apr,  posted-at = {2011-11-21 17:08:26},  priority = {2},  publisher = {Wiley},  title = {{Sensitivity Analysis in Practice: A Guide to Assessing Scientific Models}},  url = {http://www.worldcat.org/isbn/0470870931},  year = {2004}  }  @article{citeulike:10005235,  abstract = {{Computer science and biology have enjoyed a long and fruitful relationship for decades. Biologists rely on computational methods to analyze and integrate large data sets, while several computational methods were inspired by the high-level design principles of biological systems. Recently, these two directions have been converging. In this review, we argue that thinking computationally about biological processes may lead to more accurate models, which in turn can be used to improve the design of algorithms. We discuss the similar mechanisms and requirements shared by computational and biological processes and then present several recent studies that apply this joint analysis strategy to problems related to coordination, network analysis, and tracking and vision. We also discuss additional biological processes that can be studied in a similar manner and link them to potential computational problems. With the rapid accumulation of data detailing the inner workings of biological systems, we expect this direction of coupling biological and computational studies to greatly expand in the future.}},  author = {Navlakha, Saket and Bar-Joseph, Ziv},  citeulike-article-id = {10005235},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/msb.2011.78},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/msb201178},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261700/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/22068329},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=22068329},  day = {08},  doi = {10.1038/msb.2011.78},  issn = {1744-4292},  journal = {Molecular Systems Biology},  keywords = {transversal},  month = nov,  number = {1},  pmcid = {PMC3261700},  pmid = {22068329},  posted-at = {2011-11-12 18:10:51},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Algorithms in nature: the convergence of systems biology and computational thinking}},  url = {http://dx.doi.org/10.1038/msb.2011.78},  volume = {7},  year = {2011}  }  @article{citeulike:10004716,  abstract = {{  We show that difficulties in regulating cellular behavior with synthetic biological circuits may be circumvented using in silico feedback control. By tracking a circuit's output in Saccharomyces cerevisiae in real time, we precisely control its behavior using an in silico feedback algorithm to compute regulatory inputs implemented through a genetically encoded light-responsive module. Moving control functions outside the cell should enable more sophisticated manipulation of cellular processes whenever real-time measurements of cellular variables are possible.  }},  author = {Milias-Argeitis, Andreas and Summers, Sean and Stewart-Ornstein, Jacob and Zuleta, Ignacio and Pincus, David and El-Samad, Hana and Khammash, Mustafa and Lygeros, John},  citeulike-article-id = {10004716},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt.2018},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt.2018},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/22057053},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=22057053},  day = {06},  doi = {10.1038/nbt.2018},  issn = {1087-0156},  journal = {Nature Biotechnology},  keywords = {synbio-dna},  month = nov,  number = {12},  pages = {1114--1116},  pmid = {22057053},  posted-at = {2011-11-12 18:09:52},  priority = {2},  publisher = {Nature Publishing Group},  title = {{In silico feedback for in vivo regulation of a gene expression circuit}},  url = {http://dx.doi.org/10.1038/nbt.2018},  volume = {29},  year = {2011}  }  @article{citeulike:10016895,  abstract = {{Negative and positive transcriptional feedback loops are present in natural and synthetic genetic oscillators. A single gene with negative transcriptional feedback needs a time delay and sufficiently strong nonlinearity in the transmission of the feedback signal in order to produce biochemical rhythms. A single gene with only positive transcriptional feedback does not produce oscillations. Here, we demonstrate that this single-gene network in conjunction with a simple negative interaction can also easily produce rhythms. We examine a model comprised of two well-differentiated parts. The first is a positive feedback created by a protein that binds to the promoter of its own gene and activates the transcription. The second is a negative interaction in which a repressor molecule prevents this protein from binding to its promoter. A stochastic study shows that the system is robust to noise. A deterministic study identifies that the dynamics of the oscillator are mainly driven by two types of biomolecules: the protein, and the complex formed by the repressor and this protein. The main conclusion of this paper is that a simple and usual negative interaction, such as degradation, sequestration or inhibition, acting on the positive transcriptional feedback of a single gene is a sufficient condition to produce reliable oscillations. One gene is enough and the positive transcriptional feedback signal does not need to activate a second repressor gene. This means that at the genetic level an explicit negative feedback loop is not necessary. The model needs neither cooperative binding reactions nor the formation of protein multimers. Therefore, our findings could help to clarify the design principles of cellular clocks and constitute a new efficient tool for engineering synthetic genetic oscillators.}},  author = {Mir\'{o}-Bueno, Jes\'{u}s M. and Rodr\'{\i}guez-Pat\'{o}n, Alfonso},  citeulike-article-id = {10016895},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0027414},  day = {10},  doi = {10.1371/journal.pone.0027414},  issn = {1932-6203},  journal = {PLoS ONE},  keywords = {synbio-dna},  month = nov,  number = {11},  pages = {e27414+},  posted-at = {2011-11-12 18:09:04},  priority = {2},  publisher = {Public Library of Science},  title = {{A Simple Negative Interaction in the Positive Transcriptional Feedback of a Single Gene Is Sufficient to Produce Reliable Oscillations}},  url = {http://dx.doi.org/10.1371/journal.pone.0027414},  volume = {6},  year = {2011}  }  @article{citeulike:9998611,  abstract = {{The presence of a plasmid, containing gene sequences for DNA immunotherapy that are not expressed in microbial culture, imposed a degradation in bioreactor performance in cultures of the host E. coli strain. Significant decreases in growth rate (24\%) and biomass yield (7\%) and a corresponding increase in overflow metabolism were observed in a strain containing a therapeutic sequence (a hepatitis B antigen under the control of a CMV promotor). The observed increase in overflow metabolism was incorporated into a Metabolic Flux Analysis (MFA) model (as acetate secretion). Metabolic flux analysis revealed an increase in TCA cycle flux, consistent with an increased respiration rate observed in plasmid-containing cells. These effects are thought to result from increased ATP synthesis requirements (24\%) arising from the expression of the Kanr plasmid marker gene whose product accounted for 18\% of the cell protein of the plasmid-containing strain. These factors will necessitate significantly higher aeration and agitation rates or lower nutrient feed rates in high-density cultures than would be expected for plasmid-free cultures.}},  author = {Rozkov, A. and Avignone-Rossa, C. A. and Ertl, P. F. and Jones, P. and O'Kennedy, R. D. and Smith, J. J. and Dale, J. W. and Bushell, M. E.},  citeulike-article-id = {9998611},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/bit.20327},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15532038},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15532038},  day = {30},  doi = {10.1002/bit.20327},  issn = {0006-3592},  journal = {Biotechnology and bioengineering},  keywords = {bacterial-biology},  month = dec,  number = {7},  pages = {909--915},  pmid = {15532038},  posted-at = {2011-11-06 16:29:57},  priority = {2},  title = {{Characterization of the metabolic burden on Escherichia coli DH1 cells imposed by the presence of a plasmid containing a gene therapy sequence.}},  url = {http://dx.doi.org/10.1002/bit.20327},  volume = {88},  year = {2004}  }  @book{citeulike:9982820,  author = {Alberts, Bruce and Raff, Martin},  citeulike-article-id = {9982820},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0815320450},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0815320450},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0815320450},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0815320450},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0815320450/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0815320450},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0815320450},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0815320450},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0815320450\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0815320450},  day = {01},  edition = {Har/Cdr},  howpublished = {Hardcover},  isbn = {0815320450},  keywords = {books},  month = jul,  posted-at = {2011-11-03 06:24:16},  priority = {2},  publisher = {Garland},  title = {{Essential Cell Biology: An introducton to the Molecular Biology of the Cell}},  url = {http://www.worldcat.org/isbn/0815320450},  year = {1997}  }  @article{citeulike:8420583,  abstract = {{Spatially explicit models like cellular automata are widely used in ecology. The spatio-temporal order of events is a new feature of these models that does not have to be considered in equivalent non-spatial models. We considered simple stochastic cellular automata to test sensitivity of model response under different spatial and temporal sequences of events. The results indicate that very important differences in model output can be found as spatio-temporal ordering is changed, even in a very simple model. A careful choice of the way events are evaluated has to be made: the spatio-temporal ordering must be selected to match the biological characteristics of the target ecological system to be modelled. Further, a complete description of the details of this ordering should be specified in order to let others reproduce published simulation experiments.}},  author = {Ruxton, G.},  citeulike-article-id = {8420583},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0304-3800(97)00179-8},  day = {1},  doi = {10.1016/s0304-3800(97)00179-8},  issn = {03043800},  journal = {Ecological Modelling},  keywords = {simulation-and-modeling},  month = apr,  number = {2-3},  pages = {105--112},  posted-at = {2011-11-01 10:25:41},  priority = {0},  title = {{The need for biological realism in the updating of cellular automata models}},  url = {http://dx.doi.org/10.1016/s0304-3800(97)00179-8},  volume = {107},  year = {1998}  }  @article{citeulike:9972449,  abstract = {{Using a simple cellular automaton model, I demonstrate that the timing mechanism for events on different sites within the model can have a large impact on macroscopic model predictions. This implies that modellers must consider how to iterate their models so as to produce timing of events which match the biology of the problem rather than allowing a potentially unbiological timing (and hence an unrealistic model) to be imposed unintentionally by computational expedience. I discuss how to achieve this and suggest that model presentation should always describe the timing mechanism fully in order to allow others to repeat published simulation experiments.}},  author = {Ruxton, G.},  citeulike-article-id = {9972449},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/0304-3800(94)00145-6},  doi = {10.1016/0304-3800(94)00145-6},  issn = {03043800},  journal = {Ecological Modelling},  keywords = {simulation-and-modeling},  month = jan,  number = {1-3},  pages = {311--314},  posted-at = {2011-10-31 18:23:12},  priority = {0},  title = {{Effects of the spatial and temporal ordering of events on the behaviour of a simple cellular automaton}},  url = {http://dx.doi.org/10.1016/0304-3800(94)00145-6},  volume = {84},  year = {1996}  }  @article{citeulike:9962564,  abstract = {{DNA plasmids of Escherichia coli are common vectors for recombinant protein and metabolite production and have potential therapeutic applications as genetic vaccines and therapeutics. However, plasmid maintenance imposes a metabolic burden on the host cells, resulting in reduced growth rate and cell density. In 2 L batch fermentation, DH5α cells carrying a 7.3 kb NS3 plasmid had a lower specific growth rate than the non-plasmid-bearing host (0.64 h−1 versus 0.87 h−1). In this work, global transcriptional analysis was combined with proteomics studies to evaluate the effect of plasmid maintenance on gene expression. Global transcriptional expression analysis of plasmid-bearing cells over host showed a general trend of downregulated biosynthetic/energy metabolism genes, differentially expressed transport genes and upregulated heat shock proteins. In the central metabolic pathways, most glycolytic genes were downregulated, while less expression difference was found in the pentose phosphate pathway. Expression ratios of 19 proteins identified from proteomics studies were consistent with these observations. Our findings suggest that plasmid maintenance alone perturbs global gene regulation, and leads to significant changes in central metabolic pathways in the host. This work contributes to our understanding of plasmid metabolic load at the gene expression level and could potentially aid in future metabolic engineering efforts.}},  author = {Ow, Dave S. and Nissom, Peter M. and Philp, Robin and Oh, Steve K. and Yap, Miranda G.},  citeulike-article-id = {9962564},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.enzmictec.2005.11.048},  doi = {10.1016/j.enzmictec.2005.11.048},  issn = {01410229},  journal = {Enzyme and Microbial Technology},  keywords = {bacterial-biology},  month = jul,  number = {3},  pages = {391--398},  posted-at = {2011-10-30 11:06:25},  priority = {0},  title = {{Global transcriptional analysis of metabolic burden due to plasmid maintenance in Escherichia coli DH5α during batch fermentation}},  url = {http://dx.doi.org/10.1016/j.enzmictec.2005.11.048},  volume = {39},  year = {2006}  }  @article{citeulike:9962560,  abstract = {{The effects of changing the composition of the growth medium, the dilution rate and the source of the bacterial host on maintenance of the plasmid pAT153 in Escherichia coli HB101 have been studied. In a medium supplemented with Casamino acids, the plasmid was maintained longer during phosphate-limited growth at a dilution rate of 0.3 h-1 than at 0.15 h-1. In contrast, phosphate-limited growth was not achieved when the Casamino acids were replaced by proline, leucine and thiamin to satisfy the auxotrophic requirements of the host. Although 100\% of the bacteria were still ampicillin resistant after 72 generations of growth at a dilution rate of 0.15 h-1, the original plasmid had almost totally been replaced by a structurally modified plasmid which lacked a functional tet gene. Further experiments confirmed that neither the host nor the plasmid was retained unchanged in the minimal medium. The changes were highly reproducible and reflected periodic selection of sub-populations which were either plasmid-free or carried a structurally modified plasmid, which had reverted to Leu+ or Pro+, or had acquired other chromosomal mutations which gave them a selective advantage. We conclude that in complex media the plasmid is maintained longer by E. coli HB101 at a high than at a low growth rate and that different results reported from different laboratories are largely due to differences in analytical techniques and the growth medium rather than to differences in the bacterial host or the plasmid used. A fermenter-adapted strain was isolated which reproducibly maintained the plasmid longer during phosphate-limited continuous growth than the original strain which had been cultured on laboratory media.}},  author = {Brownlie, L. and Stephenson, J. R. and Cole, J. A.},  citeulike-article-id = {9962560},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/2079631},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=2079631},  issn = {0022-1287},  journal = {Journal of general microbiology},  keywords = {bacterial-biology},  month = dec,  number = {12},  pages = {2471--2480},  pmid = {2079631},  posted-at = {2011-10-30 11:01:41},  priority = {0},  title = {{Effect of growth rate on plasmid maintenance by Escherichia coli HB101(pAT153).}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/2079631},  volume = {136},  year = {1990}  }  @article{citeulike:1704379,  abstract = {{Insights into conducting research and the writing of scientific papers are given by Prof. Whitesides in this short essay. The manuscript and its guidelines has been circulated within the Whitesides' research group since 1989.}},  address = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA},  author = {Whitesides, G. . M.},  citeulike-article-id = {1704379},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/adma.200400767},  citeulike-linkout-1 = {http://www3.interscience.wiley.com/cgi-bin/abstract/109596525/ABSTRACT},  day = {04},  doi = {10.1002/adma.200400767},  issn = {0935-9648},  journal = {Advanced Materials},  keywords = {transversal},  month = aug,  number = {15},  pages = {1375--1377},  posted-at = {2011-10-25 22:08:10},  priority = {2},  publisher = {WILEY-VCH Verlag},  title = {{Whitesides' Group: Writing a Paper}},  url = {http://dx.doi.org/10.1002/adma.200400767},  volume = {16},  year = {2004}  }  @article{citeulike:8707530,  abstract = {{Ten years after the publication of the position paper "The hallmarks of cancer" (Hanahan and Weinberg Cell 100:57-70, 2000), it has become increasingly clear that mutated cells on their way to giving rise to a tumor have also to learn how to thrive in a chronically inflamed microenvironment, evade immune recognition, and suppress immune reactivity. Genetic and molecular definition of these three immune hallmarks of cancer offers the opportunity to learn how to deploy specific countermeasures to reverse the situation in favor of the immune system and, eventually, the patient. This new information could be channeled to address what seem to be the three major hallmarks for the immune control of cancer progression: effective procedures to activate immune reactivity; characterization of not-disposable oncoantigens; and counteraction of immune suppression.}},  author = {Cavallo, Federica and De Giovanni, Carla and Nanni, Patrizia and Forni, Guido and Lollini, Pier-Luigi L.},  citeulike-article-id = {8707530},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00262-010-0968-0},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042096/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21267721},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21267721},  citeulike-linkout-4 = {http://www.springerlink.com/content/y7165m6x64l6211p},  day = {1},  doi = {10.1007/s00262-010-0968-0},  issn = {1432-0851},  journal = {Cancer immunology, immunotherapy : CII},  keywords = {cancer-system-biology},  month = mar,  number = {3},  pages = {319--326},  pmcid = {PMC3042096},  pmid = {21267721},  posted-at = {2011-10-25 22:05:44},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  title = {{2011: the immune hallmarks of cancer.}},  url = {http://dx.doi.org/10.1007/s00262-010-0968-0},  volume = {60},  year = {2011}  }  @article{citeulike:6389349,  abstract = {{Most natural environments harbour a stunningly diverse collection of microbial species. In these communities, bacteria compete with their neighbours for space and resources. Laboratory experiments with pure and mixed cultures have revealed many active mechanisms by which bacteria can impair or kill other microorganisms. In addition, a growing body of theoretical and experimental population studies indicates that the interactions within and between bacterial species can have a profound impact on the outcome of competition in nature. The next challenge is to integrate the findings of these laboratory and theoretical studies and to evaluate the predictions that they generate in more natural settings.}},  author = {Hibbing, Michael E. and Fuqua, Clay and Parsek, Matthew R. and Peterson, S. Brook},  citeulike-article-id = {6389349},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrmicro2259},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrmicro2259},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879262/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19946288},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19946288},  day = {30},  doi = {10.1038/nrmicro2259},  issn = {1740-1534},  journal = {Nature reviews. Microbiology},  keywords = {system-biology},  month = jan,  number = {1},  pages = {15--25},  pmcid = {PMC2879262},  pmid = {19946288},  posted-at = {2011-10-24 21:23:02},  priority = {0},  publisher = {Nature Publishing Group},  title = {{Bacterial competition: surviving and thriving in the microbial jungle.}},  url = {http://dx.doi.org/10.1038/nrmicro2259},  volume = {8},  year = {2010}  }  @article{citeulike:9149840,  author = {Sutherland, Ian W.},  citeulike-article-id = {9149840},  citeulike-linkout-0 = {http://mic.sgmjournals.org/content/147/1/3.full.abstract},  citeulike-linkout-1 = {http://mic.sgmjournals.org/content/147/1/3.full.full.pdf},  citeulike-linkout-2 = {http://mic.sgmjournals.org/cgi/content/abstract/147/1/3},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/11160795},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=11160795},  day = {1},  journal = {Microbiology},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {3--9},  pmid = {11160795},  posted-at = {2011-10-24 19:35:24},  priority = {2},  title = {{Biofilm exopolysaccharides: a strong and sticky framework}},  url = {http://mic.sgmjournals.org/content/147/1/3.full.abstract},  volume = {147},  year = {2001}  }  @book{citeulike:781881,  abstract = {{The study of strategic action (game theory) is moving from a formal science of  rational behavior to an evolutionary tool kit for studying behavior in a broad  array of social settings. In this problem-oriented introduction to the field,  Herbert Gintis exposes students to the techniques and applications of game  theory through a wealth of sophisticated and surprisingly fun-to-solve  problems involving human (and even animal) behavior.  \_Game Theory Evolving\_ is innovative in several ways. First, it reflects game  theory's expansion into such areas as cooperation in teams, networks, the  evolution and diffusion of preferences, the connection between biology and  economics, artificial life simulations, and experimental economics. Second,  the book--recognizing that students learn by doing and that most game theory  texts are weak on problems--is organized around problems, and introduces  principles through practice. Finally, the quality of the problems is simply  unsurpassed, and each chapter provides a study plan for instructors interested  in teaching evolutionary game theory.  Reflecting the growing consensus that in many important contexts outside of  anonymous markets, human behavior is not well described by classical  "rationality," Gintis shows students how to apply game theory to model how  people behave in ways that reflect the special nature of human sociality and  individuality. This book is perfect for upper undergraduate and graduate  economics courses as well as a terrific introduction for ambitious do-it-  yourselfers throughout the behavioral sciences.}},  author = {Gintis, Herbert},  citeulike-article-id = {781881},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0691009430},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0691009430},  citeulike-linkout-10 = {http://www.worldcat.org/oclc/318276523},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0691009430},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0691009430},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0691009430/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0691009430},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0691009430},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0691009430},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0691009430\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0691009430},  day = {22},  howpublished = {Paperback},  isbn = {0691009430},  keywords = {books},  month = may,  posted-at = {2011-10-23 16:49:42},  priority = {2},  publisher = {Princeton University Press},  title = {{Game Theory Evolving}},  url = {http://www.worldcat.org/isbn/0691009430},  year = {2000}  }  @article{citeulike:668899,  abstract = {{A fundamental aspect of all biological systems is cooperation. Cooperative interactions are required for many levels of biological organization ranging from single cells to groups of animals1, 2, 3, 4. Human society is based to a large extent on mechanisms that promote cooperation5, 6, 7. It is well known that in unstructured populations, natural selection favours defectors over cooperators. There is much current interest, however, in studying evolutionary games in structured populations and on graphs8, 9, 10, 11, 12, 13, 14, 15, 16, 17. These efforts recognize the fact that who-meets-whom is not random, but determined by spatial relationships or social networks18, 19, 20, 21, 22, 23, 24. Here we describe a surprisingly simple rule that is a good approximation for all graphs that we have analysed, including cycles, spatial lattices, random regular graphs, random graphs and scale-free networks25, 26: natural selection favours cooperation, if the benefit of the altruistic act, b, divided by the cost, c, exceeds the average number of neighbours, k, which means b/c > k. In this case, cooperation can evolve as a consequence of 'social viscosity' even in the absence of reputation effects or strategic complexity.}},  author = {Ohtsuki, Hisashi and Hauert, Christoph and Lieberman, Erez and Nowak, Martin A.},  citeulike-article-id = {668899},  citeulike-linkout-0 = {http://www.biomedexperts.com/Abstract.bme/16724065},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature04605},  citeulike-linkout-2 = {http://dx.doi.org/10.1038/nature04605},  citeulike-linkout-3 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430087/},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/16724065},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=16724065},  day = {25},  doi = {10.1038/nature04605},  issn = {0028-0836},  journal = {Nature},  keywords = {transversal},  month = may,  number = {7092},  pages = {502--505},  pmcid = {PMC2430087},  pmid = {16724065},  posted-at = {2011-10-15 20:38:39},  priority = {2},  publisher = {Nature Publishing Group},  title = {{A simple rule for the evolution of cooperation on graphs and social networks}},  url = {http://dx.doi.org/10.1038/nature04605},  volume = {441},  year = {2006}  }  @inproceedings{citeulike:9848828,  abstract = {{Processes that occur in many biological systems are not synchronous, but are governed by asynchronous updating. Although some previous models of multi agent systems have incorporated asynchronous updating in an informal or implicit way, the importance of asynchronous behaviour has been largely overlooked. However, the update scheme chosen is very important in determining the overall system behaviour. We illustrate this point using several updating schemes in simple models. The implication is that care should be given to selecting an update scheme that is appropriate for the modelling application. We also observe that certain ordered asynchronous processes play a role in emergent modularity: an important process in the evolution of complexity in living systems.}},  address = {Cambridge, MA, USA},  author = {Cornforth, David and Green, David G. and Newth, David and Kirley, Michael},  booktitle = {Proceedings of the eighth international conference on Artificial life},  citeulike-article-id = {9848828},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=860301},  isbn = {0-262-69281-3},  keywords = {individual-based-modeling},  pages = {28--32},  posted-at = {2011-10-04 07:45:59},  priority = {2},  publisher = {MIT Press},  title = {{Do artificial ants march in step? ordered asynchronous processes and modularity in biological systems}},  url = {http://portal.acm.org/citation.cfm?id=860301},  year = {2003}  }  @book{citeulike:9848800,  author = {Stubberud, Allen and Williams, Ivan and DiStefano, Joseph},  citeulike-article-id = {9848800},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0070170525},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0070170525},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0070170525},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0070170525},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0070170525/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0070170525},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0070170525},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0070170525},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0070170525\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0070170525},  day = {01},  edition = {2},  howpublished = {Paperback},  isbn = {0070170525},  keywords = {books},  month = oct,  posted-at = {2011-10-04 07:41:56},  priority = {2},  publisher = {McGraw-Hill},  title = {{Schaum's Outline of Feedback and Control Systems (Schaum's)}},  url = {http://www.worldcat.org/isbn/0070170525},  year = {1994}  }  @article{citeulike:9706267,  abstract = {{ Large-scale cancer genomics, proteomics and RNA-sequencing efforts are currently mapping in fine detail the genetic and biochemical alterations that occur in cancer. However, it is becoming clear that it is difficult to integrate and interpret these data and to translate them into treatments. This difficulty is compounded by the recognition that cancer cells evolve, and that initiation, progression and metastasis are influenced by a wide variety of factors. To help tackle this challenge, the US National Cancer Institute Physical Sciences-Oncology Centers initiative is bringing together physicists, cancer biologists, chemists, mathematicians and engineers. How are we beginning to address cancer from the perspective of the physical sciences? }},  author = {Michor, Franziska and Liphardt, Jan and Ferrari, Mauro and Widom, Jonathan},  citeulike-article-id = {9706267},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrc3092},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrc3092},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21850037},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21850037},  day = {18},  doi = {10.1038/nrc3092},  issn = {1474-175X},  journal = {Nature Reviews Cancer},  keywords = {simulation-and-modeling},  month = aug,  number = {9},  pages = {657--670},  pmid = {21850037},  posted-at = {2011-10-03 20:58:43},  priority = {0},  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},  title = {{What does physics have to do with cancer?}},  url = {http://dx.doi.org/10.1038/nrc3092},  volume = {11},  year = {2011}  }  @incollection{citeulike:9844574,  abstract = {{Cellular Automata (CA) are generally acknowledged to be a powerful way to describe and model natural phenomena [1–3]. There are even tempting claims that nature itself is one big (quantum) information processing system, e.g. [4], and that CA may actually be nature's way to do this processing [5–7]. We will not embark on this philosophical road, but ask ourselves a more mundane question. Can we use CA to model the inherently multi-scale processes in nature and use these models for efficient simulations on digital computers?}},  address = {Berlin, Heidelberg},  author = {Hoekstra, Alfons and Caiazzo, Alfonso and Lorenz, Eric and Falcone, Jean-Luc and Chopard, Bastien},  chapter = {3},  citeulike-article-id = {9844574},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-12203-3\_3},  citeulike-linkout-1 = {http://www.springerlink.com/content/k751k8512x7pl6r2},  doi = {10.1007/978-3-642-12203-3\_3},  editor = {Kroc, Jiri and Sloot, Peter M. A. and Hoekstra, Alfons G.},  isbn = {978-3-642-12202-6},  keywords = {simulation-and-modeling},  pages = {29--57},  posted-at = {2011-10-02 18:11:58},  priority = {0},  publisher = {Springer Berlin / Heidelberg},  series = {Understanding Complex Systems},  title = {{Complex Automata: Multi-scale Modeling with Coupled Cellular Automata Simulating Complex Systems by Cellular Automata}},  url = {http://dx.doi.org/10.1007/978-3-642-12203-3\_3},  volume = {0},  year = {2010}  }  @article{citeulike:8129560,  abstract = {{Interpretive and predictive tools are needed to assist in the understanding of cell invasion processes. Cell invasion involves cell motility and proliferation, and is central to many biological processes including developmental morphogenesis and tumor invasion. Experimental data can be collected across a wide range of scales, from the population scale to the individual cell scale. Standard continuum or discrete models used in isolation are insufficient to capture this wide range of data. We develop a discrete cellular automata model of invasion with experimentally motivated rules. The cellular automata algorithm is applied to a narrow two-dimensional lattice and simulations reveal the formation of invasion waves moving with constant speed. The simulation results are averaged in one dimension—these data are used to identify the time history of the leading edge to characterize the population-scale wave speed. This allows the relationship between the population-scale wave speed and the cell-scale parameters to be determined. This relationship is analogous to well-known continuum results for Fisher's equation. The cellular automata algorithm also produces individual cell trajectories within the invasion wave that are analogous to cell trajectories obtained with new experimental techniques. Our approach allows both the cell-scale and population-scale properties of invasion to be predicted in a way that is consistent with multiscale experimental data. Furthermore we suggest that the cellular automata algorithm can be used in conjunction with individual data to overcome limitations associated with identifying cell motility mechanisms using continuum models alone.}},  author = {Simpson, Matthew J. and Merrifield, Alistair and Landman, Kerry A. and Hughes, Barry D.},  citeulike-article-id = {8129560},  citeulike-linkout-0 = {http://dx.doi.org/10.1103/physreve.76.021918},  citeulike-linkout-1 = {http://link.aps.org/abstract/PRE/v76/i2/e021918},  citeulike-linkout-2 = {http://link.aps.org/pdf/PRE/v76/i2/e021918},  doi = {10.1103/physreve.76.021918},  journal = {Physical Review E},  keywords = {simulation-and-modeling},  month = aug,  number = {2},  pages = {021918+},  posted-at = {2011-10-02 12:12:08},  priority = {0},  publisher = {American Physical Society},  title = {{Simulating invasion with cellular automata: Connecting cell-scale and population-scale properties}},  url = {http://dx.doi.org/10.1103/physreve.76.021918},  volume = {76},  year = {2007}  }  @article{citeulike:4606573,  abstract = {{Oscillations play an important physiological role in a variety of biological systems. For example, respiration and carbohydrate synthesis are coupled to the circadian clock in cyanobacteria (Ishiura et al 1998 Science 281 1519) and ultradian oscillations with time periods of a few hours have been observed in immune response (NF-kB, Hoffmann et al 2002 Science 298 1241, Neson et al 2004 Science 306 704), apoptosis (p53, Lahav et al 2004 Nat. Genet. 36 53), development (Hes, Hirata et al 2002 Science 298 840) and growth hormone secretion (Plotsky and Vale 1985 Science 230 461, Zeitler et al 1991 Proc. Natl. Acad. Sci. USA 88 8920). Here we discuss how any bistable system can be 'frustrated' to produce oscillations of a desired nature--we use the term frustration, in analogy to frustrated spins in antiferromagnets, to refer to the addition of a negative feedback loop that destabilizes the bistable system. We show that the molecular implementation can use a wide variety of methods ranging from translation regulation, using small non-coding RNAs, to targeted protein modification to transcriptional regulation. We also introduce a simple graphical method for determining whether a particular implementation will produce oscillations. The shape of the resulting oscillations can be readily tuned to produce spiky and asymmetric oscillations--quite different from the shapes produced by synthetic oscillators (Elowitz and Leibler 2000 Nature 403 335, Fung et al 2005 Nature 435 118). The time period and amplitude can also be manipulated and these oscillators are easy to reset or switch on and off using a tunable external input. The mechanism of frustrated bistability could thus prove to be an easily implementable way to synthesize flexible, designable oscillators.}},  author = {Krishna, S. and Semsey, S. and Jensen, M. H.},  citeulike-article-id = {4606573},  citeulike-linkout-0 = {http://dx.doi.org/10.1088/1478-3975/6/3/036009},  doi = {10.1088/1478-3975/6/3/036009},  issn = {1478-3975},  journal = {Physical Biology},  keywords = {synbio-bacterial},  month = sep,  number = {3},  pages = {036009+},  posted-at = {2011-10-02 10:30:34},  priority = {2},  publisher = {IOP Publishing},  title = {{Frustrated bistability as a means to engineer oscillations in biological systems}},  url = {http://dx.doi.org/10.1088/1478-3975/6/3/036009},  volume = {6},  year = {2009}  }  @book{citeulike:4470156,  abstract = {{In the years following her role as the lead author of the international  bestseller, \_Limits to Growth\_—the first book to show the consequences of  unchecked growth on a finite planet— Donella Meadows remained a pioneer of  environmental and social analysis until her untimely death in 2001.  Meadows' newly released manuscript, \_Thinking in Systems\_, is a concise and  crucial book offering insight for problem solving on scales ranging from the  personal to the global. Edited by the Sustainability Institute's Diana Wright,  this essential primer brings systems thinking out of the realm of computers  and equations and into the tangible world, showing readers how to develop the  systems-thinking skills that thought leaders across the globe consider  critical for 21st-century life.  Some of the biggest problems facing the world—war, hunger, poverty, and  environmental degradation—are essentially system failures. They cannot be  solved by fixing one piece in isolation from the others, because even  seemingly minor details have enormous power to undermine the best efforts of  too-narrow thinking.  While readers will learn the conceptual tools and methods of systems thinking,  the heart of the book is grander than methodology. Donella Meadows was known  as much for nurturing positive outcomes as she was for delving into the  science behind global dilemmas. She reminds readers to pay attention to what  is important, not just what is quantifiable, to stay humble, and to stay a  learner.  In a world growing ever more complicated, crowded, and interdependent,  \_Thinking in Systems\_ helps readers avoid confusion and helplessness, the  first step toward finding proactive and effective solutions.}},  author = {Meadows, Donella H.},  citeulike-article-id = {4470156},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/1603580557},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/1603580557},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/1603580557},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/1603580557},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/1603580557/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/1603580557},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/1603580557},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN1603580557},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=1603580557\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/1603580557},  day = {03},  howpublished = {Paperback},  isbn = {1603580557},  keywords = {books},  month = dec,  posted-at = {2011-09-26 19:34:54},  priority = {0},  publisher = {Chelsea Green Publishing},  title = {{Thinking in Systems: A Primer}},  url = {http://www.worldcat.org/isbn/1603580557},  year = {2008}  }  @article{citeulike:2416308,  abstract = {{ Cancer research attracts broad resources and scientists from many disciplines, and has produced some impressive advances in the treatment and understanding of this disease. However, a comprehensive mechanistic view of the cancer process remains elusive. To achieve this it seems clear that one must assemble a physically integrated team of interdisciplinary scientists that includes mathematicians, to develop mathematical models of tumorigenesis as a complex process. Examining these models and validating their findings by experimental and clinical observations seems to be one way to reconcile molecular reductionist with quantitative holistic approaches and produce an integrative mathematical oncology view of cancer progression.}},  author = {Anderson, Alexander R. A. and Quaranta, Vito},  citeulike-article-id = {2416308},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrc2329},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrc2329},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18273038},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18273038},  day = {01},  doi = {10.1038/nrc2329},  issn = {1474-175X},  journal = {Nat Rev Cancer},  keywords = {cancer-system-biology},  month = mar,  number = {3},  pages = {227--234},  pmid = {18273038},  posted-at = {2011-08-22 15:30:42},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Integrative mathematical oncology}},  url = {http://dx.doi.org/10.1038/nrc2329},  volume = {8},  year = {2008}  }  @article{citeulike:4640063,  abstract = {{Agent-based modeling (ABM) is an in silico technique that is being used in a variety of research areas such as in social sciences, economics and increasingly in biomedicine as an interdisciplinary tool to study the dynamics of complex systems. Here, we describe its applicability to integrative tumor biology research by introducing a multi-scale tumor modeling platform that understands brain cancer as a complex dynamic biosystem. We summarize significant findings of this work, and discuss both challenges and future directions for ABM in the field of cancer research.}},  author = {Zhang, Le and Wang, Zhihui and Sagotsky, Jonathan A. and Deisboeck, Thomas S.},  booktitle = {Journal of Mathematical Biology},  citeulike-article-id = {4640063},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00285-008-0211-1},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18787828},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18787828},  citeulike-linkout-3 = {http://www.springerlink.com/content/k346070x5360l213},  citeulike-linkout-4 = {http://link.springer.com/article/10.1007/s00285-008-0211-1},  day = {1},  doi = {10.1007/s00285-008-0211-1},  issn = {0303-6812},  journal = {Journal of mathematical biology},  keywords = {cancer-system-biology},  month = apr,  number = {4-5},  pages = {545--559},  pmid = {18787828},  posted-at = {2011-08-22 15:28:43},  priority = {2},  publisher = {Springer-Verlag},  title = {{Multiscale agent-based cancer modeling.}},  url = {http://dx.doi.org/10.1007/s00285-008-0211-1},  volume = {58},  year = {2009}  }  @article{citeulike:9148783,  abstract = {{Social interaction among cells is essential for multicellular complexity. But how do molecular networks within individual cells confer the ability to interact? And how do those same networks evolve from the evolutionary conflict between individual- and population-level interests? Recent studies have dissected social interaction at the molecular level by analyzing both synthetic and natural microbial populations. These studies shed new light on the role of population structure for the evolution of cooperative interactions and revealed novel molecular mechanisms that stabilize cooperation among cells. New understanding of populations is changing our view of microbial processes, such as pathogenesis and antibiotic resistance, and suggests new ways to fight infection by exploiting social interaction. The study of social interaction is also challenging established paradigms in cancer evolution and immune system dynamics. Finding similar patterns in such diverse systems suggests that the same 'social interaction motifs' may be general to many cell populations.}},  author = {Xavier, Joao B.},  citeulike-article-id = {9148783},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/msb.2011.16},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/msb201116},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101950/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/21487402},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=21487402},  day = {12},  doi = {10.1038/msb.2011.16},  issn = {1744-4292},  journal = {Molecular systems biology},  keywords = {cancer-system-biology},  month = apr,  number = {1},  pmcid = {PMC3101950},  pmid = {21487402},  posted-at = {2011-08-22 14:09:33},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Social interaction in synthetic and natural microbial communities.}},  url = {http://dx.doi.org/10.1038/msb.2011.16},  volume = {7},  year = {2011}  }  @article{citeulike:490947,  abstract = {{Cancer research has focused on the identification of molecular differences between cancerous and healthy cells. The emerging picture is overwhelmingly complex. Molecules out of many parallel signal transduction pathways are involved. Their activities appear to be controlled by multiple factors. The action of regulatory circuits, cross-talk between pathways and the non-linear reaction kinetics of biochemical processes complicate the understanding and prediction of the outcome of intracellular signaling. In addition, interactions between tumor and other cell types give rise to a complex supra-cellular communication network. If cancer is such a complex system, how can one ever predict the effect of a mutation in a particular gene on a functionality of the entire system? And, how should one go about identifying drug targets? Here, we argue that one aspect is to recognize, where the essence resides, i.e. recognize cancer as a Systems Biology disease. Then, more cancer biologists could become systems biologists aiming to provide answers to some of the above systemic questions. To this aim, they should integrate the available knowledge stemming from quantitative experimental results through mathematical models. Models that have contributed to the understanding of complex biological systems are discussed. We show that the architecture of a signaling network is important for determining the site at which an oncologist should intervene. Finally, we discuss the possibility of applying network-based drug design to cancer treatment and how rationalized therapies, such as the application of kinase inhibitors, may benefit from Systems Biology.}},  author = {Hornberg, Jorrit J. and Bruggeman, Frank J. and Westerhoff, Hans V. and Lankelma, Jan},  citeulike-article-id = {490947},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.biosystems.2005.05.014},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16426740},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16426740},  citeulike-linkout-3 = {http://www.sciencedirect.com/science/article/B6T2K-4J2TVW8-1/2/c16f2a3aa2a345c2a3c366f6d87d0b81},  doi = {10.1016/j.biosystems.2005.05.014},  issn = {03032647},  journal = {Biosystems},  keywords = {cancer-system-biology},  month = feb,  number = {2-3},  pages = {81--90},  pmid = {16426740},  posted-at = {2011-08-22 14:06:57},  priority = {2},  title = {{Cancer: A Systems Biology disease}},  url = {http://dx.doi.org/10.1016/j.biosystems.2005.05.014},  volume = {83},  year = {2006}  }  @inproceedings{citeulike:9665962,  abstract = {{An abstract is not available.}},  address = {London, UK},  author = {Graham, John R. and Decker, Keith},  booktitle = {6th International Workshop on Intelligent Agents VI, Agent Theories, Architectures, and Languages (ATAL),},  citeulike-article-id = {9665962},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=749599},  isbn = {3-540-67200-1},  keywords = {simulation-and-modeling},  pages = {290--304},  posted-at = {2011-08-13 20:05:05},  priority = {2},  publisher = {Springer-Verlag},  title = {{Towards a Distributed, Environment-Centered Agent Framework}},  url = {http://portal.acm.org/citation.cfm?id=749599},  year = {2000}  }  @inproceedings{citeulike:9665838,  abstract = {{An abstract is not available.}},  address = {London, UK},  author = {Freiwald, Uwe and Weimar, J\"{o}rg R.},  booktitle = {Proceedings of the Fourth International Conference on Cellular Automata for Research and Industry: Theoretical and Practical Issues on Cellular Automata},  citeulike-article-id = {9665838},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=760226},  isbn = {1-85233-388-X},  keywords = {simulation-and-modeling},  pages = {47--54},  posted-at = {2011-08-13 18:59:51},  priority = {2},  publisher = {Springer-Verlag},  title = {{JCAsim - a Java System for Simulating Cellular Automata}},  url = {http://portal.acm.org/citation.cfm?id=760226},  year = {2000}  }  @article{citeulike:9562700,  abstract = {{Abstract The initiation of replication is the central event in the bacterial cell cycle. Cells control the rate of DNA synthesis by modulating the frequency with which new chains are initiated, like all macromolecular synthesis. The end of the replication cycle provides a checkpoint that must be executed for cell division to occur. This review summarizes recent insight into the biochemistry, genetics and control of the initiation of replication in bacteria, and the central role of the initiator protein DnaA.}},  author = {Messer, Walter},  citeulike-article-id = {9562700},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1574-6976.2002.tb00620.x},  doi = {10.1111/j.1574-6976.2002.tb00620.x},  journal = {FEMS Microbiology Reviews},  keywords = {bacterial-biology},  number = {4},  pages = {355--374},  posted-at = {2011-07-19 14:53:45},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication}},  url = {http://dx.doi.org/10.1111/j.1574-6976.2002.tb00620.x},  volume = {26},  year = {2002}  }  @article{citeulike:9560564,  author = {Shuvaev, A. N. and Brilkov, A. V.},  citeulike-article-id = {9560564},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/18064819},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=18064819},  issn = {1607-6729},  journal = {Doklady. Biochemistry and biophysics},  keywords = {synbio-bacterial},  pages = {233--236},  pmid = {18064819},  posted-at = {2011-07-19 11:40:50},  priority = {2},  title = {{A model of bacterial cell cycle duration based on DnaA dynamics and estimation of the population cost of bacterial plasmids.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/18064819},  volume = {416},  year = {2007}  }  @article{citeulike:9543608,  abstract = {{Mathematical models which relate the growth rate of a microorganism to a single limiting substrate concentration have long been established. In recent years, it has become apparent that, under certain conditions, the growth rate of an organism may be simultaneously limited by two or more substrates. Mathematical models of double-substrate limitation fall into two categories: interactive and noninteractive models. A discussion of both types of models is presented in both conceptual and mathematical terms. An analogous case of an enzyme which requires two different substrates to produce a single product is presented. This enzyme analog indicates that both types of double-substrate limitation models appear to be feasible under certain conditions. Based upon stoichiometry and specific growth rate-substrate concentration contour plots, a method for determining the operational conditions which will lead to double-substrate limitation is presented.}},  author = {Bader, F. G.},  citeulike-article-id = {9543608},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/bit.260200203},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/630068},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=630068},  doi = {10.1002/bit.260200203},  issn = {0006-3592},  journal = {Biotechnology and bioengineering},  keywords = {bacterial-biology},  month = feb,  number = {2},  pages = {183--202},  pmid = {630068},  posted-at = {2011-07-13 18:38:45},  priority = {2},  title = {{Analysis of double-substrate limited growth.}},  url = {http://dx.doi.org/10.1002/bit.260200203},  volume = {20},  year = {1978}  }  @article{citeulike:658356,  abstract = {{  Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.  }},  author = {Andrianantoandro, Ernesto and Basu, Subhayu and Karig, David K. and Weiss, Ron},  citeulike-article-id = {658356},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/msb4100073},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/msb4100073},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681505/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/16738572},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=16738572},  day = {16},  doi = {10.1038/msb4100073},  issn = {1744-4292},  journal = {Molecular systems biology},  keywords = {synbio-dna},  month = may,  number = {1},  pages = {msb4100073-E1--msb4100073-E14},  pmcid = {PMC1681505},  pmid = {16738572},  posted-at = {2011-07-10 17:20:41},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Synthetic biology: new engineering rules for an emerging discipline.}},  url = {http://dx.doi.org/10.1038/msb4100073},  volume = {2},  year = {2006}  }  @article{citeulike:929835,  abstract = {{Synthetic biology is interpreted as the engineering-driven building of increasingly complex biological entities for novel applications. Encouraged by progress in the design of artificial gene networks, de novo DNA synthesis and protein engineering, we review the case for this emerging discipline. Key aspects of an engineering approach are purpose-orientation, deep insight into the underlying scientific principles, a hierarchy of abstraction including suitable interfaces between and within the levels of the hierarchy, standardization and the separation of design and fabrication. Synthetic biology investigates possibilities to implement these requirements into the process of engineering biological systems. This is illustrated on the DNA level by the implementation of engineering-inspired artificial operations such as toggle switching, oscillating or production of spatial patterns. On the protein level, the functionally self-contained domain structure of a number of proteins suggests possibilities for essentially Lego-like recombination which can be exploited for reprogramming DNA binding domain specificities or signaling pathways. Alternatively, computational design emerges to rationally reprogram enzyme function. Finally, the increasing facility of de novo DNA synthesis—synthetic biology's system fabrication process—supplies the possibility to implement novel designs for ever more complex systems. Some of these elements have merged to realize the first tangible synthetic biology applications in the area of manufacturing of pharmaceutical compounds.}},  author = {Heinemann, Matthias and Panke, Sven},  citeulike-article-id = {929835},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btl469},  citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/22/22/2790.abstract},  citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/22/22/2790.full.pdf},  citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/22/2790},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/16954140},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=16954140},  day = {15},  doi = {10.1093/bioinformatics/btl469},  issn = {1460-2059},  journal = {Bioinformatics},  keywords = {synbio-dna},  month = nov,  number = {22},  pages = {2790--2799},  pmid = {16954140},  posted-at = {2011-07-10 17:17:57},  priority = {2},  publisher = {Oxford University Press},  title = {{Synthetic biology--putting engineering into biology}},  url = {http://dx.doi.org/10.1093/bioinformatics/btl469},  volume = {22},  year = {2006}  }  @book{citeulike:696933,  abstract = {{The emerging field of systems biology involves the application of experimental, theoretical, and modeling techniques to the study of biological organisms at all levels, from the molecular, through the cellular, to the behavioral. Its aim is to understand biological processes as whole systems instead of as isolated parts. Developments in the field have been made possible by advances in molecular biology--in particular, new technologies for determining DNA sequence, gene expression profiles, protein-protein interactions, and so on. Foundations of Systems Biology provides an overview of the state of the art of the field. The book covers the central topics of systems biology: comprehensive and automated measurements, reverse engineering of genes and metabolic networks from experimental data, software issues, modeling and simulation, and system-level analysis.}},  citeulike-article-id = {696933},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0262112663},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0262112663},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0262112663},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0262112663},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0262112663/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0262112663},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0262112663},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0262112663},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0262112663\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0262112663},  day = {15},  howpublished = {Hardcover},  isbn = {0262112663},  keywords = {system-biology},  month = oct,  posted-at = {2011-07-08 17:51:36},  priority = {2},  publisher = {The MIT Press},  title = {{Foundations of Systems Biology}},  url = {http://www.worldcat.org/isbn/0262112663},  year = {2001}  }  @article{citeulike:7573650,  abstract = {{Synthetic biology seeks to enable programmed control of cellular behavior though engineered biological systems. These systems typically consist of synthetic circuits that function inside, and interact with, complex host cells possessing pre-existing metabolic and regulatory networks. Nevertheless, while designing systems, a simple well-defined interface between the synthetic gene circuit and the host is frequently assumed. We describe the generation of robust but unexpected oscillations in the densities of bacterium Escherichia coli populations by simple synthetic suicide circuits containing quorum components and a lysis gene. Contrary to design expectations, oscillations required neither the quorum sensing genes (luxR and luxI) nor known regulatory elements in the PluxI promoter. Instead, oscillations were likely due to density-dependent plasmid amplification that established a population-level negative feedback. A mathematical model based on this mechanism captures the key characteristics of oscillations, and model predictions regarding perturbations to plasmid amplification were experimentally validated. Our results underscore the importance of plasmid copy number and potential impact of †hidden interactions†on the behavior of engineered gene circuits - a major challenge for standardizing biological parts. As synthetic biology grows as a discipline, increasing value may be derived from tools that enable the assessment of parts in their final context.}},  author = {Marguet, Philippe and Tanouchi, Yu and Spitz, Eric and Smith, Cameron and You, Lingchong},  citeulike-article-id = {7573650},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0011909},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20689598},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20689598},  day = {30},  doi = {10.1371/journal.pone.0011909},  issn = {1932-6203},  journal = {PLoS ONE},  keywords = {bacterial-biology},  month = jul,  number = {7},  pages = {e11909+},  pmid = {20689598},  posted-at = {2011-07-02 18:17:26},  priority = {2},  publisher = {Public Library of Science},  title = {{Oscillations by Minimal Bacterial Suicide Circuits Reveal Hidden Facets of Host-Circuit Physiology}},  url = {http://dx.doi.org/10.1371/journal.pone.0011909},  volume = {5},  year = {2010}  }  @inbook{citeulike:9436573,  author = {Cooper, Stephen},  booktitle = {Encyclopedia of Molecular Cell Biology and Molecular Medicine},  citeulike-article-id = {9436573},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/3527600906.mcb.200300079},  citeulike-linkout-1 = {http://dx.doi.org/10.1002/3527600906.mcb.200300079},  doi = {10.1002/3527600906.mcb.200300079},  isbn = {9783527600908},  keywords = {bacterial-biology},  posted-at = {2011-06-20 18:54:44},  priority = {2},  publisher = {Wiley-VCH Verlag GmbH \& Co. KGaA},  title = {{Bacterial Growth and Division}},  url = {http://dx.doi.org/10.1002/3527600906.mcb.200300079},  year = {2006}  }  @article{citeulike:9312087,  author = {Baker, Monya},  citeulike-article-id = {9312087},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/473403a},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/473403a},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21593873},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21593873},  day = {19},  doi = {10.1038/473403a},  issn = {0028-0836},  journal = {Nature},  keywords = {synbio-dna},  month = may,  number = {7347},  pages = {403--408},  pmid = {21593873},  posted-at = {2011-05-25 17:22:16},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Synthetic genomes: The next step for the synthetic genome}},  url = {http://dx.doi.org/10.1038/473403a},  volume = {473},  year = {2011}  }  @incollection{citeulike:8072755,  abstract = {{We overview a series of our research on implementing finite automata in vitro and in vivo in the framework of DNA-based computing [1,2]. First, we employ the length-encoding technique proposed and presented in [3,4] to implement finite automata in test tube. In the length-encoding method, the states and state transition functions of a target finite automaton are effectively encoded into DNA sequences, a computation (accepting) process of finite automata is accomplished by self-assembly of encoded complementary DNA strands, and the acceptance of an input string is determined by the detection of a completely hybridized double-strand DNA. Second, we report our intensive in vitro experiments in which we have implemented and executed several finite-state automata in test tube. We have designed and developed practical laboratory protocols which combine several in vitro operations such as annealing, ligation, PCR, and streptavidin-biotin bonding to execute in vitro finite automata based on the length-encoding technique. We have carried laboratory experiments on various finite automata with 2 up to 6 states for several input strings. Third, we present a novel framework to develop a programmable and autonomous in vivo computer using Escherichia coli (E. coli), and implement in vivo finite-state automata based on the framework by employing the protein-synthesis mechanism of E. coli. We show some successful experiments to run an in vivo finite-state automaton on E. coli.}},  address = {Berlin, Heidelberg},  author = {Sakakibara, Yasubumi},  booktitle = {Programs, Proofs, Processes},  chapter = {40},  citeulike-article-id = {8072755},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-13962-8\_40},  citeulike-linkout-1 = {http://www.springerlink.com/content/357w312344rv8q78},  doi = {10.1007/978-3-642-13962-8\_40},  editor = {Ferreira, Fernando and L\"{o}we, Benedikt and Mayordomo, Elvira and Mendes Gomes, Lu\'{\i}s},  isbn = {978-3-642-13961-1},  keywords = {synbio-bacterial},  pages = {362--371},  posted-at = {2011-05-09 21:18:42},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Development of a Bacteria Computer: From in silico Finite Automata to in vitro and in vivo}},  url = {http://dx.doi.org/10.1007/978-3-642-13962-8\_40},  volume = {6158},  year = {2010}  }  @incollection{citeulike:9269485,  abstract = {{We present a novel framework to develop a programmable and autonomous in vivo computer using E. coli, and implement in vivo finite-state automata based on the framework by employing the protein-synthesis mechanism of E. coli. Our fundamental idea to develop a programmable and autonomous finite-state automata on E. coli is that we first encode an input string into one plasmid, encode state-transition functions into the other plasmid, and introduce those two plasmids into an E. coli cell by electroporation. Second, we execute a protein-synthesis process in E. coli combined with four-base codon techniques to simulate a computation (accepting) process of finite automata, which has been proposed for in vitro translation-based computations in [8]. This approach enables us to develop a programmable in vivo computer by simply replacing a plasmid encoding a state-transition function with others. Further, our in vivo finite automata are autonomous because the protein-synthesis process is autonomously executed in the living E. coli cell. We show some successful experiments to run an in vivo finite-state automaton on E. coli.}},  address = {Berlin, Heidelberg},  author = {Nakagawa, Hirotaka and Sakamoto, Kensaku and Sakakibara, Yasubumi},  booktitle = {DNA Computing},  chapter = {16},  citeulike-article-id = {9269485},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/11753681\_16},  citeulike-linkout-1 = {http://www.springerlink.com/content/x3j1x0573681g1t4},  doi = {10.1007/11753681\_16},  editor = {Carbone, Alessandra and Pierce, Niles},  isbn = {978-3-540-34161-1},  keywords = {synbio-bacterial},  pages = {203--212},  posted-at = {2011-05-09 21:17:50},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Development of an n Vivo Computer Based on Escherichia coli}},  url = {http://dx.doi.org/10.1007/11753681\_16},  volume = {3892},  year = {2006}  }  @article{citeulike:9072281,  abstract = {{How is diversity maintained? Environmental heterogeneity is considered to be important, yet diversity in seemingly homogeneous environments is nonetheless observed. This, it is assumed, must either be owing to weak selection, mutational input or a fitness advantage to genotypes when rare. Here we demonstrate the possibility of a new general mechanism of stable diversity maintenance, one that stems from metabolic and physiological trade-offs. The model requires that such trade-offs translate into a fitness landscape in which the most fit has unfit near-mutational neighbours, and a lower fitness peak also exists that is more mutationally robust. The 'survival of the fittest' applies at low mutation rates, giving way to 'survival of the flattest' at high mutation rates. However, as a consequence of quasispecies-level negative frequency-dependent selection and differences in mutational robustness we observe a transition zone in which both fittest and flattest coexist. Although diversity maintenance is possible for simple organisms in simple environments, the more trade-offs there are, the wider the maintenance zone becomes. The principle may be applied to lineages within a species or species within a community, potentially explaining why competitive exclusion need not be observed in homogeneous environments. This principle predicts the enigmatic richness of metabolic strategies in clonal bacteria and questions the safety of lethal mutagenesis as an antimicrobial treatment.}},  author = {Beardmore, Robert E. and Gudelj, Ivana and Lipson, David A. and Hurst, Laurence D.},  citeulike-article-id = {9072281},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature09905},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature09905},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21441905},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21441905},  day = {27},  doi = {10.1038/nature09905},  issn = {0028-0836},  journal = {Nature},  keywords = {evolution},  month = mar,  number = {7343},  pages = {342--346},  pmid = {21441905},  posted-at = {2011-05-08 19:53:39},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Metabolic trade-offs and the maintenance of the fittest and the flattest}},  url = {http://dx.doi.org/10.1038/nature09905},  volume = {472},  year = {2011}  }  @inproceedings{citeulike:9240612,  abstract = {{High level languages greatly increase the power of a programmer at the cost of programs that consume more resources than those written at a lower level of abstraction. This inefficiency is a major concern for the programming of biological systems: although advances in synthetic biology are beginning to allow bacteria to be programmed at an "assembly language'' level, metabolic and chemical constraints currently place tight limits on the computational resources available. We find, however, that the semantics of the Proto spatial computing language appear to be a good match for engineered genetic regulatory networks, and particularly for describing the spatial differentiation necessary to construct tissues or organs. In this paper, we propose a mapping between Proto programs and standardized biological parts. We then demonstrate the plausibility of this mapping by applying it to a band detection program, finding that standard code optimization techniques can transform the inefficient program produced by the initial mapping into an efficient design equivalent to the Weiss laboratory's hand-designed band detector.}},  author = {Beal, J. and Bachrach, J.},  booktitle = {Self-Adaptive and Self-Organizing Systems Workshops, 2008. SASOW 2008. Second IEEE International Conference on},  citeulike-article-id = {9240612},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/sasow.2008.14},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=4800692},  doi = {10.1109/sasow.2008.14},  institution = {MIT CSAIL, Cambridge, MA},  isbn = {978-0-7695-3553-1},  keywords = {amorphous\_computing},  location = {Venice, Italy},  month = oct,  pages = {284--291},  posted-at = {2011-05-02 16:39:40},  priority = {2},  publisher = {IEEE},  title = {{Cells Are Plausible Targets for High-Level Spatial Languages}},  url = {http://dx.doi.org/10.1109/sasow.2008.14},  year = {2008}  }  @article{DBLP:journals/simulation/LukeCPSB05,  author = {Luke, Sean and Cioffi-Revilla, Claudio and Panait, Liviu and Sullivan, Keith and Balan, Gabriel C.},  citeulike-article-id = {9234416},  journal = {Simulation},  keywords = {simulation-and-modeling},  number = {7},  pages = {517--527},  posted-at = {2011-04-30 20:00:14},  priority = {2},  title = {{MASON: A Multiagent Simulation Environment}},  volume = {81},  year = {2005}  }  @article{citeulike:310475,  abstract = {{  This review deals with the prospective, experimental documentation of horizontal gene transfer (HGT) and its role in real-time, local adaptation. We have focused on plasmids and their function as an accessory and/or adaptive gene pool. Studies of the extent of HGT in natural environments have identified certain hot spots, and many of these involve biofilms. Biofilms are uniquely suited for HGT, as they sustain high bacterial density and metabolic activity, even in the harshest environments. Single-cell detection of donor, recipient and transconjugant bacteria in various natural environments, combined with individual-based mathematical models, has provided a new platform for HGT studies.  }},  author = {S{\o}rensen, S{\o}ren J. and Bailey, Mark and Hansen, Lars H. and Kroer, Niels and Wuertz, Stefan},  citeulike-article-id = {310475},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrmicro1232},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrmicro1232},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16138098},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16138098},  day = {01},  doi = {10.1038/nrmicro1232},  issn = {1740-1526},  journal = {Nature reviews. Microbiology},  keywords = {bacterial-biology},  month = sep,  number = {9},  pages = {700--710},  pmid = {16138098},  posted-at = {2011-04-27 16:09:26},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Studying plasmid horizontal transfer in situ: a critical review.}},  url = {http://dx.doi.org/10.1038/nrmicro1232},  volume = {3},  year = {2005}  }  @article{citeulike:9216162,  abstract = {{Abstract Quantitative models of bacterial conjugation are useful tools in environmental risk assessment and in studies of the ecology and evolution of bacterial communities. We constructed a mathematical model for gene transfer between bacteria growing on a solid surface. The model considers that donor and recipient cells will form separate colonies, which grow exponentially until nutrient exhaustion. Conjugation occurs when donor and recipient colonies meet, all recipient cells becoming transconjugants instantly, after which they act as donors. The model was tested theoretically by computer simulations that followed the histories of individual bacterial colonies and was validated for initial surface coverage of 60\% or less, where confluent growth does not occur. Model predictions of final number of donors, recipients and transconjugants were tested experimentally using a filter mating system with two isogenic strains of Pseudomonas fluorescens MON787 acting as donor and recipient of plasmid RP4. Experimental trends resulting from varying donor and recipient inoculum numbers and donor:recipient ratios were well described by the model, although it often overestimated conjugation by 0.5–2 orders of magnitude. Predictions were greatly improved, generally to within half a log unit of experimental values, by consideration of the time for conjugative transfer. The model demonstrates the relationship between spatial separation of cells and nutrient availability on numbers of transconjugants. By providing a mechanistic approach to the study conjugation on surfaces, the model may contribute to the study of gene transfer in natural environments.}},  author = {Lagido, Cristina and Wilson, Ian J. and Glover and Prosser, Jim I.},  citeulike-article-id = {9216162},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0168-6496(02)00453-1},  doi = {10.1016/s0168-6496(02)00453-1},  journal = {FEMS Microbiology Ecology},  keywords = {bacterial-biology},  number = {1},  pages = {67--78},  posted-at = {2011-04-27 16:08:15},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{A model for bacterial conjugal gene transfer on solid surfaces}},  url = {http://dx.doi.org/10.1016/s0168-6496(02)00453-1},  volume = {44},  year = {2003}  }  @article{citeulike:9203636,  abstract = {{We have developed a novel rule-based computing system of microbial interactions and communications, referred to as COSMIC-Rules, for simulating evolutionary processes within populations of virtual bacteria. The model incorporates three levels: the bacterial genome, the bacterial cell and an environment inhabited by such cells. The virtual environment in COSMIC-Rules can contain multiple substances, whose relative toxicity or nutrient status is specified by the genome of the bacterium. Each substance may be distributed uniformly or in a user-defined manner. The organisms in COSMIC-Rules possess individually-defined physical locations, size, cell division status and genomes. Genes and/or gene systems are represented by abstractions that may summate sometimes complex phenotypes. Central to COSMIC-Rules is a simplified representation of bacterial species, each containing a functional genome including, where desired, extrachromosomal elements such as plasmids and/or bacteriophages. A widely applicable computer representation of biological recognition systems based on bit string matching is essential to the model. This representation permits, for example, the modelling of protein–protein interactions, receptor–ligand interactions and DNA–DNA transactions. COSMIC-Rules is intended to inform studies on bacterial adaptation and evolution, and to predict behaviour of populations of pathogenic bacteria and their viruses. The framework is constructed for parallel execution across a large number of machines and efficiently utilises a 64 processor development cluster. It will run on any Grid system and has successfully tested simulations with millions of bacteria, of multiple species and utilising multiple substrates. The model may be used for large-scale simulations where a genealogical record for individual organisms is required.}},  author = {Gregory, R. and Saunders, V. A. and Saunders, J. R.},  citeulike-article-id = {9203636},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.biosystems.2007.09.002},  doi = {10.1016/j.biosystems.2007.09.002},  issn = {03032647},  journal = {Biosystems},  keywords = {individual-based-modeling},  month = jan,  number = {1},  pages = {216--230},  posted-at = {2011-04-24 16:14:00},  priority = {2},  title = {{Rule-based computing system for microbial interactions and communications: Evolution in virtual bacterial populations}},  url = {http://dx.doi.org/10.1016/j.biosystems.2007.09.002},  volume = {91},  year = {2008}  }  @article{citeulike:9189835,  abstract = {{  We describe a method for determining the rate parameter of conjugative plasmid transfer that is based on single estimates of donor, recipient and transconjugant densities and the growth rate in exponential phase of the mating culture. The formula for estimating the plasmid transfer rate, gamma, was derived from a mathematical model describing cell growth and plasmid transfer in batch culture. Computer simulations were used to explore the sensitivity of this method to the realities of bacterial life, such as growth rate differences, plasmid segregation and transitory derepression of pilus synthesis. As predicted by the theory, mating experiments with the plasmid R1 in Escherichia coli K12 demonstrated that the estimate gamma is unaffected by cell density, donor:recipient ratio and mating time. Unlike previous techniques, our method allows us to investigate the effect of environmental factors on plasmid transfer rates when these factors also influence population growth rates. To illustrate this, we examined the effect of temperature on the rate of plasmid transfer.  }},  author = {Simonsen, L. and Gordon, D. M. and Stewart, F. M. and Levin, B. R.},  citeulike-article-id = {9189835},  citeulike-linkout-0 = {http://dx.doi.org/10.1099/00221287-136-11-2319},  citeulike-linkout-1 = {http://mic.sgmjournals.org/cgi/content/abstract/136/11/2319},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/2079626},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=2079626},  day = {1},  doi = {10.1099/00221287-136-11-2319},  issn = {0022-1287},  journal = {Journal of general microbiology},  keywords = {bacterial-biology},  month = nov,  number = {11},  pages = {2319--2325},  pmid = {2079626},  posted-at = {2011-04-22 17:10:02},  priority = {2},  title = {{Estimating the rate of plasmid transfer: an end-point method.}},  url = {http://dx.doi.org/10.1099/00221287-136-11-2319},  volume = {136},  year = {1990}  }  @article{citeulike:9186255,  abstract = {{  A mathematical model for the population dynamics of conjugationally transmitted plasmids in bacterial populations is presented and its properties analyzed. Consideration is given to nonbacteriocinogenic factors that are incapable of incorporation into the chromosome of their host cells, and to bacterial populations maintained in either continuous (chemostat) or discrete (serial transfer) culture. The conditions for the establishment and maintenance of these infectious extrachromosomal elements and equilibrium frequencies of cells carrying them are presented for different values of the biological parameters: population growth functions, conjugational transfer and segregation rate constants. With these parameters in a biologically realistic range, the theory predicts a broad set of physical conditions, resource concentrations and dilution rates, where conjugationally transmitted plasmids can become established and where cells carrying them will maintain high frequencies in bacterial populations. This can occur even when plasmid-bearing cells are much less fit (i.e., have substantially lower growth rates) than cells free of these factors. The implications of these results and the reality and limitations of the model are discussed and the values of its parameters in natural populations speculated upon.  }},  author = {Stewart, F. M. and Levin, B. R.},  citeulike-article-id = {9186255},  citeulike-linkout-0 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1213735/},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17248761},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17248761},  issn = {0016-6731},  journal = {Genetics},  keywords = {bacterial-biology},  month = oct,  number = {2},  pages = {209--228},  pmcid = {PMC1213735},  pmid = {17248761},  posted-at = {2011-04-22 09:15:26},  priority = {2},  title = {{The Population Biology of Bacterial Plasmids: A PRIORI Conditions for the Existence of Conjugationally Transmitted Factors.}},  url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1213735/},  volume = {87},  year = {1977}  }  @article{citeulike:7890776,  abstract = {{The 'ODD' (Overview, Design concepts, and Details) protocol was published in 2006 to standardize the published descriptions of individual-based and agent-based models (ABMs). The primary objectives of ODD are to make model descriptions more understandable and complete, thereby making ABMs less subject to criticism for being irreproducible. We have systematically evaluated existing uses of the ODD protocol and identified, as expected, parts of ODD needing improvement and clarification. Accordingly, we revise the definition of ODD to clarify aspects of the original version and thereby facilitate future standardization of ABM descriptions. We discuss frequently raised critiques in ODD but also two emerging, and unanticipated, benefits: ODD improves the rigorous formulation of models and helps make the theoretical foundations of large models more visible. Although the protocol was designed for ABMs, it can help with documenting any large, complex model, alleviating some general objections against such models.}},  author = {Grimm, Volker and Berger, Uta and DeAngelis, Donald L. and Polhill, J. Gary and Giske, Jarl and Railsback, Steven F.},  citeulike-article-id = {7890776},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ecolmodel.2010.08.019},  day = {24},  doi = {10.1016/j.ecolmodel.2010.08.019},  issn = {03043800},  journal = {Ecological Modelling},  keywords = {individual-based-modeling},  month = nov,  number = {23},  pages = {2760--2768},  posted-at = {2011-04-18 17:09:27},  priority = {2},  title = {{The ODD protocol: A review and first update}},  url = {http://dx.doi.org/10.1016/j.ecolmodel.2010.08.019},  volume = {221},  year = {2010}  }  @book{citeulike:493765,  abstract = {{This is the greatly revised and greatly expanded Second Edition of the hugely  popular Numerical Recipes: The Art of Scientific Computing. The product of a  unique collaboration among four leading scientists in academic research and  industry Numerical Recipes is a complete text and reference book on scientific  computing. In a self-contained manner it proceeds from mathematical and  theoretical considerations to actual practical computer routines. With over  100 new routines bringing the total to well over 300, plus upgraded versions  of the original routines, this new edition remains the most practical,  comprehensive handbook of scientific computing available today. Highlights of  the new material include: -A new chapter on integral equations and inverse  methods -Multigrid and other methods for solving partial differential  equations -Improved random number routines - Wavelet transforms -The  statistical bootstrap method -A new chapter on "less-numerical" algorithms  including compression coding and arbitrary precision arithmetic. The book  retains the informal easy-to-read style that made the first edition so  popular, while introducing some more advanced topics. It is an ideal textbook  for scientists and engineers and an indispensable reference for anyone who  works in scientific computing. The Second Edition is availabe in FORTRAN, the  traditional language for numerical calculations and in the increasingly  popular C language.}},  author = {Press, William H. and Flannery, Brian P. and Teukolsky, Saul A. and Vetterling, William T.},  citeulike-article-id = {493765},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/052143064X},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/052143064X},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/052143064X},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/052143064X},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/052143064X/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/052143064X},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/052143064X},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN052143064X},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=052143064X\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/052143064X},  day = {25},  edition = {2},  howpublished = {Hardcover},  isbn = {052143064X},  keywords = {books},  month = sep,  posted-at = {2011-04-16 11:52:40},  priority = {2},  publisher = {Cambridge University Press},  title = {{Numerical Recipes in Fortran: The Art of Scientific Computing}},  url = {http://www.worldcat.org/isbn/052143064X},  year = {1992}  }  @article{citeulike:9155646,  abstract = {{Micro-organisms play a central role in every ecosystem and in the global biomass cycle. They are strongly involved in many fields of human interest, from medicine to the food industry and waste control. Nevertheless, most micro-organisms remain almost unknown, and nearly 99\% of them have not yet been successfully cultured in vitro. Therefore, new approaches and new tools must be developed in order to understand the collective behaviour of microbial communities in any natural or artificial setting. In particular, theoretical and practical methodologies to deal with such systems at a mesoscopic level of description (covering the range from 100 to 10(8) cells) are required. Individual-based modelling (IBM) has become a widely used tool for describing complex systems made up of autonomous entities, such as ecosystems and social networks. Individual-based models (IBMs) provide some advantages over the traditional whole-population models: (a) they are bottom-up approaches, so they describe the behaviour of a system as a whole by establishing procedural rules for the individuals and for their interactions, and thus allow more realistic assumptions for the model of the individuals than population models do; (b) they permit the introduction of randomness and individual variability, so they can reproduce the diversity found in real systems; and (c) they can account for individual adaptive behaviour to their environmental conditions, so the evolution of the whole system arises from the dynamics that govern individuals in their pursuit of optimal fitness. However, they also present some drawbacks: they lack the clarity of continuous models and may easily become rambling, which makes them difficult to analyse and communicate. All in all, IBMs supply a holistic description of microbial systems and their emerging properties. They are specifically appropriate to deal with microbial communities in non-steady states, and spatially explicit IBMs are particularly appropriate to study laboratory and natural microbiological systems with spatial heterogeneity. In this paper, we review IBM methodology applied to microbiology. We also present some results obtained from the application of Individual Discrete Simulations, an IBM of ours, to the study of bacterial communities, yeast cultures and Plasmodium falciparum-infected erythrocytes in vitro cultures of Plasmodium falciparum-infected erythrocytes.}},  author = {Ferrer, Jordi and Prats, Clara and L\'{o}pez, Daniel},  citeulike-article-id = {9155646},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s10867-008-9082-3},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577750/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19669490},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19669490},  citeulike-linkout-4 = {http://www.springerlink.com/content/7023440262243886},  day = {1},  doi = {10.1007/s10867-008-9082-3},  issn = {0092-0606},  journal = {Journal of biological physics},  keywords = {individual-based-modeling},  month = apr,  number = {1-2},  pages = {19--37},  pmcid = {PMC2577750},  pmid = {19669490},  posted-at = {2011-04-14 18:13:16},  priority = {2},  publisher = {Springer Netherlands},  title = {{Individual-based modelling: an essential tool for microbiology.}},  url = {http://dx.doi.org/10.1007/s10867-008-9082-3},  volume = {34},  year = {2008}  }  @article{doi:10.2200/S00328ED1V01Y201101DCT006,  author = {Michail, Othon and Chatzigiannakis, Ioannis and Spirakis, Paul G.},  citeulike-article-id = {9092703},  citeulike-linkout-0 = {http://www.morganclaypool.com/doi/abs/10.2200/S00328ED1V01Y201101DCT006},  citeulike-linkout-1 = {http://dx.doi.org/10.2200/S00328ED1V01Y201101DCT006},  doi = {10.2200/S00328ED1V01Y201101DCT006},  eprint = {http://www.morganclaypool.com/doi/pdf/10.2200/S00328ED1V01Y201101DCT006},  journal = {Synthesis Lectures on Distributed Computing Theory},  keywords = {population-protocols},  number = {1},  pages = {1--156},  posted-at = {2011-04-03 12:51:47},  priority = {2},  title = {{New Models for Population Protocols}},  url = {http://www.morganclaypool.com/doi/abs/10.2200/S00328ED1V01Y201101DCT006},  volume = {2},  year = {2011}  }  @inproceedings{citeulike:8958359,  abstract = {{Grid based distributed simulations are becoming more and more important with the increasing number of large-scale modeling and simulation applications. Distributed simulations are evolving with modern distributed computing techniques and are facing new challenges such as interoperability, reusability, scalability, etc. distributed interactive simulation and high level architecture have been the dominant distributed simulation standards for the past few years, and HLA is still the backbone for supporting federate based distributed simulations. However, HLA relies heavily on centralized runtime infrastructure (RTI) and is not easy to scale for large-scale applications. Also, its interoperability is limited since it does not use a fully opened standard such as service oriented architecture (SOA). Therefore, a lot research has been done to promote the next generation of simulation architecture. Such efforts result in the XMSF, which tries to integrate SOA with distributed simulation. In the meantime, peer-to-peer network based distributed simulations are also attracting more researchers to investigate the feasibility of decentralized architecture for large-scale distributed simulations. In this paper, we propose a hierarchical service oriented JXIA-core multi-layered architecture for large scale distributed simulations. Our particular design consideration is dynamic reconfigurable and realtime capable distributed simulation infrastructure, and we also aim to address most of the concerns regarding grid based large-scale distributed simulation. We further verify our design through a formal DEVS simulation based modeling. We believe that a decentralized framework will be dominant in the area of distributed simulations in the near future due to its flexibility, scalability, and the ease of reconfiguring simulation applications.}},  author = {Boukerche, Azzedine and Zhang, Ming},  citeulike-article-id = {8958359},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/anss-41.2008.9},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=4494422},  doi = {10.1109/anss-41.2008.9},  keywords = {simulation-and-modeling},  location = {Ottawa, Canada},  month = apr,  pages = {212--219},  posted-at = {2011-03-08 07:11:36},  priority = {2},  title = {{Towards Peer-to-Peer Based Distributed Simulations on a Grid Infrastructure}},  url = {http://dx.doi.org/10.1109/anss-41.2008.9},  year = {2008}  }  @book{GrimmRailsback2005,  abstract = {{

Individual-based models are an exciting and widely used new tool for ecology. These computational models allow scientists to explore the mechanisms through which population and ecosystem ecology arises from how individuals interact with each other and their environment. This book provides the first in-depth treatment of individual-based modeling and its use to develop theoretical understanding of how ecological systems work, an approach the authors call "individual-based ecology."

Grimm and Railsback start with a general primer on modeling: how to design models that are as simple as possible while still allowing specific problems to be solved, and how to move efficiently through a cycle of pattern-oriented model design, implementation, and analysis. Next, they address the problems of theory and conceptual framework for individual-based ecology: What is "theory"? That is, how do we develop reusable models of how system dynamics arise from characteristics of individuals? What conceptual framework do we use when the classical differential equation framework no longer applies? An extensive review illustrates the ecological problems that have been addressed with individual-based models. The authors then identify how the mechanics of building and using individual-based models differ from those of traditional science, and provide guidance on formulating, programming, and analyzing models. This book will be helpful to ecologists interested in modeling, and to other scientists interested in agent-based modeling.

}},  address = {Princeton},  author = {Grimm, Volker and Railsback, Steven F.},  citeulike-article-id = {608186},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/069109666X},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/069109666X},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/069109666X},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/069109666X},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/069109666X/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/069109666X},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/069109666X},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN069109666X},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=069109666X\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/069109666X},  day = {05},  howpublished = {Paperback},  isbn = {069109666X},  keywords = {individual-based-modeling},  location = {NJ},  month = jul,  posted-at = {2011-02-28 19:30:27},  priority = {2},  publisher = {Princeton University Press},  title = {{Individual-based Modeling and Ecology: (Princeton Series in Theoretical and Computational Biology)}},  url = {http://www.worldcat.org/isbn/069109666X},  year = {2005}  }  @inproceedings{citeulike:2984936,  abstract = {{Developments in simulation systems, e.g. new simulators, partitioning algorithms, modeling formalisms, or specialized user interfaces, often implies the realization of entire simulation systems from scratch. This requires significant efforts, and, in addition, it hampers the evaluation of the results achieved. The proposed plug 'n simulate concept enables developers to integrate their ideas into an existing framework and thus eases the development and the evaluation of results}},  address = {Washington, DC, USA},  author = {Himmelspach, J. and Uhrmacher, A. M.},  booktitle = {Simulation Symposium, 2007. ANSS \&\#039;07. 40th Annual},  citeulike-article-id = {2984936},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1250406},  citeulike-linkout-1 = {http://dx.doi.org/10.1109/anss.2007.34},  citeulike-linkout-2 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=4127212},  day = {12},  doi = {10.1109/anss.2007.34},  institution = {Rostock Univ.},  isbn = {0-7695-2814-7},  issn = {1080-241X},  journal = {Simulation Symposium, 2007. ANSS '07. 40th Annual},  keywords = {simulation-and-modeling},  location = {Norfolk, VA, USA},  month = mar,  pages = {137--143},  posted-at = {2011-02-28 19:25:22},  priority = {2},  publisher = {IEEE},  title = {{Plug'n Simulate}},  url = {http://dx.doi.org/10.1109/anss.2007.34},  year = {2007}  }  @article{Grimm99,  abstract = {{Each modeller who builds and analyses an individual-based model learns of course a great deal, but what has ecology as a whole learned from the individual-based models published during the last decade? Answering this question proves extremely difficult as there is no common motivation behind individual-based models. The distinction is introduced between 'pragmatic' motivation, which uses the individual-based approach as a tool without any reference to the theoretical issues which have emerged from the classical state variable approach and 'paradigmatic' motivation, which explicitly refers to theoretical ecology. A mini-review of 50 individual-based animal population models shows that the majority are driven by pragmatic motivation. Most models are very complex and special techniques to cope with this complexity during their analysis are only occasionally applied. It is suggested that in order to orient individual-based modelling more towards general theoretical issues, we need increased explicit reference to theoretical ecology and an advanced strategy for building and analysing individual-based models. To this end, a heuristic list of rules is presented which may help us to advance the practice of individual-based modelling and to learn more general lessons from individual-based modelling in the future than we have during the last decade. The main ideas behind these rules are as follows: (1) Individual-based models usually make more realistic assumptions than state variable models, but it should not be forgotten that the aim of individual-based modelling is not 'realism' but modelling. (2) The individual-based approach is a bottom-up approach which starts with the 'parts' (i.e. individuals) of a system (i.e. population) and then tries to understand how the system's properties emerge from the interaction among these parts. However, bottom-up approaches alone will never lead to theories at the systems level. State variable or top-down approaches are needed to provide an appropriate integrated view, i.e. the relevant questions at the population level.}},  author = {Grimm, V.},  citeulike-article-id = {2030155},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0304-3800(98)00188-4},  citeulike-linkout-1 = {http://www.ingentaconnect.com/content/els/03043800/1999/00000115/00000002/art00188},  citeulike-linkout-2 = {http://www.sciencedirect.com/science/article/B6VBS-3XD415P-4/2/10047b936565d36617cb6a4b02b71cad},  day = {15},  doi = {10.1016/s0304-3800(98)00188-4},  issn = {0304-3800},  journal = {Ecological Modelling},  keywords = {individual-based-modeling},  month = feb,  number = {2-3},  pages = {129--148},  posted-at = {2011-02-28 19:24:26},  priority = {2},  publisher = {Elsevier},  title = {{Ten years of individual-based modelling in ecology: what have we learned and what could we learn in the future?}},  url = {http://dx.doi.org/10.1016/s0304-3800(98)00188-4},  volume = {115},  year = {1999}  }  @inproceedings{Minsky1965,  author = {Minsky, Marvin},  booktitle = {Proceedings of IFIP Congress 65},  citeulike-article-id = {5093875},  citeulike-linkout-0 = {http://groups.csail.mit.edu/medg/people/doyle/gallery/minsky/mmm.html},  day = {3},  keywords = {simulation-and-modeling},  month = jan,  pages = {45--49},  posted-at = {2011-02-27 11:34:58},  priority = {2},  title = {{Matter, Mind and Models}},  url = {http://groups.csail.mit.edu/medg/people/doyle/gallery/minsky/mmm.html},  year = {1965}  }  @inproceedings{citeulike:8820269,  abstract = {{As an emergence technology, P2P is spreading to distributed simulation area, and many distributed simulation frameworks have used P2P as the middleware to interconnect their existing single processor's simulators to form distributed environments for simulation execution. In terms of simulation time management, most existing tools use a middleware layer to implement and support time management in a heterogeneous networking environment, and therefore, it is generally not easy to migrate a single processor's simulation to multi-processors in these frameworks. In this paper, we present a P2P based distributed simulation time management based upon JXTA API and Service Oriented Architecture (SOA), and we focus our discussion on how we implement the time management as a JXTA peer and a JXTA group service. Our time management is actually a native distributed message passing management framework, and does not rely on any middleware layer. Furthermore, we evaluate the performance of our implementations using a local Linux cluster. This work will establish a solid foundation for the more advanced distributed simulation services that have been proposed in our project [1].}},  address = {Washington, DC, USA},  author = {Boukerche, Azzedine and Zhang, Ming and Xie, Hengheng},  booktitle = {Proceedings of the 2008 12th IEEE/ACM International Symposium on Distributed Simulation and Real-Time Applications},  citeulike-article-id = {8820269},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1468003},  citeulike-linkout-1 = {http://dx.doi.org/10.1109/ds-rt.2008.39},  doi = {10.1109/ds-rt.2008.39},  isbn = {978-0-7695-3425-1},  keywords = {simulation-and-modeling},  pages = {167--172},  posted-at = {2011-02-14 22:17:55},  priority = {2},  publisher = {IEEE Computer Society},  series = {DS-RT '08},  title = {{An Efficient Time Management Scheme for Large-Scale Distributed Simulation Based on JXTA Peer-to-Peer Network}},  url = {http://dx.doi.org/10.1109/ds-rt.2008.39},  year = {2008}  }  @article{citeulike:4940654,  abstract = {{Micromachines and nanoscale devices can act together for high-resolution monitoring and action on multiple size scales within physical materials and biological organisms. Such multiscale systems require robust distributed controls responsive to heterogeneous and poorly characterized microenvironments. To develop such controls, this paper extends the partially observable Markov decision process formalism to machines operating asynchronously at multiple scales and with delays. We show how an approximation to this formalism readily provides aggregate performance measures needed for designing distributed controls. This approach identifies the aggregate behavior as arising from differential-delay equations approximating the system's dynamics. We illustrate this approach to distributed controls for chemical sensor networks consisting of micro- and nanoscale devices in the context of high-resolution biomedical diagnostics and treatment through localized drug delivery.}},  author = {Hogg, Tad},  citeulike-article-id = {4940654},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s12213-009-0018-1},  citeulike-linkout-1 = {http://www.springerlink.com/content/57503228r1h7v10g},  day = {1},  doi = {10.1007/s12213-009-0018-1},  issn = {1865-3928},  journal = {Journal of Micro - Nano Mechatronics},  keywords = {simulation-and-modeling},  month = dec,  number = {4},  pages = {168--177},  posted-at = {2011-02-14 22:15:44},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  title = {{Distributed control of multiscale microscopic chemical sensor networks}},  url = {http://dx.doi.org/10.1007/s12213-009-0018-1},  volume = {4},  year = {2008}  }  @article{citeulike:8802803,  abstract = {{Bacterial populations meet the challenges of dynamic spatially heterogeneous environments with fluctuating biotic and abiotic factors in a number of ways. The motivation for the work presented here has been to transfer ideas from bacterial adaptability and evolvability to computational problem solving. Following a brief comment on some examples of the ways bacteria solve problems, a bacterially-inspired computational architecture for simulating aspects of problem solving is described. We then examine three case studies. The first, a study of the mutational impact of a remediation to toxic (fitness-reducing) material, highlights how a sufficiently pre-engineered adaptive system can solve a difficult problem quite easily. The second study looks at why it is difficult to evolve complex problem solving behaviours and how artificial selection mechanisms coupled with pre-engineering the system can help. Specifically, this refers to quorum sensing and tactic behaviours. A further study looked at ways in which a quorum sensing analogue could help computational agents find multiple peaks in a landscape. The paper concludes with a discussion of an investigation of bacteria that had both quorum sensing and tactic capabilities.}},  address = {Hingham, MA, USA},  author = {Paton, R. C. and Vlachos, C. and Wu, Q. H. and Saunders, J. R.},  citeulike-article-id = {8802803},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1111657},  issn = {1567-7818},  keywords = {individual-based-modeling},  month = mar,  pages = {43--65},  posted-at = {2011-02-10 21:30:25},  priority = {2},  publisher = {Kluwer Academic Publishers},  title = {{Simulated Bacterially-Inspired Problem Solving --- The Behavioural Domain}},  url = {http://portal.acm.org/citation.cfm?id=1111657},  volume = {5},  year = {2006}  }  @article{citeulike:7789338,  abstract = {{Biological systems are inherently inhomogeneous and spatial effects play a significant role in processes such as pattern formation. At the cellular level proteins are often localised either through static attachment or via a dynamic equilibrium. As well as spatial heterogeneity many cellular processes exhibit stochastic fluctuations and so to make inferences about the location of molecules there is a need for spatial stochastic models. A test case for spatial models has been bacterial chemotaxis which has been studied extensively as a model of signal transduction. By creating specific models of a cellular system that incorporate the spatial distributions of molecules we have shown how the fit between simulated and experimental data can be used to make inferences about localisation, in the case of bacterial chemotaxis. This method allows the robust comparison of different spatial models through alternative model parameterisations. By using detailed statistical analysis we can reliably infer the parameters for the spatial models, and also to evaluate alternative models. The statistical methods employed in this case are particularly powerful as they reduce the need for a large number of simulation replicates. The technique is also particularly useful when only limited molecular level data is available or where molecular data is not quantitative.}},  author = {Yu, Yoon-Dong and Choi, Yoonjoo and Teo, Yik-Ying and Dalby, Andrew R.},  citeulike-article-id = {7789338},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0010464},  day = {13},  doi = {10.1371/journal.pone.0010464},  journal = {PLoS ONE},  keywords = {individual-based-modeling},  month = may,  number = {5},  pages = {e10464+},  posted-at = {2011-02-10 21:28:39},  priority = {2},  publisher = {Public Library of Science},  title = {{Developing Stochastic Models for Spatial Inference: Bacterial Chemotaxis}},  url = {http://dx.doi.org/10.1371/journal.pone.0010464},  volume = {5},  year = {2010}  }  @article{citeulike:8802776,  abstract = {{We present two approaches to the individual-based modeling (IbM) of bacterial ecologies and evolution using computational tools. The IbM approach is introduced, and its important complementary role to biosystems modeling is discussed. A fine-grained model of bacterial evolution is then presented that is based on networks of interactivity between computational objects representing genes and proteins. This is followed by a coarser grained agent-based model, which is designed to explore the evolvability of adaptive behavioral strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of the two proposed individual-based bacterial models are discussed, and some results from simulation experiments are presented, illustrating their adaptive properties.}},  author = {Paton, R. and Gregory, R. and Vlachos, C. and Saunders, J. and Wu, H.},  citeulike-article-id = {8802776},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/tnb.2004.833701},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=1331346},  doi = {10.1109/tnb.2004.833701},  issn = {1536-1241},  journal = {IEEE Transactions on Nanobioscience},  keywords = {individual-based-modeling},  month = sep,  number = {3},  pages = {208--216},  posted-at = {2011-02-10 21:25:12},  priority = {2},  title = {{Evolvable Social Agents for Bacterial Systems Modeling}},  url = {http://dx.doi.org/10.1109/tnb.2004.833701},  volume = {3},  year = {2004}  }  @article{citeulike:172811,  abstract = {{Pattern formation is a hallmark of coordinated cell behaviour in both single and multicellular organisms1, 2, 3. It typically involves cell–cell communication and intracellular signal processing. Here we show a synthetic multicellular system in which genetically engineered 'receiver' cells are programmed to form ring-like patterns of differentiation based on chemical gradients of an acyl-homoserine lactone (AHL) signal that is synthesized by 'sender' cells. In receiver cells, 'band-detect' gene networks respond to user-defined ranges of AHL concentrations. By fusing different fluorescent proteins as outputs of network variants, an initially undifferentiated 'lawn' of receivers is engineered to form a bullseye pattern around a sender colony. Other patterns, such as ellipses and clovers, are achieved by placing senders in different configurations. Experimental and theoretical analyses reveal which kinetic parameters most significantly affect ring development over time. Construction and study of such synthetic multicellular systems can improve our quantitative understanding of naturally occurring developmental processes and may foster applications in tissue engineering, biomaterial fabrication and biosensing.}},  author = {Basu, Subhayu and Gerchman, Yoram and Collins, Cynthia H. and Arnold, Frances H. and Weiss, Ron},  citeulike-article-id = {172811},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature03461},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature03461},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/15858574},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=15858574},  day = {28},  doi = {10.1038/nature03461},  issn = {0028-0836},  journal = {Nature},  keywords = {bacterial-biology},  month = apr,  number = {7037},  pages = {1130--1134},  pmid = {15858574},  posted-at = {2011-02-10 05:37:56},  priority = {2},  publisher = {Nature Publishing Group},  title = {{A synthetic multicellular system for programmed pattern formation}},  url = {http://dx.doi.org/10.1038/nature03461},  volume = {434},  year = {2005}  }  @book{citeulike:2125850,  abstract = {{This textbook on the theory of nonlinear dynamical systems for nonmathematical advanced undergraduate or graduate students is also a reference book for researchers in the physical and social sciences. It provides a comprehensive introduction including linear systems, stability theory of nonlinear systems, bifurcation theory, chaotic dynamics. Discussion of the measure--theoretic approach to dynamical systems and the relation between deterministic systems and stochastic processes is featured. There are a hundred exercises and an associated website provides a software program, computer exercises and answers to selected book exercises.} {A systematic and comprehensive introduction to the study of nonlinear dynamical systems, in both discrete and continuous time, for nonmathematical students and researchers working in applied fields. An understanding of linear systems and the classical theory of stability are essential although basic reviews of the relevant material are provided. Further chapters are devoted to the stability of invariant sets, bifurcation theory, chaotic dynamics and the transition to chaos. In the final two chapters the authors approach the subject from a measure-theoretical point of view and compare results to those given for the geometrical or topological approach of the first eight chapters. Includes about one hundred exercises. A Windows-compatible software programme called DMC, provided free of charge through a website dedicated to the book, allows readers to perform numerical and graphical analysis of dynamical systems. Also available on the website are computer exercises and solutions to selected book exercises. See www.cambridge.org/economics/resources}},  author = {Medio, Alfredo and Lines, Marji},  citeulike-article-id = {2125850},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0521551862},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0521551862},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0521551862},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0521551862},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0521551862/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0521551862},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0521551862},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0521551862},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0521551862\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0521551862},  day = {15},  edition = {1st},  howpublished = {Paperback},  isbn = {0521558743},  keywords = {books},  month = dec,  posted-at = {2011-02-05 18:11:43},  priority = {2},  publisher = {Cambridge University Press},  title = {{Nonlinear Dynamics}},  url = {http://www.worldcat.org/isbn/0521551862},  year = {2001}  }  @article{citeulike:2801447,  abstract = {{As data and knowledge about cell-biological systems increases so does the need for simulation tools to support a hypothesis driven wet-lab experimentation. Discrete event simulation has received a lot of attention lately, however, often its application is hampered by its lack of performance. One solution are parallel, distributed approaches, however, their application is limited by the amount of parallelism available in the model. Recent studies have shown that spatial aspects are crucial for cell biological dynamics and they are also a promising candidate to exploit parallelism. Promises and specific requirements imposed by a spatial simulation of cell biological systems will be illuminated by a parallel and distributed variant of the Next-Subvolume Method (NSM), which augments the Stochastic Simulation Algorithm (SSA) with spatial features, and its realization in a grid-inspired simulation system called Aurora.}},  address = {New York, NY, USA},  author = {Jeschke, Matthias and Ewald, Roland and Park, Alfred and Fujimoto, Richard and Uhrmacher, Adelinde M.},  citeulike-article-id = {2801447},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1364652},  citeulike-linkout-1 = {http://dx.doi.org/10.1145/1364644.1364652},  doi = {10.1145/1364644.1364652},  issn = {0163-5999},  journal = {SIGMETRICS Perform. Eval. Rev.},  keywords = {simulation-and-modeling},  month = mar,  number = {4},  pages = {22--31},  posted-at = {2011-02-05 17:01:48},  priority = {2},  publisher = {ACM},  title = {{A parallel and distributed discrete event approach for spatial cell-biological simulations}},  url = {http://dx.doi.org/10.1145/1364644.1364652},  volume = {35},  year = {2008}  }  @article{citeulike:144442,  abstract = {{How cells utilize intracellular spatial features to optimize their signaling characteristics is still not clearly understood. The physical distance between the cell-surface receptor and the gene expression machinery, fast reactions, and slow protein diffusion coefficients are some of the properties that contribute to their intricacy. This article reviews computational frameworks that can help biologists to elucidate the implications of space in signaling pathways. We argue that intracellular macromolecular crowding is an important modeling issue, and describe how recent simulation methods can reproduce this phenomenon in either implicit, semi-explicit or fully explicit representation.}},  author = {Takahashi, K. and Arjunan, S. and Tomita, M.},  citeulike-article-id = {144442},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.febslet.2005.01.072},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15763552},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15763552},  citeulike-linkout-3 = {http://www.sciencedirect.com/science/article/B6T36-4FG4SNS-4/2/985b8f5ba22f012850d8b21571560681},  day = {21},  doi = {10.1016/j.febslet.2005.01.072},  issn = {00145793},  journal = {FEBS Letters},  keywords = {simulation-and-modeling},  month = mar,  number = {8},  pages = {1783--1788},  pmid = {15763552},  posted-at = {2011-02-04 16:13:45},  priority = {2},  title = {{Space in systems biology of signaling pathways ? towards intracellular molecular crowding in silico}},  url = {http://dx.doi.org/10.1016/j.febslet.2005.01.072},  volume = {579},  year = {2005}  }  @book{citeulike:8754502,  citeulike-article-id = {8754502},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/3540963057},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/3540963057},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/3540963057},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/3540963057},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/3540963057/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/3540963057},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/3540963057},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN3540963057},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=3540963057\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/3540963057},  day = {31},  howpublished = {Hardcover},  isbn = {3540963057},  keywords = {books},  month = dec,  posted-at = {2011-02-03 07:07:07},  priority = {2},  publisher = {Springer-Verlag Berlin and Heidelberg GmbH \& Co. K},  title = {{Non-Uniform Random Variate Generation}},  url = {http://www.worldcat.org/isbn/3540963057},  year = {1986}  }  @article{citeulike:8750368,  abstract = {{This article highlights the role of biophysical principles in biofilm growth and propagation in food environments, an area that is of increasing concern to food processors due to the high resistance of biofilms to conventional remediation methodologies. First, the general characteristics of biofilms are discussed including their structure and physiological characteristics. Transfer and propagation mechanisms consisting of attachment followed by growth and subsequent detachment are reviewed. General growth models that are currently used in laboratories focusing on biofilm research are compared and emerging characterization techniques are discussed. An overview over current practices and techniques to remediate biofilms in a variety of environments is given. Remediation techniques that are reviewed include application of sanitizers and detergents. Finally, future research needs are briefly summarized.}},  author = {McLandsborough, L. and Rodriguez, A. and P\'{e}rez-Conesa, D. and Weiss, J.},  citeulike-article-id = {8750368},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s11483-005-9004-x},  citeulike-linkout-1 = {http://www.springerlink.com/content/xt55k5033m7677l7},  day = {1},  doi = {10.1007/s11483-005-9004-x},  issn = {1557-1858},  journal = {Food Biophysics},  keywords = {bacterial-biology},  month = jun,  number = {2},  pages = {94--114},  posted-at = {2011-02-02 20:59:35},  priority = {2},  publisher = {Springer New York},  title = {{Biofilms: At the Interface between Biophysics and Microbiology}},  url = {http://dx.doi.org/10.1007/s11483-005-9004-x},  volume = {1},  year = {2006}  }  @article{citeulike:6284624,  abstract = {{Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research, reveal that, under specific growth conditions, bacterial cells form patterns of interconnected microcolonies. In the present work, we use an individual-based model to assess the involvement of bacteria motility and self-produced extracellular substance in the formation of these patterns. In our simulations, the pattern of interconnected microcolonies appears only when bacteria motility is reduced by excreted extracellular macromolecules. Immotile bacteria form isolated microcolonies and constantly motile bacteria form flat biofilms. Based on experimental data and computer simulations, we suggest a mechanism that could be responsible for these interconnected microcolonies.}},  author = {Mabrouk, Nabil and Deffuant, Guillaume and Tolker-Nielsen, Tim and Lobry, Claude},  citeulike-article-id = {6284624},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s12064-009-0078-8},  citeulike-linkout-1 = {http://www.springerlink.com/content/r276t7018n41pq23},  day = {1},  doi = {10.1007/s12064-009-0078-8},  issn = {1431-7613},  journal = {Theory in Biosciences},  keywords = {individual-based-modeling},  month = jun,  number = {1},  pages = {1--13},  posted-at = {2011-02-02 20:55:35},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  title = {{Bacteria can form interconnected microcolonies when a self-excreted product reduces their surface motility: evidence from individual-based model simulations}},  url = {http://dx.doi.org/10.1007/s12064-009-0078-8},  volume = {129},  year = {2010}  }  @article{citeulike:8750291,  abstract = {{  We present an individual-based experimental framework to identify and estimate the main parameters governing bacterial conjugation at the individual cell scale. From this analysis, we have established that transient periods of unregulated plasmid transfer within newly formed transconjugant cells, together with contact mechanics arising from cellular growth and division, are the two main processes determining the emergent inability of the pWW0 TOL plasmid to fully invade spatially structured Pseudomonas putida populations. We have also shown that pWW0 conjugation occurs mainly at advanced stages of the growth cycle and that nongrowing cells, even when exposed to high nutrient concentrations, do not display conjugal activity. These results do not support previous hypotheses relating conjugation decay in the deeper cell layers of bacterial biofilms to nutrient depletion and low physiological activity. We observe, however, that transient periods of elevated plasmid transfer in newly formed transconjugant cells are offset by unfavorable cell-to-cell contact mechanics, which ultimately precludes the pWWO TOL plasmid from fully invading tightly packed multicellular P. putida populations such as microcolonies and biofilms.  {\copyright} 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.  }},  author = {Seoane, Jose and Yankelevich, Tatiana and Dechesne, Arnaud and Merkey, Brian and Sternberg, Claus and Smets, Barth F.},  citeulike-article-id = {8750291},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1574-6941.2010.00994.x},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/21091520},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=21091520},  doi = {10.1111/j.1574-6941.2010.00994.x},  issn = {1574-6941},  journal = {FEMS microbiology ecology},  keywords = {individual-based-modeling},  month = jan,  number = {1},  pages = {17--27},  pmid = {21091520},  posted-at = {2011-02-02 20:43:47},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{An individual-based approach to explain plasmid invasion in bacterial populations.}},  url = {http://dx.doi.org/10.1111/j.1574-6941.2010.00994.x},  volume = {75},  year = {2011}  }  @article{citeulike:8420624,  abstract = {{The individual-based (aka agent-based) approach is now well established in ecological modeling. Traditionally, most applications have been to organisms at higher trophic levels, where the importance of population heterogeneity (intra-population variability), complete life cycles and behavior adapted to internal and external conditions has been recognized for some time. However, advances in molecular biology and biochemistry have brought about an increase in the application of individual-based modeling (IBM) to microbes as well. This literature review summarizes 46 IBM papers for bacteria in wastewater treatment plants, phytoplankton in ocean and inland waters, bacteria in biofilms, bacteria in food and other environs, and ” digital organisms” and ” domesticated computer viruses” in silico. The use of IBM in these applications was motivated by population heterogeneity (45\%), emergence (24\%), absence of a continuum (5\%), and other unknown reasons (26\%). In general, the challenges and concepts of IBM modeling for microbes and higher trophic levels are similar. However, there are differences in the microbe population dynamics and their environment that create somewhat different challenges, which have led to somewhat different modeling concepts. Several topics are discussed, including producing, maintaining and changing population heterogeneity (different life histories, internal variability, positive feedback, inter-generation memory), dealing with very large numbers of individuals (different up-scaling methods, including representative space vs. super-individual, number vs. biomass based, discrete vs. continuous kinetics, various agent accounting methods), handling space, simulating interactions with the extracellular environment (hybrid Eulerian–Lagrangian approach), modeling agent–agent interaction (self-shading, predation, shoving) and passive transport (random walk with spatially variable diffusivity, well-mixed reactors). Overall, the literature indicates that the application of IBM to microbes is developing into a mature field. However, several challenges remain, including simulating various types of agent–agent interactions (formation and function of colonies or filaments, sexual reproduction) and even smaller individuals (viruses, genes). Further increases in intracellular detail and complexity in microbe IBMs may be considered the combination of systems biology and systems ecology, or the new field of systems bioecology.}},  author = {Hellweger, Ferdi L. and Bucci, Vanni},  citeulike-article-id = {8420624},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ecolmodel.2008.09.004},  day = {10},  doi = {10.1016/j.ecolmodel.2008.09.004},  issn = {03043800},  journal = {Ecological Modelling},  keywords = {individual-based-modeling},  month = jan,  number = {1},  pages = {8--22},  posted-at = {2011-02-02 19:24:55},  priority = {2},  title = {{A bunch of tiny individuals --- Individual-based modeling for microbes}},  url = {http://dx.doi.org/10.1016/j.ecolmodel.2008.09.004},  volume = {220},  year = {2009}  }  @book{citeulike:8745260,  author = {Lynch, Stephen and Lynch, Stephen and Birkhauser},  citeulike-article-id = {8745260},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0817643214},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0817643214},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0817643214},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0817643214},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0817643214/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0817643214},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0817643214},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0817643214},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0817643214\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0817643214},  day = {10},  edition = {1},  howpublished = {Paperback},  isbn = {0817643214},  keywords = {books},  month = jun,  posted-at = {2011-02-02 11:15:23},  priority = {2},  publisher = {Birkh\"{a}user Boston},  title = {{Dynamical Systems with Applications using MATLAB}},  url = {http://www.worldcat.org/isbn/0817643214},  year = {2004}  }  @article{citeulike:3878676,  abstract = {{doi: 10.1021/j100540a008}},  author = {Gillespie, Daniel T.},  booktitle = {The Journal of Physical Chemistry},  citeulike-article-id = {3878676},  citeulike-linkout-0 = {http://dx.doi.org/10.1021/j100540a008},  citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/j100540a008},  day = {1},  doi = {10.1021/j100540a008},  journal = {J. Phys. Chem.},  keywords = {simulation-and-modeling},  month = dec,  number = {25},  pages = {2340--2361},  posted-at = {2011-02-01 22:48:52},  priority = {2},  publisher = {American Chemical Society},  title = {{Exact stochastic simulation of coupled chemical reactions}},  url = {http://dx.doi.org/10.1021/j100540a008},  volume = {81},  year = {1977}  }  @book{citeulike:233804,  abstract = {{This is the first textbook to be explicitly designed for use as a course text for an undergraduate/graduate course on multi-agent systems. Assuming only a basic understanding of computer science, this text provides an introduction to all the main issues in the theory and practice of intelligent agents and multi-agent systems.

* The companion Web Site includes sample exercises, lecture slidest and hyperlinks to software referred to in the book
* Introduces agents, explains what agents are, how they are constructed and how they can be made to co-operate effectively with one another in large-scale systems
* Introduces the main issues surrounding the design of intelligent agents
* Introduces a number of typical applications for agent technology

} {Multiagent systems represent a new way of conceptualising and implementing distributed software. An Introduction to MultiAgent Systems is the first modern textbook on this important topic. It provides a comprehensive introduction to intelligent agents and multiagent systems. The book assumes no specialist knowledge. It introduces the idea of agents as software systems that can act autonomously, and leads the reader through a detailed discussion of: ways that agents can be built how agents can reach agreements the languages that agents can use to communicate with one-another co-operation and co-ordination in agent systems and the applications of agent technology. Designed and written specifically for undergraduates and computing professionals, the book is supported by extensive online teaching resources, including a complete set of lecture slides. Illustrated with many informal examples, and packed with more than 500 references, An Introduction to MultiAgent Systems is a must-read for students and practitioners of agent systems alike.}},  author = {Wooldridge, Michael},  citeulike-article-id = {233804},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/047149691X},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/047149691X},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/047149691X},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/047149691X},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/047149691X/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/047149691X},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/047149691X},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN047149691X},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=047149691X\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/047149691X},  day = {12},  edition = {1st},  howpublished = {Paperback},  isbn = {047149691X},  keywords = {books},  month = jun,  posted-at = {2011-01-29 20:08:20},  priority = {2},  publisher = {John Wiley \& Sons},  title = {{An Introduction to MultiAgent Systems}},  url = {http://www.worldcat.org/isbn/047149691X},  year = {2002}  }  @book{ChaosBook,  address = {Copenhagen},  author = {Cvitanovi\'{c}, P. and Artuso, R. and Mainieri, R. and Tanner, G. and Vattay, G.},  citeulike-article-id = {8704575},  comment = {{\tt \href{http://ChaosBook.org}{ChaosBook.org}}},  keywords = {books},  posted-at = {2011-01-29 11:49:14},  priority = {2},  publisher = {Niels Bohr Institute},  title = {{Chaos: Classical and Quantum}},  year = {2010}  }  @book{citeulike:8703893,  author = {Myers, Jerome L. and Well, Arnold D.},  citeulike-article-id = {8703893},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0805820671},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0805820671},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0805820671},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0805820671},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0805820671/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0805820671},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0805820671},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0805820671},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0805820671\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0805820671},  day = {01},  edition = {1},  howpublished = {Hardcover},  isbn = {0805820671},  keywords = {books},  month = jun,  posted-at = {2011-01-29 09:46:04},  priority = {2},  publisher = {Routledge},  title = {{Research Design \& Statistical Analysis}},  url = {http://www.worldcat.org/isbn/0805820671},  year = {1995}  }  @book{citeulike:1604142,  abstract = {{**** Virtually every computing system today is part of a distributed system.  Programmers, developers, and engineers need to understand the underlying  principles and paradigms as well as the real-world application of those  principles. Now, internationally renowned expert Andrew S. Tanenbaum – with  colleague Martin van Steen – presents a complete introduction that identifies  the seven key principles of distributed systems, with extensive examples of  each. **** Adds a completely new chapter on architecture to address the  principle of organizing distributed systems. Provides extensive new material  on peer-to-peer systems, grid computing and Web services, virtualization, and  application-level multicasting. Updates material on clock synchronization,  data-centric consistency, object-based distributed systems, and file systems  and Web systems coordination. **** For all developers, software engineers, and  architects who need an in-depth understanding of distributed systems.}},  author = {Tanenbaum, Andrew S. and Van Steen, Maarten},  citeulike-article-id = {1604142},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0132392275},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0132392275},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0132392275},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0132392275},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0132392275/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0132392275},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0132392275},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0132392275},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0132392275\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0132392275},  day = {12},  edition = {2},  howpublished = {Hardcover},  isbn = {0132392275},  keywords = {books},  month = oct,  posted-at = {2011-01-29 09:44:31},  priority = {2},  publisher = {Prentice Hall},  title = {{Distributed Systems: Principles and Paradigms (2nd Edition)}},  url = {http://www.worldcat.org/isbn/0132392275},  year = {2006}  }  @article{citeulike:1104508,  abstract = {{Previous studies have suggested that members of the Geobacteraceae can use electrodes as electron acceptors for anaerobic respiration. In order to better understand this electron transfer process for energy production, Geobacter sulfurreducens was inoculated into chambers in which a graphite electrode served as the sole electron acceptor and acetate or hydrogen was the electron donor. The electron-accepting electrodes were maintained at oxidizing potentials by connecting them to similar electrodes in oxygenated medium (fuel cells) or to potentiostats that poised electrodes at +0.2 V versus an Ag/AgCl reference electrode (poised potential). When a small inoculum of G. sulfurreducens was introduced into electrode-containing chambers, electrical current production was dependent upon oxidation of acetate to carbon dioxide and increased exponentially, indicating for the first time that electrode reduction supported the growth of this organism. When the medium was replaced with an anaerobic buffer lacking nutrients required for growth, acetate-dependent electrical current production was unaffected and cells attached to these electrodes continued to generate electrical current for weeks. This represents the first report of microbial electricity production solely by cells attached to an electrode. Electrode-attached cells completely oxidized acetate to levels below detection (<10 μM), and hydrogen was metabolized to a threshold of 3 Pa. The rates of electron transfer to electrodes (0.21 to 1.2 μmol of electrons/mg of protein/min) were similar to those observed for respiration with Fe(III) citrate as the electron acceptor (Eo′ =+0.37 V). The production of current in microbial fuel cell (65 mA/m2 of electrode surface) or poised-potential (163 to 1,143 mA/m2) mode was greater than what has been reported for other microbial systems, even those that employed higher cell densities and electron-shuttling compounds. Since acetate was completely oxidized, the efficiency of conversion of organic electron donor to electricity was significantly higher than in previously described microbial fuel cells. These results suggest that the effectiveness of microbial fuel cells can be increased with organisms such as G. sulfurreducens that can attach to electrodes and remain viable for long periods of time while completely oxidizing organic substrates with quantitative transfer of electrons to an electrode.}},  author = {Bond, Daniel R. and Lovley, Derek R.},  citeulike-article-id = {1104508},  citeulike-linkout-0 = {http://dx.doi.org/10.1128/aem.69.3.1548},  citeulike-linkout-1 = {http://aem.asm.org/content/69/3/1548.abstract},  citeulike-linkout-2 = {http://aem.asm.org/content/69/3/1548.full.pdf},  citeulike-linkout-3 = {http://aem.asm.org/cgi/content/abstract/69/3/1548},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/12620842},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=12620842},  day = {01},  doi = {10.1128/aem.69.3.1548},  issn = {1098-5336},  journal = {Applied and Environmental Microbiology},  keywords = {bacterial-biology},  month = mar,  number = {3},  pages = {1548--1555},  pmid = {12620842},  posted-at = {2011-01-28 12:36:59},  priority = {2},  publisher = {American Society for Microbiology},  title = {{Electricity Production by Geobacter sulfurreducens Attached to Electrodes}},  url = {http://dx.doi.org/10.1128/aem.69.3.1548},  volume = {69},  year = {2003}  }  @article{citeulike:235180,  abstract = {{Microbes that can transfer electrons to extracellular electron acceptors, such as Fe(iii) oxides, are important in organic matter degradation and nutrient cycling in soils and sediments1, 2. Previous investigations on electron transfer to Fe(iii) have focused on the role of outer-membrane c-type cytochromes1, 3. However, some Fe(iii) reducers lack c-cytochromes4. Geobacter species, which are the predominant Fe(iii) reducers in many environments1, must directly contact Fe(iii) oxides to reduce them5, and produce monolateral pili6 that were proposed1, 2, on the basis of the role of pili in other organisms7, 8, to aid in establishing contact with the Fe(iii) oxides. Here we report that a pilus-deficient mutant of Geobacter sulfurreducens could not reduce Fe(iii) oxides but could attach to them. Conducting-probe atomic force microscopy revealed that the pili were highly conductive. These results indicate that the pili of G. sulfurreducens might serve as biological nanowires, transferring electrons from the cell surface to the surface of Fe(iii) oxides. Electron transfer through pili indicates possibilities for other unique cell-surface and cell–cell interactions, and for bioengineering of novel conductive materials.}},  author = {Reguera, Gemma and McCarthy, Kevin D. and Mehta, Teena and Nicoll, Julie S. and Tuominen, Mark T. and Lovley, Derek R.},  citeulike-article-id = {235180},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature03661},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature03661},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/15973408},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=15973408},  day = {23},  doi = {10.1038/nature03661},  issn = {0028-0836},  journal = {Nature},  keywords = {bacterial-biology},  month = jun,  number = {7045},  pages = {1098--1101},  pmid = {15973408},  posted-at = {2011-01-28 11:54:21},  priority = {2},  publisher = {Macmillian Magazines Ltd.},  title = {{Extracellular electron transfer via microbial nanowires}},  url = {http://dx.doi.org/10.1038/nature03661},  volume = {435},  year = {2005}  }  @article{citeulike:5396651,  abstract = {{Computer simulations are increasingly used in biological fields. The amazing power, storage ability, and processing speeds available nowadays have enabled the implementation of computer individual-based models (IbMs) to simulate really complex biological populations. Computers can easily keep track of thousands of individuals (often called 'agents'), whose complex behaviours and large amounts of associated data were daunting only 20 years ago. As such, computer modelling has just entered a field where traditional PDE models used to reign alone. A study of the exchange and non-trivial relationship between these two fields, computer IbMs versus classic partial differential equations (PDEs), is appropriate. The aim of this paper is to compare both approaches through a relevant example, namely the evolution of a yeast population in a batch culture. Thus, this paper deals with the utilization of both classical mathematics and computer science in the solution of problems arising in microbiology. First, an IbM approach to study the evolution of a yeast batch culture is presented. Second, an equivalent PDE model is derived by using some techniques from the interacting particle systems field. Third, a comparison and discussion on the advantages and drawbacks of both modelling tools is given.}},  address = {Tarrytown, NY, USA},  author = {Mourelo, Pablo G. and Ginovart, Marta},  citeulike-article-id = {5396651},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1596087},  citeulike-linkout-1 = {http://dx.doi.org/10.1016/j.camwa.2009.05.024},  day = {03},  doi = {10.1016/j.camwa.2009.05.024},  issn = {0898-1221},  journal = {Comput. Math. Appl.},  keywords = {individual-based-modeling},  month = oct,  number = {7},  pages = {1360--1369},  posted-at = {2011-01-27 16:07:55},  priority = {2},  publisher = {Pergamon Press, Inc.},  title = {{The differential equation counterpart of an individual-based model for yeast population growth}},  url = {http://dx.doi.org/10.1016/j.camwa.2009.05.024},  volume = {58},  year = {2009}  }  @article{citeulike:451545,  abstract = {{An individual-based model has been developed and designed to simulate the growth and behaviour of bacterial colonies. The simulator is called INDISIM, which stands for INDividual DIScrete SIMulations. INDISIM is discrete in space and time, and controls a group of bacterial cells at each time step, using a set of random, time-dependent variables for each bacterium. These variables are used to characterize its position in space, biomass, state in the cellular reproduction cycle as well as other individual properties. The space where the bacterial colony evolves is also discrete. A physical lattice is introduced, subject to the appropriate boundary conditions. The lattice is subdivided into spatial cells, also defined by a set of random, time-dependent variables. These variables may include concentrations of different types of particles, nutrients, reaction products and residual products. Random variables are used to characterize the individual bacterium and the individual particle, as well as the updating of individual rules. Thus, the simulations are stochastic rather than deterministic. The whole set of variables, those that characterize the bacterial population and the environment where they evolve, enables the simulator to study the behaviour of each microorganism-such as its motion, uptake, metabolism, and viability-according to given rules suited for the system under study. These rules require the input of only a few parameters. Once this information is inputted, INDISIM simulates the behaviour of the system providing insights into the global properties of the system from the assumptions made on the properties of the individual bacteria. The relation between microscopic and global properties of the bacterial colony is obtained by using statistical averaging. In this work INDISIM has been used to study (a) biomass distributions, (b) the relationship between the rate of growth of a bacterial colony and the nutrient concentration and temperature, and (c) metabolic oscillations in batch bacterial colonies. The simulation results are found to be in very good qualitative agreement with available experimental data, and provide useful insights into the mechanisms involved in each case.}},  address = {Escola Superior d'Agricultura de Barcelona (EUETAB-CEIB), Universitat Polit\`{e}cnica de Catalunya, Urgell 187, 08036 Barcelona, Spain. [email protected]},  author = {Ginovart, Marta and L\'{o}pez, Daniel and Valls, Joaquim},  citeulike-article-id = {451545},  citeulike-linkout-0 = {http://dx.doi.org/10.1006/jtbi.2001.2466},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/11812180},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=11812180},  day = {21},  doi = {10.1006/jtbi.2001.2466},  issn = {0022-5193},  journal = {Journal of theoretical biology. },  keywords = {individual-based-modeling},  month = jan,  number = {2},  pages = {305--319},  pmid = {11812180},  posted-at = {2011-01-27 16:04:36},  priority = {2},  title = {{INDISIM, an individual-based discrete simulation model to study bacterial cultures.}},  url = {http://dx.doi.org/10.1006/jtbi.2001.2466},  volume = {214},  year = {2002}  }  @article{citeulike:8691376,  abstract = {{We illustrate and extend the techniques of computational mechanics in explicating the structures that emerge in the space-time behavior of elementary one-dimensional cellular automaton rule 54. The dominant regular domain of the cellular automation is identified and a domain filter is constructed to locate and classify defects in the domain. The primary particles are identified and a range of interparticle interactions is studied. The deterministic equation of motion of the filtered space-time behavior is derived. Filters of increasing sophistication are constructed for the efficient gathering of particle statistics and for the identification of higher-level defects, particle interactions, and secondary domains. We define the emergence time at which the space-time behavior condenses into configurations consisting only of domains, particles, and particle interactions. Taken together, these techniques serve as the basis for the investigation of pattern evolution and self-organization in this representative system.}},  author = {Hanson, James E. and Crutchfield, James P.},  citeulike-article-id = {8691376},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0167-2789(96)00259-x},  day = {15},  doi = {10.1016/s0167-2789(96)00259-x},  issn = {01672789},  journal = {Physica D: Nonlinear Phenomena},  keywords = {simulation-and-modeling},  month = apr,  number = {1-4},  pages = {169--189},  posted-at = {2011-01-25 16:43:33},  priority = {2},  title = {{Computational mechanics of cellular automata: An example}},  url = {http://dx.doi.org/10.1016/s0167-2789(96)00259-x},  volume = {103},  year = {1997}  }  @article{citeulike:5042820,  abstract = {{The main focus of this article is to present and relate four different frameworks in which spatially explicit individual-based models (IBMs) can be defined. These frameworks differ in the way space and time are modeled; each can be treated either discretely or continuously. The emphasis is put on constructing and simulating one of the simplest single-species IBMs in each spatio-temporal framework, discussing some of their technical subtleties, and deriving corresponding mean-field models when the homogeneous mixing conditions are assumed to hold. The four frameworks are more supplements than competitors. Since at almost every step of IBM construction several alternatives are a priori plausible I discuss the most important ones in more details. This article seems to be the first attempt to collect and synthesize information of this kind that is scattered over the literature.}},  author = {Berec, Lud\v{e}k},  citeulike-article-id = {5042820},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0304-3800(01)00463-x},  day = {15},  doi = {10.1016/s0304-3800(01)00463-x},  issn = {03043800},  journal = {Ecological Modelling},  keywords = {individual-based-modeling},  month = apr,  number = {1-2},  pages = {55--81},  posted-at = {2011-01-25 16:15:44},  priority = {2},  title = {{Techniques of spatially explicit individual-based models: construction, simulation, and mean-field analysis}},  url = {http://dx.doi.org/10.1016/s0304-3800(01)00463-x},  volume = {150},  year = {2002}  }  @article{citeulike:8684280,  abstract = {{Plasmids classified to the IncP-1 incompatibility group belong to the most stably maintained mobile elements among low copy number plasmids known to date. The remarkable persistence is achieved by various tightly controlled stability mechanisms like active partitioning, efficient conjugative transfer system, killing of plasmid-free segregants and multimer resolution. The unique feature of IncP-1 plasmids is the central control operon coding for global regulators which control the expression of genes involved in vegetative replication, stable maintenance and conjugative transfer. The multivalent regulatory network provides means for coordinated expression of all plasmid functions. The current state of knowledge about two fully sequenced plasmids RK2 and R751, representatives of the IncP-1alpha and IncP-1beta subgroups, is presented.}},  author = {Adamczyk, Ma{\l}gorzata and Jagura-Burdzy, Grazyna},  citeulike-article-id = {8684280},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/12833168},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=12833168},  issn = {0001-527X},  journal = {Acta biochimica Polonica},  keywords = {bacterial-biology},  number = {2},  pages = {425--453},  pmid = {12833168},  posted-at = {2011-01-23 22:09:41},  priority = {2},  title = {{Spread and survival of promiscuous IncP-1 plasmids.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/12833168},  volume = {50},  year = {2003}  }  @article{citeulike:8682012,  abstract = {{Magnetosomes are intracellular, iron-rich, membrane-enclosed magnetic particles that allow magnetotactic bacteria to orient in the earth's geomagnetic field as they swim. The magnetosomes of most magnetotactic bacteria contain iron oxide particles, but some magnetotactic species contain iron sulfide particles instead. Phylogenetic analyses of small subunit ribosomal RNA sequences showed that all known magnetotactic bacteria of the iron oxide type are associated with the a subgroup of the Proteobacteria in the domain Bacteria. In contrast, uncultured magnetotactic bacteria of the iron sulfide type are specifically related to the dissimilatory sulfate-reducing bacteria within the delta subdivision of the Proteobacteria. These findings indicate a polyphyletic origin for magnetotactic bacteria and suggest that magnetotaxis based on iron oxides and iron sulfides evolved independently.}},  author = {Delong, E. F. and Frankel, R. B. and Bazylinski, D. A.},  citeulike-article-id = {8682012},  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.259.5096.803},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17809345},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17809345},  day = {5},  doi = {10.1126/science.259.5096.803},  issn = {0036-8075},  journal = {Science (New York, N.Y.)},  keywords = {bacterial-biology},  month = feb,  number = {5096},  pages = {803--806},  pmid = {17809345},  posted-at = {2011-01-23 10:41:29},  priority = {2},  title = {{Multiple evolutionary origins of magnetotaxis in bacteria.}},  url = {http://dx.doi.org/10.1126/science.259.5096.803},  volume = {259},  year = {1993}  }  @article{citeulike:4443193,  abstract = {{Summary The organization of magnetosome genes was analysed in all available complete or partial genomic sequences of magnetotactic bacteria (MTB), including the magnetosome island (MAI) of the magnetotactic marine vibrio strain MV-1 determined in this study. The MAI was found to differ in gene content and organization between Magnetospirillum species and strains MV-1 or MC-1. Although a similar organization of magnetosome genes was found in all MTB, distinct variations in gene order and sequence similarity were uncovered that may account for the observed diversity of biomineralization, cell biology and magnetotaxis found in various MTB. While several magnetosome genes were present in all MTB, others were confined to Magnetospirillum species, indicating that the minimal set of genes required for magnetosome biomineralization might be smaller than previously suggested. A number of novel candidate genes were implicated in magnetosome formation by gene cluster comparison. Based on phylogenetic and compositional evidence we present a model for the evolution of magnetotaxis within the Alphaproteobacteria, which suggests the independent horizontal transfer of magnetosome genes from an unknown ancestor of magnetospirilla into strains MC-1 and MV-1.}},  author = {Jogler, Christian and Kube, Michael and Sch\"{u}bbe, Sabrina and Ullrich, Susanne and Teeling, Hanno and Bazylinski, Dennis A. and Reinhardt, Richard and Sch\"{u}ler, Dirk},  citeulike-article-id = {4443193},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1462-2920.2009.01854.x},  citeulike-linkout-1 = {http://www.ingentaconnect.com/content/bsc/emi/2009/00000011/00000005/art00019},  doi = {10.1111/j.1462-2920.2009.01854.x},  issn = {1462-2912},  journal = {Environmental Microbiology},  keywords = {bacterial-biology},  number = {5},  pages = {1267--1277},  posted-at = {2011-01-23 10:28:27},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{Comparative analysis of magnetosome gene clusters in magnetotactic bacteria provides further evidence for horizontal gene transfer}},  url = {http://dx.doi.org/10.1111/j.1462-2920.2009.01854.x},  volume = {11},  year = {2009}  }  @article{citeulike:8681921,  abstract = {{The magnetosomes of magnetotactic bacteria are prokaryotic organelles consisting of a magnetite crystal bounded by a phospholipid bilayer that contains a distinct set of proteins with various functions. Because of their unique magnetic and crystalline properties, magnetosome particles are potentially useful as magnetic nanoparticles in a number of applications, which in many cases requires the coupling of functional moieties to the magnetosome membrane. In this work, we studied the use of green fluorescent protein (GFP) as a reporter for the magnetosomal localization and expression of fusion proteins in the microaerophilic Magnetospirillum gryphiswaldense by flow cytometry, fluorescence microscopy, and biochemical analysis. Although optimum conditions for high fluorescence and magnetite synthesis were mutually exclusive, we established oxygen-limited growth conditions, which supported growth, magnetite biomineralization, and GFP fluorophore formation at reasonable rates. Under these optimized conditions, we studied the subcellular localization and expression of the GFP-tagged magnetosome proteins MamC, MamF, and MamG by fluorescence microscopy and immunoblotting. While all fusions specifically localized at the magnetosome membrane, MamC-GFP displayed the strongest expression and fluorescence. MamC-GFP-tagged magnetosomes purified from cells displayed strong fluorescence, which was sensitive to detergents but stable under a wide range of temperature and salt concentrations. In summary, our data demonstrate the use of GFP as a reporter for protein localization under magnetite-forming conditions and the utility of MamC as an anchor for magnetosome-specific display of heterologous gene fusions.}},  author = {Lang, Claus and Sch\"{u}ler, Dirk},  citeulike-article-id = {8681921},  citeulike-linkout-0 = {http://dx.doi.org/10.1128/aem.00231-08},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18539817},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18539817},  doi = {10.1128/aem.00231-08},  issn = {1098-5336},  journal = {Applied and environmental microbiology},  keywords = {bacterial-biology},  month = aug,  number = {15},  pages = {4944--4953},  pmid = {18539817},  posted-at = {2011-01-23 10:17:04},  priority = {2},  title = {{Expression of green fluorescent protein fused to magnetosome proteins in microaerophilic magnetotactic bacteria.}},  url = {http://dx.doi.org/10.1128/aem.00231-08},  volume = {74},  year = {2008}  }  @article{citeulike:2374692,  abstract = {{The ability to manipulate systems on the molecular scale naturally leads to speculation about the rational design of molecular-scale machines. Cells might be the ultimate molecular-scale machines and our ability to engineer them is relatively advanced when compared with our ability to control the synthesis and direct the assembly of man-made materials. Indeed, engineered whole cells deployed in biosensors can be considered one of the practical successes of molecular-scale devices. However, these devices explore only a small portion of cellular functionality. Individual cells or self-organized groups of cells perform extremely complex functions that include sensing, communication, navigation, cooperation and even fabrication of synthetic nanoscopic materials. In natural systems, these capabilities are controlled by complex genetic regulatory circuits, which are only partially understood and not readily accessible for use in engineered systems. Here, we focus on efforts to mimic the functionality of man-made information-processing systems within whole cells.}},  author = {Simpson, M.},  citeulike-article-id = {2374692},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0167-7799(01)01691-2},  citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6TCW-43F7CD0-X/2/e4750617766ce7b9148ed726c6fb3911},  day = {1},  doi = {10.1016/s0167-7799(01)01691-2},  issn = {01677799},  journal = {Trends in Biotechnology},  keywords = {bacterial-biology},  month = aug,  number = {8},  pages = {317--323},  posted-at = {2011-01-23 10:14:18},  priority = {2},  title = {{Whole-cell biocomputing}},  url = {http://dx.doi.org/10.1016/s0167-7799(01)01691-2},  volume = {19},  year = {2001}  }  @book{citeulike:1314150,  abstract = {{Thorough and accessible, this book presents the design principles of  biological systems, and highlights the recurring circuit elements that make up  biological networks. It provides a simple mathematical framework which can be  used to understand and even design biological circuits. The textavoids  specialist terms, focusing instead on several well-studied biological systems  that concisely demonstrate key principles.  **An Introduction to Systems Biology: Design Principles of Biological Circuits  **builds a solid foundation for the intuitive understanding of general  principles. It encourages the reader to ask \_why\_ a system is designed in a  particular way and then proceeds to answer with simplified models.}},  author = {Alon, Uri},  citeulike-article-id = {1314150},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/1584886420},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/1584886420},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/1584886420},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/1584886420},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/1584886420/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/1584886420},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/1584886420},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN1584886420},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=1584886420\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/1584886420},  day = {07},  edition = {1},  howpublished = {Paperback},  isbn = {1584886420},  keywords = {books},  month = jul,  posted-at = {2011-01-22 11:25:27},  priority = {2},  publisher = {Chapman and Hall/CRC},  title = {{An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman \& Hall/CRC Mathematical and Computational Biology)}},  url = {http://www.worldcat.org/isbn/1584886420},  year = {2006}  }  @article{citeulike:5336751,  abstract = {{ Nano-sized magnetic particles are increasingly being used across a wide spectrum of biomedical fields. Upon functionalization to enable specific binding, magnetic particles and their targets can be conveniently positioned in vitro and in vivo by the distal application of magnetic fields. Furthermore, such particles can be magnetically heated after reaching their in vivo targets, thus inducing localized cell death that has a considerable therapeutic value in, for instance, cancer therapy. In this context, innovative biomedical research has produced novel applications that have exciting clinical potential. Such applications include magnetically enhanced transfection, magnetically assisted gene therapy, magnetically induced hyperthermia and magnetic-force-based tissue engineering, and the principles and utilities of these applications will be discussed here. }},  author = {Corchero, Jos\'{e} L. and Villaverde, Antonio},  citeulike-article-id = {5336751},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.tibtech.2009.04.003},  doi = {10.1016/j.tibtech.2009.04.003},  issn = {01677799},  journal = {Trends in Biotechnology},  keywords = {bacterial-biology},  month = aug,  number = {8},  pages = {468--476},  posted-at = {2011-01-20 21:47:14},  priority = {2},  title = {{Biomedical applications of distally controlled magnetic nanoparticles}},  url = {http://dx.doi.org/10.1016/j.tibtech.2009.04.003},  volume = {27},  year = {2009}  }  @article{citeulike:8663692,  abstract = {{We developed a series of ligand-inducible riboswitches that control gene expression in diverse species of Gram-negative and Gram-positive bacteria, including human pathogens that have few or no previously reported inducible expression systems. We anticipate that these riboswitches will be useful tools for genetic studies in a wide range of bacteria.}},  author = {Topp, Shana and Reynoso, Colleen M. K. and Seeliger, Jessica C. and Goldlust, Ian S. and Desai, Shawn K. and Murat, Dorothee and Shen, Aimee and Puri, Aaron W. and Komeili, Arash and Bertozzi, Carolyn R. and Scott, June R. and Gallivan, Justin P.},  citeulike-article-id = {8663692},  citeulike-linkout-0 = {http://dx.doi.org/10.1128/aem.01537-10},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20935124},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20935124},  day = {8},  doi = {10.1128/aem.01537-10},  journal = {Appl. Environ. Microbiol.},  keywords = {bacterial-biology},  month = oct,  pages = {01537+},  pmid = {20935124},  posted-at = {2011-01-20 21:45:58},  priority = {2},  title = {{Synthetic Riboswitches that Induce Gene Expression in Diverse Bacterial Species}},  url = {http://dx.doi.org/10.1128/aem.01537-10},  year = {2010}  }  @article{citeulike:8663675,  abstract = {{Magnetic particles offer high technological potential since they can be conveniently collected with an external magnetic field. Magnetotactic bacteria synthesize bacterial magnetic particles (BacMPs) with well-controlled size and morphology. BacMPs are individually covered with thin organic membrane, which confers high and even dispersion in aqueous solutions compared with artificial magnetites, making them ideal biotechnological materials. Recent molecular studies including genome sequence, mutagenesis, gene expression and proteome analyses indicated a number of genes and proteins which play important roles for BacMP biomineralization. Some of the genes and proteins identified from these studies have allowed us to express functional proteins efficiently onto BacMPs, through genetic engineering, permitting the preservation of the protein activity, leading to a simple preparation of functional protein–magnetic particle complexes. They were applicable to high-sensitivity immunoassay, drug screening and cell separation. Furthermore, fully automated single nucleotide polymorphism discrimination and DNA recovery systems have been developed to use these functionalized BacMPs. The nano-sized fine magnetic particles offer vast potential in new nano-techniques.}},  author = {Arakaki, Atsushi and Nakazawa, Hidekazu and Nemoto, Michiko and Mori, Tetsushi and Matsunaga, Tadashi},  citeulike-article-id = {8663675},  citeulike-linkout-0 = {http://dx.doi.org/10.1098/rsif.2008.0170},  citeulike-linkout-1 = {http://rsif.royalsocietypublishing.org/content/5/26/977.abstract},  citeulike-linkout-2 = {http://rsif.royalsocietypublishing.org/content/5/26/977.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18559314},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18559314},  day = {6},  doi = {10.1098/rsif.2008.0170},  journal = {Journal of The Royal Society Interface},  keywords = {bacterial-biology},  month = sep,  number = {26},  pages = {977--999},  pmid = {18559314},  posted-at = {2011-01-20 21:38:49},  priority = {2},  title = {{Formation of magnetite by bacteria and its application}},  url = {http://dx.doi.org/10.1098/rsif.2008.0170},  volume = {5},  year = {2008}  }  @article{citeulike:4264351,  author = {Frankel, Richard},  citeulike-article-id = {4264351},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00343-009-0001-7},  citeulike-linkout-1 = {http://www.springerlink.com/content/34008tlj424662w5},  day = {1},  doi = {10.1007/s00343-009-0001-7},  issn = {0254-4059},  journal = {Chinese Journal of Oceanology and Limnology},  keywords = {bacterial-biology},  month = feb,  number = {1},  pages = {1--2},  posted-at = {2011-01-20 21:34:53},  priority = {2},  publisher = {Science Press, co-published with Springer-Verlag GmbH},  title = {{The discovery of magnetotactic/magnetosensitive bacteria}},  url = {http://dx.doi.org/10.1007/s00343-009-0001-7},  volume = {27},  year = {2009}  }  @book{citeulike:7323465,  citeulike-article-id = {7323465},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/3642122027},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/3642122027},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/3642122027},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/3642122027},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/3642122027/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/3642122027},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/3642122027},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN3642122027},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=3642122027\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/3642122027},  day = {16},  edition = {1st Edition.},  howpublished = {Hardcover},  isbn = {3642122027},  keywords = {books},  month = jun,  posted-at = {2011-01-19 18:27:59},  priority = {2},  publisher = {Springer},  title = {{Simulating Complex Systems by Cellular Automata (Understanding Complex Systems)}},  url = {http://www.worldcat.org/isbn/3642122027},  year = {2010}  }  @article{citeulike:8599792,  abstract = {{  Computational and biological systems are often distributed so that processors (cells) jointly solve a task, without any of them receiving all inputs or observing all outputs. Maximal independent set (MIS) selection is a fundamental distributed computing procedure that seeks to elect a set of local leaders in a network. A variant of this problem is solved during the development of the fly's nervous system, when sensory organ precursor (SOP) cells are chosen. By studying SOP selection, we derived a fast algorithm for MIS selection that combines two attractive features. First, processors do not need to know their degree; second, it has an optimal message complexity while only using one-bit messages. Our findings suggest that simple and efficient algorithms can be developed on the basis of biologically derived insights.  }},  author = {Afek, Yehuda and Alon, Noga and Barad, Omer and Hornstein, Eran and Barkai, Naama and Bar-Joseph, Ziv},  citeulike-article-id = {8599792},  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1193210},  citeulike-linkout-1 = {http://www.sciencemag.org/content/331/6014/183.abstract},  citeulike-linkout-2 = {http://www.sciencemag.org/content/331/6014/183.full.pdf},  citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/331/6014/183},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/21233379},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=21233379},  day = {14},  doi = {10.1126/science.1193210},  issn = {1095-9203},  journal = {Science},  keywords = {bacterial-biology},  month = jan,  number = {6014},  pages = {183--185},  pmid = {21233379},  posted-at = {2011-01-18 17:22:52},  priority = {2},  publisher = {American Association for the Advancement of Science},  title = {{A Biological Solution to a Fundamental Distributed Computing Problem}},  url = {http://dx.doi.org/10.1126/science.1193210},  volume = {331},  year = {2011}  }  @article{citeulike:7797125,  abstract = {{Mixed microbial communities exhibit emergent biochemical properties not found in clonal monocultures. We report a new type of synthetic genetic interaction, synthetic mutualism in trans (SMIT), in which certain pairs of auxotrophic Escherichia coli mutants complement one another's growth by cross-feeding essential metabolites. We find significant metabolic synergy in 17\% of 1035 such pairs tested, with SMIT partners identified throughout the metabolic network. Cooperative phenotypes show more growth on average by aiding the proliferation of their conjugate partner, thereby expanding the source of their own essential metabolites. We construct a quantitative, predictive, framework for describing SMIT interactions as governed by stoichiometric models of the metabolic networks of the interacting strains.}},  author = {Wintermute, Edwin H. and Silver, Pamela A.},  citeulike-article-id = {7797125},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/msb.2010.66},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/msb201066},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964121/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/20823845},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=20823845},  day = {07},  doi = {10.1038/msb.2010.66},  issn = {1744-4292},  journal = {Molecular Systems Biology},  keywords = {bacterial-biology},  month = sep,  number = {1},  pmcid = {PMC2964121},  pmid = {20823845},  posted-at = {2011-01-17 19:58:05},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Emergent cooperation in microbial metabolism}},  url = {http://dx.doi.org/10.1038/msb.2010.66},  volume = {6},  year = {2010}  }  @article{citeulike:8512184,  abstract = {{A central challenge of synthetic biology is to enable the growth of living systems using parts that are not derived from nature, but designed and synthesized in the laboratory. As an initial step toward achieving this goal, we probed the ability of a collection of >106de novo designed proteins to provide biological functions necessary to sustain cell growth. Our collection of proteins was drawn from a combinatorial library of 102-residue sequences, designed by binary patterning of polar and nonpolar residues to fold into stable 4-helix bundles. We probed the capacity of proteins from this library to function in vivo by testing their abilities to rescue 27 different knockout strains of Escherichia coli, each deleted for a conditionally essential gene. Four different strains – ΔserB, ΔgltA, ΔilvA, and Δfes – were rescued by specific sequences from our library. Further experiments demonstrated that a strain simultaneously deleted for all four genes was rescued by co-expression of four novel sequences. Thus, cells deleted for \~{}0.1\% of the E. coli genome (and \~{}1\% of the genes required for growth under nutrient-poor conditions) can be sustained by sequences designed de novo.}},  author = {Fisher, Michael A. and McKinley, Kara L. and Bradley, Luke H. and Viola, Sara R. and Hecht, Michael H.},  citeulike-article-id = {8512184},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0015364},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014984/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21245923},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21245923},  day = {4},  doi = {10.1371/journal.pone.0015364},  issn = {1932-6203},  journal = {PLoS ONE},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {e15364+},  pmcid = {PMC3014984},  pmid = {21245923},  posted-at = {2011-01-17 08:29:58},  priority = {2},  publisher = {Public Library of Science},  title = {{De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth}},  url = {http://dx.doi.org/10.1371/journal.pone.0015364},  volume = {6},  year = {2011}  }  @article{citeulike:8630329,  abstract = {{Bacterial actuation and manipulation are demonstrated where Magnetospirillum gryphiswaldense magnetotactic bacteria (MTB) are used to push 3   μ m beads at an average velocity of 7.5   μ m   s -1 along preplanned paths by modifying the torque on a chain of magnetosomes in the bacterium with a directional magnetic field of at least 0.5   G generated from a small programmed electrical current. But measured average thrusts of 0.5 and 4   pN of the flagellar motor of a single Magnetospirillum gryphiswaldense and MC-1 MTB suggest that average velocities greater than 16 and 128   μ m   s -1 , respectively could be achieved.}},  author = {Martel, Sylvain and Tremblay, Charles C. and Ngakeng, Serge and Langlois, Guillaume},  citeulike-article-id = {8630329},  citeulike-linkout-0 = {http://dx.doi.org/10.1063/1.2402221},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=4823737},  doi = {10.1063/1.2402221},  issn = {00036951},  journal = {Applied Physics Letters},  keywords = {bacterial-biology},  number = {23},  pages = {233904+},  posted-at = {2011-01-16 20:56:22},  priority = {2},  title = {{Controlled manipulation and actuation of micro-objects with magnetotactic bacteria}},  url = {http://dx.doi.org/10.1063/1.2402221},  volume = {89},  year = {2006}  }  @article{citeulike:8630328,  abstract = {{PMID: 19548666 Escherichia coli O157:H7 is detected using a remote-query (wireless, passive) magnetoelastic sensor platform to which a 1 μm thick layer of Bayhydrol 110 and then a layer of functionalized mannose is applied. The multivalent binding of lectin concanavalin A (Con A) to the E. coli surface O-antigen and mannose favors the strong adhesion of E. coli to the mannose-modified magnetoelastic sensor; E. coli is rigidly and strongly attached on the mannose-modified sensor through Con A, which works as a bridge to bind E. coli to the mannose-modified sensor surface. As E. coli is bound to the sensor, its resonance frequency shifts, enabling quantification of E. coli concentration with a limit of detection of 60 cells/mL and a linear logarithmic response range of 6.0 × 101 to 6.1 × 109 cells/mL. The analysis can be directly conducted without incubation and completed in 3 h or less.}},  author = {Lu, Qingzhu and Lin, Hailan and Ge, Shutian and Luo, Shenglian and Cai, Qingyun and Grimes, Craig A.},  citeulike-article-id = {8630328},  citeulike-linkout-0 = {http://dx.doi.org/10.1021/ac9008572},  citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ac9008572},  day = {15},  doi = {10.1021/ac9008572},  journal = {Analytical Chemistry},  keywords = {bacterial-biology},  month = jul,  number = {14},  pages = {5846--5850},  posted-at = {2011-01-16 20:54:06},  priority = {2},  title = {{Wireless, Remote-Query, and High Sensitivity Escherichia coli O157:H7 Biosensor Based on the Recognition Action of Concanavalin A}},  url = {http://dx.doi.org/10.1021/ac9008572},  volume = {81},  year = {2009}  }  @article{citeulike:8630327,  abstract = {{Magnetotactic bacteria contain magnetic particles that constitute a permanent magnetic dipole and cause each cell to orient and migrate along geomagnetic field lines. Recent results relevant to the biomineralization process and to the function of magnetotaxis are discussed.}},  author = {Frankel, Richard B. and Bazylinski, Dennis A.},  citeulike-article-id = {8630327},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/bf02069123},  citeulike-linkout-1 = {http://www.springerlink.com/content/v73k4634l7w44616},  day = {1},  doi = {10.1007/bf02069123},  issn = {0304-3834},  journal = {Hyperfine Interactions},  keywords = {bacterial-biology},  month = dec,  number = {1},  pages = {135--142},  posted-at = {2011-01-16 20:51:36},  priority = {2},  publisher = {Springer Netherlands},  title = {{Magnetotaxis and magnetic particles in bacteria}},  url = {http://dx.doi.org/10.1007/bf02069123},  volume = {90},  year = {1994}  }  @article{citeulike:5846085,  abstract = {{Abstract The ability of magnetotactic bacteria (MTB) to orient in magnetic fields is based on the synthesis of magnetosomes, which are unique prokaryotic organelles comprising membrane-enveloped, nano-sized crystals of a magnetic iron mineral that are aligned in well-ordered intracellular chains. Magnetosome crystals have species-specific morphologies, sizes, and arrangements. The magnetosome membrane, which originates from the cytoplasmic membrane by invagination, represents a distinct subcellular compartment and has a unique biochemical composition. The roughly 20 magnetosome-specific proteins have functions in vesicle formation, magnetosomal iron transport, and the control of crystallization and intracellular arrangement of magnetite particles. The assembly of magnetosome chains is under genetic control and involves the action of an acidic protein that links magnetosomes to a novel cytoskeletal structure, presumably formed by a specific actin-like protein. A total of 28 conserved genes present in various magnetic bacteria were identified to be specifically associated with the magnetotactic phenotype, most of which are located in the genomic magnetosome island. The unique properties of magnetosomes attracted broad interdisciplinary interest, and MTB have recently emerged as a model to study prokaryotic organelle formation and evolution.}},  address = {Faculty of Biology, Microbiology, Ludwig Maximilians University, Mnchen, Germany},  author = {Sch\"{u}ler, Dirk},  citeulike-article-id = {5846085},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1574-6976.2008.00116.x},  citeulike-linkout-1 = {http://www3.interscience.wiley.com/cgi-bin/abstract/120085028/ABSTRACT},  doi = {10.1111/j.1574-6976.2008.00116.x},  issn = {1574-6976},  journal = {FEMS Microbiology Reviews},  keywords = {bacterial-biology},  number = {4},  pages = {654--672},  posted-at = {2011-01-16 20:48:07},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{Genetics and cell biology of magnetosome formation in magnetotactic bacteria}},  url = {http://dx.doi.org/10.1111/j.1574-6976.2008.00116.x},  volume = {32},  year = {2008}  }  @incollection{citeulike:8630325,  abstract = {{The detection of bacterial signaling molecules in liquid or gaseous environments has been occurring in nature for billions of years. More recently, man-made materials and systems has also allowed for the detection of small molecules in liquid or gaseous environments. This chapter will outline some examples of these man-made detection systems by detailing several acoustic-wave sensor systems applicable to quorum sensing. More importantly though, a comparison will be made between existing bacterial quorum sensing signaling systems, such as the Vibrio harveyi two-component system and that of man-made detection systems, such as acoustic-wave sensor systems and digital communication receivers similar to those used in simple cell phone technology. It will be demonstrated that the system block diagrams for either bacterial quorum sensing systems or man-made detection systems are all very similar, and that the established modeling techniques for digital communications and acoustic-wave sensors can also be transformed to quorum sensing systems.}},  address = {Totowa, NJ},  author = {Edmonson, Peter and Stubbs, Desmond and Hunt, William},  booktitle = {Quorum Sensing},  chapter = {7},  citeulike-article-id = {8630325},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-1-60761-971-0\_7},  citeulike-linkout-1 = {http://www.springerlink.com/content/h0829646241156x7},  doi = {10.1007/978-1-60761-971-0\_7},  editor = {Rumbaugh, Kendra P.},  isbn = {978-1-60761-970-3},  keywords = {bacterial-biology},  pages = {83--100},  posted-at = {2011-01-16 20:41:27},  priority = {2},  publisher = {Humana Press},  series = {Methods in Molecular Biology},  title = {{Detection of Bacterial Signaling Molecules in Liquid or Gaseous Environments}},  url = {http://dx.doi.org/10.1007/978-1-60761-971-0\_7},  volume = {692},  year = {2011}  }  @article{citeulike:5697383,  abstract = {{In order to obtain accurate and reliable network planning in the Radio Frequency Identification (RFID) communication system, the locations of readers and the associated values for each of the reader parameters have to be determined. All these choices must optimize a set of objectives, such as tag coverage, economic efficiency, load balance, and interference level between readers. This paper proposes a novel optimization algorithm, namely the multi-colony bacteria foraging optimization (MC-BFO), to solve complex RFID network planning problem. The main idea of MC-BFO is to extend the single population bacterial foraging algorithm to the interacting multi-colony model by relating the chemotactic behavior of single bacterial cell to the cell-to-cell communication of bacterial community. With this multi-colony cooperative approach, a suitable diversity in the whole bacterial community can be maintained. At the same time, the cell-to-cell communication mechanism significantly speeds up the bacterial community to converge to the global optimum. Then a mathematical model for planning RFID networks is developed based on the proposed MC-BFO. The performance of MC-BFO is compared to both GA and PSO on RFID network planning problem, demonstrating its superiority.}},  author = {Chen, Hanning and Zhu, Yunlong and Hu, Kunyuan},  citeulike-article-id = {5697383},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.asoc.2009.08.023},  day = {28},  doi = {10.1016/j.asoc.2009.08.023},  issn = {15684946},  journal = {Applied Soft Computing},  keywords = {transversal},  month = mar,  number = {2},  pages = {539--547},  posted-at = {2011-01-16 20:40:45},  priority = {2},  title = {{Multi-colony bacteria foraging optimization with cell-to-cell communication for RFID network planning}},  url = {http://dx.doi.org/10.1016/j.asoc.2009.08.023},  volume = {10},  year = {2010}  }  @article{citeulike:8630324,  abstract = {{Most methods in evolutionary computation are biologically inspired by chromosome crossover and mutation, two of the main sources of genetic variability in biological populations, as well as in genetic algorithms. In fact, this is a very important feature of the biological populations and their counterpart in genetic algorithms since the efficiency of the Darwinian natural selection depends on the degree of genetic variation that is achieved with the genetic mechanism or operator responsible for the population variability. Furthermore, in Nature, several other genetic mechanisms are used by populations as sources of variability such as bacterial conjugation, that is the transfer of genetic material between bacteria. In this paper, we introduce a biologically inspired conjugation operator simulating the genetic mechanism exhibited by bacterial colonies. The efficiency of the bacterial conjugation operator is illustrated designing with a genetic algorithm based on this operator an AM radio receiver, optimizing the main features of the electronic components of the AM radio circuit, as well as those of the radio enclosure.}},  author = {Perales-Gravin, Carlos and Lahoz-Beltra, Rafael},  citeulike-article-id = {8630324},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/tevc.2007.895271},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=4358767},  doi = {10.1109/tevc.2007.895271},  issn = {1089-778X},  journal = {IEEE Transactions on Evolutionary Computation},  keywords = {transversal},  number = {2},  pages = {129--142},  posted-at = {2011-01-16 20:39:56},  priority = {2},  title = {{An AM Radio Receiver Designed With a Genetic Algorithm Based on a Bacterial Conjugation Genetic Operator}},  url = {http://dx.doi.org/10.1109/tevc.2007.895271},  volume = {12},  year = {2008}  }  @article{citeulike:4150926,  abstract = {{A novel property of DNA is described: the capacity of some bacterial DNA sequences to induce electromagnetic waves at high aqueous dilutions. It appears to be a resonance phenomenon triggered by the ambient electromagnetic background of very low frequency waves. The genomic DNA of most pathogenic bacteria contains sequences which are able to generate such signals. This opens the way to the development of highly sensitive detection system for chronic bacterial infections in human and animal diseases.}},  author = {Bl\"{u}m, Claudia and Scheibel, Thomas},  citeulike-article-id = {4150926},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s12539-009-0036-7},  citeulike-linkout-1 = {http://www.springerlink.com/content/0557v31188m3766x},  day = {2},  doi = {10.1007/s12539-009-0036-7},  issn = {2191-1630},  journal = {BioNanoScience},  keywords = {bacterial-biology},  month = feb,  number = {2},  pages = {81--90},  posted-at = {2011-01-16 20:37:25},  priority = {2},  publisher = {International Association of Scientists in the Interdisciplinary Areas, co-published with Springer-Verlag GmbH},  title = {{Control of Drug Loading and Release Properties of Spider Silk Sub-Microparticles}},  url = {http://dx.doi.org/10.1007/s12539-009-0036-7},  volume = {1},  year = {2012}  }  @article{citeulike:8347499,  abstract = {{Isolated, clonal populations of cells are rarely found in nature. The emergent properties of microbial consortia present a challenge for the systems approach to biology, as chances for competition, communication, or collaboration multiply with the number of interacting agents. This review focuses on recent work on intercourse within biofilms, among quorum-sensing populations, and between cross-feeding metabolic cooperators. New tools from synthetic biology allow microbial interactions to be designed and tightly controlled, creating valuable model systems. We address both natural and synthetic partnerships, with an emphasis on how system behaviors derive from the properties of their components. Essential features of microbial biology arose in the context of a very mixed culture and cannot be understood without unscrambling it.}},  author = {Wintermute, Edwin H. and Silver, Pamela A.},  citeulike-article-id = {8347499},  citeulike-linkout-0 = {http://dx.doi.org/10.1101/gad.1985210},  citeulike-linkout-1 = {http://genesdev.cshlp.org/content/24/23/2603.abstract},  citeulike-linkout-2 = {http://genesdev.cshlp.org/content/24/23/2603.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/21123647},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=21123647},  day = {1},  doi = {10.1101/gad.1985210},  issn = {1549-5477},  journal = {Genes \& Development},  keywords = {bacterial-biology},  month = dec,  number = {23},  pages = {2603--2614},  pmid = {21123647},  posted-at = {2011-01-16 19:44:29},  priority = {2},  title = {{Dynamics in the mixed microbial concourse}},  url = {http://dx.doi.org/10.1101/gad.1985210},  volume = {24},  year = {2010}  }  @article{citeulike:8630249,  author = {Shuvaev, A. and Brilkov, A.},  citeulike-article-id = {8630249},  citeulike-linkout-0 = {http://dx.doi.org/10.1134/s1607672907050018},  citeulike-linkout-1 = {http://www.springerlink.com/content/m885v137x4w24w58},  day = {1},  doi = {10.1134/s1607672907050018},  issn = {1607-6729},  journal = {Doklady Biochemistry and Biophysics},  keywords = {bacterial-biology},  month = oct,  number = {1},  pages = {233--236},  posted-at = {2011-01-16 19:34:07},  priority = {2},  publisher = {MAIK Nauka/Interperiodica distributed exclusively by Springer Science+Business Media LLC.},  title = {{A model of bacterial cell cycle duration based on DnaA dynamics and estimation of the population cost of bacterial plasmids}},  url = {http://dx.doi.org/10.1134/s1607672907050018},  volume = {416},  year = {2007}  }  @article{citeulike:7417599,  abstract = {{Several factors can affect the density of mobile DNA in bacterial genomes including rates of exposure to novel gene pools, recombination, and reductive evolution. These traits are difficult to measure across a broad range of bacterial species, but the ecological niches occupied by an organism provide some indication of the relative magnitude of these forces. Here, by analyzing 384 bacterial genomes assigned to three ecological categories (obligate intracellular, facultative intracellular, and extracellular), we address two, related questions: How does the density of mobile DNA vary across the Bacteria? And is there a statistically supported relationship between ecological niche and mobile element gene density? We report three findings. First, the fraction of mobile element genes in bacterial genomes ranges from 0 to 21\% and decreases significantly: facultative intracellular \> extracellular \> obligate intracellular bacteria. Results further show that the obligate intracellular bacteria that host switch have a higher mobile DNA gene density than the obligate intracellular bacteria that are vertically transmitted. Second, while bacteria from the three ecological niches differ in their average mobile DNA contents, the ranges of mobile DNA found in each category overlap a surprising extent, suggesting bacteria with different lifestyles can tolerate similar amounts of mobile DNA. Third, mobile DNA gene densities increase with genome size across the entire dataset, and the significance of this correlation is dependent on the obligate intracellular bacteria. Further, mobile DNA gene densities do not correlate with evolutionary relationships in a 16S rDNA phylogeny. These findings statistically support a compelling link between mobile element evolution and bacterial ecology.}},  author = {Newton, Irene and Bordenstein, Seth},  citeulike-article-id = {7417599},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00284-010-9693-3},  citeulike-linkout-1 = {http://www.springerlink.com/content/92678672w6701570},  day = {1},  doi = {10.1007/s00284-010-9693-3},  issn = {0343-8651},  journal = {Current Microbiology},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {198--208},  posted-at = {2011-01-15 13:45:28},  priority = {2},  publisher = {Springer New York},  title = {{Correlations Between Bacterial Ecology and Mobile DNA}},  url = {http://dx.doi.org/10.1007/s00284-010-9693-3},  volume = {62},  year = {2011}  }  @article{citeulike:8530584,  abstract = {{The P1 ParB protein is required for active partition and thus stable inheritance of the plasmid prophage. ParB and the Escherichia coli protein integration host factor (IHF) participate in the assembly of a partition complex at the centromere-like site parS. In this report the role of IHF in the formation of the partition complex has been explored. First, ParB protein was purified for these studies, which revealed that ParB forms a dimer in solution. Next, the IHF binding site was mapped to a 29-base pair region within parS, including the sequence TAACTGACTGTTT (which differs from the IHF consensus in two positions). IHF induced a strong bend in the DNA at its binding site. Versions of parS which have lost or damaged the IHF binding site bound ParB with greatly reduced affinity in vitro and in vivo. Measurements of binding constants showed that IHF increased ParB affinity for the wild-type parS site by about 10,000-fold. Finally, DNA supercoiling improved ParB binding in the presence of IHF but not in its absence. These observations led to the proposal that IHF and superhelicity assist ParB by promoting its precise positioning at parS, a spatial arrangement that results in a high affinity of ParB for parS.}},  author = {Funnell, B. E.},  citeulike-article-id = {8530584},  citeulike-linkout-0 = {http://www.jbc.org/content/266/22/14328.abstract},  citeulike-linkout-1 = {http://www.jbc.org/content/266/22/14328.full.pdf},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/1860842},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=1860842},  day = {5},  journal = {Journal of Biological Chemistry},  keywords = {bacterial-biology},  month = aug,  number = {22},  pages = {14328--14337},  pmid = {1860842},  posted-at = {2011-01-10 20:32:26},  priority = {2},  title = {{The P1 plasmid partition complex at parS. The influence of Escherichia coli integration host factor and of substrate topology.}},  url = {http://www.jbc.org/content/266/22/14328.abstract},  volume = {266},  year = {1991}  }  @book{citeulike:329746,  abstract = {{"Emergence" is the notion that the whole is more than the sum of its parts. John Holland, a MacArthur Fellow known as the "father of genetic algorithms," says this seemingly simple notion will be at the heart of the development of machines that can think for themselves. And while he claims that he'd rather do science than write about it, this is his second scientific philosophy book intended to increase public understanding of difficult concepts (his first was Hidden Order: How Adaptation Builds Complexity). One of the questions that Holland says emergence theory can help answer is: can we build systems from which more comes out than was put in? Think of the food replicators in the imaginary future of Star Trek--with some basic chemical building blocks and simple rules, those machines can produce everything from Klingon delicacies to Earl Grey tea. If scientists can understand and apply the knowledge they gather from studying emergent systems, we may soon witness the development of artificial intelligence, nanotech, biological machines, and other creations heretofore confined to science fiction. Using games, molecules, maps, and scientific theories as examples, Holland outlines how emergence works, emphasizing the interrelationships of simple rules and parts in generating a complex whole. Because of the theoretical depth, this book probably won't appeal to the casual reader of popular science, but those interested in delving a little deeper into the future of science and engineering will be fascinated. Holland's writing, while sometimes self-consciously precise, is clear, and he links his theoretical arguments to examples in the real world whenever possible. Emergence offers insight not just to scientific advancement, but across many areas of human endeavor--business, the arts, even the evolution of society and the generation of new ideas. --Therese Littleton } {In this important book, John H. Holland dramatically shows us that the "emergence" of order from chaos has much to teach us about life, mind, and organizations. Creative activities in both the arts and the sciences depend upon an ability to model the world. The most creative of those models exhibits emergent properties, so that "what comes out is more than what goes in." From the ingenious checkers-playing computer that started beating its creator in game after game, to the emotive creations of the poet, Emergence shows that Holland's theory successfully predicts many complex behaviors in art and science.}},  author = {Holland, John H.},  citeulike-article-id = {329746},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0738201421},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0738201421},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0738201421},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0738201421},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0738201421/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0738201421},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0738201421},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0738201421},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0738201421\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0738201421},  day = {23},  howpublished = {Paperback},  isbn = {0738201421},  keywords = {books},  month = apr,  posted-at = {2011-01-10 05:19:50},  priority = {2},  publisher = {Basic Books},  title = {{Emergence: From Chaos To Order (Helix Books)}},  url = {http://www.worldcat.org/isbn/0738201421},  year = {1999}  }  @book{citeulike:4820792,  abstract = {{Evolutionary game theory attempts to predict individual behavior (whether of  humans or other species) when interactions between individuals are modeled as  a noncooperative game. Most dynamic analyses of evolutionary games are based  on their normal forms, despite the fact that many interesting games are  specified more naturally through their extensive forms. Because every  extensive form game has a normal form representation, some theorists hold that  the best way to analyze an extensive form game is simply to ignore the  extensive form structure and study the game in its normal form representation.  This book rejects that suggestion, arguing that a game's normal form  representation often omits essential information from the perspective of  dynamic evolutionary game theory. The book offers a synthesis of current  knowledge about extensive form games from an evolutionary perspective,  emphasizing connections between the extensive form representation and dynamic  models that traditionally have been applied to biological and economic  phenomena. It develops a general theory to analyze dynamically arbitrary  extensive form games and applies this theory to a range of examples. It lays  the foundation for the analysis of specific extensive form models of behavior  and for the further theoretical study of extensive form evolutionary games.}},  author = {Cressman, Ross},  citeulike-article-id = {4820792},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0262033054},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0262033054},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0262033054},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0262033054},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0262033054/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0262033054},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0262033054},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0262033054},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0262033054\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0262033054},  day = {13},  edition = {illustrated edition},  howpublished = {Hardcover},  isbn = {0262033054},  keywords = {books},  month = jul,  posted-at = {2011-01-10 05:16:28},  priority = {2},  publisher = {The MIT Press},  title = {{Evolutionary Dynamics and Extensive Form Games (Economic Learning and Social Evolution)}},  url = {http://www.worldcat.org/isbn/0262033054},  year = {2003}  }  @book{citeulike:8529333,  author = {Hicks, Charles R.},  citeulike-article-id = {8529333},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0195122739},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0195122739},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0195122739},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0195122739},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0195122739/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0195122739},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0195122739},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0195122739},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0195122739\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0195122739},  day = {25},  edition = {4},  howpublished = {Hardcover},  isbn = {0195122739},  keywords = {books},  month = mar,  posted-at = {2011-01-10 05:10:22},  priority = {2},  publisher = {Oxford University Press, USA},  title = {{Fundamental Concepts in the Design of Experiments}},  url = {http://www.worldcat.org/isbn/0195122739},  year = {1993}  }  @book{ComputationalComplexity2009,  abstract = {{This beginning graduate textbook describes both recent achievements andclassical results of computational complexity theory. Requiring essentially nobackground apart from mathematical maturity, the book can be used as areference for self-study for anyone interested in complexity, includingphysicists, mathematicians, and other scientists, as well as a textbook for avariety of courses and seminars. More than 300 exercises are included with aselected hint set.}},  author = {Arora, Sanjeev and Barak, Boaz},  citeulike-article-id = {4781854},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0521424267},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0521424267},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0521424267},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0521424267},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0521424267/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0521424267},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0521424267},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0521424267},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0521424267\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0521424267},  day = {20},  edition = {1},  howpublished = {Hardcover},  isbn = {0521424267},  keywords = {books},  month = apr,  posted-at = {2011-01-10 05:05:30},  priority = {2},  publisher = {Cambridge University Press},  title = {{Computational Complexity: A Modern Approach}},  url = {http://www.worldcat.org/isbn/0521424267},  year = {2009}  }  @book{EssentionBioinformatics2006,  abstract = {{Essential Bioinformatics is a concise yet comprehensive textbook of  bioinformatics, which provides a broad introduction to the entire field.  Written specifically for a life science audience, the basics of bioinformatics  are explained, followed by discussions of the state-of-the-art computational  tools available to solve biological research problems. All key areas of  bioinformatics are covered including biological databases, sequence alignment,  genes and promoter prediction, molecular phylogenetics, structural  bioinformatics, genomics and proteomics. The book emphasizes how computational  methods work and compares the strengths and weaknesses of different methods.  This balanced yet easily accessible text will be invaluable to students who do  not have sophisticated computational backgrounds. Technical details of  computational algorithms are explained with a minimum use of mathematical  formulae; graphical illustrations are used in their place to aid  understanding. The effective synthesis of existing literature as well as in-  depth and up-to-date coverage of all key topics in bioinformatics make this an  ideal textbook for all bioinformatics courses taken by life science students  and for researchers wishing to develop their knowledge of bioinformatics to  facilitate their own research.}},  author = {Xiong, Jin},  citeulike-article-id = {3882572},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0521600820},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0521600820},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0521600820},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0521600820},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0521600820/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0521600820},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0521600820},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0521600820},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0521600820\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0521600820},  day = {13},  edition = {1},  howpublished = {Paperback},  isbn = {0521600820},  keywords = {books},  month = mar,  posted-at = {2011-01-09 16:11:51},  priority = {2},  publisher = {Cambridge University Press},  title = {{Essential Bioinformatics}},  url = {http://www.worldcat.org/isbn/0521600820},  year = {2006}  }  @book{NonLinearWorkBook2005,  abstract = {{The study of nonlinear dynamical systems has advanced tremendously in the last 20 years, making a big impact on science and technology. This book provides all the techniques and methods used in nonlinear dynamics. The concepts and underlying mathematics are discussed in detail.

The numerical and symbolic methods are implemented in C++, SymbolicC++ and Java. Object-oriented techniques are also applied. The book contains more than 150 ready-to-run programs.

The text has also been designed for a one-year course at both the junior and senior levels in nonlinear dynamics. The topics discussed in the book are part of e-learning and distance learning courses conducted by the International School for Scientific Computing.}},  author = {Steeb, Willi-Hans},  citeulike-article-id = {479143},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/9812562788},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/9812562788},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/9812562788},  citeulike-linkout-3 = {http://www.amazon.co.uk/exec/obidos/ASIN/9812562788/citeulike00-21},  citeulike-linkout-4 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/9812562788},  citeulike-linkout-5 = {http://www.worldcat.org/isbn/9812562788},  citeulike-linkout-6 = {http://books.google.com/books?vid=ISBN9812562788},  citeulike-linkout-7 = {http://www.amazon.com/gp/search?keywords=9812562788\&index=books\&linkCode=qs},  citeulike-linkout-8 = {http://www.librarything.com/isbn/9812562788},  day = {25},  howpublished = {Hardcover},  isbn = {9812562788},  keywords = {books},  month = jun,  posted-at = {2011-01-09 16:08:49},  priority = {2},  publisher = {World Scientific Publishing Company},  title = {{The Nonlinear Workbook}},  url = {http://www.worldcat.org/isbn/9812562788},  year = {2005}  }  @article{ScientificModelingSimulations2009,  author = {Tom\'{a}s Diaz de la Rubia and Yip, Sidney},  citeulike-article-id = {3631570},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s10820-008-9099-8},  citeulike-linkout-1 = {http://www.springerlink.com/content/k48112qltn6307q2},  doi = {10.1007/s10820-008-9099-8},  isbn = {978-1-4020-9741-6},  issn = {1439-7358},  journal = {Scientific Modeling and Simulation},  keywords = {books},  posted-at = {2011-01-09 15:55:44},  priority = {2},  title = {{Scientific Modeling and Simulations}},  url = {http://dx.doi.org/10.1007/s10820-008-9099-8},  year = {2009}  }  @book{Shonkwiler:2008:MBI:1481388,  author = {Shonkwiler, Ronald W.},  citeulike-article-id = {8528589},  edition = {2nd},  keywords = {books},  posted-at = {2011-01-09 15:47:28},  priority = {2},  publisher = {Springer Publishing Company, Incorporated},  title = {{Mathematical Biology: An Introduction with Maple and Matlab}},  year = {2008}  }  @article{citeulike:8528587,  citeulike-article-id = {8528587},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/dvg.1020080207},  doi = {10.1002/dvg.1020080207},  editor = {Hardy, K. G.},  isbn = {0-19-963444-0},  keywords = {books},  posted-at = {2011-01-09 15:42:48},  priority = {2},  publisher = {Oxford University Press},  title = {{Plasmids: A practical approach.}},  url = {http://dx.doi.org/10.1002/dvg.1020080207},  year = {1993}  }  @book{HorizontalGenePool:2000,  abstract = {{Every molecular biologist perceives the usefulness of bacterial plasmids in recombinant DNA technology. Indeed, it is difficult to imagine how the biosciences revolution which is currently taking place could have occurred without the development of plasmid-based gene cloning and over expression strategies. However, the importance of plasmids in bacterial persistence, diversity and evolution, and as model systems for analysing processes such as DNA replication and segregation, is less widely appreciated. This book, like David Summers' The Biology of Plasmids (1996), attempts to bring together many aspects of plasmid biology into a single volume. However, unlike Summers' less daunting volume, which is largely accessible to readers with a fundamental but inexhaustive knowledge of molecular biology, this book is best appreciated by those comfortable with the intricacies and jargon of current molecular biosciences.  The strongest aspect of the book is in the overviews of the fundamental mechanisms by which plasmids replicate, segregate, transfer and evolve. The editor, Chris Thomas, has successfully melded the opinions of many experts in these topics without sacrificing coherence. The emphasis in these chapters is on providing relatively detailed factual descriptions of the best understood systems, albeit with some inevitable bias towards the authors' favourite plasmids. Although few new concepts are presented, the contributors wisely emphasize that much remains to be learned. The comprehensive reference lists which accompany these chapters are useful pointers for those wishing to investigate the topics more fully. Chapters devoted to plasmid ecology, the contribution of plasmids to bacterial population genetics, and the isolation and characterization of plasmids from environmental samples, provide an interesting counterbalance to the more molecular-orientated chapters, but the over-riding impression is that the former studies suffer greatly from the fact 'that only a minor proportion of bacteria is accessible to cultivation techniques'. As the characterization of plasmids in environmental studies frequently requires bacterial cultivation before plasmid isolation, with a consequent bias towards the analysis of plasmids from culturable bacteria, plasmid ecological and population studies seem fraught with uncertainties.  A collaborative book of this sort inevitably lacks reference to a number of interesting developments which have taken place in the last two years. As an example, no mention is made of the recent structural studies of the integrase family of site-specific recombinases. Nevertheless, this book is a mandatory addition to the bookshelves of every research group with a strong interest in plasmid biology, and will also serve as an invaluable reference tool for every molecular microbiology laboratory for some years to come. The book's appeal to those outside these communities is less apparent, especially considering that it is not inexpensive. It is to be hoped that updated editions of the book will emerge at regular intervals.}},  citeulike-article-id = {8528305},  editor = {Thomas, Christopher M.},  isbn = {90-5702-462-4},  keywords = {books},  location = {Amsterdam},  posted-at = {2011-01-09 15:30:07},  priority = {2},  publisher = {Harwood Academic Publishers},  title = {{The Horizontal Gene Pool -- Bacterial Plasmids and Gene Spread}},  year = {2000}  }  @article{citeulike:3158738,  abstract = {{WikiGenes is the first wiki system to combine the collaborative and largely altruistic possibilities of wikis with explicit authorship. In view of the extraordinary success of Wikipedia there remains no doubt about the potential of collaborative publishing, yet its adoption in science has been limited. Here I discuss a dynamic collaborative knowledge base for the life sciences that provides authors with due credit and that can evolve via continual revision and traditional peer review into a rigorous scientific tool.}},  author = {Hoffmann, Robert},  citeulike-article-id = {3158738},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/ng.f.217},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/ng.f.217},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18728691},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18728691},  day = {27},  doi = {10.1038/ng.f.217},  issn = {1061-4036},  journal = {Nature Genetics},  keywords = {bacterial-biology},  month = aug,  number = {9},  pages = {1047--1051},  pmid = {18728691},  posted-at = {2011-01-08 21:54:19},  priority = {2},  publisher = {Nature Publishing Group},  title = {{A wiki for the life sciences where authorship matters}},  url = {http://dx.doi.org/10.1038/ng.f.217},  volume = {40},  year = {2008}  }  @article{citeulike:4132355,  abstract = {{An essential feature of bacterial plasmids is their ability to replicate as autonomous genetic elements in a controlled way within the host. Therefore, they can be used to explore the mechanisms involved in DNA replication and to analyze the different strategies that couple DNA replication to other critical events in the cell cycle. In this review, we focus on replication and its control in circular plasmids. Plasmid replication can be conveniently divided into three stages: initiation, elongation, and termination. The inability of DNA polymerases to initiate de novo replication makes necessary the independent generation of a primer. This is solved, in circular plasmids, by two main strategies: (i) opening of the strands followed by RNA priming (theta and strand displacement replication) or (ii) cleavage of one of the DNA strands to generate a 3′-OH end (rolling-circle replication). Initiation is catalyzed most frequently by one or a few plasmid-encoded initiation proteins that recognize plasmid-specific DNA sequences and determine the point from which replication starts (the origin of replication). In some cases, these proteins also participate directly in the generation of the primer. These initiators can also play the role of pilot proteins that guide the assembly of the host replisome at the plasmid origin. Elongation of plasmid replication is carried out basically by DNA polymerase III holoenzyme (and, in some cases, by DNA polymerase I at an early stage), with the participation of other host proteins that form the replisome. Termination of replication has specific requirements and implications for reinitiation, studies of which have started. The initiation stage plays an additional role: it is the stage at which mechanisms controlling replication operate. The objective of this control is to maintain a fixed concentration of plasmid molecules in a growing bacterial population (duplication of the plasmid pool paced with duplication of the bacterial population). The molecules involved directly in this control can be (i) RNA (antisense RNA), (ii) DNA sequences (iterons), or (iii) antisense RNA and proteins acting in concert. The control elements maintain an average frequency of one plasmid replication per plasmid copy per cell cycle and can †sense†and correct deviations from this average. Most of the current knowledge on plasmid replication and its control is based on the results of analyses performed with pure cultures under steady-state growth conditions. This knowledge sets important parameters needed to understand the maintenance of these genetic elements in mixed populations and under environmental conditions.}},  author = {Solar, Gloria D. and Giraldo, Rafael and Ruiz-Echevarr\'{\i}a, Mar\'{\i}a J. and Espinosa, Manuel and D\'{\i}az-Orejas, Ram\'{o}n},  citeulike-article-id = {4132355},  citeulike-linkout-0 = {http://mmbr.asm.org/content/62/2/434.abstract},  citeulike-linkout-1 = {http://mmbr.asm.org/content/62/2/434.full.pdf},  citeulike-linkout-2 = {http://mmbr.asm.org/cgi/content/abstract/62/2/434},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/9618448},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=9618448},  day = {01},  issn = {1098-5557},  journal = {Microbiology and Molecular Biology Reviews},  keywords = {bacterial-biology},  month = jun,  number = {2},  pages = {434--464},  pmid = {9618448},  posted-at = {2011-01-08 12:49:24},  priority = {2},  publisher = {American Society for Microbiology},  title = {{Replication and Control of Circular Bacterial Plasmids}},  url = {http://mmbr.asm.org/content/62/2/434.abstract},  volume = {62},  year = {1998}  }  @article{citeulike:8426527,  abstract = {{Objections to Darwinian evolution are often based on the time required to carry out the necessary mutations. Seemingly, exponential numbers of mutations are needed. We show that such estimates ignore the effects of natural selection, and that the numbers of necessary mutations are thereby reduced to about K log L, rather than KL, where L is the length of the genomic †word,†and K is the number of possible †letters†that can occupy any position in the word. The required theory makes contact with the theory of radix-exchange sorting in theoretical computer science, and the asymptotic analysis of certain sums that occur there.}},  author = {Wilf, Herbert S. and Ewens, Warren J.},  citeulike-article-id = {8426527},  citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.1016207107},  citeulike-linkout-1 = {http://www.pnas.org/content/early/2010/12/06/1016207107.abstract},  citeulike-linkout-2 = {http://www.pnas.org/content/early/2010/12/06/1016207107.full.pdf},  citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/107/52/22454},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/21149677},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=21149677},  day = {28},  doi = {10.1073/pnas.1016207107},  issn = {1091-6490},  journal = {Proceedings of the National Academy of Sciences},  keywords = {transversal},  month = dec,  number = {52},  pages = {22454--22456},  pmid = {21149677},  posted-at = {2011-01-07 12:52:29},  priority = {2},  publisher = {National Academy of Sciences},  title = {{There's plenty of time for evolution}},  url = {http://dx.doi.org/10.1073/pnas.1016207107},  volume = {107},  year = {2010}  }  @article{RPNovick03011976,  author = {Novick, R. P. and Clowes, R. C. and Cohen, S. N. and Curtiss, 3rd and Datta, N. and Falkow, S.},  citeulike-article-id = {8512051},  citeulike-linkout-0 = {http://mmbr.asm.org},  eprint = {http://mmbr.asm.org/cgi/reprint/40/1/168.pdf},  journal = {Microbiol. Mol. Biol. Rev.},  keywords = {bacterial-biology},  number = {1},  pages = {168--189},  posted-at = {2011-01-06 18:27:57},  priority = {2},  title = {{Uniform nomenclature for bacterial plasmids: a proposal.}},  url = {http://mmbr.asm.org},  volume = {40},  year = {1976}  }  @misc{citeulike:8511955,  author = {Ong, Yan and Ward, John and Nagl, Sylvia},  citeulike-article-id = {8511955},  citeulike-linkout-0 = {http://www.biochem.ucl.ac.uk/bsm/PLASMID/mainpage.htm},  howpublished = {Online},  institution = {Department of Biochemistry and Molecular Biology},  keywords = {bacterial-biology},  posted-at = {2011-01-06 17:16:45},  priority = {2},  school = {UCL},  title = {{Genome Database of Naturally Occurring Plasmids}},  url = {http://www.biochem.ucl.ac.uk/bsm/PLASMID/mainpage.htm},  year = {2010}  }  @article{citeulike:8506150,  abstract = {{Genetic switch systems with mutual repression of two transcription factors, encoded on plasmids, are studied using stochastic methods. The plasmid copy number is found to strongly affect the behavior of these systems. More specifically, the average time between spontaneous switching events quickly increases with the number of plasmids. It was shown before that for a single copy encoded on the chromosome, the exclusive switch is more stable than the general switch. Here we show that when the switch is encoded on a sufficiently large number of plasmids, the situation is reversed and the general switch is more stable than the exclusive switch. These predictions can be tested experimentally using methods of synthetic biology.}},  author = {Loinger, Adiel and Biham, Ofer},  citeulike-article-id = {8506150},  citeulike-linkout-0 = {http://dx.doi.org/10.1103/physrevlett.103.068104},  citeulike-linkout-1 = {http://link.aps.org/abstract/PRL/v103/i6/e068104},  citeulike-linkout-2 = {http://link.aps.org/pdf/PRL/v103/i6/e068104},  doi = {10.1103/physrevlett.103.068104},  journal = {Physical Review Letters},  keywords = {bacterial-biology},  month = aug,  number = {6},  pages = {068104+},  posted-at = {2011-01-04 22:13:23},  priority = {2},  publisher = {American Physical Society},  title = {{Analysis of Genetic Toggle Switch Systems Encoded on Plasmids}},  url = {http://dx.doi.org/10.1103/physrevlett.103.068104},  volume = {103},  year = {2009}  }  @article{citeulike:4292765,  abstract = {{Next-generation DNA sequencing machines are generating an enormous amount of sequence data, placing unprecedented demands on traditional single-processor read-mapping algorithms. CloudBurst is a new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping and personal genomics. It is modeled after the short read-mapping program RMAP, and reports either all alignments or the unambiguous best alignment for each read with any number of mismatches or differences. This level of sensitivity could be prohibitively time consuming, but CloudBurst uses the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes. CloudBurst's running time scales linearly with the number of reads mapped, and with near linear speedup as the number of processors increases. In a 24-processor core configuration, CloudBurst is up to 30 times faster than RMAP executing on a single core, while computing an identical set of alignments. Using a larger remote compute cloud with 96 cores, CloudBurst improved performance by >100-fold, reducing the running time from hours to mere minutes for typical jobs involving mapping of millions of short reads to the human genome. CloudBurst is available open-source as a model for parallelizing algorithms with MapReduce at (http://cloudburst-bio.sourceforge.net/).}},  author = {Schatz, Michael C.},  citeulike-article-id = {4292765},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp236},  citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/btp236/.abstract},  citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/btp236/.full.pdf},  citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/11/1363?etoc},  citeulike-linkout-4 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682523/},  citeulike-linkout-5 = {http://view.ncbi.nlm.nih.gov/pubmed/19357099},  citeulike-linkout-6 = {http://www.hubmed.org/display.cgi?uids=19357099},  day = {1},  doi = {10.1093/bioinformatics/btp236},  issn = {1367-4811},  journal = {Bioinformatics (Oxford, England)},  keywords = {transversal},  month = jun,  number = {11},  pages = {1363--1369},  pmcid = {PMC2682523},  pmid = {19357099},  posted-at = {2011-01-04 12:38:52},  priority = {2},  publisher = {Oxford University Press},  title = {{CloudBurst: highly sensitive read mapping with MapReduce.}},  url = {http://dx.doi.org/10.1093/bioinformatics/btp236},  volume = {25},  year = {2009}  }  @article{citeulike:8467579,  abstract = {{BACKGROUND:Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce.DESCRIPTION:An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date.CONCLUSIONS:Hadoop and the MapReduce programming paradigm already have a substantial base in the bioinformatics community, especially in the field of next-generation sequencing analysis, and such use is increasing. This is due to the cost-effectiveness of Hadoop-based analysis on commodity Linux clusters, and in the cloud via data upload to cloud vendors who have implemented Hadoop/HBase; and due to the effectiveness and ease-of-use of the MapReduce method in parallelization of many data analysis algorithms.}},  author = {Taylor, Ronald},  citeulike-article-id = {8467579},  citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-11-s12-s1},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040523/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21210976},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21210976},  doi = {10.1186/1471-2105-11-s12-s1},  issn = {1471-2105},  journal = {BMC Bioinformatics},  keywords = {transversal},  number = {Suppl 12},  pages = {S1+},  pmcid = {PMC3040523},  pmid = {21210976},  posted-at = {2011-01-04 12:12:59},  priority = {2},  title = {{An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics}},  url = {http://dx.doi.org/10.1186/1471-2105-11-s12-s1},  volume = {11},  year = {2010}  }  @article{citeulike:8489030,  abstract = {{Abstract Transmissible plasmids can be classified according to their mobilization ability, as being conjugative (self-transmissible) or mobilizable (transmissible only in the presence of additional conjugative functions). Naturally occurring mobilizable plasmids carry the genetic information necessary for relaxosome formation and processing, but lack the functions required for mating pair formation. Mobilizable plasmids have a tremendous impact in horizontal gene transfer in nature, including the spread of antibiotic resistance. However, analysis of their promiscuity and diversity has attracted less attention than that of conjugative plasmids. This review will focus on the analysis of the diversity of mobilizable plasmids. For this purpose, we primarily compared the amino acid sequences of their relaxases and, when pertinent, we compared these enzymes with conjugative plasmid relaxases. In this way, we established phylogenetic relationships among the members of each superfamily. We conducted a database and literature analysis that led us to propose a classification system for small mobilizable plasmids in families and superfamilies according to their mobilization regions. This review outlines the genetic organization of each family of mobilization regions, as well as the most relevant properties and relationships among their constituent encoded proteins. In this respect, the present review constitutes a first approach to the characterization of the global gene pool of mobilization regions of small mobilizable plasmids.}},  author = {Francia and Varsaki, Athanasia and Garcill\'{a}n-Barcia and Latorre, Amparo and Drainas, Constantin and de la Cruz, Fernando},  citeulike-article-id = {8489030},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.femsre.2003.09.001},  doi = {10.1016/j.femsre.2003.09.001},  journal = {FEMS Microbiology Reviews},  keywords = {bacterial-biology},  number = {1},  pages = {79--100},  posted-at = {2010-12-28 14:45:36},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{A classification scheme for mobilization regions of bacterial plasmids}},  url = {http://dx.doi.org/10.1016/j.femsre.2003.09.001},  volume = {28},  year = {2004}  }  @article{citeulike:4636639,  abstract = {{The epidemiological importance of tracing plasmids conferring drug resistance prompted us to develop a PCR method based on replicons (inc/rep PCR) of the major plasmid incompatibility groups among Enterobacteriaceae. Eighteen pairs of primers were designed to perform 5 multiplex- and 3 simplex-PCRs, recognizing FIA, FIB, FIC, HI1, HI2, I1-Iγ, L/M, N, P, W, T, A/C, K, B/O, X, Y, F, and FIIA. The specificity of the method was tested on a collection of 61 reference plasmids and on 20 Salmonella enterica strains of different serotypes isolated in Italy. Results indicated that the inc/rep PCR method demonstrates high specificity and sensitivity in detecting replicons on reference plasmids and also revealed the presence of recurrent and common plasmids in epidemiologically unrelated Salmonella isolates of different serotypes. These results suggest that the method is potentially applicable to a large number of strains to trace the diffusion of specific multi-drug resistance plasmids in different environments.}},  author = {Carattoli, A. and Bertini, A. and Villa, L. and Falbo, V. and Hopkins, K. and Threlfall, E.},  citeulike-article-id = {4636639},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.mimet.2005.03.018},  doi = {10.1016/j.mimet.2005.03.018},  issn = {01677012},  journal = {Journal of Microbiological Methods},  keywords = {bacterial-biology},  month = dec,  number = {3},  pages = {219--228},  posted-at = {2010-12-28 14:44:40},  priority = {2},  title = {{Identification of plasmids by PCR-based replicon typing}},  url = {http://dx.doi.org/10.1016/j.mimet.2005.03.018},  volume = {63},  year = {2005}  }  @article{citeulike:8489022,  author = {Couturier, M. and Bex, F. and Bergquist, P. L. and Maas, W. K.},  citeulike-article-id = {8489022},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/3054468},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=3054468},  issn = {0146-0749},  journal = {Microbiological reviews},  keywords = {bacterial-biology},  month = sep,  number = {3},  pages = {375--395},  pmid = {3054468},  posted-at = {2010-12-28 14:43:54},  priority = {2},  title = {{Identification and classification of bacterial plasmids.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/3054468},  volume = {52},  year = {1988}  }  @article{citeulike:5405606,  abstract = {{The transfer of the self-transmissible plasmids, RP4 and pJP4, from introduced bacteria to indigenous bacteria was examined in soil and slurry microcosms. The introduced plasmids persisted in indigenous transconjugants despite the low survival of introduced donors. The potential of the transconjugants for growth and conjugation affects the persistence of introduced plasmids in soil.}},  author = {Inoue, Daisuke and Soda, Satoshi and Tsutsui, Hirofumi and Yamazaki, Yuji and Murashige, Katsushi and Sei, Kazunari and Fujita, Masanori and Ike, Michihiko},  citeulike-article-id = {5405606},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jbiosc.2009.03.014},  doi = {10.1016/j.jbiosc.2009.03.014},  issn = {13891723},  journal = {Journal of Bioscience and Bioengineering},  keywords = {bacterial-biology},  month = sep,  number = {3},  pages = {231--234},  posted-at = {2010-12-20 23:05:35},  priority = {2},  title = {{Occurrence and persistence of indigenous transconjugants carrying conjugative plasmids in soil}},  url = {http://dx.doi.org/10.1016/j.jbiosc.2009.03.014},  volume = {108},  year = {2009}  }  @article{citeulike:2755966,  abstract = {{When it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be used as a guide to improve them. There are nevertheless many open problems, particularly to describe DNA at the scale of a few tens of base pairs, which is relevant for many biological phenomena.}},  author = {Peyrard, Michel and Cuesta-L\'{o}pez, Santiago and James, Guillaume},  citeulike-article-id = {2755966},  citeulike-linkout-0 = {http://dx.doi.org/10.1088/0951-7715/21/6/t02},  citeulike-linkout-1 = {http://www.ingentaconnect.com/content/iop/non/2008/00000021/00000006/art00t02},  citeulike-linkout-2 = {http://iopscience.iop.org/0951-7715/21/6/T02},  day = {01},  doi = {10.1088/0951-7715/21/6/t02},  issn = {0951-7715},  journal = {Nonlinearity},  keywords = {transversal},  month = jun,  number = {6},  pages = {T91--T100},  posted-at = {2010-12-20 23:03:10},  priority = {2},  publisher = {Institute of Physics Publishing},  title = {{Modelling DNA at the mesoscale: a challenge for nonlinear science?}},  url = {http://dx.doi.org/10.1088/0951-7715/21/6/t02},  volume = {21},  year = {2008}  }  @article{citeulike:4054364,  abstract = {{The base pairs that encode the genetic information in DNA show large amplitude localized excitations called DNA breathing. We discuss the experimental observations of this phenomenon and its theoretical analysis. Starting from a model introduced to study the thermal denaturation of DNA, we show that it can qualitatively describe DNA breathing but is quantitatively not satisfactory. We show how the model can be modified to be quantitatively correct. This defines a nonlinear lattice model, which is interesting in itself because it has nonlinear localized excitations, forming a new class of discrete breather.}},  author = {Peyrard, M. and Cuesta-L\'{o}pez, S. and James, G.},  citeulike-article-id = {4054364},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s10867-009-9127-2},  citeulike-linkout-1 = {http://www.springerlink.com/content/l3p403502w335056},  day = {1},  doi = {10.1007/s10867-009-9127-2},  issn = {0092-0606},  journal = {Journal of Biological Physics},  keywords = {transversal},  month = feb,  number = {1},  pages = {73--89},  posted-at = {2010-12-20 23:00:50},  priority = {2},  publisher = {Springer Netherlands},  title = {{Nonlinear Analysis of the Dynamics of DNA Breathing}},  url = {http://dx.doi.org/10.1007/s10867-009-9127-2},  volume = {35},  year = {2009}  }  @article{citeulike:6031815,  abstract = {{A pair of genes designated parA and parB are encoded by many low copy number plasmids and bacterial chromosomes. They work with one or more cis-acting sites termed centromere-like sequences to ensure better than random predivisional partitioning of the DNA molecule that encodes them. The centromere-like sequences nucleate binding of ParB and titrate sufficient protein to create foci, which are easily visible by immuno-fluorescence microscopy. These foci normally follow the plasmid or the chromosomal replication oriC complexes. ParA is a membrane-associated ATPase that is essential for this symmetric movement of the ParB foci. In Bacillus subtilis ParA oscillates from end to end of the cell as does MinD of E. coli, a relative of the ParA family. ParA may facilitate ParB movement along the inner surface of the cytoplasmic membrane to encounter and become tethered to the next replication zone. The ATP-bound form of ParA appears to adopt the conformation needed to drive partition. Hydrolysis to create ParA-ADP or free ParA appears to favour a form that is not located at the pole and binds to DNA rather than the partition complex. Definition of the protein domains needed for interaction with membranes and the conformational changes that occur on interaction with ATP/ADP will provide insights into the partitioning mechanism and possible targets for inhibitors of partitioning.}},  author = {Bignell, C. and Thomas, C. M.},  citeulike-article-id = {6031815},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/11522360},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=11522360},  day = {13},  issn = {0168-1656},  journal = {Journal of biotechnology},  keywords = {bacterial-biology},  month = sep,  number = {1},  pages = {1--34},  pmid = {11522360},  posted-at = {2010-12-19 21:33:18},  priority = {2},  title = {{The bacterial ParA-ParB partitioning proteins.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/11522360},  volume = {91},  year = {2001}  }  @article{citeulike:8422705,  abstract = {{ColE1-like plasmids constitute the most popular vectors for recombinant protein expression. ColE1 plasmid replication is tightly controlled by an antisense RNA mechanism that is highly dynamic, tuning plasmid metabolic burden to the physiological state of the host. Plasmid homeostasis is upset upon induction of recombinant protein expression because of non-physiological levels of expression and because of the frequently biased amino acid composition of recombinant proteins. Disregulation of plasmid replication is the main cause of collapse of plasmid-based expression systems because of a simultaneous increase in the metabolic burden (due to increased average copy number) and in the probability of generation of plasmid-free cells (due to increased copy number variation). Interference between regulatory elements of co-resident plasmids causes comparable effects on plasmid stability (plasmid incompatibility). Modulating plasmid copy number for recombinant gene expression aims at achieving a high gene dosage while preserving the stability of the expression system. Here I present strategies targeting plasmid replication for optimizing recombinant gene expression. Specifically, I review approaches aimed at modulating the antisense regulatory system (as well as their implications for plasmid incompatibility) and innovative strategies involving modulation of host factors, of R-loop formation, and of the timing of recombinant gene expression.}},  author = {Camps, Manel},  citeulike-article-id = {8422705},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/20218961},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=20218961},  issn = {1872-2156},  journal = {Recent patents on DNA \& gene sequences},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {58--73},  pmid = {20218961},  posted-at = {2010-12-13 22:32:46},  priority = {2},  title = {{Modulation of ColE1-like plasmid replication for recombinant gene expression.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/20218961},  volume = {4},  year = {2010}  }  @article{citeulike:8415917,  abstract = {{Summary The mitotic apparatus that a plasmid uses to ensure its stable inheritance responds to the appearance of an additional copy of the plasmid's centromere by segregating it from the pre-existing copies: if the new copy arises by replication of the plasmid the result is partition, if it arrives on a different plasmid the result is incompatibility. Incompatibility thus serves as a probe of the partition mechanism. Coupling of distinct plasmids via their shared centromeres to form mixed pairs has been the favoured explanation for centromere-based incompatibility, because it supports a long-standing assumption that pairing of plasmid replicas is a prerequisite for their partition into daughter cells. Recent results from molecular genetic and fluorescence microscopy studies challenge this mixed pairing model. Partition incompatibility is seen to result from various processes, including titration, randomized positioning and a form of mixed pairing that is based on co-activation of the same partition event rather than direct contact between partition complexes. The perspectives thus opened onto the partition mechanism confirm the continuing utility of incompatibility as an approach to understanding bacterial mitosis. The results considered are compatible with the view that direct pairing of plasmids is not essential to plasmid partition.}},  author = {Bouet, Jean-Yves and Nordstr\"{o}m, Kurt and Lane, David},  citeulike-article-id = {8415917},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1365-2958.2007.05882.x},  doi = {10.1111/j.1365-2958.2007.05882.x},  journal = {Molecular Microbiology},  keywords = {bacterial-biology},  number = {6},  pages = {1405--1414},  posted-at = {2010-12-12 11:38:35},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{Plasmid partition and incompatibility -- the focus shifts}},  url = {http://dx.doi.org/10.1111/j.1365-2958.2007.05882.x},  volume = {65},  year = {2007}  }  @article{citeulike:8413629,  abstract = {{It is generally accepted that plasmids containing the same origin of replication are incompatible. We have re-examined this concept in terms of the plasmid copy number, by introducing plasmids containing the same origin of replication and different antibiotic resistance genes into bacteria. By selecting for resistance to only one antibiotic, we were able to examine the persistence of plasmids carrying resistances to other antibiotics. We find that plasmids are not rapidly lost, but are able to persist in bacteria for multiple overnight growth cycles, with some dependence upon the nature of the antibiotic selected for. By carrying out the experiments with different origins of replication, we have been able to show that higher copy number leads to longer persistence, but even with low copy plasmids, persistence occurs to a significant degree. This observation holds significance for the field of protein engineering, as the presence of two or more plasmids within bacteria weakens, and confuses, the connection between screened phenotype and genotype, with the potential to wrongly assign specific phenotypes to incorrect genotypes.}},  author = {Velappan, Nileena and Sblattero, Daniele and Chasteen, Leslie and Pavlik, Peter and Bradbury, Andrew R. M.},  citeulike-article-id = {8413629},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/protein/gzm005},  citeulike-linkout-1 = {http://peds.oxfordjournals.org/content/20/7/309.abstract},  citeulike-linkout-2 = {http://peds.oxfordjournals.org/content/20/7/309.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/17332010},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=17332010},  day = {1},  doi = {10.1093/protein/gzm005},  journal = {Protein Engineering Design and Selection},  keywords = {bacterial-biology},  month = jul,  number = {7},  pages = {309--313},  pmid = {17332010},  posted-at = {2010-12-11 20:13:21},  priority = {2},  title = {{Plasmid incompatibility: more compatible than previously thought?}},  url = {http://dx.doi.org/10.1093/protein/gzm005},  volume = {20},  year = {2007}  }  @article{citeulike:8387435,  abstract = {{Computation underlies the organization of cells into higher-order structures, for example during development or the spatial association of bacteria in a biofilm. Each cell performs a simple computational operation, but when combined with cell-cell communication, intricate patterns emerge. Here we study this process by combining a simple genetic circuit with quorum sensing to produce more complex computations in space. We construct a simple NOR logic gate in Escherichia coli by arranging two tandem promoters that function as inputs to drive the transcription of a repressor. The repressor inactivates a promoter that serves as the output. Individual colonies of E. coli carry the same NOR gate, but the inputs and outputs are wired to different orthogonal quorum-sensing 'sender' and 'receiver' devices. The quorum molecules form the wires between gates. By arranging the colonies in different spatial configurations, all possible two-input gates are produced, including the difficult XOR and EQUALS functions. The response is strong and robust, with 5- to >300-fold changes between the 'on' and 'off' states. This work helps elucidate the design rules by which simple logic can be harnessed to produce diverse and complex calculations by rewiring communication between cells.}},  author = {Tamsir, Alvin and Tabor, Jeffrey J. and Voigt, Christopher A.},  citeulike-article-id = {8387435},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature09565},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature09565},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21150903},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21150903},  day = {13},  doi = {10.1038/nature09565},  issn = {0028-0836},  journal = {Nature},  keywords = {bacterial-biology},  month = jan,  number = {7329},  pages = {212--215},  pmid = {21150903},  posted-at = {2010-12-09 22:28:42},  priority = {2},  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},  title = {{Robust multicellular computing using genetically encoded NOR gates and chemical /`wires/'}},  url = {http://dx.doi.org/10.1038/nature09565},  volume = {469},  year = {2011}  }  @article{citeulike:8387036,  abstract = {{Ongoing efforts within synthetic and systems biology have been directed towards the building of artificial computational devices using engineered biological units as basic building blocks. Such efforts, inspired in the standard design of electronic circuits, are limited by the difficulties arising from wiring the basic computational units (logic gates) through the appropriate connections, each one to be implemented by a different molecule. Here, we show that there is a logically different form of implementing complex Boolean logic computations that reduces wiring constraints thanks to a redundant distribution of the desired output among engineered cells. A practical implementation is presented using a library of engineered yeast cells, which can be combined in multiple ways. Each construct defines a logic function and combining cells and their connections allow building more complex synthetic devices. As a proof of principle, we have implemented many logic functions by using just a few engineered cells. Of note, small modifications and combination of those cells allowed for implementing more complex circuits such as a multiplexer or a 1-bit adder with carry, showing the great potential for re-utilization of small parts of the circuit. Our results support the approach of using cellular consortia as an efficient way of engineering complex tasks not easily solvable using single-cell implementations.}},  author = {Regot, Sergi and Macia, Javier and Conde, Nuria and Furukawa, Kentaro and Kjellen, Jimmy and Peeters, Tom and Hohmann, Stefan and de Nadal, Eulalia and Posas, Francesc and Sole, Ricard},  citeulike-article-id = {8387036},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature09679},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature09679},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21150900},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21150900},  day = {13},  doi = {10.1038/nature09679},  issn = {0028-0836},  journal = {Nature},  keywords = {bacterial-biology},  month = jan,  number = {7329},  pages = {207--211},  pmid = {21150900},  posted-at = {2010-12-09 06:12:10},  priority = {2},  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},  title = {{Distributed biological computation with multicellular engineered networks}},  url = {http://dx.doi.org/10.1038/nature09679},  volume = {469},  year = {2011}  }  @article{citeulike:8393093,  abstract = {{Targeting of DNA molecules to specific subcellular positions is essential for efficient segregation, but the mechanisms underlying these processes are poorly understood. In Escherichia coli, several plasmids belonging to different incompatibility groups (F, P1 and RK2) localize preferentially near the midcell and quartercell positions. Here we compare the relative positions of these three plasmids using fluorescence in situ hybridization. When plasmids F and P1 were localized simultaneously using differentially labeled probes, the majority of foci (75\%) were well separated from each other. Similar results were found when we compared the subcellular localization of F with RK2, and RK2 with P1: regardless of the number of foci per cell or growth conditions, most of the foci (70–80\%) were not in close proximity to one another. We also localized RK2 in Pseudomonas aeruginosa and Vibrio cholerae, and found that plasmid RK2 localization is conserved across bacterial species. Our results suggest that each plasmid has its own unique subcellular address, implying a mechanism for the stable co-existence of plasmids in which subcelluar targeting plays a major role.}},  author = {Ho, Thanh Q. and Zhong, Zhenping and Aung, Stefan and Pogliano, Joe},  citeulike-article-id = {8393093},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/emboj/21.7.1864},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/7594405a},  day = {01},  doi = {10.1093/emboj/21.7.1864},  journal = {The EMBO Journal},  keywords = {bacterial-biology},  month = apr,  number = {7},  pages = {1864--1872},  posted-at = {2010-12-09 06:10:38},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Compatible bacterial plasmids are targeted to independent cellular locations in Escherichia coli}},  url = {http://dx.doi.org/10.1093/emboj/21.7.1864},  volume = {21},  year = {2002}  }  @article{citeulike:8393044,  abstract = {{Recent studies have shown that plasmids are organized inside bacterial cells in a remarkably complex way. Plasmids containing active partitioning systems are tethered to specific regions of the cell, and the number and position of plasmid molecules within the cell are coordinated with the bacterial host cell cycle and growth rate. Plasmids belonging to different incompatibility groups are also tethered to different sites within the cell, and segregate at different times relative to one another and to the bacterial cell cycle. Recent studies suggest that many of these observations regarding subcellular plasmid dynamics formulated for Escherichia coli plasmids may be broadly conserved. Plasmids inside bacterial cells are organised in remarkably complex patterns and are actively segregated into daughter cells by plasmid-encoded partitioning systems.}},  author = {Pogliano, J.},  citeulike-article-id = {8393044},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s1369-5274(02)00370-3},  day = {01},  doi = {10.1016/s1369-5274(02)00370-3},  issn = {13695274},  journal = {Current Opinion in Microbiology},  keywords = {bacterial-biology},  month = dec,  number = {6},  pages = {586--590},  posted-at = {2010-12-09 06:03:10},  priority = {2},  title = {{Dynamic cellular location of bacterial plasmids}},  url = {http://dx.doi.org/10.1016/s1369-5274(02)00370-3},  volume = {5},  year = {2002}  }  @article{citeulike:8392968,  abstract = {{Abstract The long-term dynamics of mobile plasmids in natural environments are unclear. This is the first study of the long-term dynamics of introduced plasmids with xenobiotic degradation abilities using a mathematical model that describes the horizontal gene transfer (HGT) of plasmids into indigenous bacteria via conjugation. We focussed on negative feedback between the spread of plasmids and their selective advantage, i.e. the severe competition between plasmid-bearing and plasmid-free bacteria resulting from a decrease in xenobiotic concentration caused by the gene expression of plasmids, favoring plasmid-free bacteria. Two types of HGT enhanced the persistence of plasmids and the degradation of the xenobiotic in different conditions: a relatively low rate of 'intergeneric HGT' from introduced to indigenous bacteria and a high rate of 'intraindigenous HGT' from indigenous to indigenous bacteria. In addition, when the indigenous resource supply rate was high and when the cost of bearing plasmids was low, both types of HGT made large contributions to xenobiotic degradation compared to the contribution of vertical transfer via plasmid replication within the introduced host population. Initial conditions were also important; a higher initial density of introduced plasmid-bearing bacteria led to a lower degradation rate over a long time scale.}},  author = {Miki, Takeshi and Ueki, Masaya and Kawabata, Zen'ichiro and Yamamura, Norio},  citeulike-article-id = {8392968},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1574-6941.2007.00357.x},  doi = {10.1111/j.1574-6941.2007.00357.x},  journal = {FEMS Microbiology Ecology},  keywords = {bacterial-biology},  number = {2},  pages = {211--221},  posted-at = {2010-12-09 05:53:29},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{Long-term dynamics of catabolic plasmids introduced to a microbial community in a polluted environment: a mathematical model}},  url = {http://dx.doi.org/10.1111/j.1574-6941.2007.00357.x},  volume = {62},  year = {2007}  }  @article{citeulike:8378788,  abstract = {{The conjugative streptococcal transposon Tn916 was found to transfer naturally between a variety of gram-positive and gram-negative eubacteria. Enterococcus faecalis hosting the transposon could serve as a donor for Alcaligenes eutrophus, Citrobacter freundii, and Escherichia coli at frequencies of 10(-6) to 10(-8). No transfer was observed with several phototrophic species. Mating of an E. coli strain carrying Tn916 yielded transconjugants with Bacillus subtilis, Clostridium acetobutylicum, Enterococcus faecalis, and Streptococcus lactis subsp. diacetylactis at frequencies of 10(-4) to 10(-6). Acetobacterium woodii was the only gram-positive organism tested that did not accept the transposon from a gram-negative donor. The results prove the ability of conjugative transposable elements such as Tn916 for natural cross-species gene transfer, thus potentially contributing to bacterial evolution.}},  author = {Bertram, J. and Stratz, M. and Durre, P.},  citeulike-article-id = {8378788},  citeulike-linkout-0 = {http://jb.asm.org/cgi/content/abstract/173/2/443},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/1846142},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=1846142},  day = {1},  journal = {J. Bacteriol.},  keywords = {bacterial-biology},  month = jan,  number = {2},  pages = {443--448},  pmid = {1846142},  posted-at = {2010-12-07 20:35:38},  priority = {2},  title = {{Natural transfer of conjugative transposon Tn916 between gram-positive and gram-negative bacteria.}},  url = {http://jb.asm.org/cgi/content/abstract/173/2/443},  volume = {173},  year = {1991}  }  @article{citeulike:8378785,  abstract = {{Conjugative transposons are highly ubiquitous elements found throughout the bacterial world. Members of the Tn916–Tn1545 family carry the widely disseminated tetracycline-resistance determinant Tet M, as well as additional resistance genes. They have been found naturally in, or been introduced into, over 50 different species and 24 genera of bacteria. Recent investigations have led to insights into the molecular basis of movement of these interesting mobile elements.}},  author = {Clewell, D.},  citeulike-article-id = {8378785},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0966-842x(00)88930-1},  doi = {10.1016/s0966-842x(00)88930-1},  issn = {0966842X},  journal = {Trends in Microbiology},  keywords = {bacterial-biology},  month = jun,  number = {6},  pages = {229--236},  posted-at = {2010-12-07 20:34:38},  priority = {2},  title = {{Unconstrained bacterial promiscuity: the Tn916--Tn1545 family of conjugative transposons}},  url = {http://dx.doi.org/10.1016/s0966-842x(00)88930-1},  volume = {3},  year = {1995}  }  @article{citeulike:8366801,  abstract = {{Multicopy plasmids are often chosen for the expression of recombinant genes in Escherichia coli. The high copy number is generally desired for maximum gene expression; however, the metabolic burden effects that usually result from multiple plasmid copies could prove to be detrimental for maximum productivity in certain metabolic engineering applications. In this study, low-copy mini-F plasmids were compared to high-copy pMB1-based plasmids for production of two metabolites in E. coli: polyphosphate (polyP) and lycopene derived from isopentenyl diphosphate (IPP). The stationary-phase accumulation of polyP on a per cell basis was enhanced approximately 80\% when either high- or low-copy plasmids were used, from 120 micromol/g DCW without augmented polyP kinase (PPK) activity to approximately 220 micromol/g DCW. The cell density of the high-copy plasmid-containing culture at stationary phase was approximately 24\% lower than the low-copy culture and 30\% lower than the control culture. This difference in cell density is likely a metabolic burden effect and resulted in a lower overall product concentration for the high-copy culture (approximately 130 micromol/L culture) relative to the low-copy culture (approximately 160 micromol/L culture). When the gene for DXP (1-deoxy-D-xylulose 5-phosphate) synthase, the first enzyme in the IPP mevalonate-independent biosynthetic pathway, was expressed from the tac promoter on multicopy and low-copy plasmids, lycopene production was enhanced two- to threefold over that found in cells expressing the chromosomal copy only. Cell growth and lycopene production decreased substantially when isopropyl beta-D-thiogalactosidase (IPTG) was added to the high-copy plasmid-containing culture, suggesting that overexpression of DXP synthase was a significant metabolic burden. In the low-copy plasmid-containing culture, no differences in cell growth or lycopene production were observed with any IPTG concentrations. When dxs was placed under the control of the arabinose-inducible promoter (P(BAD)) on the low-copy plasmid, the amount of lycopene produced was proportional to the arabinose concentration and no significant changes in cell growth resulted. These results suggest that low-copy plasmids may be useful in metabolic engineering applications, particularly when one or more of the substrates used in the recombinant pathway are required for normal cellular metabolism.}},  author = {Jones, K. L. and Kim, S. W. and Keasling, J. D.},  citeulike-article-id = {8366801},  citeulike-linkout-0 = {http://dx.doi.org/10.1006/mben.2000.0161},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/11120644},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=11120644},  doi = {10.1006/mben.2000.0161},  issn = {1096-7176},  journal = {Metabolic engineering},  keywords = {bacterial-biology},  month = oct,  number = {4},  pages = {328--338},  pmid = {11120644},  posted-at = {2010-12-06 21:28:37},  priority = {2},  title = {{Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria.}},  url = {http://dx.doi.org/10.1006/mben.2000.0161},  volume = {2},  year = {2000}  }  @article{citeulike:8366795,  abstract = {{Many expression systems in research and industry use plasmids as vectors for the production of recombinant proteins or non-proteinous recombinant substances. Plasmids have an essential impact on productivity. Related factors are plasmid copy number, structural plasmid stability and segregational plasmid stability. Plasmid copy number determines the gene dosage accessible for expression and many plasmids lead generally to a high productivity. To analyze an expression system the quantification of plasmid copy number is very helpful. Therefore, different methods for the determination of plasmid copy number are described. Structural plasmid stability exists, when all generated plasmids have the correct base sequence. The analysis of structural instabilities is not trivial and some methods are reported. When all daughter cells get at least one plasmid during cell division, the culture is segregational stable. The development of plasmid free cells can lead to a significant loss in productivity. Different methods for lab scale and industrial scale help to avoid segregational instability. Since plasmids are used as pharmaceuticals, additional aspects of stability have to be taken into account. These include stability during downstream processing, stability after application and stability during storage and shipping.}},  author = {Friehs, Karl},  citeulike-article-id = {8366795},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/15088763},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=15088763},  issn = {0724-6145},  journal = {Advances in biochemical engineering/biotechnology},  keywords = {bacterial-biology},  pages = {47--82},  pmid = {15088763},  posted-at = {2010-12-06 21:27:31},  priority = {2},  title = {{Plasmid copy number and plasmid stability.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/15088763},  volume = {86},  year = {2004}  }  @article{citeulike:8366770,  abstract = {{Horizontal gene transfer is a principal source of evolution leading to change in the ecological character of bacterial species1. Bacterial conjugation2, which promotes the horizontal transfer of genetic material between donor and recipient cells by physical contact, is a phenomenon of fundamental evolutionary consequence3. Although conjugation has been studied primarily in liquid, most natural bacterial populations are found associated with environmental surfaces in complex multispecies communities called biofilms4. Biofilms are ideally suited to the exchange of genetic material of various origins, and it has been shown that bacterial conjugation occurs within biofilms5, 6. Here I investigate the direct contribution of conjugative plasmids themselves to the capacity of the bacterial host to form a biofilm. Natural conjugative plasmids expressed factors that induced planktonic bacteria to form or enter biofilm communities, which favour the infectious transfer of the plasmid. This general connection between conjugation and biofilms suggests that medically relevant plasmid-bearing strains are more likely to form a biofilm. This may influence both the chances of biofilm-related infection risks and of conjugational spread of virulence factors.}},  author = {Ghigo, Jean-Marc},  citeulike-article-id = {8366770},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/35086581},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/412442a0},  day = {26},  doi = {10.1038/35086581},  issn = {0028-0836},  journal = {Nature},  keywords = {bacterial-biology},  month = jul,  number = {6845},  pages = {442--445},  posted-at = {2010-12-06 21:22:47},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Natural conjugative plasmids induce bacterial biofilm development}},  url = {http://dx.doi.org/10.1038/35086581},  volume = {412},  year = {2001}  }  @article{citeulike:8364351,  abstract = {{Bacteria have evolved numerous mechanisms for cell-cell communication, many of which have important consequences for human health. Among these is conjugation, the direct transfer of DNA from one cell to another. For gram-negative bacteria, conjugation requires thin, flexible filaments (conjugative pili) that are elaborated by DNA donor cells. The structure, function, and especially the dynamics of conjugative pili are poorly understood. Here, we have applied live-cell imaging to characterize the dynamics of F-pili (conjugative pili encoded by the F plasmid of Escherichia coli). We establish that F-pili normally undergo cycles of extension and retraction in the absence of any obvious triggering event, such as contact with a recipient cell. When made, such contacts are able to survive the shear forces felt by bacteria in liquid media. Our data emphasize the role of F-pilus flexibility both in efficiently sampling a large volume surrounding donor cells in liquid culture and in establishing and maintaining cell-cell contact. Additionally and unexpectedly, we infer that extension and retraction are accompanied by rotation about the long axis of the filament.}},  author = {Clarke, Margaret and Maddera, Lucinda and Harris, Robin L. and Silverman, Philip M.},  citeulike-article-id = {8364351},  citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0806786105},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19004777},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19004777},  day = {18},  doi = {10.1073/pnas.0806786105},  issn = {1091-6490},  journal = {Proceedings of the National Academy of Sciences of the United States of America},  keywords = {bacterial-biology},  month = nov,  number = {46},  pages = {17978--17981},  pmid = {19004777},  posted-at = {2010-12-06 14:58:35},  priority = {2},  title = {{F-pili dynamics by live-cell imaging.}},  url = {http://dx.doi.org/10.1073/pnas.0806786105},  volume = {105},  year = {2008}  }  @article{citeulike:228158,  abstract = {{The human genome was analyzed for evidence that genes had been laterally transferred into the genome from prokaryotic organisms. Protein sequence comparisons of the proteomes of human, fruit fly, nematode worm, yeast, mustard weed, eukaryotic parasites, and all completed prokaryote genomes were performed, and all genes shared between human and each of the other groups of organisms were collected. About 40 genes were found to be exclusively shared by humans and bacteria and are candidate examples of horizontal transfer from bacteria to vertebrates. Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation.}},  address = {The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. [email protected]},  author = {Salzberg, Steven L. and White, Owen and Peterson, Jeremy and Eisen, Jonathan A.},  citeulike-article-id = {228158},  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1061036},  citeulike-linkout-1 = {http://www.sciencemag.org/content/292/5523/1903.abstract},  citeulike-linkout-2 = {http://www.sciencemag.org/content/292/5523/1903.full.pdf},  citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/292/5523/1903},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/11358996},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=11358996},  day = {8},  doi = {10.1126/science.1061036},  issn = {0036-8075},  journal = {Science},  keywords = {bacterial-biology},  month = jun,  number = {5523},  pages = {1903--1906},  pmid = {11358996},  posted-at = {2010-12-06 12:55:19},  priority = {2},  title = {{Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss?}},  url = {http://dx.doi.org/10.1126/science.1061036},  volume = {292},  year = {2001}  }  @article{citeulike:8361522,  abstract = {{The enterococcal, conjugative, cytolysin plasmid pAD1 confers a mating response to the peptide sex pheromone cAD1 secreted by plasmid-free strains of Enterococcus faecalis. Cells carrying pAM714, a pAD1::Tn917 derivative with wild-type conjugation properties, were mutagenized with ethyl methanesulfonate to obtain variants that were induced (in the absence of pheromone) to transfer plasmid DNA upon shifting from 32 to 42 degrees C. Of 31 such mutants generated, the results of analyses of 7 are presented in detail. All seven strains were thermosensitive in the E. faecalis host FA2-2; colony morphology, clumping, and DNA transfer correlated well with each other at the two temperatures. In the nonisogenic host E. faecalis OG1X, however, only one derivative (pAM2725) exhibited correlation of all three traits at both temperatures. Three (pAM2700, pAM2703, and pAM2717) clumped and had colonies characteristic of pheromone-induced cells at 32 degrees C but transferred plasmid DNA at a higher frequency only at the elevated temperature. The other three (pAM2708, pAM2709, and pAM2712) were derepressed at both temperatures for all three characteristics. Four of the mutations, including that of pAM2725, mapped within the traA determinant, whereas two mapped identically in a previously unnoted open reading frame (designated traD) putatively encoding a short (23-amino-acid) peptide downstream of the inhibitor peptide determinant iad and in the opposite orientation. One mutant could not be located in the regions sequenced. Studies showed that the traA and traD mutations could be complemented in trans with a DNA fragment carrying the corresponding regions.}},  author = {de Freire Bastos, M. C. and Tanimoto, K. and Clewell, D. B.},  citeulike-article-id = {8361522},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/9150221},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=9150221},  issn = {0021-9193},  journal = {Journal of bacteriology},  keywords = {bacterial-biology},  month = may,  number = {10},  pages = {3250--3259},  pmid = {9150221},  posted-at = {2010-12-05 20:33:12},  priority = {2},  title = {{Regulation of transfer of the Enterococcus faecalis pheromone-responding plasmid pAD1: temperature-sensitive transfer mutants and identification of a new regulatory determinant, traD.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/9150221},  volume = {179},  year = {1997}  }  @article{citeulike:8354083,  abstract = {{TrbC propilin is the precursor of the pilin subunit TrbC of IncP conjugative pili in Escherichia coli.Likewise, its homologue, VirB2 propilin, is processed into T pilin of the Ti plasmid T pilus in Agrobacterium tumefaciens. TrbC and VirB2 propilin are truncated post-translationally at the N terminus by the removal of a 36/47-residue leader peptide, respectively. TrbC propilin undergoes a second processing step by the removal of 27 residues at the C terminus by host-encoded functions followed by the excision of four additional C-terminal residues by a plasmid-borne serine protease. The final product TrbC of 78 residues is cyclized via an intramolecular covalent head-to-tail peptide bond. The T pilin does not undergo additional truncation but is likewise cyclized. The circular structures of these pilins, as verified by mass spectrometry, represent novel primary configurations that conform and assemble into the conjugative apparatus.}},  author = {Eisenbrandt, Ralf and Kalkum, Markus and Lai, Erh-Min and Lurz, Rudi and Kado, Clarence I. and Lanka, Erich},  citeulike-article-id = {8354083},  citeulike-linkout-0 = {http://dx.doi.org/10.1074/jbc.274.32.22548},  citeulike-linkout-1 = {http://www.jbc.org/content/274/32/22548.abstract},  citeulike-linkout-2 = {http://www.jbc.org/content/274/32/22548.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/10428832},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=10428832},  day = {6},  doi = {10.1074/jbc.274.32.22548},  journal = {Journal of Biological Chemistry},  keywords = {bacterial-biology},  month = aug,  number = {32},  pages = {22548--22555},  pmid = {10428832},  posted-at = {2010-12-03 18:38:39},  priority = {2},  title = {{Conjugative Pili of IncP Plasmids, and the Ti Plasmid T Pilus Are Composed of Cyclic Subunits}},  url = {http://dx.doi.org/10.1074/jbc.274.32.22548},  volume = {274},  year = {1999}  }  @article{citeulike:7263158,  abstract = {{Broad-host-range (BHR) IncP-1 plasmids have the ability to transfer between and replicate in nearly all species of the Alpha-, Beta- and Gammaproteobacteria, but surprisingly few data are available on the stability of these plasmids in strains within their host range. Moreover, even though molecular interactions between the bacterial host and its plasmid(s) exist, no systematic study to date has compared the stability of the same plasmid among different hosts. The goal of this study was to examine whether the stability characteristics of an IncP-1 plasmid can be variable between strains within the host range of the plasmid. Therefore, 19 strains within the Alpha-, Beta- or Gammaproteobacteria carrying the IncP-1beta plasmid pB10 were serially propagated in non-selective medium and the fraction of segregants was monitored through replica-picking. Remarkably, a large variation in the stability of pB10 in different strains was found, even between strains within the same genus or species. Ten strains showed no detectable plasmid loss over about 200 generations, and in two strains plasmid-free clones were only sporadically observed. In contrast, three strains, Pseudomonas koreensis R28, Pseudomonas putida H2 and Stenotrophomonas maltophilia P21, exhibited rapid plasmid loss within 80 generations. Parameter estimation after mathematical modelling of these stability data suggested high frequencies of segregation (about 0.04 per generation) or high plasmid cost (i.e. a relative fitness decrease in plasmid-bearing cells of about 15 and 40 \%), which was confirmed experimentally. The models also suggested that plasmid reuptake by conjugation only played a significant role in plasmid stability in one of the three strains. Four of the 19 strains lost the plasmid very slowly over about 600 generations. The erratic decrease of the plasmid-containing fraction and simulation of the data with a new mathematical model suggested that plasmid cost was variable over time due to compensatory mutations. The findings of this study demonstrate that the ability of a so-called 'BHR' plasmid to persist in a bacterial population is influenced by strain-specific traits, and therefore observations made for one strain should not be generalized for the entire species or genus.}},  author = {De Gelder, Leen and Ponciano, Jos\'{e} M. and Joyce, Paul and Top, Eva M.},  citeulike-article-id = {7263158},  citeulike-linkout-0 = {http://dx.doi.org/10.1099/mic.0.2006/001784-0},  citeulike-linkout-1 = {http://mic.sgmjournals.org/cgi/content/abstract/153/2/452},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17259616},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17259616},  day = {1},  doi = {10.1099/mic.0.2006/001784-0},  issn = {1350-0872},  journal = {Microbiology (Reading, England)},  keywords = {bacterial-biology},  month = feb,  number = {Pt 2},  pages = {452--463},  pmid = {17259616},  posted-at = {2010-12-03 11:33:12},  priority = {2},  title = {{Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship.}},  url = {http://dx.doi.org/10.1099/mic.0.2006/001784-0},  volume = {153},  year = {2007}  }  @article{citeulike:8349297,  abstract = {{Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bioelements may have profound evolutionary and geochemical significance.}},  author = {Wolfe-Simon, Felisa and Blum, Jodi S. and Kulp, Thomas R. and Gordon, Gwyneth W. and Hoeft, Shelley E. and Pett-Ridge, Jennifer and Stolz, John F. and Webb, Samuel M. and Weber, Peter K. and Davies, Paul C. W. and Anbar, Ariel D. and Oremland, Ronald S.},  citeulike-article-id = {8349297},  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1197258},  citeulike-linkout-1 = {http://www.sciencemag.org/content/early/2010/12/01/science.1197258.abstract},  citeulike-linkout-2 = {http://www.sciencemag.org/content/early/2010/12/01/science.1197258.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/21127214},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=21127214},  day = {03},  doi = {10.1126/science.1197258},  issn = {1095-9203},  journal = {Science},  keywords = {bacterial-biology},  month = jun,  number = {6034},  pages = {1163--1166},  pmid = {21127214},  posted-at = {2010-12-03 11:26:35},  priority = {2},  publisher = {American Association for the Advancement of Science},  title = {{A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus}},  url = {http://dx.doi.org/10.1126/science.1197258},  volume = {332},  year = {2011}  }  @article{citeulike:3393478,  abstract = {{Protein export by Gram-negative bacteria requires devoted machineries to allow for the passage of hydrolytic enzymes and toxins through the cell envelope. The Type II export machinery has a number of distinct characteristics, which include its role as an extension of Sec-dependent secretion, its ability to recognize and export fully folded substrates efficiently and, perhaps most significantly, the relationship between a subset of its gene products with the Type IV pilus-biogenesis apparatus. An important question is whether we can extrapolate our knowledge, albeit limited, of Type IV pilus biogenesis to understand the structure and function of the Type II export apparatus. This and other questions relating to the energetics of assembly and specificity of the apparatus are addressed in this article.}},  author = {Nunn, D.},  citeulike-article-id = {3393478},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0962-8924(99)01634-7},  day = {01},  doi = {10.1016/s0962-8924(99)01634-7},  issn = {09628924},  journal = {Trends in Cell Biology},  keywords = {bacterial-biology},  month = oct,  number = {10},  pages = {402--408},  posted-at = {2010-12-03 11:11:58},  priority = {2},  title = {{Bacterial Type II protein export and pilus biogenesis: more than just homologies?}},  url = {http://dx.doi.org/10.1016/s0962-8924(99)01634-7},  volume = {9},  year = {1999}  }  @article{citeulike:6194880,  abstract = {{A classification system for plasmids isolated from enterococci and other Gram-positive bacteria was developed based on 111 published plasmid sequences from enterococci and other Gram-positive bacteria; mostly staphylococci. Based on PCR amplification of conserved areas of the replication initiating genes (rep), alignment of these sequences and using a cutoff value of 80\% identity on both protein and DNA level, 19 replicon families (rep-families) were defined together with several unique sequences. The prevalence of these rep-families was tested on 79 enterococcal isolates from a collection of isolates of animal and human origin. Difference in prevalence of the designed rep-families were detected with rep9 being most prevalent in Enterococcus faecalis and rep2 in Enterococcus faecium. In 33\% of the tested E. faecium and 32\% of the tested E. faecalis no positive amplicons were detected. Furthermore, conjugation experiments were performed obtaining 30 transconjugants when selecting for antimicrobial resistance. Among them 19 gave no positive amplicons indicating presence of rep-families not tested for in this experimental setup.}},  author = {Jensen, L. B. and Garcia-Migura, L. and Valenzuela, A. J. S. and L{\o}hr, M. and Hasman, H. and Aarestrup, F. M.},  citeulike-article-id = {6194880},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.mimet.2009.10.012},  day = {29},  doi = {10.1016/j.mimet.2009.10.012},  issn = {01677012},  journal = {Journal of Microbiological Methods},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {25--43},  posted-at = {2010-12-03 06:33:26},  priority = {2},  title = {{A classification system for plasmids from enterococci and other Gram-positive bacteria}},  url = {http://dx.doi.org/10.1016/j.mimet.2009.10.012},  volume = {80},  year = {2010}  }  @article{citeulike:6593541,  abstract = {{Little is known about the range of hosts in which broad-host-range (BHR) plasmids can persist in the absence of selection for plasmid-encoded traits, and whether this "long-term host range" can evolve over time. Previously, the BHR multidrug resistance plasmid pB10 was shown to be highly unstable in Stenotrophomonas maltophilia P21 and Pseudomonas putida H2. To investigate whether this plasmid can adapt to such unfavorable hosts, we performed evolution experiments wherein pB10 was maintained in strain P21, strain H2, and alternatingly in P21 and H2. Plasmids that evolved in P21 and in both hosts showed increased stability and decreased cost in ancestral host P21. However, the latter group showed higher variability in stability patterns, suggesting that regular switching between distinct hosts hampered adaptive plasmid evolution. The plasmids evolved in P21 were also equally or more stable in other hosts compared to pB10, which suggested true host-range expansion. The complete genome sequences of four evolved plasmids with improved stability showed only one or two genetic changes. The stability of plasmids evolved in H2 improved only in their coevolved hosts, not in the ancestral host. Thus a BHR plasmid can adapt to an unfavorable host and thereby expand its long-term host range.}},  author = {De Gelder, Leen and Williams, Julia J. and Ponciano, Jose M. and Sota, Masahiro and Top, Eva M.},  citeulike-article-id = {6593541},  citeulike-linkout-0 = {http://dx.doi.org/10.1534/genetics.107.084475},  citeulike-linkout-1 = {http://www.genetics.org/cgi/content/abstract/178/4/2179},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18430943},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18430943},  day = {1},  doi = {10.1534/genetics.107.084475},  journal = {Genetics},  keywords = {bacterial-biology},  month = apr,  number = {4},  pages = {2179--2190},  pmid = {18430943},  posted-at = {2010-12-03 06:29:43},  priority = {2},  title = {{Adaptive Plasmid Evolution Results in Host-Range Expansion of a Broad-Host-Range Plasmid}},  url = {http://dx.doi.org/10.1534/genetics.107.084475},  volume = {178},  year = {2008}  }  @article{citeulike:5892264,  abstract = {{Microbes engage in a remarkable array of cooperative behaviors, secreting shared proteins that are essential for foraging, shelter, microbial warfare, and virulence.}},  author = {Nogueira, Teresa and Rankin, Daniel J. and Touchon, Marie and Taddei, Fran\c{c}ois and Brown, Sam P. and Rocha, Eduardo P. C.},  citeulike-article-id = {5892264},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.cub.2009.08.056},  citeulike-linkout-1 = {http://www.f1000.com/1570986},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19800234},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19800234},  day = {3},  doi = {10.1016/j.cub.2009.08.056},  issn = {1879-0445},  journal = {Current biology : CB},  keywords = {bacterial-biology},  month = nov,  number = {20},  pages = {1683--1691},  pmid = {19800234},  posted-at = {2010-12-03 06:25:59},  priority = {2},  title = {{Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence.}},  url = {http://dx.doi.org/10.1016/j.cub.2009.08.056},  volume = {19},  year = {2009}  }  @article{citeulike:6727387,  abstract = {{BACKGROUND:Prokaryotic plasmids have a dual importance in the microbial world: first they have a great impact on the metabolic functions of the host cell, providing additional traits that can be accumulated in the cell without altering the gene content of the bacterial chromosome. Additionally and/or alternatively, from a genome perspective, plasmids can provide a basis for genomic rearrangements via homologous recombination and so they can facilitate the loss or acquisition of genes during these events, which eventually may lead to horizontal gene transfer (HGT). Given their importance for conferring adaptive traits to the host organisms, the interest in plasmid sequencing is growing and now many complete plasmid sequences are available online.RESULTS:By using the newly developed Blast2Network bioinformatic tool, a comparative analysis was performed on the plasmid and chromosome sequence data available for bacteria belonging to the genus Acinetobacter, an ubiquitous and clinically important group of gamma-proteobacteria. Data obtained showed that, although most of the plasmids lack mobilization and transfer functions, they have probably a long history of rearrangements with other plasmids and with chromosomes. Indeed, traces of transfers between different species can be disclosed.CONCLUSIONS:We show that, by combining plasmid and chromosome similarity, identity based, network analysis, an evolutionary scenario can be described even for highly mobile genetic elements that lack extensively shared genes. In particular we found that transposases and selective pressure for mercury resistance seem to have played a pivotal role in plasmid evolution in Acinetobacter genomes sequenced so far.}},  author = {Fondi, Marco and Bacci, Giovanni and Brilli, Matteo and Papaleo, Maria and Mengoni, Alessio and Vaneechoutte, Mario and Dijkshoorn, Lenie and Fani, Renato},  citeulike-article-id = {6727387},  citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2148-10-59},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20181243},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20181243},  day = {24},  doi = {10.1186/1471-2148-10-59},  issn = {1471-2148},  journal = {BMC Evolutionary Biology},  keywords = {bacterial-biology},  month = feb,  number = {1},  pages = {59+},  pmid = {20181243},  posted-at = {2010-12-03 06:05:38},  priority = {2},  title = {{Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome}},  url = {http://dx.doi.org/10.1186/1471-2148-10-59},  volume = {10},  year = {2010}  }  @article{citeulike:8351190,  abstract = {{Despite the prevalence of Arthrobacter in the environment little is known about their plasmids, or the capacity of Arthrobacter plasmids to mediate horizontal gene transfer. In this study, we compared eight plasmids from five Arthrobacter strains in order to identify putative core maintenance genes for replication, segregation, and conjugation. Iteron like sequences were identified on some of the plasmids; however, no genes with obvious similarity to known replication sequences such as an origin of replication, or rep genes were identified. All eight plasmids contained a putative conjugation system. Genes with similarity to a relaxase, coupling protein, and various components of a type IV secretion system were identified on each plasmid; it appears that three different systems may be present. Putative parA partitioning genes were found in all of the plasmids. Each of the Arthrobacter strains examined contained a putative parB gene; however, of the three plasmids in Arthrobacter strain FB24 only one plasmid had a putative parB gene. Cluster analysis of many of the Arthrobacter genes suggested that they often formed branches within existing families of plasmid maintenance genes. Comparison of a concatenation of all the maintenance genes from each plasmid suggests that the eight Arthrobacter plasmids represent multiple evolutionary pathways.}},  author = {Jerke, K. and Nakatsu, C. and Beasley, F. and Konopka, A.},  citeulike-article-id = {8351190},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2007.12.003},  doi = {10.1016/j.plasmid.2007.12.003},  issn = {0147619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = mar,  number = {2},  pages = {73--85},  posted-at = {2010-12-03 06:02:23},  priority = {2},  title = {{Comparative analysis of eight Arthrobacter plasmids}},  url = {http://dx.doi.org/10.1016/j.plasmid.2007.12.003},  volume = {59},  year = {2008}  }  @article{citeulike:8351184,  author = {Zhou, Jizhong},  citeulike-article-id = {8351184},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1751-7915.2009.00090\_21.x},  doi = {10.1111/j.1751-7915.2009.00090\_21.x},  journal = {Microbial Biotechnology},  keywords = {bacterial-biology},  number = {2},  pages = {154--156},  posted-at = {2010-12-03 06:00:45},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{Predictive microbial ecology}},  url = {http://dx.doi.org/10.1111/j.1751-7915.2009.00090\_21.x},  volume = {2},  year = {2009}  }  @incollection{citeulike:8351179,  abstract = {{In this chapter, we present some of the biologically-inspired approaches, developed within the context of the European project BIONETS for enabling autonomic pervasive computing environments. The set of problems addressed include networking as well as service management issues. The approach pursued is based on the use of evolutionary techniques — properly embedded in the system components — as a means to achieve fully autonomic behaviour.}},  address = {Berlin, Heidelberg},  author = {Miorandi, Daniele and Carreras, Iacopo and Altman, Eitan and Yamamoto, Lidia and Chlamtac, Imrich},  booktitle = {Bio-Inspired Computing and Communication},  chapter = {20},  citeulike-article-id = {8351179},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-540-92191-2\_20},  citeulike-linkout-1 = {http://www.springerlink.com/content/e66082010m20725p},  doi = {10.1007/978-3-540-92191-2\_20},  editor = {Li\`{o}, Pietro and Yoneki, Eiko and Crowcroft, Jon and Verma, Dinesh},  isbn = {978-3-540-92190-5},  issn = {0302-9743},  keywords = {transversal},  pages = {217--228},  posted-at = {2010-12-03 05:55:49},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Bio-Inspired Approaches for Autonomic Pervasive Computing Systems}},  url = {http://dx.doi.org/10.1007/978-3-540-92191-2\_20},  volume = {5151},  year = {2008}  }  @article{citeulike:7297807,  abstract = {{A key interest of microbial ecology is to understand the role of environmental heterogeneity in shaping bacterial diversity and fitness. However, quantifying relevant selection pressures and their effects is challenging due to the number of parameters that must be considered and the multiple scales over which they act. In the current study, a model system was employed to investigate the effects of a spatially heterogeneous mercuric ion (Hg2+) selection pressure on a population comprising Hg-sensitive and Hg-resistant pseudomonads. The Hg-sensitive bacteria were Pseudomonas fluorescens SBW25::rfp and Hg-resistant bacteria were P. fluorescens SBW25 carrying a gfp-labelled, Hg resistance plasmid. In the absence of Hg, the plasmid confers a considerable fitness cost on the host, with µmax for plasmid-carrying cells relative to plasmid-free cells of only 0.66. Two image analysis techniques were developed to investigate the structure that developed in biofilms about foci of Hg (cellulose fibres imbued with HgCl2). Both techniques indicated selection for the resistant phenotype occurred only in small areas of approximately 178–353 μm (manually defined contour region analysis) or 275–350 μm (daime analysis) from foci. Hg also elicited toxic effects that reduced the growth of both Hg-sensitive and Hg-resistant bacteria up to 250 μm from foci. Selection for the Hg resistance phenotype was therefore highly localised when Hg was spatially heterogeneous. As such, for this model system, we define here the spatial scale over which selection operates. The ability to quantify changes in the strength of selection for particular phenotypes over sub-millimetre scales is useful for understanding the scale over which environmental variables affect bacterial populations.}},  author = {Slater, Frances and Bruce, Kenneth and Ellis, Richard and Lilley, Andrew and Turner, Sarah},  citeulike-article-id = {7297807},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00248-010-9687-5},  citeulike-linkout-1 = {http://www.springerlink.com/content/05308184477xt441},  day = {1},  doi = {10.1007/s00248-010-9687-5},  issn = {0095-3628},  journal = {Microbial Ecology},  keywords = {bacterial-biology},  month = nov,  number = {4},  pages = {873--884},  posted-at = {2010-12-03 05:54:40},  priority = {2},  publisher = {Springer New York},  title = {{Determining the Effects of a Spatially Heterogeneous Selection Pressure on Bacterial Population Structure at the Sub-millimetre Scale}},  url = {http://dx.doi.org/10.1007/s00248-010-9687-5},  volume = {60},  year = {2010}  }  @article{citeulike:8347480,  abstract = {{An abstract is not available.}},  address = {New York, NY, USA},  author = {King, Valerie and Saia, Jared},  citeulike-article-id = {8347480},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1855136},  citeulike-linkout-1 = {http://dx.doi.org/10.1145/1855118.1855136},  doi = {10.1145/1855118.1855136},  issn = {0163-5700},  journal = {SIGACT News},  keywords = {simulation-and-modeling},  month = sep,  pages = {89--104},  posted-at = {2010-12-02 08:40:53},  priority = {2},  publisher = {ACM},  title = {{Scalable byzantine computation}},  url = {http://dx.doi.org/10.1145/1855118.1855136},  volume = {41},  year = {2010}  }  @electronic{citeulike:7234264,  abstract = {{The developments in the communication and networking technologies have yielded many existing and envisioned information network architectures such as cognitive radio networks, sensor and actor networks, quantum communication networks, terrestrial next generation Internet, and InterPlaNetary Internet. However, there exist many common significant challenges to be addressed for the practical realization of these current and envisioned networking paradigms such as the increased complexity with large scale networks, their dynamic nature, resource constraints, heterogeneous architectures, absence or impracticality of centralized control and infrastructure, need for survivability, and unattended resolution of potential failures. These challenges have been successfully dealt with by Nature, which, as a result of millions of years of evolution, have yielded many biological systems and processes with intrinsic appealing characteristics such as adaptivity to varying environmental conditions, inherent resiliency to failures and damages, successful and collaborative operation on the basis of a limited set of rules and with global intelligence which is larger than superposition of individuals, self-organization, survivability, and evolvability. Inspired by these characteristics, many researchers are currently engaged in developing innovative design paradigms to address the networking challenges of existing and envisioned information systems. In this paper, the current stateof-the-art}},  author = {Dressler, Falko and Ozgur},  citeulike-article-id = {7234264},  citeulike-linkout-0 = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.149.6037},  keywords = {simulation-and-modeling},  posted-at = {2010-12-02 08:40:34},  priority = {2},  title = {{A Survey on Bio-inspired Networking}},  url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.149.6037}  }  @inproceedings{citeulike:8347479,  abstract = {{Autonomous networking is a challenging research area. Systems, in this case networks, are composed of many independent entities that perform a predefined task. The behavior of the global system is a result of the interaction of all the autonomous entities. The programming paradigms shift to the development of just these small entities. Self-organization is the solution for managing such environments. In this paper we demonstrate the possibilities which evolve by the application of cell biology for computer networking. With the focus on autonomous networking, the combination with methodologies known from swarm intelligence is evaluated. We show the capabilities of this combination and derive destinations and goals for self-organization in communication networks showing a more efficient and scalable behavior. Povzetek: Pregled komunikacij v avtonomnih mre\v{z}ah na osnovi biolo\v{s}kih mehanizmov. 1}},  author = {Dressler, Falko},  booktitle = {Informatica - Special Issue on Ant Colony \& Multi-Agent Systems},  citeulike-article-id = {8347479},  citeulike-linkout-0 = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.138.5613},  keywords = {simulation-and-modeling},  pages = {183--188},  posted-at = {2010-12-02 08:40:14},  priority = {2},  title = {{Efficient and Scalable Communication in Autonomous Networking using Bio-inspired Mechanisms - An Overview}},  url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.138.5613},  volume = {29},  year = {2005}  }  @article{citeulike:7511525,  abstract = {{Synthetic biology encompasses the design of new biological parts and systems as well as the modulation of existing biological networks to generate novel functions. In recent years, increasing emphasis has been placed on the engineering of population-level behaviors using cell–cell communication. From the engineering perspective, cell–cell communication serves as a versatile regulatory module that enables coordination among cells in and between populations and facilitates the generation of reliable dynamics. In addition to exploring biological 'design principles' via the construction of increasingly complex dynamics, communication-based synthetic systems can be used as well-defined model systems to study ecological and social interactions such as competition, cooperation, and predation. Here we discuss the dynamic properties of cell–cell communication modules, how they can be engineered for synthetic circuit design, and applications of these systems}},  author = {Pai, Anand and Tanouchi, Yu and Collins, Cynthia H. and You, Lingchong},  citeulike-article-id = {7511525},  citeulike-linkout-0 = {http://pubget.com/paper/19733047},  citeulike-linkout-1 = {http://www.sciencedirect.com/science?\_ob=ArticleURL\&\#38;\_udi=B6VRV-4X4Y5BR-2\&\#38;\_user=10\&\#38;\_coverDate=08/31/2009\&\#38;\_rdoc=1\&\#38;\_fmt=high\&\#38;\_orig=search\&\#38;\_sort=d\&\#38;\_docanchor=\&\#38;view=c\&\#38;\_acct=C000050221\&\#38;\_version=1\&\#38;\_urlVersion=0\&\#38;\_userid=10\&\#38;md5=ff823edecf78a2283a02efa667d2c454},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pubmed/19733047},  journal = {ScienceDirect},  keywords = {bacterial-biology},  month = sep,  posted-at = {2010-12-02 08:31:54},  priority = {2},  title = {{Engineering multicellular systems by cell–cell communication}},  url = {http://pubget.com/paper/19733047},  year = {2009}  }  @article{citeulike:8341685,  abstract = {{In this review we focus on the ecological and evolutionary forces that determine the frequency and diversity of colicins inEscherichia coli. To begin, we describe that this killing phenotype is ubiquitous inE. coli, with as many as 50\% of the isolates from a population producing colicin toxins, and that each population sampled has its own unique distribution of the more than 20 known colicin types. Next, we explore the dynamics of colicinogeny, which exhibits a typical form of frequency dependence, where the likelihood of successful colicin invasion into a population increases as the initial density of colicinogenic cells increases. We then incorporate thoughts on the evolution of chromosomal resistance to colicins and describe how resistance might influence the dynamics of colicinogen invasion and maintenance and the resulting colicin diversity. The final section deals with a genetic and phylogenetic characterization of colicins and a discussion of the evolutionary mechanisms responsible for generating colicin diversity. In this final section we provide details of the different molecular mechanisms known to play a role in generating colicin diversity, including the two most dominant forces in colincin evolution: recombination and positive, deversifying, selection.}},  author = {Riley, M. A. and Gordon, D. M.},  citeulike-article-id = {8341685},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/bf01574688},  citeulike-linkout-1 = {http://www.springerlink.com/content/lvu1k462u6628731},  day = {1},  doi = {10.1007/bf01574688},  issn = {0169-4146},  journal = {Journal of Industrial Microbiology \& Biotechnology},  keywords = {bacterial-biology},  month = sep,  number = {3},  pages = {151--158},  posted-at = {2010-12-02 08:28:40},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  title = {{The ecology and evolution of bacteriocins}},  url = {http://dx.doi.org/10.1007/bf01574688},  volume = {17},  year = {1996}  }  @article{citeulike:401226,  abstract = {{A survey of the emerging field termed †control of chaos†is given. Several major branches of research are discussed in detail: feedforward or †nonfeedback control†(based on periodic excitation of the system); †OGY method†(based on linearization of the Poincar\'{e} map), †Pyragas method†(based on a time-delay feedback), traditional control engineering methods including linear, nonlinear and adaptive control, neural networks and fuzzy control. Some unsolved problems concerning the justification of chaos control methods are presented. Other directions of active research such as chaotic mixing, chaotization, etc. are outlined. Applications in various fields of engineering are discussed.}},  citeulike-article-id = {401226},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.arcontrol.2005.01.001},  citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6V0H-4FY3P79-1/2/c7d581b31d629479432a0b9f3870f63f},  doi = {10.1016/j.arcontrol.2005.01.001},  issn = {13675788},  journal = {Annual Reviews in Control},  keywords = {simulation-and-modeling},  number = {1},  pages = {33--56},  posted-at = {2010-12-02 05:47:05},  priority = {2},  title = {{Control of chaos: Methods and applications in engineering}},  url = {http://dx.doi.org/10.1016/j.arcontrol.2005.01.001},  volume = {29},  year = {2005}  }  @incollection{citeulike:3408241,  abstract = {{We consider models of emergence, adding downward causation to conventional models where causation permeates from low-level elements to high-level behaviour. We describe an architecture and prototype simulation medium for tagging and modelling emergent features in CA-like systems. This is part of ongoing work on engineering emergence. Keyword: Cellular Automata, emergence, , simulation.}},  address = {Berlin, Heidelberg},  author = {Polack, Fiona and Stepney, Susan and Turner, Heather and Welch, Peter and Barnes, Fred},  booktitle = {Advances in Artificial Life},  chapter = {44},  citeulike-article-id = {3408241},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/11553090\_44},  citeulike-linkout-1 = {http://www.springerlink.com/content/65qrvdhaa957qk7x},  doi = {10.1007/11553090\_44},  editor = {Capcarrere, Mathieu S. and Freitas, Alex A. and Bentley, Peter J. and Johnson, Colin G. and Timmis, Jon},  isbn = {978-3-540-28848-0},  journal = {Advances in Artificial Life},  keywords = {simulation-and-modeling},  pages = {433--442},  posted-at = {2010-12-02 05:42:25},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{An Architecture for Modelling Emergence in CA-Like Systems}},  url = {http://dx.doi.org/10.1007/11553090\_44},  volume = {3630},  year = {2005}  }  @article{citeulike:2825356,  abstract = {{Complex systems can be identified by what they do (display organization without a central organizing authority — emergence), and also by how they may or may not be analysed (as decomposing the system and analysing sub-parts do not necessarily give a clue as to the behaviour of the whole). Systems that fall within the scope of complex systems include metabolic pathways, ecosystems, the web, the US power grid and the propagation of HIV infections.}},  author = {Ottino, J. M.},  citeulike-article-id = {2825356},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/427399a},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/427399a},  day = {29},  doi = {10.1038/427399a},  issn = {0028-0836},  journal = {Nature},  keywords = {simulation-and-modeling},  month = jan,  number = {6973},  pages = {399},  posted-at = {2010-12-02 05:40:28},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Engineering complex systems}},  url = {http://dx.doi.org/10.1038/427399a},  volume = {427},  year = {2004}  }  @inproceedings{citeulike:8346849,  abstract = {{We explore various definitions and characteristics of emergence, how we might recognise and measure emergence, and how we might engineer emergent systems. We discuss the TUNA (Theory Underpinning Nanotech Assemblers) project, which is investigating emergent engineering in the context of molecular nanotechnology, and use the TUNA case study to explore an architecture suitable for emergent complex systems}},  author = {Stepney, S. and Polack, F. A. C. and Turner, H. R.},  citeulike-article-id = {8346849},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/iceccs.2006.1690358},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=1690358},  doi = {10.1109/iceccs.2006.1690358},  keywords = {simulation-and-modeling},  location = {Stanford, CA, USA},  pages = {9+},  posted-at = {2010-12-02 05:39:20},  priority = {2},  title = {{Engineering emergence}},  url = {http://dx.doi.org/10.1109/iceccs.2006.1690358}  }  @electronic{citeulike:8346841,  abstract = {{Emergent behaviours are often characterised by the recurrent and recognizable events observable in a system's macro-scale environment, which result from simple local interactions between system components. Such interactions are governed by simple rule sets, which lead to complex higher-level global behaviour. Hence, engineering emergence is a necessarily subtle process subject to the impacts of system evolution with minor changes at micro-scale giving completely different outcomes, to those envisaged, at the global system level. Thus, to harness the self-organisation and emergence as a design principle for the build and management of assured and trusted systems requires a principled approach to specification and reasoning on emergence. In this paper the authors advocate the use of a formal approach/method to specify component interactions, system evolution, and runtime global states. The proposed method provides a formal specification for the engineering of known emergence and runtime deliberation on the emergence observable in the global system. 1.}},  author = {Martin, R. and Zhu, Hong and Taleb-bendiab, A.},  citeulike-article-id = {8346841},  citeulike-linkout-0 = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.68.6648},  keywords = {simulation-and-modeling},  posted-at = {2010-12-02 05:38:24},  priority = {2},  title = {{A Formal Approach to the Engineering of Emergence and its Recurrence}},  url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.68.6648}  }  @article{citeulike:8345116,  abstract = {{Lateral gene transfer has played a prominent role in bacterial evolution, but the mechanisms allowing bacteria to tolerate the acquisition of foreign DNA have been incompletely defined. Recent studies show that H-NS, an abundant nucleoid-associated protein in enteric bacteria and related species, can recognize and selectively silence the expression of foreign DNA with higher adenine and thymine content relative to the resident genome, a property that has made this molecule an almost universal regulator of virulence determinants in enteric bacteria. These and other recent findings challenge the ideas that curvature is the primary determinant recognized by H-NS and that activation of H-NS-silenced genes in response to environmental conditions occurs through a change in the structure of H-NS itself. Derepression of H-NS-silenced genes can occur at specific promoters by several mechanisms including competition with sequence-specific DNA-binding proteins, thereby enabling the regulated expression of foreign genes. The possibility that microorganisms maintain and exploit their characteristic genomic GC ratios for the purpose of self/non-self-discrimination is discussed.}},  author = {Navarre, William W. and McClelland, Michael and Libby, Stephen J. and Fang, Ferric C.},  citeulike-article-id = {8345116},  citeulike-linkout-0 = {http://dx.doi.org/10.1101/gad.1543107},  citeulike-linkout-1 = {http://genesdev.cshlp.org/content/21/12/1456.abstract},  citeulike-linkout-2 = {http://genesdev.cshlp.org/content/21/12/1456.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/17575047},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=17575047},  day = {15},  doi = {10.1101/gad.1543107},  journal = {Genes \& Development},  keywords = {bacterial-biology},  month = jun,  number = {12},  pages = {1456--1471},  pmid = {17575047},  posted-at = {2010-12-01 21:26:23},  priority = {2},  title = {{Silencing of xenogeneic DNA by H-NS - facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA}},  url = {http://dx.doi.org/10.1101/gad.1543107},  volume = {21},  year = {2007}  }  @article{citeulike:1065611,  abstract = {{The interpretation of recent environmental genomics data exposes the  far-reaching influence of horizontal gene transfer, and is changing our basic  concepts of organism, species and evolution itself.}},  archivePrefix = {arXiv},  author = {Goldenfeld, Nigel and Woese, Carl},  citeulike-article-id = {1065611},  citeulike-linkout-0 = {http://arxiv.org/abs/q-bio/0702015},  citeulike-linkout-1 = {http://arxiv.org/pdf/q-bio/0702015},  citeulike-linkout-2 = {http://dx.doi.org/10.1038/445369a},  citeulike-linkout-3 = {http://dx.doi.org/10.1038/445369a},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/17251963},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=17251963},  day = {14},  doi = {10.1038/445369a},  eprint = {q-bio/0702015},  issn = {0028-0836},  journal = {Nature},  keywords = {bacterial-biology},  month = jul,  number = {7126},  pages = {369},  pmid = {17251963},  posted-at = {2010-11-28 19:45:49},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Biology's next revolution}},  url = {http://dx.doi.org/10.1038/445369a},  volume = {445},  year = {2009}  }  @article{citeulike:8316417,  abstract = {{Type IV secretory systems are transmembrane bacterial multiprotein complexes. They are pivotal for conjugation, bacterial-induced plant tumour formation, toxin secretion and mammalian pathogen intracellular activity. These systems are involved in the spread of antibiotic resistance genes among bacteria by enabling conjugative DNA transfer. When such translocons transport DNA, they require the assistance of multimeric integral inner membrane proteins, the type IV coupling proteins. Its structural prototype is plasmid R388 TrwB protein, responsible for coupling the relaxosome with the DNA transport apparatus during bacterial conjugation. Its monomeric molecular structure is reminiscent of ring helicases and AAA ATPases. The quaternary structure is made up by six equivalent protomers featuring a flattened sphere resembling F1-ATPase, with a central channel traversing the particle, thus connecting cytoplasm and periplasm.}},  author = {Gomis-R\"{u}th, F. Xavier and de la Cruz, Fernando and Coll, Miquel},  citeulike-article-id = {8316417},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/12066890},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=12066890},  issn = {0923-2508},  journal = {Research in microbiology},  keywords = {bacterial-biology},  month = may,  number = {4},  pages = {199--204},  pmid = {12066890},  posted-at = {2010-11-28 12:37:37},  priority = {2},  title = {{Structure and role of coupling proteins in conjugal DNA transfer.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/12066890},  volume = {153},  year = {2002}  }  @article{citeulike:8316416,  abstract = {{TraG-like proteins are essential components of type IV secretion systems. During secretion, TraG is thought to translocate defined substrates through the inner cell membrane. The energy for this transport is presumably delivered by its potential nucleotide hydrolase (NTPase) activity. TraG of conjugative plasmid RP4 is a membrane-anchored oligomer that binds RP4 relaxase and DNA. TrwB (R388) is a hexameric TraG-like protein that binds ATP. Both proteins, however, lack NTPase activity under in vitro conditions. We characterized derivatives of TraG and TrwB truncated by the N-terminal membrane anchor (TraGdelta2 and TrwBdelta1) and/or containing a point mutation at the putative nucleotide-binding site (TraGdelta2K187T and TraGK187T). Unlike TraG and TrwB, truncated derivatives behaved as monomers without the tendency to form oligomers or aggregates. Surface plasmon resonance analysis with immobilized relaxase showed that mutant TraGK187T was as good a binding partner as the wild-type protein, whereas truncated TraG monomers were unable to bind relaxase. TraGdelta2 and TrwBdelta1 bound ATP and, with similar affinity, ADP. Binding of ATP and ADP was strongly inhibited by the presence of Mg(2+) or single-stranded DNA and was competed for by other nucleotides. Compared to the activity of TraGdelta2, the ATP- and ADP-binding activity of the point mutation derivative TraGdelta2K187T was significantly reduced. Each TraG derivative bound DNA with an affinity similar to that of the native protein. DNA binding was inhibited or competed for by ATP, ADP, and, most prominently, Mg(2+). Thus, both nucleotide binding and DNA binding were sensitive to Mg(2+) and were competitive with respect to each other.}},  author = {Schr\"{o}der, Gunnar and Lanka, Erich},  citeulike-article-id = {8316416},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/12867445},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=12867445},  issn = {0021-9193},  journal = {Journal of bacteriology},  keywords = {bacterial-biology},  month = aug,  number = {15},  pages = {4371--4381},  pmid = {12867445},  posted-at = {2010-11-28 12:36:29},  priority = {2},  title = {{TraG-like proteins of type IV secretion systems: functional dissection of the multiple activities of TraG (RP4) and TrwB (R388).}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/12867445},  volume = {185},  year = {2003}  }  @article{plasmid-inc,  author = {Novick, R. P.},  citeulike-article-id = {5192740},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/3325793},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=3325793},  issn = {0146-0749},  journal = {Microbiological reviews},  keywords = {bacterial-biology},  month = dec,  number = {4},  pages = {381--395},  pmid = {3325793},  posted-at = {2010-11-27 17:30:43},  priority = {2},  title = {{Plasmid incompatibility.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/3325793},  volume = {51},  year = {1987}  }  @article{citeulike:6297600,  abstract = {{Conjugative transfer of bacterial plasmids is the most efficient way of horizontal gene spread, and it is therefore considered one of the major reasons for the increase in the number of bacteria exhibiting multiple-antibiotic resistance. Thus, conjugation and spread of antibiotic resistance represents a severe problem in antibiotic treatment, especially of immunosuppressed patients and in intensive care units. While conjugation in gram-negative bacteria has been studied in great detail over the last decades, the transfer mechanisms of antibiotic resistance plasmids in gram-positive bacteria remained obscure. In the last few years, the entire nucleotide sequences of several large conjugative plasmids from gram-positive bacteria have been determined. Sequence analyses and data bank comparisons of their putative transfer (tra) regions have revealed significant similarities to tra regions of plasmids from gram-negative bacteria with regard to the respective DNA relaxases and their targets, the origins of transfer (oriT), and putative nucleoside triphosphatases NTP-ases with homologies to type IV secretion systems. In contrast, a single gene encoding a septal DNA translocator protein is involved in plasmid transfer between micelle-forming streptomycetes. Based on these clues, we propose the existence of two fundamentally different plasmid-mediated conjugative mechanisms in gram-positive microorganisms, namely, the mechanism taking place in unicellular gram-positive bacteria, which is functionally similar to that in gram-negative bacteria, and a second type that occurs in multicellular gram-positive bacteria, which seems to be characterized by double-stranded DNA transfer. 10.1128/MMBR.67.2.277-301.2003}},  author = {Grohmann, Elisabeth and Muth, Gunther and Espinosa, Manuel},  booktitle = {Microbiol. Mol. Biol. Rev.},  citeulike-article-id = {6297600},  citeulike-linkout-0 = {http://dx.doi.org/10.1128/mmbr.67.2.277-301.2003},  citeulike-linkout-1 = {http://mmbr.asm.org/cgi/content/abstract/67/2/277},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/12794193},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=12794193},  day = {1},  doi = {10.1128/mmbr.67.2.277-301.2003},  keywords = {bacterial-biology},  month = jun,  number = {2},  pages = {277--301},  pmid = {12794193},  posted-at = {2010-11-27 17:30:34},  priority = {2},  title = {{Conjugative Plasmid Transfer in Gram-Positive Bacteria}},  url = {http://dx.doi.org/10.1128/mmbr.67.2.277-301.2003},  volume = {67},  year = {2003}  }  @article{citeulike:551955,  abstract = {{Nucleotide sequence analysis, and more recently whole genome analysis, shows that bacterial evolution has often proceeded by horizontal gene flow between different species and genera. In bacteria, gene transfer takes place by transformation, transduction, or conjugation and this review examines the roles of these gene transfer processes, between different bacteria, in a wide variety of ecological niches in the natural environment. This knowledge is necessary for our understanding of plasmid evolution and ecology, as well as for risk assessment. The rise and spread of multiple antibiotic resistance plasmids in medically important bacteria are consequences of intergeneric gene transfer coupled to the selective pressures posed by the increasing use and misuse of antibiotics in medicine and animal feedstuffs. Similarly, the evolution of degradative plasmids is a response to the increasing presence of xenobiotic pollutants in soil and water. Finally, our understanding of the role of horizontal gene transfer in the environment is essential for the evaluation of the possible consequences of the deliberate environmental release of natural or recombinant bacteria for agricultural and bioremediation purposes.}},  address = {Institut National de la Recherche Agronomique, Route de Saint Cyr, Versailles, F-78026, France. [email protected]},  author = {Davison, J.},  citeulike-article-id = {551955},  citeulike-linkout-0 = {http://dx.doi.org/10.1006/plas.1999.1421},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/10489325},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=10489325},  doi = {10.1006/plas.1999.1421},  issn = {0147-619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = sep,  number = {2},  pages = {73--91},  pmid = {10489325},  posted-at = {2010-11-27 17:30:07},  priority = {2},  title = {{Genetic exchange between bacteria in the environment.}},  url = {http://dx.doi.org/10.1006/plas.1999.1421},  volume = {42},  year = {1999}  }  @article{citeulike:5184864,  abstract = {{The IncQ plasmids have a broader host-range than any other known replicating element in bacteria. Studies on the replication and conjugative mobilization of these plasmids, which have mostly been focused on the nearly identical RSF1010 and R1162, are summarized with a view to understanding how this broad host-range is achieved. Several significant features of IncQ plasmids emerge from these studies: (1) initiation of replication, involving DnaA-independent activation of the origin and a dedicated primase, is strictly host-independent. (2) The plasmids can be conjugatively mobilized by a variety of different type IV transporters, including those engaged in the secretion of proteins involved in pathogenesis. (3) Stability is insured by a combination of high copy-number and modulated gene expression to reduce metabolic load.}},  author = {Meyer, Richard},  citeulike-article-id = {5184864},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2009.05.001},  day = {22},  doi = {10.1016/j.plasmid.2009.05.001},  issn = {0147619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = sep,  number = {2},  pages = {57--70},  posted-at = {2010-11-25 17:47:54},  priority = {2},  title = {{Replication and conjugative mobilization of broad host-range IncQ plasmids}},  url = {http://dx.doi.org/10.1016/j.plasmid.2009.05.001},  volume = {62},  year = {2009}  }  @article{citeulike:2479045,  abstract = {{COSMIC-rules, an individual-based model for bacterial adaptation and evolution, has been used to study virtual transmission of plasmids within bacterial populations, in an environment varying between supportive and inhibitory. The simulations demonstrate spread of antibiotic resistance (R) plasmids, both compatible and incompatible, by the bacterial gene transfer process of conjugation. This paper describes the behaviour of virtual plasmids, their modes of exchange within bacterial populations and the impact of antibiotics, together with the rules governing plasmid transfer. Three case studies are examined: transfer of an R plasmid within an antibiotic-susceptible population, transfer of two incompatible R plasmids and transfer of two compatible R plasmids. R plasmid transfer confers antibiotic resistance on recipients. For incompatible plasmids, one or other plasmid could be maintained in bacterial cells and only that portion of the population acquiring the appropriate plasmid-encoded resistance survives exposure to the antibiotics. By contrast, the compatible plasmids transfer and mix freely within the bacterial population that survives in its entirety in the presence of the antibiotics. These studies are intended to inform models for examining adaptive evolution in bacteria. They provide proof of principle in simple systems as a platform for predicting the behaviour of bacterial populations in more complex situations, for example in response to changing environments or in multi-species bacterial assemblages.}},  address = {Department of Computer Science, Ashton Building, University of Liverpool, Liverpool L69 3BX, United Kingdom. [email protected]},  author = {Gregory, R. and Saunders, J. R. and Saunders, V. A.},  citeulike-article-id = {2479045},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.biosystems.2007.09.003},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18023962},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18023962},  doi = {10.1016/j.biosystems.2007.09.003},  issn = {0303-2647},  journal = {Biosystems},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {201--215},  pmid = {18023962},  posted-at = {2010-11-25 17:44:48},  priority = {2},  title = {{Rule-based modelling of conjugative plasmid transfer and incompatibility.}},  url = {http://dx.doi.org/10.1016/j.biosystems.2007.09.003},  volume = {91},  year = {2008}  }  @misc{citeulike:8273254,  abstract = {{Evolution is the fundamental physical process that gives rise to biological  phenomena. Yet it is widely treated as a subset of population genetics, and  thus its scope is artificially limited. As a result, the key issues of how  rapidly evolution occurs, and its coupling to ecology have not been  satisfactorily addressed and formulated. The lack of widespread appreciation  for, and understanding of, the evolutionary process has arguably retarded the  development of biology as a science, with disastrous consequences for its  applications to medicine, ecology and the global environment. This review  focuses on evolution as a problem in non-equilibrium statistical mechanics,  where the key dynamical modes are collective, as evidenced by the plethora of  mobile genetic elements whose role in shaping evolution has been revealed by  modern genomic surveys. We discuss how condensed matter physics concepts might  provide a useful perspective in evolutionary biology, the conceptual failings  of the modern evolutionary synthesis, the open-ended growth of complexity, and  the quintessentially self-referential nature of evolutionary dynamics.}},  archivePrefix = {arXiv},  author = {Goldenfeld, Nigel and Woese, Carl},  citeulike-article-id = {8273254},  citeulike-linkout-0 = {http://arxiv.org/abs/1011.4125},  citeulike-linkout-1 = {http://arxiv.org/pdf/1011.4125},  day = {18},  eprint = {1011.4125},  keywords = {bacterial-biology},  month = nov,  posted-at = {2010-11-24 18:31:25},  priority = {2},  title = {{Life is physics: evolution as a collective phenomenon far from equilibrium}},  url = {http://arxiv.org/abs/1011.4125},  year = {2010}  }  @article{citeulike:2652813,  abstract = {{Horizontal gene transfer (HGT) has played a major role in bacterial evolution and is fairly common in certain unicellular eukaryotes. However, the prevalence and importance of HGT in the evolution of multicellular eukaryotes remain unclear. Recent studies indicate that plant mitochondrial genomes are unusually active in HGT relative to all other organellar and nuclear genomes of multicellular eukaryotes. Although little about the mechanisms of plant HGT is known, several studies have implicated parasitic plants as both donors and recipients of mitochondrial genes. Most cases uncovered thus far have involved a single transferred gene per species; however, recent work has uncovered a case of massive HGT in Amborella trichopoda involving acquisition of at least a few dozen and probably hundreds of foreign mitochondrial genes. These foreign genes came from multiple donors, primarily eudicots and mosses. This review will examine the implications of such massive transfer, the potential mechanisms and consequences of plant-to-plant mitochondrial HGT in general, as well as the limited evidence for HGT in plant chloroplast and nuclear genomes.}},  address = {Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA.},  author = {Richardson, A. O. and Palmer, J. D.},  citeulike-article-id = {2652813},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/17030541},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=17030541},  issn = {0022-0957},  journal = {Journal of experimental botany},  keywords = {bacterial-biology},  number = {1},  pages = {1--9},  pmid = {17030541},  posted-at = {2010-11-24 14:51:40},  priority = {2},  title = {{Horizontal gene transfer in plants.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/17030541},  volume = {58},  year = {2007}  }  @article{citeulike:691380,  abstract = {{In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred genetic material. Such transfers have the potential to give rise to extremely dynamic genomes where a significant proportion of their coding DNA has been contributed by external sources. Because of the impact of these horizontal transfers on the ecological and pathogenic character of the recipient organisms, methods are continuously sought that are able to computationally determine which of the genes of a given genome are products of transfer events. In this paper, we introduce and discuss a novel computational method for identifying horizontal transfers that relies on a gene's nucleotide composition and obviates the need for knowledge of codon boundaries. In addition to being applicable to individual genes, the method can be easily extended to the case of clusters of horizontally transferred genes. With the help of an extensive and carefully designed set of experiments on 123 archaeal and bacterial genomes, we demonstrate that the new method exhibits significant improvement in sensitivity when compared to previously published approaches. In fact, it achieves an average relative improvement across genomes of between 11 and 41\% compared to the Codon Adaptation Index method in distinguishing native from foreign genes. Our method's horizontal gene transfer predictions for 123 microbial genomes are available online at http://cbcsrv.watson.ibm.com/HGT/.}},  address = {New York University, Computer Science New York, NY 10021, USA.},  author = {Tsirigos, A. and Rigoutsos, I.},  citeulike-article-id = {691380},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/15716310},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=15716310},  issn = {1362-4962},  journal = {Nucleic Acids Res},  keywords = {bacterial-biology},  number = {3},  pages = {922--933},  pmid = {15716310},  posted-at = {2010-11-24 14:48:16},  priority = {2},  title = {{A new computational method for the detection of horizontal gene transfer events.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/15716310},  volume = {33},  year = {2005}  }  @article{citeulike:8133718,  abstract = {{Bacteria frequently exhibit cooperative behaviors but cooperative strains are vulnerable to invasion by cheater strains that reap the benefits of cooperation but do not perform the cooperative behavior themselves. Bacterial genomes often contain mobile genetic elements such as plasmids. When a gene for cooperative behavior exists on a plasmid, cheaters can be forced to cooperate by infection with this plasmid, rescuing cooperation in a population in which mutation or migration has allowed cheaters to arise. Here we introduce a second plasmid that does not code for cooperation and show that the social dilemma repeats itself at the plasmid level in both within-patch and metapopulation scenarios, and under various scenarios of plasmid incompatibility. Our results suggest that although plasmid carriage of cooperative genes can provide a transient defense against defection in structured environments, plasmid and chromosomal defection remain the only stable strategies in an unstructured environment. We discuss our results in the light of recent bioinformatic evidence that cooperative genes are overrepresented on mobile elements. {\copyright} 2010 The Author(s). Evolution{\copyright} 2010 The Society for the Study of Evolution.}},  author = {Mc Ginty, Sorcha E. and Rankin, Daniel J. and Brown, Sam P.},  citeulike-article-id = {8133718},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1558-5646.2010.01121.x},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038327/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20825481},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20825481},  day = {1},  doi = {10.1111/j.1558-5646.2010.01121.x},  issn = {1558-5646},  journal = {Evolution; international journal of organic evolution},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {21--32},  pmcid = {PMC3038327},  pmid = {20825481},  posted-at = {2010-11-24 14:48:09},  priority = {2},  publisher = {Blackwell Publishing Inc},  title = {{Horizontal gene transfer and the evolution of bacterial cooperation.}},  url = {http://dx.doi.org/10.1111/j.1558-5646.2010.01121.x},  volume = {65},  year = {2011}  }  @article{citeulike:6593552,  abstract = {{Horizontal gene transfer is the gene exchange between different organisms or different organelles, which occurs frequently in prokaryotes. Many newly identified horizontal transfer events in eukaryotes indicates that it is a common phenomenon in all organisms. This paper describes the concept of horizontal gene transfer, the standard for judging a horizontal gene transfer events, the character, the mode, the way of horizontal gene transfer, and its impact on gene and genome evolution. The analyses of phylogenetic tree, base composition, selection pressure, intron sequence comparison, inserted special sequence, and biased nucleotide substitution are the most common methods used in previous researches. Evidence accumulated demonstrated that transposable sequences are most likely undergoing horizontal transferring. Transformation, conjugation, and transduction are the main forms of horizontal gene transfer in prokaryotes, but no clear clue was related with the mechanism of horizontal gene transfer in eukaryotes. Horizontal gene transfer plays a special role in genetic, genomic, and the biological evolution.}},  author = {Li, Zhi-Jiang J. and Li, Hai-Quan Q. and Diao, Xian-Min M.},  citeulike-article-id = {6593552},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/18779166},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=18779166},  issn = {0253-9772},  journal = {Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji},  keywords = {bacterial-biology},  month = sep,  number = {9},  pages = {1108--1114},  pmid = {18779166},  posted-at = {2010-11-24 14:47:45},  priority = {2},  title = {{[Methods for the identification of horizontal gene transfer (HGT) events and progress in related fields].}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/18779166},  volume = {30},  year = {2008}  }  @article{citeulike:7509466,  abstract = {{Integrative and conjugative elements (ICEs) are a diverse group of mobile genetic elements found in both Gram-positive and Gram-negative bacteria. These elements primarily reside in a host chromosome but retain the ability to excise and to transfer by conjugation. Although ICEs use a range of}},  author = {Wozniak, Rachel A. F. and Waldor, Matthew K.},  citeulike-article-id = {7509466},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrmicro2382},  day = {05},  doi = {10.1038/nrmicro2382},  issn = {1740-1526},  journal = {Nature Reviews Microbiology},  keywords = {bacterial-biology},  month = jul,  number = {8},  pages = {552--563},  posted-at = {2010-11-24 14:47:32},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow}},  url = {http://dx.doi.org/10.1038/nrmicro2382},  volume = {8},  year = {2010}  }  @article{rankin10,  abstract = {{Although similar to any other organism, prokaryotes can transfer genes vertically from mother cell to daughter cell, they can also exchange certain genes horizontally. Genes can move within and between genomes at fast rates because of mobile genetic elements (MGEs). Although mobile elements are fundamentally self-interested entities, and thus replicate for their own gain, they frequently carry genes beneficial for their hosts and/or the neighbours of their hosts. Many genes that are carried by mobile elements code for traits that are expressed outside of the cell. Such traits are involved in bacterial sociality, such as the production of public goods, which benefit a cell's neighbours, or the production of bacteriocins, which harm a cell's neighbours. In this study we review the patterns that are emerging in the types of genes carried by mobile elements, and discuss the evolutionary and ecological conditions under which mobile elements evolve to carry their peculiar mix of parasitic, beneficial and cooperative genes.}},  author = {Rankin, D. J. and Rocha, E. P. C. and Brown, S. P.},  citeulike-article-id = {6913895},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/hdy.2010.24},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/hdy201024a},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20332804},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20332804},  day = {24},  doi = {10.1038/hdy.2010.24},  issn = {0018-067X},  journal = {Heredity},  keywords = {bacterial-biology},  month = mar,  number = {1},  pages = {1--10},  pmid = {20332804},  posted-at = {2010-11-24 14:46:31},  priority = {2},  publisher = {Nature Publishing Group},  title = {{What traits are carried on mobile genetic elements, and why?}},  url = {http://dx.doi.org/10.1038/hdy.2010.24},  volume = {106},  year = {2010}  }  @article{citeulike:3577912,  abstract = {{In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by the ICTV nomenclature, as well as with the current tendency to classify both endogenous and exogenous retroviruses by three major classes (I, II and III). Our inference indicates that all protein domains codified by the gag-pro-pol internal region of these two groups agree in a collective presentation of a particular evolutionary history, which may be used as a main criterion to differentiate their molecular diversity in a comprehensive collection of phylogenies and non-redundant molecular profiles useful in the identification of new Ty3/Gypsy and Retroviridae species. The GyDB project is available at http://gydb.uv.es. 10.1093/nar/gkm697}},  author = {Llorens, C. and Futami, R. and Bezemer, D. and Moya, A.},  citeulike-article-id = {3577912},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkm697},  citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl\_1/D38},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17895280},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17895280},  day = {11},  doi = {10.1093/nar/gkm697},  issn = {1362-4962},  journal = {Nucl. Acids Res.},  keywords = {bacterial-biology},  month = jan,  number = {suppl\_1},  pages = {D38--46},  pmid = {17895280},  posted-at = {2010-11-24 14:46:20},  priority = {2},  title = {{The Gypsy Database (GyDB) of mobile genetic elements}},  url = {http://dx.doi.org/10.1093/nar/gkm697},  volume = {36},  year = {2008}  }  @article{citeulike:6144143,  abstract = {{The contribution of horizontal gene transfer to evolution has been controversial since it was suggested to be a force driving evolution in the microbial world. In this paper, I review the current standpoint on horizontal gene transfer in evolutionary thinking and discuss how important horizontal gene transfer is in evolution in the broad sense, and particularly in prokaryotic evolution. I review recent literature, asking, first, which processes are involved in the evolutionary success of transferred genes and, secondly, about the extent of horizontal gene transfer towards different evolutionary times. Moreover, I discuss the feasibility of reconstructing ancient phylogenetic relationships in the face of horizontal gene transfer. Finally, I discuss how horizontal gene transfer fits in the current neo-Darwinian evolutionary paradigm and conclude there is a need for a new evolutionary paradigm that includes horizontal gene transfer as well as other mechanisms in the explanation of evolution.}},  author = {Boto, Luis},  citeulike-article-id = {6144143},  citeulike-linkout-0 = {http://dx.doi.org/10.1098/rspb.2009.1679},  citeulike-linkout-1 = {http://rspb.royalsocietypublishing.org/content/early/2009/10/27/rspb.2009.1679.abstract},  citeulike-linkout-2 = {http://rspb.royalsocietypublishing.org/content/early/2009/10/27/rspb.2009.1679.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19864285},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19864285},  day = {28},  doi = {10.1098/rspb.2009.1679},  journal = {Proceedings of the Royal Society B: Biological Sciences},  keywords = {bacterial-biology},  month = oct,  number = {1683},  pages = {819--827},  pmid = {19864285},  posted-at = {2010-11-24 14:46:13},  priority = {2},  title = {{Horizontal gene transfer in evolution: facts and challenges}},  url = {http://dx.doi.org/10.1098/rspb.2009.1679},  volume = {277},  year = {2009}  }  @article{citeulike:6129403,  abstract = {{  Comparative genomics have identified two loosely defined classes of genes: widely distributed core genes that encode proteins for central functions in the cell and accessory genes that are patchily distributed across lineages and encode taxa-specific functions. Studies of microbial eukaryotes show that both categories undergo horizontal gene transfer (HGT) from prokaryotes, but also between eukaryotic organisms. Intra-domain gene transfers of most core genes seem to be relatively infrequent and therefore comparatively easy to detect using phylogenetic methods. In contrast, phylogenies of accessory genes often have complex topologies with little or no resemblance of organismal relationships typically with eukaryotes and prokaryotes intermingled, making detailed evolutionary histories difficult to interpret. Nevertheless, this suggests significant rates of gene transfer between and among the three domains of life for many of these genes, affecting a considerably diversity of eukaryotic microbes, although the current depth of taxonomic sampling usually is insufficient to pin down individual transfer events. The occurrence of intra-domain transfer among microbial eukaryotes has important implications for studies of organismal phylogeny as well as eukaryote genome evolution in general.  }},  author = {Andersson, Jan O.},  citeulike-article-id = {6129403},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-1-60327-853-9\_27},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19271202},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19271202},  citeulike-linkout-3 = {http://www.springerlink.com/content/g323633871386415},  doi = {10.1007/978-1-60327-853-9\_27},  issn = {1064-3745},  journal = {Methods in molecular biology (Clifton, N.J.)},  keywords = {bacterial-biology},  pages = {473--487},  pmid = {19271202},  posted-at = {2010-11-24 14:46:02},  priority = {2},  title = {{Horizontal gene transfer between microbial eukaryotes.}},  url = {http://dx.doi.org/10.1007/978-1-60327-853-9\_27},  volume = {532},  year = {2009}  }  @incollection{citeulike:3743753,  abstract = {{Transposable elements (TEs) are ubiquitous components of all living organisms, and in the course of their coexistence with their respective host genomes, these parasitic DNAs have played important roles in the evolution of complex genetic networks. The interaction between mobile DNAs and their host genomes are quite diverse, ranging from modifications of gene structure and regulation to alterations in general genome architecture. Thus over evolutionary time these elements can be regarded as natural molecular tools in shaping the organization, structure, and function of eukaryotic genes and genomes. Based on their intrinsic properties and features, mobile DNAs are widely applied at present as a technical †toolbox,†essential for studying a diverse spectrum of biological questions. In this chapter we aim to review both the evolutionary impact of TEs on genome evolution and their valuable and diverse methodological applications as the molecular tools presented in this book.}},  address = {New Jersey},  author = {Miller, Wolfgang J. and Capy, Pierre},  booktitle = {Mobile Genetic Elements },  citeulike-article-id = {3743753},  citeulike-linkout-0 = {http://dx.doi.org/10.1385/1-59259-755-6:001},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15020798},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15020798},  citeulike-linkout-3 = {http://www.springerlink.com/content/ltgt54532l746213},  day = {15},  doi = {10.1385/1-59259-755-6:001},  isbn = {1-59259-755-6},  issn = {1064-3745},  journal = {Mobile Genetic Elements},  keywords = {bacterial-biology},  month = mar,  pages = {1--20},  pmid = {15020798},  posted-at = {2010-11-24 14:45:55},  priority = {2},  publisher = {Humana Press},  title = {{Mobile Genetic Elements as Natural Tools for Genome Evolution}},  url = {http://dx.doi.org/10.1385/1-59259-755-6:001},  volume = {260},  year = {2004}  }  @article{citeulike:8298094,  abstract = {{Conjugation is one mechanism for intra- and inter-species horizontal gene transfer among bacteria. Conjugative elements have been instrumental in many bacterial species to face the threat of antibiotics, by allowing them to evolve and adapt to these hostile conditions. Conjugative plasmids are transferred to plasmidless recipient cells as single-stranded DNA. We used lacZ and gfp fusions to address whether conjugation induces the SOS response and the integron integrase. The SOS response controls a series of genes responsible for DNA damage repair, which can lead to recombination and mutagenesis. In this manuscript, we show that conjugative transfer of ssDNA induces the bacterial SOS stress response, unless an anti-SOS factor is present to alleviate this response. We also show that integron integrases are up-regulated during this process, resulting in increased cassette rearrangements. Moreover, the data we obtained using broad and narrow host range plasmids strongly suggests that plasmid transfer, even abortive, can trigger chromosomal gene rearrangements and transcriptional switches in the recipient cell. Our results highlight the importance of environments concentrating disparate bacterial communities as reactors for extensive genetic adaptation of bacteria.}},  author = {Baharoglu, Zeynep and Bikard, David and Mazel, Didier},  citeulike-article-id = {8298094},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pgen.1001165},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958807/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20975940},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20975940},  day = {21},  doi = {10.1371/journal.pgen.1001165},  issn = {1553-7404},  journal = {PLoS genetics},  keywords = {bacterial-biology},  month = oct,  number = {10},  pages = {e1001165+},  pmcid = {PMC2958807},  pmid = {20975940},  posted-at = {2010-11-23 22:54:55},  priority = {2},  publisher = {Public Library of Science},  title = {{Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation.}},  url = {http://dx.doi.org/10.1371/journal.pgen.1001165},  volume = {6},  year = {2010}  }  @article{citeulike:8297749,  abstract = {{The ecological aspects of the transfer and spread of mobile genetic elements (MGE) are reviewed in the context of the emerging evidence for the dominant role that horizontal gene transfer (HGT) has played in the evolutionary shaping of bacterial communities. Novel tools are described that allow a refined analysis of HGT in natural settings. The occurrence of HGT processes in soil and water, as affected by environmental factors, is then discussed. Examples are provided that illustrate how MGE can influence the behavior of microorganisms in their natural habitats. The occurrence of microorganisms as groups of cells in structured communities, such as those found in biofilms, is used as a framework in order to review the data and pose further questions on the evolutionary role and significance of contemporary gene transfer processes in nature. Selection by the environment is likely to be the dominant force in shaping the genetic make-up of bacterial communities. In fact, selective force can act as an apparent accelerator of gene transfer processes, mainly as a result of the enhancement of survival and persistence of favorably selected products of gene transfer processes (genes, metabolic pathways, microbial cells and communities). However, the current understanding of the triggering and impact of HGT in nature remains limited by our lack of understanding of the very nature and variety of the selective forces that act on microorganisms in situ. Hence, the relevant questions with respect to these triggers acting in natural habitats need to be answered using advanced approaches for studying HGT processes in nature, such as those discussed in this review.}},  author = {Vanelsas, J. and Bailey, M.},  citeulike-article-id = {8297749},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0168-6496(02)00373-2},  doi = {10.1016/s0168-6496(02)00373-2},  issn = {01686496},  journal = {FEMS Microbiology Ecology},  keywords = {bacterial-biology},  month = nov,  number = {2},  pages = {187--197},  posted-at = {2010-11-23 21:49:40},  priority = {2},  title = {{The ecology of transfer of mobile genetic elements}},  url = {http://dx.doi.org/10.1016/s0168-6496(02)00373-2},  volume = {42},  year = {2002}  }  @inbook{citeulike:8297746,  author = {Ferguson, G. and Heinemann, J.},  booktitle = {Horizontal Gene Transfer},  citeulike-article-id = {8297746},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/b978-012680126-2/50004-9},  doi = {10.1016/b978-012680126-2/50004-9},  isbn = {978-0-12-680126-2},  keywords = {bacterial-biology},  pages = {3--17},  posted-at = {2010-11-23 21:45:17},  priority = {2},  publisher = {Elsevier},  title = {{Recent History of Trans-kingdom Conjugation}},  url = {http://dx.doi.org/10.1016/b978-012680126-2/50004-9},  year = {2002}  }  @article{citeulike:8297738,  abstract = {{Abstract Bacterial conjugation is an efficient and sophisticated mechanism of DNA transfer among bacteria. While mobilizable plasmids only encode a minimal MOB machinery that allows them to be transported by other plasmids, conjugative plasmids encode a complete set of transfer genes (MOB+T4SS). The only essential ingredient of the MOB machinery is the relaxase, the protein that initiates and terminates conjugative DNA processing. In this review we compared the sequences and properties of the relaxase proteins contained in gene sequence databases. Proteins were arranged in families and phylogenetic trees constructed from the family alignments. This allowed the classification of conjugative transfer systems in six MOB families: MOBF, MOBH, MOBQ, MOBC, MOBP and MOBV . The main characteristics of each family were reviewed. The phylogenetic relationships of the coupling proteins were also analysed and resulted in phylogenies congruent to those of the cognate relaxases. We propose that the sequences of plasmid relaxases can be used for plasmid classification. We hope our effort will provide researchers with a useful tool for further mining and analysing the plasmid universe both experimentally and in silico.}},  author = {Garcill\'{a}n-Barcia, Mar\'{\i}a P. and Francia, Mar\'{\i}a V. and De La Cruz, Fernando},  citeulike-article-id = {8297738},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1574-6976.2009.00168.x},  doi = {10.1111/j.1574-6976.2009.00168.x},  journal = {FEMS Microbiology Reviews},  keywords = {bacterial-biology},  number = {3},  pages = {657--687},  posted-at = {2010-11-23 21:41:53},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{The diversity of conjugative relaxases and its application in plasmid classification}},  url = {http://dx.doi.org/10.1111/j.1574-6976.2009.00168.x},  volume = {33},  year = {2009}  }  @article{citeulike:8296637,  abstract = {{Abstract Bacterial conjugation in Gram-negative bacteria is triggered by a signal that connects the relaxosome to the coupling protein (T4CP) and transferosome, a type IV secretion system. The relaxosome, a nucleoprotein complex formed at the origin of transfer (oriT), consists of a relaxase, directed to the nic site by auxiliary DNA-binding proteins. The nic site undergoes cleavage and religation during vegetative growth, but this is converted to a cleavage and unwinding reaction when a competent mating pair has formed. Here, we review the biochemistry of relaxosomes and ponder some of the remaining questions about the nature of the signal that begins the process.}},  author = {De La Cruz, Fernando and Frost, Laura S. and Meyer, Richard J. and Zechner, Ellen L.},  citeulike-article-id = {8296637},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1574-6976.2009.00195.x},  doi = {10.1111/j.1574-6976.2009.00195.x},  journal = {FEMS Microbiology Reviews},  keywords = {bacterial-biology},  number = {1},  pages = {18--40},  posted-at = {2010-11-23 18:14:51},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{Conjugative DNA metabolism in Gram-negative bacteria}},  url = {http://dx.doi.org/10.1111/j.1574-6976.2009.00195.x},  volume = {34},  year = {2010}  }  @article{citeulike:227017,  abstract = {{Unlike eukaryotes, which evolve principally through the modification of existing genetic information, bacteria have obtained a significant proportion of their genetic diversity through the acquisition of sequences from distantly related organisms. Horizontal gene transfer produces extremely dynamic genomes in which substantial amounts of DNA are introduced into and deleted from the chromosome. These lateral transfers have effectively changed the ecological and pathogenic character of bacterial species.}},  address = {Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721-0088, USA.},  author = {Ochman, Howard and Lawrence, Jeffrey G. and Groisman, Eduardo A.},  citeulike-article-id = {227017},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/35012500},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/405299a0},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/10830951},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=10830951},  day = {18},  doi = {10.1038/35012500},  issn = {0028-0836},  journal = {Nature},  keywords = {bacterial-biology},  month = may,  number = {6784},  pages = {299--304},  pmid = {10830951},  posted-at = {2010-11-23 18:09:19},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Lateral gene transfer and the nature of bacterial innovation}},  url = {http://dx.doi.org/10.1038/35012500},  volume = {405},  year = {2000}  }  @article{citeulike:411521,  abstract = {{It has been suggested that horizontal gene transfer (HGT) is the "essence of phylogeny." In contrast, much data suggest that this is an exaggeration resulting in part from a reliance on inadequate methods to identify HGT events. In addition, the assumption that HGT is a ubiquitous influence throughout evolution is questionable. Instead, rampant global HGT is likely to have been relevant only to primitive genomes. In modern organisms we suggest that both the range and frequencies of HGT are constrained most often by selective barriers. As a consequence those HGT events that do occur most often have little influence on genome phylogeny. Although HGT does occur with important evolutionary consequences, classical Darwinian lineages seem to be the dominant mode of evolution for modern organisms.}},  address = {Department of Molecular Evolution, Evolutionary Biology Centre, University of Uppsala, S-75236 Uppsala, Sweden.},  author = {Kurland, C. G. and Canback, B. and Berg, Otto G.},  citeulike-article-id = {411521},  citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.1632870100},  citeulike-linkout-1 = {http://www.pnas.org/content/100/17/9658.full.abstract},  citeulike-linkout-2 = {http://www.pnas.org/content/100/17/9658.full.full.pdf},  citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/100/17/9658},  citeulike-linkout-4 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC187805/},  citeulike-linkout-5 = {http://view.ncbi.nlm.nih.gov/pubmed/12902542},  citeulike-linkout-6 = {http://www.hubmed.org/display.cgi?uids=12902542},  day = {19},  doi = {10.1073/pnas.1632870100},  issn = {0027-8424},  journal = {Proceedings of the National Academy of Sciences of the United States of America},  keywords = {bacterial-biology},  month = aug,  number = {17},  pages = {9658--9662},  pmcid = {PMC187805},  pmid = {12902542},  posted-at = {2010-11-23 15:55:30},  priority = {2},  title = {{Horizontal gene transfer: a critical view.}},  url = {http://dx.doi.org/10.1073/pnas.1632870100},  volume = {100},  year = {2003}  }  @article{citeulike:8296000,  abstract = {{This review explores examples of horizontal genetic transfer in eukaryotes and prokaryotes. The best understood of these involves various conserved families of transposable elements, but examples of non-transposable-element-based movement of genes or gene clusters have also been identified in prokaryotic genomes. A unifying theme is the structural and DNA-sequence homology of transposable elements from widely unrelated genomes, suggesting evolutionarily conserved mechanisms for horizontal transfer. This is reinforced by the fundamental similarity in the enzymatic mechanisms of retro viral integration (by integrases) and of transposition (by transposases). The review deals with various types of horizontal transfer, the mechanisms available for such transfer, potential barriers, and the evolutionary significance of horizontal genetic transfer.}},  author = {Krishnapillai, Viji},  citeulike-article-id = {8296000},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/bf02931763},  citeulike-linkout-1 = {http://www.springerlink.com/content/tr43755h77678776},  day = {1},  doi = {10.1007/bf02931763},  issn = {0022-1333},  journal = {Journal of Genetics},  keywords = {bacterial-biology},  month = aug,  number = {2},  pages = {219--232},  posted-at = {2010-11-23 15:44:56},  priority = {2},  publisher = {Springer India, in co-publication with Indian Academy of Sciences},  title = {{Horizontal gene transfer}},  url = {http://dx.doi.org/10.1007/bf02931763},  volume = {75},  year = {1996}  }  @article{citeulike:8295717,  abstract = {{Prokaryotic mobile elements have traditionally been classified as bacteriophages, plasmids, and transposons. We propose here a global classification of these and other bacterial and archaeal mobile elements based on their modular structure. This would allow for setting up interconnected databases where mobile elements could be stored as combinations of functional modules. Such a database would be very helpful. It would, for instance, allow for analyzing the phylogeny of individual blocks within an element, to understand how modules get associated and properly express the functions they carry in various bacterial hosts. Modules of practical importance, as for instance those that encode toxins or other virulence factors, could be identified and compared, and probes devised to test bacterial populations for the presence of such modules.}},  author = {Toussaint, Ariane and Merlin, Christophe},  citeulike-article-id = {8295717},  citeulike-linkout-0 = {http://dx.doi.org/10.1006/plas.2001.1552},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/11798283},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=11798283},  doi = {10.1006/plas.2001.1552},  issn = {0147-619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {26--35},  pmid = {11798283},  posted-at = {2010-11-23 12:07:10},  priority = {2},  title = {{Mobile elements as a combination of functional modules.}},  url = {http://dx.doi.org/10.1006/plas.2001.1552},  volume = {47},  year = {2002}  }  @article{citeulike:8295688,  abstract = {{Bacterial genomes have been viewed as collections of genes, with each gene and genome evolving more-or-less independently through the acquisition of mutational changes. This historical view has been overturned by the finding that genomes of even closely-related taxa differ widely in gene content. Yet, genomes are more than ever-shuffling collections of genes. Some genes within a genome are more transient than others, conferring a layer of phenotypic lability over a core of genotypic stability; this core decreases in size as the taxa included become increasingly diverse. In addition, some lineages no longer experience high rates of gene turnover, and gene content alters primarily through slow rates of gene loss. More importantly, the cell and molecular biology of the bacterial cell imposes constraints on chromosome composition, maintaining a stable architecture in the face of gene turnover. As a result, genomes reflect the sum of processes that introduce variability, which is then arbitrated by processes that maintain stability.}},  author = {Lawrence, Jeffrey G. and Hendrickson, Heather},  citeulike-article-id = {8295688},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.mib.2005.08.005},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16122972},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16122972},  doi = {10.1016/j.mib.2005.08.005},  issn = {1369-5274},  journal = {Current opinion in microbiology},  keywords = {bacterial-biology},  month = oct,  number = {5},  pages = {572--578},  pmid = {16122972},  posted-at = {2010-11-23 11:30:21},  priority = {2},  title = {{Genome evolution in bacteria: order beneath chaos.}},  url = {http://dx.doi.org/10.1016/j.mib.2005.08.005},  volume = {8},  year = {2005}  }  @article{citeulike:558914,  abstract = {{The various methods for detecting potential lateral gene transfer events typically uncover different sets of genes. Because the procedures used to recognize transferred genes ask different types of questions, the sets of genes identified by each procedure must be interpreted in the appropriate context. The integration of biological information, along with these analytical procedures, makes it possible to assess the total impact of lateral gene transfer on microbial genomes. Utilization of the different analytical procedures available for detecting lateral gene transfer provides the best information to assess the scope of gene transfer between microbial genomes.}},  author = {Lawrence, Jeffrey G. and Ochman, Howard},  citeulike-article-id = {558914},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0966-842x(01)02282-x},  citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6TD0-44NW0W9-1/2/baa000a6028389988bffe4ab0795d655},  day = {1},  doi = {10.1016/s0966-842x(01)02282-x},  issn = {0966842X},  journal = {Trends in Microbiology},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {1--4},  posted-at = {2010-11-22 23:25:40},  priority = {2},  title = {{Reconciling the many faces of lateral gene transfer}},  url = {http://dx.doi.org/10.1016/s0966-842x(01)02282-x},  volume = {10},  year = {2002}  }  @article{citeulike:8294771,  abstract = {{In bacteria, horizontal gene transfer (HGT) is widely recognized as the mechanism responsible for the widespread distribution of antibiotic resistance genes, gene clusters encoding biodegradative pathways and pathogenicity determinants. We propose that HGT is also responsible for speciation and sub-speciation in bacteria, and that HGT mechanisms exist in eukaryotes.}},  author = {de la Cruz, F.},  citeulike-article-id = {8294771},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0966-842x(00)01703-0},  day = {1},  doi = {10.1016/s0966-842x(00)01703-0},  issn = {0966842X},  journal = {Trends in Microbiology},  keywords = {bacterial-biology},  month = mar,  number = {3},  pages = {128--133},  posted-at = {2010-11-22 23:23:28},  priority = {2},  title = {{Horizontal gene transfer and the origin of species: lessons from bacteria}},  url = {http://dx.doi.org/10.1016/s0966-842x(00)01703-0},  volume = {8},  year = {2000}  }  @article{citeulike:4067307,  abstract = {{Abstract Bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. Besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. The horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. A significant part of the horizontal gene transfer is or has been facilitated by genomic islands (GEIs). GEIs are discrete DNA segments, some of which are mobile and others which are not, or are no longer mobile, which differ among closely related strains. A number of GEIs are capable of integration into the chromosome of the host, excision, and transfer to a new host by transformation, conjugation or transduction. GEIs play a crucial role in the evolution of a broad spectrum of bacteria as they are involved in the dissemination of variable genes, including antibiotic resistance and virulence genes leading to generation of hospital 'superbugs', as well as catabolic genes leading to formation of new metabolic pathways. Depending on the composition of gene modules, the same type of GEIs can promote survival of pathogenic as well as environmental bacteria.}},  address = {Clinical Microbiology and Infectious Diseases, Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland; Departments of Zoology and Statistics, University of Oxford, Oxford, UK; Molecular Infectious Diseases Group, The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK},  author = {Juhas, Mario and Van Der Meer, Jan R. and Gaillard, Muriel and Harding, Rosalind M. and Hood, Derek W. and Crook, Derrick W.},  citeulike-article-id = {4067307},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1574-6976.2008.00136.x},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19178566},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19178566},  citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/121495628/ABSTRACT},  doi = {10.1111/j.1574-6976.2008.00136.x},  issn = {1574-6976},  journal = {FEMS Microbiology Reviews},  keywords = {bacterial-biology},  month = mar,  number = {2},  pages = {376--393},  pmid = {19178566},  posted-at = {2010-11-22 23:06:12},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{Genomic islands: tools of bacterial horizontal gene transfer and evolution}},  url = {http://dx.doi.org/10.1111/j.1574-6976.2008.00136.x},  volume = {33},  year = {2009}  }  @article{citeulike:559157,  abstract = {{Bacteria evolve rapidly not only by mutation and rapid multiplication, but also by transfer of DNA, which can result in strains with beneficial mutations from more than one parent. Transformation involves the release of naked DNA followed by uptake and recombination. Homologous recombination and DNA-repair processes normally limit this to DNA from similar bacteria. However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition.}},  author = {Thomas, Christopher M. and Nielsen, Kaare M.},  citeulike-article-id = {559157},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrmicro1234},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrmicro1234},  day = {01},  doi = {10.1038/nrmicro1234},  issn = {1740-1526},  journal = {Nature Reviews Microbiology},  keywords = {bacterial-biology},  month = sep,  number = {9},  pages = {711--721},  posted-at = {2010-11-22 22:20:41},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria}},  url = {http://dx.doi.org/10.1038/nrmicro1234},  volume = {3},  year = {2005}  }  @article{citeulike:8294733,  abstract = {{Conjugative plasmids of Escherichia coli can mobilize DNA transmission from this bacterium to the yeast Saccharomyces cerevisiae. The process shares some of the features of conjugation between bacteria and could be evolutionarily significant in promoting trans-kingdom genetic exchange.}},  author = {Heinemann, J. A. and Sprague, G. F.},  citeulike-article-id = {8294733},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/340205a0},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/2666856},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=2666856},  day = {20},  doi = {10.1038/340205a0},  issn = {0028-0836},  journal = {Nature},  keywords = {bacterial-biology},  month = jul,  number = {6230},  pages = {205--209},  pmid = {2666856},  posted-at = {2010-11-22 22:18:29},  priority = {2},  title = {{Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast.}},  url = {http://dx.doi.org/10.1038/340205a0},  volume = {340},  year = {1989}  }  @article{citeulike:401504,  abstract = {{The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54\%) of which have functional assignments and 863 (46\%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T.maritima has the highest percentage (24\%) of genes that are most similar to archaeal genes. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.}},  address = {Institute for Genomic Research, Rockville, Maryland 20850, USA.},  author = {Nelson, Karen E. and Clayton, Rebecca A. and Gill, Steven R. and Gwinn, Michelle L. and Dodson, Robert J. and Haft, Daniel H. and Hickey, Erin K. and Peterson, Jeremy D. and Nelson, William C. and Ketchum, Karen A. and McDonald, Lisa and Utterback, Teresa R. and Malek, Joel A. and Linher, Katja D. and Garrett, Mina M. and Stewart, Ashley M. and Cotton, Matthew D. and Pratt, Matthew S. and Phillips, Cheryl A. and Richardson, Delwood and Heidelberg, John and Sutton, Granger G. and Fleischmann, Robert D. and Eisen, Jonathan A. and White, Owen and Salzberg, Steven L. and Smith, Hamilton O. and Venter, J. Craig and Fraser, Claire M.},  citeulike-article-id = {401504},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/20601},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/399323a0},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/10360571},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=10360571},  day = {27},  doi = {10.1038/20601},  issn = {0028-0836},  journal = {Nature},  keywords = {bacterial-biology},  month = may,  number = {6734},  pages = {323--329},  pmid = {10360571},  posted-at = {2010-11-22 21:46:42},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima}},  url = {http://dx.doi.org/10.1038/20601},  volume = {399},  year = {1999}  }  @article{citeulike:8294664,  abstract = {{Abstract The ecological aspects of the transfer and spread of mobile genetic elements (MGE) are reviewed in the context of the emerging evidence for the dominant role that horizontal gene transfer (HGT) has played in the evolutionary shaping of bacterial communities. Novel tools are described that allow a refined analysis of HGT in natural settings. The occurrence of HGT processes in soil and water, as affected by environmental factors, is then discussed. Examples are provided that illustrate how MGE can influence the behavior of microorganisms in their natural habitats. The occurrence of microorganisms as groups of cells in structured communities, such as those found in biofilms, is used as a framework in order to review the data and pose further questions on the evolutionary role and significance of contemporary gene transfer processes in nature. Selection by the environment is likely to be the dominant force in shaping the genetic make-up of bacterial communities. In fact, selective force can act as an apparent accelerator of gene transfer processes, mainly as a result of the enhancement of survival and persistence of favorably selected products of gene transfer processes (genes, metabolic pathways, microbial cells and communities). However, the current understanding of the triggering and impact of HGT in nature remains limited by our lack of understanding of the very nature and variety of the selective forces that act on microorganisms in situ. Hence, the relevant questions with respect to these triggers acting in natural habitats need to be answered using advanced approaches for studying HGT processes in nature, such as those discussed in this review.}},  author = {van Elsas, Jan D. and Bailey, Mark J.},  citeulike-article-id = {8294664},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1574-6941.2002.tb01008.x},  doi = {10.1111/j.1574-6941.2002.tb01008.x},  journal = {FEMS Microbiology Ecology},  keywords = {bacterial-biology},  number = {2},  pages = {187--197},  posted-at = {2010-11-22 20:44:01},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{The ecology of transfer of mobile genetic elements}},  url = {http://dx.doi.org/10.1111/j.1574-6941.2002.tb01008.x},  volume = {42},  year = {2002}  }  @article{citeulike:3091007,  abstract = {{The body plan of modular organisms is based on an indeterminate structure composed of iterated units or modules arrayed at various levels of complexity (such as leaves, twigs, and branches). Examples of modular organisms include plants and many sessile benthic invertebrates. In contrast, the body of unitary organisms is a determinate structure consisting usually of a strictly defined number of parts (such as legs or wings) established only during embryogenesis. Mobile animals are examples. Unlike that of unitary creatures, the form of a modular organism derives from a characteristic pattern of branching or budding of modules, which may remain attached or become separated to live physiologically independent lives as parts of a clone. Modular organisms tend to be sessile or passively mobile and, as genetic individuals, have the capacity for exponential increase in size. They do not necessarily undergo systemic senescence, and do not segregate somatic from germ line cells. It is argued here that bacteria are essentially modular organisms where the bacterial cell, microcolony, and macrocolony are modules of different levels of complexity analogous to modules of macroorganisms. This interpretation provides a broad conceptual basis for understanding the natural history of bacteria, and may illuminate the evolutionary origins and developmental biology of modular creatures.}},  address = {Department of Plant Pathology, University of Wisconsin, Madison 53706, USA. [email protected]},  author = {Andrews, John H.},  citeulike-article-id = {3091007},  citeulike-linkout-0 = {http://www.annualreviews.org/doi/abs/10.1146/annurev.micro.52.1.105},  citeulike-linkout-1 = {http://dx.doi.org/10.1146/annurev.micro.52.1.105},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/9891795},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=9891795},  doi = {10.1146/annurev.micro.52.1.105},  issn = {0066-4227},  journal = {Annual Review of Microbiology},  keywords = {bacterial-biology},  number = {1},  pages = {105--126},  pmid = {9891795},  posted-at = {2010-11-22 20:09:40},  priority = {2},  title = {BACTERIA AS MODULAR ORGANISMS},  url = {http://dx.doi.org/10.1146/annurev.micro.52.1.105},  volume = {52},  year = {1998}  }  @article{citeulike:8294634,  abstract = {{Most plasmids replicate only within a particular genus or family.}},  author = {Bryksin, Anton V. and Matsumura, Ichiro},  citeulike-article-id = {8294634},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0013244},  day = {8},  doi = {10.1371/journal.pone.0013244},  journal = {PLoS ONE},  keywords = {bacterial-biology},  month = oct,  number = {10},  pages = {e13244+},  posted-at = {2010-11-22 20:02:54},  priority = {2},  publisher = {Public Library of Science},  title = {{Rational Design of a Plasmid Origin That Replicates Efficiently in Both Gram-Positive and Gram-Negative Bacteria}},  url = {http://dx.doi.org/10.1371/journal.pone.0013244},  volume = {5},  year = {2010}  }  @article{citeulike:310473,  abstract = {{Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage — and avoid the dangers — of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.}},  author = {Frost, Laura S. and Leplae, Raphael and Summers, Anne O. and Toussaint, Ariane},  citeulike-article-id = {310473},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrmicro1235},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrmicro1235},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16138100},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16138100},  day = {01},  doi = {10.1038/nrmicro1235},  issn = {1740-1526},  journal = {Nat Rev Micro},  keywords = {bacterial-biology},  month = sep,  number = {9},  pages = {722--732},  pmid = {16138100},  posted-at = {2010-11-22 18:43:15},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Mobile genetic elements: the agents of open source evolution}},  url = {http://dx.doi.org/10.1038/nrmicro1235},  volume = {3},  year = {2005}  }  @article{citeulike:8293052,  abstract = {{Retrospective studies clearly indicate that mobile genetic elements (MGEs) play a major role in the in situ spread and even de novo construction of catabolic pathways in bacteria, allowing bacterial communities to rapidly adapt to new xenobiotics. The construction of novel pathways seems to occur by an assembly process that involves horizontal gene transfer: different appropriate genes or gene modules that encode different parts of the novel pathway are recruited from phylogenetically related or distant hosts into one single host. Direct evidence for the importance of catabolic MGEs in bacterial adaptation to xenobiotics stems from observed correlations between catabolic gene transfer and accelerated biodegradation in several habitats and from studies that monitor catabolic MGEs in polluted sites.}},  author = {Top, Eva M. and Springael, Dirk},  citeulike-article-id = {8293052},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/12849778},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=12849778},  issn = {0958-1669},  journal = {Current opinion in biotechnology},  keywords = {bacterial-biology},  month = jun,  number = {3},  pages = {262--269},  pmid = {12849778},  posted-at = {2010-11-22 18:42:06},  priority = {2},  title = {{The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/12849778},  volume = {14},  year = {2003}  }  @incollection{citeulike:8293045,  abstract = {{The pool of mobile genetic elements (MGE) in microbial communities consists of viruses, plasmids, and associated elements (insertion sequences, transposons, and integrons) that are either self-transmissible or use mobile plasmids and viruses as vehicles for their dissemination. This mobilome facilitates the horizontal transfer of genes that promote the evolution and adaptation of microbial communities. Efforts to characterize MGEs from microbial populations resident in a variety of ecological habitats have revealed a surprisingly novel and seemingly untapped biodiversity. To better understand the impact of horizontal gene transfer (HGT), as well as the agents that promote HGT in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of the mobilome in marine microbial communities, information on the distribution, diversity, and ecological traits of the marine mobilome is presented. In this chapter we discuss recent insights gained from different methodological approaches used to characterize the biodiversity and ecology of MGE in marine environments and their contributions to HGT. In addition, we present case studies that highlight specific HGT examples in coastal, open-ocean, and deep-sea marine ecosystems.}},  address = {Totowa, NJ},  author = {Sobecky, Patricia A. and Hazen, Tracy H.},  booktitle = {Horizontal Gene Transfer},  chapter = {25},  citeulike-article-id = {8293045},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-1-60327-853-9\_25},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19271200},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19271200},  citeulike-linkout-3 = {http://www.springerlink.com/content/u400050660184268},  doi = {10.1007/978-1-60327-853-9\_25},  editor = {Gogarten, Maria B. and Gogarten, Johann P. and Olendzenski, Lorraine C.},  isbn = {978-1-60327-852-2},  issn = {1064-3745},  journal = {Methods in molecular biology (Clifton, N.J.)},  keywords = {bacterial-biology},  pages = {435--453},  pmid = {19271200},  posted-at = {2010-11-22 18:40:59},  priority = {2},  publisher = {Humana Press},  series = {Methods in Molecular Biology},  title = {{Horizontal Gene Transfer and Mobile Genetic Elements in Marine Systems}},  url = {http://dx.doi.org/10.1007/978-1-60327-853-9\_25},  volume = {532},  year = {2009}  }  @article{citeulike:551965,  abstract = {{The European Science Foundation (ESF) funds a limited number of exploratory workshops each year that enable scientists to meet and develop plans for a program of integrated research which would benefit from a coordinated European effort. In summer 2003, the Standing Committee for Life and Environmental Sciences (LESC) sponsored such a workshop called The Horizontal Gene Pool: The Functional Role of Mobile Genetic Information--How Bacteria Perceive, Sample, and Utilize Genetic Elements in evolution and Local Adaptation. The workshop took place at St. Catherine's College, Oxford, UK. Its purpose was to identify how recent advances in the application of genomics and microbial ecology can be harnessed to determine the genetic mechanisms that underpin the biological role of the horizontal gene pool. Scientific excellence at the workshop was contributed by senior scientists and young investigators from research institutes located in nine European countries.}},  address = {Institute f\"{u}r Molekularbiologie, Biochemie, und Mikrobiologie, Universit\"{a}t Graz, Graz, Austria. [email protected]},  author = {Zechner, E. L. and Bailey, M. J.},  citeulike-article-id = {551965},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/15068024},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=15068024},  issn = {0147-619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = mar,  number = {2},  pages = {67--74},  pmid = {15068024},  posted-at = {2010-11-22 18:38:16},  priority = {2},  title = {{The Horizontal Gene Pool: an ESF workshop summary.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/15068024},  volume = {51},  year = {2004}  }  @article{citeulike:3720347,  abstract = {{Plasmids and bacteriophage represent the classical vectors for gene transfer within the horizontal gene pool. However, the more recent discovery of an increasing array of other mobile genetic elements (MGE) including genomic islands (GIs), conjugative transposons (CTns), and mobilizable transposons (MTns) which each integrate within the chromosome, offer an increasingly diverse assemblage contributing to bacterial adaptation and evolution. Molecular characterisation of these elements has revealed that they are comprised of functional modules derived from phage, plasmids, and transposons, and further that these modules are combined to generate a continuum of mosaic MGE. In particular, they are comprised of any one of three distinct types of recombinase, together with plasmid-derived transfer and mobilisation gene functions. This review highlights both the similarities and distinctions between these integrating transferable elements resulting from combination of the MGE toolbox.}},  author = {Osborn, A. Mark and B\"{o}ltner, Dietmar},  citeulike-article-id = {3720347},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/12460536},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=12460536},  issn = {0147-619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = nov,  number = {3},  pages = {202--212},  pmid = {12460536},  posted-at = {2010-11-22 18:37:57},  priority = {2},  title = {{When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/12460536},  volume = {48},  year = {2002}  }  @article{citeulike:988488,  abstract = {{  Horizontal plasmid transfer plays a key role in bacterial adaptation. In harsh environments, bacterial populations adapt by sampling genetic material from a horizontal gene pool through self-transmissible plasmids, and that allows persistence of these mobile genetic elements. In the absence of selection for plasmid-encoded traits it is not well understood if and how plasmids persist in bacterial communities. Here we present three models of the dynamics of plasmid persistence in the absence of selection. The models consider plasmid loss (segregation), plasmid cost, conjugative plasmid transfer, and observation error. Also, we present a stochastic model in which the relative fitness of the plasmid-free cells was modeled as a random variable affected by an environmental process using a hidden Markov model (HMM). Extensive simulations showed that the estimates from the proposed model are nearly unbiased. Likelihood-ratio tests showed that the dynamics of plasmid persistence are strongly dependent on the host type. Accounting for stochasticity was necessary to explain four of seven time-series data sets, thus confirming that plasmid persistence needs to be understood as a stochastic process. This work can be viewed as a conceptual starting point under which new plasmid persistence hypotheses can be tested.  }},  address = {University of Idaho.},  author = {Ponciano, Jos\'{e} M. and De Gelder, Leen and Top, Eva M. and Joyce, Paul},  citeulike-article-id = {988488},  citeulike-linkout-0 = {http://dx.doi.org/10.1534/genetics.106.061937},  citeulike-linkout-1 = {http://www.genetics.org/cgi/content/abstract/176/2/957},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894622/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/17151258},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=17151258},  day = {1},  doi = {10.1534/genetics.106.061937},  issn = {0016-6731},  journal = {Genetics},  keywords = {bacterial-biology},  month = jun,  number = {2},  pages = {957--968},  pmcid = {PMC1894622},  pmid = {17151258},  posted-at = {2010-11-22 18:37:51},  priority = {2},  title = {{The population biology of bacterial plasmids: a hidden Markov model approach.}},  url = {http://dx.doi.org/10.1534/genetics.106.061937},  volume = {176},  year = {2007}  }  @article{citeulike:8292861,  abstract = {{Summary 10.1002/9781444313741.ch2.abs This chapter contains sections titled: * Essential plasmid functions * Plasmids and prokaryote evolution * Structural fluidity of plasmid genomes * Where do plasmids come from?}},  author = {Summers, David K.},  booktitle = {The Biology of Plasmids},  citeulike-article-id = {8292861},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/9781444313741.ch2},  doi = {10.1002/9781444313741.ch2},  keywords = {bacterial-biology},  pages = {20--30},  posted-at = {2010-11-22 18:07:36},  priority = {2},  publisher = {Blackwell Publishing Ltd.},  title = {{The Unity of Plasmid Biology}},  url = {http://dx.doi.org/10.1002/9781444313741.ch2},  year = {2009}  }  @article{citeulike:8292860,  abstract = {{Summary 10.1002/9781444313741.ch1.abs This chapter contains sections titled: * Early plasmid research * Plasmid-encoded phenotypes * Plasmid classification * The structure and organization of plasmids * The preparation of plasmid DNA * Plasmid anatomy revisited}},  author = {Summers, David K.},  booktitle = {The Biology of Plasmids},  citeulike-article-id = {8292860},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/9781444313741.ch1},  doi = {10.1002/9781444313741.ch1},  keywords = {bacterial-biology},  pages = {1--19},  posted-at = {2010-11-22 18:06:48},  priority = {2},  publisher = {Blackwell Publishing Ltd.},  title = {{The Anatomy of Bacterial Plasmids}},  url = {http://dx.doi.org/10.1002/9781444313741.ch1},  year = {2009}  }  @incollection{citeulike:8292859,  abstract = {{In 1952, Joshua Lederberg coined the term plasmid to describe any bacterial genetic element that exists in an extrachromosomal state for at least part of its replication cycle (1). As this description included bacterial viruses, the definition of what constitutes a plasmid was subsequently refined to describe exclusively or predominantly extrachromosomal genetic elements that replicate autonomously. Plasmids are now known to be present in most species of Eubacteria that have been examined, as well as in Archaea and lower Eukarya (2).}},  author = {Hayes, Finbarr},  booktitle = {\<i\>E. coli\</i\> Plasmid Vectors},  citeulike-article-id = {8292859},  citeulike-linkout-0 = {http://dx.doi.org/10.1385/1-59259-409-3:1},  citeulike-linkout-1 = {http://www.springerlink.com/content/l5x3u11n278r68jq},  citeulike-linkout-2 = {http://www.springerprotocols.com/Abstract/doi/10.1385/1-59259-409-3:1},  doi = {10.1385/1-59259-409-3:1},  editor = {Casali,, Nicola and Preston,, Andrew},  keywords = {bacterial-biology},  pages = {1--17},  posted-at = {2010-11-22 18:05:43},  priority = {2},  publisher = {Humana Press},  series = {Methods in Molecular Biology},  title = {{The Function and Organization of Plasmids}},  url = {http://dx.doi.org/10.1385/1-59259-409-3:1},  volume = {235},  year = {2003}  }  @article{citeulike:8292687,  author = {Carattoli, Alessandra},  citeulike-article-id = {8292687},  citeulike-linkout-0 = {http://dx.doi.org/10.1128/aac.01707-08},  citeulike-linkout-1 = {http://aac.asm.org/cgi/content/abstract/53/6/2227},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19307361},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19307361},  day = {1},  doi = {10.1128/aac.01707-08},  journal = {Antimicrobial Agents and Chemotherapy},  keywords = {bacterial-biology},  month = jun,  number = {6},  pages = {2227--2238},  pmid = {19307361},  posted-at = {2010-11-22 17:22:19},  priority = {2},  title = {{Resistance Plasmid Families in Enterobacteriaceae}},  url = {http://dx.doi.org/10.1128/aac.01707-08},  volume = {53},  year = {2009}  }  @article{citeulike:7179176,  abstract = {{The conjugative transfer system of Yersinia enterocolitica 29930 present on the cryptic plasmid p29930 comprises a mating pore formation system (Mpf) related to that of the IncX plasmid R6K and a DNA transfer and replication system (Dtr) with close relationship to the mob region of the mobilizable plasmid CloDF13. Two regions of the transfer system were selected for more detailed analyses of basic functions of conjugative transfer. The putative open reading frame orf22 located in the Mpf region confers the entry exclusion phenotype to possible recipient cells and inhibited conjugative transfer, when it was inserted into the coding region of the cat gene of pACYC184 in sense direction. Mobilization experiments with recombinant plasmids revealed that a 611 bp fragment of the Dtr region containing two repeat sequences were required for a functional oriT by the conjugation system of Y. enterocolitica. While the conjugative transfer of cryptic plasmids harbouring the complete conjugation system had not been demonstrated previously, plasmid pBK17 containing the functional oriT was successfully mobilized from Y. enterocolitica strains into Escherichia coli, thus proving that the transfer system could contribute to the spread of these plasmids in nature.}},  author = {Kraushaar, Britta and Appel, Bernd and Lanka, Erich and Strauch, Eckhard},  citeulike-article-id = {7179176},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2010.05.001},  day = {12},  doi = {10.1016/j.plasmid.2010.05.001},  issn = {0147619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = sep,  number = {2},  pages = {79--84},  posted-at = {2010-11-22 17:11:15},  priority = {2},  title = {{Entry exclusion and oriT of a conjugative system encoded by the cryptic plasmid p29930 of Yersinia enterocolitica}},  url = {http://dx.doi.org/10.1016/j.plasmid.2010.05.001},  volume = {64},  year = {2010}  }  @article{citeulike:8292610,  abstract = {{Bacterial plasmids are exemplary subjects for study, being conveniently isolated, dissected, reassembled, and introduced into various hosts. Their versatility and power make them eminently worthy of our attention. In what follows I consider some consequences of simply doubling the dosage of particular plasmid genes or of forming a plasmid dimer. These consequences can be perverse, paradoxical, or informative. They bear on questions of cell viability, copy number limitation, clonal homogeneity, check-point control, and the recovery of mutants. They have relevance to biotechnology, evolution and medicine. In reviewing these effects, my motivation is largely to share my enthusiasm for certain kinds of biological narratives, the nature of which is best left for the reader to discern.}},  author = {Yarmolinsky, Michael B.},  citeulike-article-id = {8292610},  citeulike-linkout-0 = {http://dx.doi.org/10.1046/j.1365-2958.2000.02127.x},  doi = {10.1046/j.1365-2958.2000.02127.x},  journal = {Molecular Microbiology},  keywords = {bacterial-biology},  number = {1},  pages = {1--7},  posted-at = {2010-11-22 16:23:45},  priority = {2},  publisher = {Blackwell Science Ltd},  title = {{A pot-pourri of plasmid paradoxes: effects of a second copy}},  url = {http://dx.doi.org/10.1046/j.1365-2958.2000.02127.x},  volume = {38},  year = {2000}  }  @inproceedings{citeulike:8283573,  abstract = {{We developed and implemented two highly optimized optimistic discrete event simulation techniques based on an efficient and scalable Parallel Heap data structure as a global event queue. The primary results are (i) the design of an optimistic simulation algorithm, namely SyncSim, which does not rely on traditional state and message saving data structures, but employs only one backup state per state variable, (ii) a demonstration, through implementation of SyncSim, of an optimistic technique which overcomes the two main mutually conflicting and unbounded overheads of the existing optimistic simulation algorithms: SyncSim bounds the additional space requirements to just one copy per state variable and drastically limits the number of rollbacks encountered. Furthermore, SyncSim beats the highly optimized traditional simulator simglobal on a wide variety of large networks on an Origin-2000 computer. The algorithm SyncSim could form a basis for a good parallelizing engine attachable relatively easily to an existing serial simulator.}},  author = {Prasad, Sushil K. and Cao, Zhiyong},  booktitle = {Proceedings of the 35th conference on Winter simulation: driving innovation},  citeulike-article-id = {8283573},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1030933},  isbn = {0-7803-8132-7},  keywords = {simulation-and-modeling},  location = {New Orleans, Louisiana},  pages = {872--880},  posted-at = {2010-11-20 13:18:48},  priority = {2},  publisher = {Winter Simulation Conference},  series = {WSC '03},  title = {{Parallel distributed simulation and modeling methods: SyncSim: a synchronous simple optimistic simulation technique based on a global parallel heap event queue}},  url = {http://portal.acm.org/citation.cfm?id=1030933},  year = {2003}  }  @article{citeulike:7252351,  abstract = {{This is a brief review of the current situation concerning practical pseudorandom number generation for Monte Carlo calculations. The conclusion is that pseudorandom number generators with the required properties are now available, but the generators actually used are often not good enough. Portable Fortran code is given for three different pseudorandom number generators, all of which have much better properties than any of the traditional generators commonly supplied in most program libraries.}},  author = {James, F.},  citeulike-article-id = {7252351},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/0010-4655(90)90032-v},  doi = {10.1016/0010-4655(90)90032-v},  issn = {00104655},  journal = {Computer Physics Communications},  keywords = {simulation-and-modeling},  month = oct,  number = {3},  pages = {329--344},  posted-at = {2010-11-17 17:15:01},  priority = {2},  title = {{A review of pseudorandom number generators}},  url = {http://dx.doi.org/10.1016/0010-4655(90)90032-v},  volume = {60},  year = {1990}  }  @article{citeulike:7746727,  abstract = {{Summary: Plasmids are key vectors of horizontal gene transfer and essential genetic engineering tools. They code for genes involved in many aspects of microbial biology, including detoxication, virulence, ecological interactions, and antibiotic resistance. While many studies have decorticated the mechanisms of mobility in model plasmids, the identification and characterization of plasmid mobility from genome data are unexplored. By reviewing the available data and literature, we established a computational protocol to identify and classify conjugation and mobilization genetic modules in 1,730 plasmids. This allowed the accurate classification of proteobacterial conjugative or mobilizable systems in a combination of four mating pair formation and six relaxase families. The available evidence suggests that half of the plasmids are nonmobilizable and that half of the remaining plasmids are conjugative. Some conjugative systems are much more abundant than others and preferably associated with some clades or plasmid sizes. Most very large plasmids are nonmobilizable, with evidence of ongoing domestication into secondary chromosomes. The evolution of conjugation elements shows ancient divergence between mobility systems, with relaxases and type IV coupling proteins (T4CPs) often following separate paths from type IV secretion systems. Phylogenetic patterns of mobility proteins are consistent with the phylogeny of the host prokaryotes, suggesting that plasmid mobility is in general circumscribed within large clades. Our survey suggests the existence of unsuspected new relaxases in archaea and new conjugation systems in cyanobacteria and actinobacteria. Few genes, e.g., T4CPs, relaxases, and VirB4, are at the core of plasmid conjugation, and together with accessory genes, they have evolved into specific systems adapted to specific physiological and ecological contexts.}},  author = {Smillie, Chris and Garcill\'{a}n-Barcia, M. Pilar and Francia, M. Victoria and Rocha, Eduardo P. C. and de la Cruz, Fernando},  citeulike-article-id = {7746727},  citeulike-linkout-0 = {http://dx.doi.org/10.1128/mmbr.00020-10},  citeulike-linkout-1 = {http://mmbr.asm.org/content/74/3/434.abstract},  citeulike-linkout-2 = {http://mmbr.asm.org/content/74/3/434.full.pdf},  citeulike-linkout-3 = {http://mmbr.asm.org/cgi/content/abstract/74/3/434},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/20805406},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=20805406},  day = {1},  doi = {10.1128/mmbr.00020-10},  issn = {1098-5557},  journal = {Microbiology and Molecular Biology Reviews},  keywords = {bacterial-biology},  month = sep,  number = {3},  pages = {434--452},  pmid = {20805406},  posted-at = {2010-11-17 16:42:38},  priority = {0},  publisher = {American Society for Microbiology},  title = {{Mobility of Plasmids}},  url = {http://dx.doi.org/10.1128/mmbr.00020-10},  volume = {74},  year = {2010}  }  @article{citeulike:7100429,  abstract = {{Abstract Plasmid-mediated horizontal gene transfer influences bacterial community structure and evolution. However, an understanding of the forces which dictate the fate of plasmids in bacterial populations remains elusive. This is in part due to the enormous diversity of plasmids, in terms of size, structure, transmission, evolutionary history and accessory phenotypes, coupled with the lack of a standard theoretical framework within which to investigate them. This review discusses how ecological factors, such as spatial structure and temporal fluctuations, shape both the population dynamics and the physical features of plasmids. Novel data indicate that larger plasmids are more likely to be harboured by hosts in complex environments. Plasmid size may therefore be determined by environmentally mediated fitness trade-offs. As the correlation between replicon size and complexity of environment is similar for plasmids and chromosomes, plasmids could be used as tractable tools to investigate the influence of ecological factors on chromosomes. Parallels are drawn between plasmids and bacterial facultative symbionts, including the evolution of some members of both groups to a more obligate relationship with their host. The similarity between the influences of ecological factors on plasmids and bacterial symbionts suggests that it may be appropriate to study plasmids within a classical ecological framework.}},  address = {The Centre for Ecology and Hydrology, Oxford, UK; King's College London, Pharmaceutical Sciences Research Division, London, UK},  author = {Slater, Frances R. and Bailey, Mark J. and Tett, Adrian J. and Turner, Sarah L.},  citeulike-article-id = {7100429},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1574-6941.2008.00505.x},  citeulike-linkout-1 = {http://www3.interscience.wiley.com/cgi-bin/abstract/120121792/ABSTRACT},  doi = {10.1111/j.1574-6941.2008.00505.x},  issn = {1574-6941},  journal = {FEMS Microbiology Ecology},  keywords = {bacterial-biology},  number = {1},  pages = {3--13},  posted-at = {2010-11-17 16:37:01},  priority = {0},  publisher = {Blackwell Publishing Ltd},  title = {{Progress towards understanding the fate of plasmids in bacterial communities}},  url = {http://dx.doi.org/10.1111/j.1574-6941.2008.00505.x},  volume = {66},  year = {2008}  }  @article{citeulike:8217073,  abstract = {{A wide variety of loss-of-function mutations are observed in BioBrick-assembled genetic circuits including point mutations, small insertions and deletions, large deletions, and insertion sequence (IS) element insertions that often occur in the scar sequence between parts. Promoter mutations are selected for more than any other biological part. Genetic circuits can be re-engineered to be more evolutionary robust with a few simple design principles: high expression of genetic circuits comes with the cost of low evolutionary stability, avoid repeated sequences, and the use of inducible promoters increases stability. Inclusion of an antibiotic resistance gene within the circuit does not ensure evolutionary stability.}},  author = {Sleight, Sean C. and Bartley, Bryan A. and Lieviant, Jane A. and Sauro, Herbert M.},  citeulike-article-id = {8217073},  citeulike-linkout-0 = {http://dx.doi.org/10.1186/1754-1611-4-12},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/21040586},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=21040586},  doi = {10.1186/1754-1611-4-12},  issn = {1754-1611},  journal = {Journal of biological engineering},  keywords = {synbio-dna},  number = {1},  pages = {12+},  pmid = {21040586},  posted-at = {2010-11-07 21:41:04},  priority = {2},  title = {{Designing and engineering evolutionary robust genetic circuits.}},  url = {http://dx.doi.org/10.1186/1754-1611-4-12},  volume = {4},  year = {2010}  }  @article{citeulike:7762620,  abstract = {{BACKGROUND:Positive feedback is a common mechanism used in the regulation of many gene circuits as it can amplify the response to inducers and also generate binary outputs and hysteresis. In the context of electrical circuit design, positive feedback is often considered in the design of amplifiers. Similar approaches, therefore, may be used for the design of amplifiers in synthetic gene circuits with applications, for example, in cell-based sensors.RESULTS:We developed a modular positive feedback circuit that can function as a genetic signal amplifier, heightening the sensitivity to inducer signals as well as increasing maximum expression levels without the need for an external cofactor. The design utilizes a constitutively active, autoinducer-independent variant of the quorum-sensing regulator LuxR. We experimentally tested the ability of the positive feedback module to separately amplify the output of a one-component tetracycline sensor and a two-component aspartate sensor. In each case, the positive feedback module amplified the response to the respective inducers, both with regards to the dynamic range and sensitivity.CONCLUSIONS:The advantage of our design is that the actual feedback mechanism depends only on a single gene and does not require any other modulation. Furthermore, this circuit can amplify any transcriptional signal, not just one encoded within the circuit or tuned by an external inducer. As our design is modular, it can potentially be used as a component in the design of more complex synthetic gene circuits.}},  author = {Nistala, Goutam and Wu, Kang and Rao, Christopher and Bhalerao, Kaustubh},  citeulike-article-id = {7762620},  citeulike-linkout-0 = {http://dx.doi.org/10.1186/1754-1611-4-4},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20187959},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20187959},  doi = {10.1186/1754-1611-4-4},  issn = {1754-1611},  journal = {Journal of Biological Engineering},  keywords = {synbio-dna},  number = {1},  pages = {4+},  pmid = {20187959},  posted-at = {2010-11-07 20:37:04},  priority = {2},  title = {{A modular positive feedback-based gene amplifier}},  url = {http://dx.doi.org/10.1186/1754-1611-4-4},  volume = {4},  year = {2010}  }  @article{citeulike:7817856,  abstract = {{State diagrams (stategraphs) are suitable for describing the behavior of dynamic systems. However, when they are used to model large and complex systems, determining the states and transitions among them can be overwhelming, due to their flat, unstratified structure. In this article, we present the use of statecharts as a novel way of modeling complex gene networks. Statecharts extend conventional state diagrams with features such as nested hierarchy, recursion, and concurrency. These features are commonly utilized in engineering for designing complex systems and can enable us to model complex gene networks in an efficient and systematic way. We modeled five key gene network motifs, simple regulation, autoregulation, feed-forward loop, single-input module, and dense overlapping regulon, using statecharts. Specifically, utilizing nested hierarchy and recursion, we were able to model a complex interlocked feed-forward loop network in a highly structured way, demonstrating the potential of our approach for modeling large and complex gene networks.}},  author = {Shin, Yong-Jun and Nourani, Mehrdad},  citeulike-article-id = {7817856},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0009376},  day = {23},  doi = {10.1371/journal.pone.0009376},  journal = {PLoS ONE},  keywords = {synbio-dna},  month = feb,  number = {2},  pages = {e9376+},  posted-at = {2010-11-05 11:37:29},  priority = {2},  publisher = {Public Library of Science},  title = {{Statecharts for Gene Network Modeling}},  url = {http://dx.doi.org/10.1371/journal.pone.0009376},  volume = {5},  year = {2010}  }  @inproceedings{citeulike:3210356,  abstract = {{The program system JCASim is a general-purpose system for simulating cellular automata in Java. It includes a stand-alone application and an applet for web presentations. The cellular automata can be specified in Java, in CDL, or using an interactive dialogue. The system supports many different lattice geometries (1-D, 2-D square, hexagonal, triangular, 3-D), neighborhoods, boundary conditions, and can display the cells using colors, text, or icons. We use three kinds of cellular automata for reaction-diffusion systems to demonstrate the wide applicability of the simulation system. These are microscopic block-CA, reactive lattice gas CA, and macroscopic CA related to finite difference methods. }},  author = {Weimar, J\"{o}rg R.},  booktitle = {Discrete Modelling and Discrete Algorithms in Continuum Mechanics},  citeulike-article-id = {3210356},  citeulike-linkout-0 = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.16.9227},  keywords = {simulation-and-modeling},  pages = {217--226},  posted-at = {2010-11-04 16:15:24},  priority = {2},  title = {{Simulating reaction-diffusion cellular automata with JCASim}},  url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.16.9227},  year = {2001}  }  @article{citeulike:7847175,  abstract = {{Summary: Computational pipelines are common place in scientific research. However, most of the resources for constructing pipelines are heavyweight systems with graphical user interfaces. Ruffus is a library for the creation of computational pipelines. Its lightweight and unobtrusive design recommends it for use even for the most trivial of analyses. At the same time, it is powerful enough to have been used for complex workflows involving more than 50 interdependent stages.}},  author = {Goodstadt, Leo},  citeulike-article-id = {7847175},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btq524},  citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/26/21/2778.abstract},  citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/26/21/2778.full.pdf},  citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/21/2778},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/20847218},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=20847218},  day = {01},  doi = {10.1093/bioinformatics/btq524},  issn = {1460-2059},  journal = {Bioinformatics},  month = nov,  number = {21},  pages = {2778--2779},  pmid = {20847218},  posted-at = {2010-11-04 06:29:21},  priority = {2},  publisher = {Oxford University Press},  title = {{Ruffus: a lightweight Python library for computational pipelines}},  url = {http://dx.doi.org/10.1093/bioinformatics/btq524},  volume = {26},  year = {2010}  }  @article{citeulike:305755,  abstract = {{Collaborative tagging describes the process by which many users add metadata  in the form of keywords to shared content. Recently, collaborative tagging has  grown in popularity on the web, on sites that allow users to tag bookmarks,  photographs and other content. In this paper we analyze the structure of  collaborative tagging systems as well as their dynamical aspects. Specifically,  we discovered regularities in user activity, tag frequencies, kinds of tags  used, bursts of popularity in bookmarking and a remarkable stability in the  relative proportions of tags within a given url. We also present a dynamical  model of collaborative tagging that predicts these stable patterns and relates  them to imitation and shared knowledge.}},  archivePrefix = {arXiv},  author = {Golder, Scott and Huberman, Bernardo A.},  citeulike-article-id = {305755},  citeulike-linkout-0 = {http://arxiv.org/abs/cs.DL/0508082},  citeulike-linkout-1 = {http://arxiv.org/pdf/cs.DL/0508082},  day = {18},  eprint = {cs.DL/0508082},  keywords = {transversal},  month = aug,  posted-at = {2010-11-03 16:41:46},  priority = {2},  title = {{The Structure of Collaborative Tagging Systems}},  url = {http://arxiv.org/abs/cs.DL/0508082},  year = {2005}  }  @article{citeulike:481248,  abstract = {{Coupled biological and chemical systems, neural networks, social interacting species, the Internet and the World Wide Web, are only a few examples of systems composed by a large number of highly interconnected dynamical units. The first approach to capture the global properties of such systems is to model them as graphs whose nodes represent the dynamical units, and whose links stand for the interactions between them. On the one hand, scientists have to cope with structural issues, such as characterizing the topology of a complex wiring architecture, revealing the unifying principles that are at the basis of real networks, and developing models to mimic the growth of a network and reproduce its structural properties. On the other hand, many relevant questions arise when studying complex networks' dynamics, such as learning how a large ensemble of dynamical systems that interact through a complex wiring topology can behave collectively. We review the major concepts and results recently achieved in the study of the structure and dynamics of complex networks, and summarize the relevant applications of these ideas in many different disciplines, ranging from nonlinear science to biology, from statistical mechanics to medicine and engineering.}},  author = {Boccaletti, S. and Latora, V. and Moreno, Y. and Chavez, M. and Hwang, D.},  citeulike-article-id = {481248},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.physrep.2005.10.009},  citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6TVP-4J0WTM2-1/2/739f254d99ff14ca96565d3d34a6d77a},  doi = {10.1016/j.physrep.2005.10.009},  issn = {03701573},  journal = {Physics Reports},  keywords = {transversal},  month = feb,  number = {4-5},  pages = {175--308},  posted-at = {2010-11-03 16:40:38},  priority = {2},  title = {{Complex networks: Structure and dynamics}},  url = {http://dx.doi.org/10.1016/j.physrep.2005.10.009},  volume = {424},  year = {2006}  }  @article{citeulike:1263124,  author = {Bourne, Philip E.},  citeulike-article-id = {1263124},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.0030077},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17500596},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17500596},  day = {27},  doi = {10.1371/journal.pcbi.0030077},  issn = {1553-7358},  journal = {PLoS Comput Biol},  keywords = {transversal},  month = apr,  number = {4},  pages = {e77+},  pmid = {17500596},  posted-at = {2010-11-03 16:38:41},  priority = {2},  publisher = {Public Library of Science},  title = {{Ten Simple Rules for Making Good Oral Presentations}},  url = {http://dx.doi.org/10.1371/journal.pcbi.0030077},  volume = {3},  year = {2007}  }  @article{citeulike:2492402,  abstract = {{Principal component analysis is often incorporated into genome-wide expression studies, but what is it and how can it be used to explore high-dimensional data? Several measurement techniques used in the life sciences gather data for many more variables per sample than the typical number of samples assayed. For instance, DNA microarrays and mass spectrometers can measure levels of thousands of mRNAs or proteins in hundreds of samples.}},  author = {Ringn\'{e}r, Markus},  citeulike-article-id = {2492402},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt0308-303},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt0308-303},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18327243},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18327243},  day = {01},  doi = {10.1038/nbt0308-303},  issn = {1546-1696},  journal = {Nature biotechnology},  keywords = {transversal},  month = mar,  number = {3},  pages = {303--304},  pmid = {18327243},  posted-at = {2010-11-03 16:38:10},  priority = {2},  publisher = {Nature Publishing Group},  title = {{What is principal component analysis?}},  url = {http://dx.doi.org/10.1038/nbt0308-303},  volume = {26},  year = {2008}  }  @article{citeulike:1022846,  abstract = {{The current practice in multiagent systems typically associates the environment with resources that are external to agents and their communication infrastructure. Advanced uses of the environment include infrastructures for indirect coordination, such as digital pheromones, or support for governed interaction in electronic institutions. Yet, in general, the notion of environment is not well defined. Functionalities of the environment are often dealt with implicitly or in an ad hoc manner. This is not only poor engineering practice, it also hinders engineers to exploit the full potential of the environment in multiagent systems. In this paper, we put forward the environment as an explicit part of multiagent systems.We give a definition stating that the environment in a multiagent system is a first-class abstraction with dual roles: (1) the environment provides the surrounding conditions for agents to exist, which implies that the environment is an essential part of every multiagent system, and (2) the environment provides an exploitable design abstraction for building multiagent system applications. We discuss the responsibilities of such an environment in multiagent systems and we present a reference model for the environment that can serve as a basis for environment engineering. To illustrate the power of the environment as a design abstraction, we show how the environment is successfully exploited in a real world application. Considering the environment as a first-class abstraction in multiagent systems opens up new horizons for research and development in multiagent systems.}},  author = {Weyns, Danny and Omicini, Andrea and Odell, James},  citeulike-article-id = {1022846},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s10458-006-0012-0},  citeulike-linkout-1 = {http://www.ingentaconnect.com/content/klu/agnt/2007/00000014/00000001/00000012},  citeulike-linkout-2 = {http://www.springerlink.com/content/w571550106301124},  day = {1},  doi = {10.1007/s10458-006-0012-0},  issn = {1387-2532},  journal = {Autonomous Agents and Multi-Agent Systems},  keywords = {simulation-and-modeling},  month = feb,  number = {1},  pages = {5--30},  posted-at = {2010-11-03 07:10:04},  priority = {2},  publisher = {Springer Netherlands},  title = {{Environment as a first class abstraction in multiagent systems}},  url = {http://dx.doi.org/10.1007/s10458-006-0012-0},  volume = {14},  year = {2007}  }  @article{citeulike:8031501,  abstract = {{A situation is an abstraction for a pattern of observations made by a distributed system such as a sensor network. Situations have previously been studied in different domains, as composite events in distributed event based systems, service composition in multi-agent systems, and macro-programming in sensor networks. However, existing languages do not address the specific challenges posed by sensor networks. This article presents a novel language for representing situations in sensor networks that addresses these challenges. Three algorithms for recognizing situations in relevant fields are reviewed and adapted to sensor networks. In particular, distributed commitment machines are introduced and demonstrated to be the most suitable algorithm among the three for recognizing situations in sensor networks.}},  author = {Cardell-Oliver, Rachel and Liu, Wei},  citeulike-article-id = {8031501},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/mcom.2010.5434382},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=5434382},  doi = {10.1109/mcom.2010.5434382},  issn = {0163-6804},  journal = {IEEE Communications Magazine},  keywords = {simulation-and-modeling},  month = mar,  number = {3},  pages = {112--117},  posted-at = {2010-11-03 07:08:44},  priority = {2},  title = {{Representation and recognition of situations in sensor networks}},  url = {http://dx.doi.org/10.1109/mcom.2010.5434382},  volume = {48},  year = {2010}  }  @inproceedings{citeulike:8183517,  abstract = {{The DPC algorithm developed in our previous work is an efficient way of computing optimal trajectories for multiple robots in a distributed fashion with time-parameterized constraints on the distances between pairs of robots. In the present work we extend DPC to the problem of multiple task execution. While this extended problem inherits all the objectives, complexities and constraints of the basic DPC algorithm, each robot is also given an unordered set of tasks that it has to execute before it reaches its goal. There is no specific order imposed on the tasks assigned to a particular robot. The algorithm decides the order of execution of the tasks such that an optimal solution is attained while the time-parametrized distance constraints are satisfied along with successful execution of the tasks. We solve this problem by designing a †State-task Graph†that represents a product of the state-space graph and the task graph. We then develop an efficient heuristic function for performing searches in this graph.}},  author = {Bhattacharya, Subhrajit and Likhachev, Maxim and Kumar, Vijay},  citeulike-article-id = {8183517},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/robot.2010.5509713},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=5509713},  doi = {10.1109/robot.2010.5509713},  keywords = {simulation-and-modeling},  location = {Anchorage, AK, USA},  month = may,  pages = {953--959},  posted-at = {2010-11-03 07:07:59},  priority = {2},  title = {{Multi-agent path planning with multiple tasks and distance constraints}},  url = {http://dx.doi.org/10.1109/robot.2010.5509713},  year = {2010}  }  @inproceedings{Yamins:2008:AGP:1402298.1402310,  address = {Richland, SC},  author = {Yamins, Daniel and Nagpal, Radhika},  booktitle = {Proceedings of the 7th international joint conference on Autonomous agents and multiagent systems - Volume 2},  citeulike-article-id = {8183515},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1402298.1402310},  location = {Estoril, Portugal},  pages = {615--622},  posted-at = {2010-11-03 07:07:12},  priority = {2},  publisher = {International Foundation for Autonomous Agents and Multiagent Systems},  series = {AAMAS '08},  title = {{Automated global-to-local programming in 1-D spatial multi-agent systems}},  url = {http://portal.acm.org/citation.cfm?id=1402298.1402310},  year = {2008}  }  @phdthesis{Yamins:2008:TLA:1467941,  address = {Cambridge, MA, USA},  author = {Yamins, Daniel},  citeulike-article-id = {8183483},  comment = {AAI3312578},  keywords = {simulation-and-modeling},  posted-at = {2010-11-03 07:02:38},  priority = {2},  publisher = {Harvard University},  title = {{A theory of local-to-global algorithms for one-dimensional spatial multi-agent systems}},  year = {2008}  }  @inproceedings{Chen:2007:SDA:1357910.1358062,  address = {San Diego, CA, USA},  author = {Chen, Chih-Chun and Nagl, Sylvia B. and Clack, Christopher D.},  booktitle = {Proceedings of the 2007 summer computer simulation conference},  citeulike-article-id = {8183439},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1357910.1358062},  keywords = {simulation-and-modeling},  location = {San Diego, California},  pages = {969--976},  posted-at = {2010-11-03 06:58:36},  priority = {2},  publisher = {Society for Computer Simulation International},  series = {SCSC},  title = {{Specifying, detecting and analysing emergent behaviours in multi-level agent-based simulations}},  url = {http://portal.acm.org/citation.cfm?id=1357910.1358062},  year = {2007}  }  @incollection{citeulike:7960006,  abstract = {{A method is proposed, which is intended for constructing a probabilistic cellular automaton (CA), whose evolution simulates a spatially distributed process, given by a PDE. The heart of the method is the transformation of a real spatial function into a Boolean array whose averaged form approximates the given function. Two parts of a given PDE (a differential operator and a function) are approximated by a combination of their Boolean counterparts. The resulting CA transition function has a basic (standard) part, modeling the differential operator and the updating part modifying it according to the function value. Special attention is paid to the reaction-diffusion type of PDE. Some experimental results of simple processes simulation are given and perspectives of the proposed method application are discussed.}},  address = {Berlin, Heidelberg},  author = {Bandman, Olga},  booktitle = {Cellular Automata},  chapter = {2},  citeulike-article-id = {7960006},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/3-540-45830-1\_2},  citeulike-linkout-1 = {http://www.springerlink.com/content/6chv7rtk46vc87qc},  day = {26},  doi = {10.1007/3-540-45830-1\_2},  editor = {Bandini, Stefania and Chopard, Bastien and Tomassini, Marco},  isbn = {978-3-540-44304-9},  keywords = {simulation-and-modeling},  month = sep,  pages = {10--19},  posted-at = {2010-11-02 21:36:34},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Simulating Spatial Dynamics by Probabilistic Cellular Automata}},  url = {http://dx.doi.org/10.1007/3-540-45830-1\_2},  volume = {2493},  year = {2002}  }  @article{citeulike:7054290,  abstract = {{Engineering biological systems and organisms is a costly team effort and may be incompatible with an open-source regulatory environment, finds Michael A. Goldman. By focusing his book only on those biological components that can be combined as if they were Lego bricks, Robert Carlson ignores much of biology. Nevertheless, in Biology is Technology, he presents an informative view of the future prospects for biotechnology and its regulation.}},  author = {Goldman, Michael A.},  citeulike-article-id = {7054290},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/4641129a},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/4641129a},  day = {21},  doi = {10.1038/4641129a},  issn = {0028-0836},  journal = {Nature},  keywords = {system-biology},  month = apr,  number = {7292},  pages = {1129--1130},  posted-at = {2010-11-02 21:35:17},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Building life from the bottom up}},  url = {http://dx.doi.org/10.1038/4641129a},  volume = {464},  year = {2010}  }  @article{citeulike:5842862,  abstract = {{Choosing good problems is essential for being a good scientist. But what is a good problem, and how do you choose one? The subject is not usually discussed explicitly within our profession. Scientists are expected to be smart enough to figure it out on their own and through the observation of their teachers. This lack of explicit discussion leaves a vacuum that can lead to approaches such as choosing problems that can give results that merit publication in valued journals, resulting in a job and tenure.}},  author = {Alon, Uri},  citeulike-article-id = {5842862},  citeulike-linkout-0 = {http://www.cell.com/molecular-cell/abstract/S1097-2765(09)00641-8},  citeulike-linkout-1 = {http://dx.doi.org/10.1016/j.molcel.2009.09.013},  citeulike-linkout-2 = {http://www.f1000.com/1165779},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19782018},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19782018},  day = {24},  doi = {10.1016/j.molcel.2009.09.013},  issn = {10972765},  journal = {Molecular Cell},  keywords = {transversal},  month = sep,  number = {6},  pages = {726--728},  pmid = {19782018},  posted-at = {2010-11-02 21:33:41},  priority = {0},  publisher = {Cell Press},  title = {{How To Choose a Good Scientific Problem}},  url = {http://dx.doi.org/10.1016/j.molcel.2009.09.013},  volume = {35},  year = {2009}  }  @incollection{citeulike:8180470,  abstract = {{Cells of the embryonic vertebrate limb in high-density culture undergo chondrogenic pattern formation, which results in the formation of regularly spaced islands of cartilage analogous to the cartilage primordia of the developing limb skeleton. In this chapter a discrete, multiscale agent-based stochastic model is described, which is based on an extended cell representation coupled with biologically motivated reaction-diffusion processes and cell-matrix adhesion, for studying the behavior of limb bud precartilage mesenchymal cells. The model is calibrated using experimental data, and the sensitivity of key parameters is studied.}},  address = {Boston, MA},  author = {Christley, Scott and Newman, Stuart A. and Alber, Mark S.},  booktitle = {Mathematical Modeling of Biological Systems, Volume I},  chapter = {13},  citeulike-article-id = {8180470},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-0-8176-4558-8\_13},  citeulike-linkout-1 = {http://www.springerlink.com/content/r2295x47j670gm31},  doi = {10.1007/978-0-8176-4558-8\_13},  editor = {Deutsch,, Andreas and Brusch,, Lutz and Byrne,, Helen and Vries,, Gerda e. and Herzel,, Hanspeter},  isbn = {978-0-8176-4557-1},  keywords = {simulation-and-modeling},  pages = {149--161},  posted-at = {2010-11-02 17:57:52},  priority = {2},  publisher = {Birkh\"{a}user Boston},  series = {Modeling and Simulation in Science, Engineering and Technology},  title = {{Agent-Based Model for Developmental Pattern Formation with Multiscale Dynamics and Varying Cell Geometry}},  url = {http://dx.doi.org/10.1007/978-0-8176-4558-8\_13},  year = {2007}  }  @article{citeulike:8180447,  author = {Macal, C. M. and North, M. J.},  citeulike-article-id = {8180447},  citeulike-linkout-0 = {http://dx.doi.org/10.1057/jos.2010.3},  doi = {10.1057/jos.2010.3},  issn = {1747-7778},  keywords = {simulation-and-modeling},  month = sep,  number = {3},  pages = {151--162},  posted-at = {2010-11-02 17:54:12},  priority = {2},  publisher = {Operational Research Society},  title = {{Tutorial on agent-based modelling and simulation}},  url = {http://dx.doi.org/10.1057/jos.2010.3},  volume = {4},  year = {2010}  }  @inproceedings{citeulike:8180418,  abstract = {{The AGRE model proposed by Ferber et al. is based on an interesting generalization of both physical and social environments. In this paper we revisit the AGRE model and extend it with richer social concepts such as powers, norms and a dependency relationship which is similar to the count as operator introduced by Searle to describe the construction of social reality. Our main contribution consists in the fact that we attribute to the environment the main role in describing and controlling (social) interaction.}},  address = {Berlin, Heidelberg},  author = {Jos\'{e} Antonio B\'{a}ez Barranco and Stratulat, Tiberiu and Ferber, Jacques},  booktitle = {E4MAS'06: Proceedings of the 3rd international conference on Environments for multi-agent systems III},  citeulike-article-id = {8180418},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1759346},  isbn = {978-3-540-71102-5},  keywords = {simulation-and-modeling},  location = {Hakodate, Japan},  pages = {41--50},  posted-at = {2010-11-02 17:49:20},  priority = {2},  publisher = {Springer-Verlag},  title = {{A unified model for physical and social environments}},  url = {http://portal.acm.org/citation.cfm?id=1759346},  year = {2007}  }  @incollection{citeulike:8180299,  abstract = {{In this paper, we introduce the GAMA (Gis \& Agent-based Modelling Architecture) simulation platform, which aims at providing field experts, modellers, and computer scientists with a complete modelling and simulation development environment for building spatially explicit multi-agent simulations. The most important requirements of spatially explicit multi-agent simulations that our platform fulfils are: (1) the ability to transparently use complex Geographical Information System (GIS) data as an environment for the agents; (2) the ability to handle a vast number of (heterogeneous) agents (3); the ability to offer a platform for automated controlled experiments (by automatically varying parameters, recording statistics, etc.); (4) the possibility to let non-computer scientists design models and interact with the agents during simulations. While still in its implementation phase, the platform is currently used for two main applications. One is about the modelling of the spread of avian influenza in a province of North Vietnam in collaboration with CIRAD (French Agricultural Research Centre working for International Development). Its goal is to simulate the poultry value chain of a whole province using geolocalised data, and to use this to optimise a monitoring network. A second application conducted with the Institute for Marine Geology and Geophysics (VAST, Hanoi) is about using an interactive simulation for supporting decision-making during urban post-disaster situations. This application relies on geolocalised data as well, and requires facilities of interaction between users and the simulation.}},  address = {Berlin, Heidelberg},  author = {Amouroux, Edouard and Chu, Thanh-Quang and Boucher, Alain and Drogoul, Alexis},  booktitle = {Agent Computing and Multi-Agent Systems},  chapter = {32},  citeulike-article-id = {8180299},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-01639-4\_32},  citeulike-linkout-1 = {http://www.springerlink.com/content/88006131542n1204},  doi = {10.1007/978-3-642-01639-4\_32},  editor = {Ghose, Aditya and Governatori, Guido and Sadananda, Ramakoti},  isbn = {978-3-642-01638-7},  keywords = {simulation-and-modeling},  pages = {359--371},  posted-at = {2010-11-02 17:47:17},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{GAMA: An Environment for Implementing and Running Spatially Explicit Multi-agent Simulations}},  url = {http://dx.doi.org/10.1007/978-3-642-01639-4\_32},  volume = {5044},  year = {2009}  }  @article{citeulike:1022842,  abstract = {{Real environments in which agents operate are inherently dynamic—the environment changes beyond the agents' control. We advocate that, for multi-agent simulation, this dynamism must be modeled explicitly as part of the simulated environment, preferably using concepts and constructs that relate to the real world. In this paper, we describe such concepts and constructs, and we provide a formal framework to unambiguously specify their relations and meaning. We apply the formal framework to model a dynamic RoboCup Soccer environment and elaborate on how the framework poses new challenges for exploring the modeling of environments in multi-agent simulation.}},  author = {Helleboogh, Alexander and Vizzari, Giuseppe and Uhrmacher, Adelinde and Michel, Fabien},  citeulike-article-id = {1022842},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s10458-006-0014-y},  citeulike-linkout-1 = {http://www.ingentaconnect.com/content/klu/agnt/2007/00000014/00000001/00000014},  citeulike-linkout-2 = {http://www.springerlink.com/content/f17gq312307v8264},  day = {1},  doi = {10.1007/s10458-006-0014-y},  issn = {1387-2532},  journal = {Autonomous Agents and Multi-Agent Systems},  keywords = {simulation-and-modeling},  month = feb,  number = {1},  pages = {87--116},  posted-at = {2010-11-02 17:40:37},  priority = {2},  publisher = {Springer Netherlands},  title = {{Modeling dynamic environments in multi-agent simulation}},  url = {http://dx.doi.org/10.1007/s10458-006-0014-y},  volume = {14},  year = {2007}  }  @article{citeulike:8179048,  abstract = {{  Conjugative plasmids of Gram-negative bacteria have both vertical and horizontal modes of transmission: they are segregated to daughter cells during division, and transferred between hosts by plasmid-encoded conjugative machinery. Despite maintaining horizontal mobility, many plasmids carry fertility inhibition (fin) systems that repress their own conjugative transfer. To assess the ecological basis of self-transfer repression, we compared the invasion of bacterial populations by fin(+) and fin(-) variants of the plasmid R1 using a computational model and co-culture competitions. We observed that the fin(+) variant had a modest cost to the host (measured by reduction in growth rate), while the fin(-) variant incurred a larger cost. In simulations and empirical competitions the fin(-) plasmid invaded cultures quickly, but was subsequently displaced by the fin(+) plasmid. This indicated a competitive advantage to reducing horizontal transmission and allowing increased host replication. Computational simulations predicted that the advantage associated with reduced cost to the host would be maintained over a wide range of environmental conditions and plasmid costs. We infer that vertical transmission in concert with competitive exclusion favour decreased horizontal mobility of plasmids. Similar dynamics may exert evolutionary pressure on parasites, such as temperate bacteriophages and vertically transmitted animal viruses, to limit their rates of horizontal transfer.  }},  author = {Haft, Rembrandt J. and Mittler, John E. and Traxler, Beth},  citeulike-article-id = {8179048},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/ismej.2009.22},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/ismej200922a},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19340086},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19340086},  day = {02},  doi = {10.1038/ismej.2009.22},  issn = {1751-7370},  journal = {The ISME journal},  keywords = {bacterial-biology},  month = jul,  number = {7},  pages = {761--769},  pmid = {19340086},  posted-at = {2010-11-02 16:31:55},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Competition favours reduced cost of plasmids to host bacteria.}},  url = {http://dx.doi.org/10.1038/ismej.2009.22},  volume = {3},  year = {2009}  }  @article{citeulike:3564461,  abstract = {{In spite of the importance of plasmids in bacterial adaptation, we have a poor understanding of their dynamics. It is not known if or how plasmids persist in and spread through (invade) a bacterial population when there is no selection for plasmid-encoded traits. Moreover, the differences in dynamics between spatially structured and mixed populations are poorly understood. Through a joint experimental/theoretical approach, we tested the hypothesis that self-transmissible IncP-1 plasmids can invade a bacterial population in the absence of selection when initially very rare, but only in spatially structured habitats and when nutrients are regularly replenished. Using protocols that differed in the degree of spatial structure and nutrient levels, the invasiveness of plasmid pB10 in Escherichia coli was monitored during at least 15 days, with an initial fraction of plasmid-bearing (p+) cells as low as 10−7. To further explore the mechanisms underlying plasmid dynamics, we developed a spatially explicit mathematical model. When cells were grown on filters and transferred to fresh medium daily, the p+ fraction increased to 13\%, whereas almost complete invasion occurred when the population structure was disturbed daily. The plasmid was unable to invade in liquid. When carbon source levels were lower or not replenished, plasmid invasion was hampered. Simulations of the mathematical model closely matched the experimental results and produced estimates of the effects of alternative experimental parameters. This allowed us to isolate the likely mechanisms most responsible for the observations. In conclusion, spatial structure and nutrient availability can be key determinants in the invasiveness of plasmids.}},  author = {Fox, Randal E. and Zhong, Xue and Krone, Stephen M. and Top, Eva M.},  citeulike-article-id = {3564461},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/ismej.2008.53},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/ismej200853a},  day = {05},  doi = {10.1038/ismej.2008.53},  issn = {1751-7362},  journal = {The ISME Journal},  keywords = {bacterial-biology},  month = jun,  number = {10},  pages = {1024--1039},  posted-at = {2010-11-02 16:31:08},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations}},  url = {http://dx.doi.org/10.1038/ismej.2008.53},  volume = {2},  year = {2008}  }  @article{citeulike:8175810,  abstract = {{A microorganism has to adapt to changing environmental conditions in order to survive. Cells could follow one of two basic strategies to address such environmental fluctuations. On the one hand, cells could anticipate a fluctuating environment by spontaneously generating a phenotypically diverse population of cells, with each subpopulation exhibiting different capacities to flourish in the different conditions. Alternatively, cells could sense changes in the surrounding conditions - such as temperature, nutritional availability or the presence of other individuals - and modify their behavior to provide an appropriate response to that information. As we describe, examples of both strategies abound among different microorganisms. Moreover, successful application of either strategy requires a level of memory and information processing that has not been normally associated with single cells, suggesting that such organisms do in fact have the capacity to 'think'.}},  author = {Ramanathan, S. and Broach, J. R.},  citeulike-article-id = {8175810},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00018-007-7001-6},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17530173},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17530173},  doi = {10.1007/s00018-007-7001-6},  issn = {1420-682X},  journal = {Cellular and molecular life sciences : CMLS},  keywords = {bacterial-biology},  month = jul,  number = {14},  pages = {1801--1804},  pmid = {17530173},  posted-at = {2010-11-02 13:11:22},  priority = {2},  title = {{Do cells think?}},  url = {http://dx.doi.org/10.1007/s00018-007-7001-6},  volume = {64},  year = {2007}  }  @inproceedings{citeulike:7355642,  abstract = {{In this tutorial we present techniques for building valid and credible simulation models. Ideas to be discussed include the importance of a definitive problem formulation, discus- sions with subject-matter experts, interacting with the deci- sion-maker on a regular basis, development of a written conceptual model, structured walk-through of the concep- tual model, use of sensitivity analysis to determine impor- tant model factors, and comparison of model and system output data for an existing system (if any). Each idea will be illustrated by one or more real-world examples. We will also discuss the difficulty in using formal statistical techniques (e.g., confidence intervals) to validate simula- tion models.}},  author = {Law, Averill M.},  booktitle = {Proceedings of the 2005 Winter Simulation Conference},  citeulike-article-id = {7355642},  editor = {Kuhl, M. E. and Steiger, N. M. and Armstrong, F. B. and Joines, J. A.},  keywords = {simulation-and-modeling},  location = {Baltimore, US},  pages = {24--32},  posted-at = {2010-11-01 18:51:27},  priority = {2},  title = {{How to build valid and credible simulation models}},  year = {2005}  }  @article{citeulike:2080311,  abstract = {{Evolutionary processes generating biodiversity and ecological mechanisms maintaining biodiversity seem to be diverse themselves. Conventional explanations of biodiversity such as niche differentiation, density-dependent predation pressure, or habitat heterogeneity seem satisfactory to explain diversity in communities of macrobial organisms such as higher plants and animals. For a long time the often high diversity among microscopic organisms in seemingly uniform environments, the famous †paradox of the plankton,†has been difficult to understand. The biodiversity in bacterial communities has been shown to be sometimes orders of magnitudes higher than the diversity of known macrobial systems. Based on a spatially explicit game theoretical model with multiply cyclic dominance structures, we suggest that antibiotic interactions within microbial communities may be very effective in maintaining diversity.}},  author = {Cz\'{a}r\'{a}n, Tam\'{a}s L. and Hoekstra, Rolf F. and Pagie, Ludo},  citeulike-article-id = {2080311},  citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.012399899},  citeulike-linkout-1 = {http://www.pnas.org/content/99/2/786.abstract},  citeulike-linkout-2 = {http://www.pnas.org/content/99/2/786.full.pdf},  citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/99/2/786},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/11792831},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=11792831},  day = {22},  doi = {10.1073/pnas.012399899},  journal = {Proceedings of the National Academy of Sciences of the United States of America},  keywords = {bacterial-biology},  month = jan,  number = {2},  pages = {786--790},  pmid = {11792831},  posted-at = {2010-10-28 17:37:51},  priority = {2},  title = {{Chemical warfare between microbes promotes biodiversity}},  url = {http://dx.doi.org/10.1073/pnas.012399899},  volume = {99},  year = {2002}  }  @article{citeulike:8137322,  abstract = {{Simple combinations of common competitive mechanisms can easily result in cyclic competitive dominance relationships between species. The topological features of such competitive networks allow for complex spatial coexistence patterns. We investigate self-organization and coexistence in a lattice model, describing the spatial population dynamics of competing bacterial strains. With increasing diffusion rate the community of the nine possible toxicity/resistance types undergoes two phase transitions. Below a critical level of diffusion, the system exhibits expanding domains of three different defensive alliances, each consisting of three cyclically dominant species. Due to the neutral relationship between these alliances and the finite system size effect, ultimately only one of them remains. At large diffusion rates the system admits three coexisting domains, each containing mutually neutral species. Because of the cyclical dominance between these domains, a long term stable coexistence of all species is ensured. In the third phase at intermediate diffusion the spatial structure becomes even more complicated with domains of mutually neutral species persisting along the borders of defensive alliances. The study reveals that cyclic competitive relationships may produce a large variety of complex coexistence patterns, exhibiting common features of natural ecosystems, like hierarchical organization, phase transitions and sudden, large-scale fluctuations.}},  author = {Szab\'{o}, P\'{e}ter and Cz\'{a}r\'{a}n, Tam\'{a}s and Szab\'{o}, Gy\"{o}rgy},  citeulike-article-id = {8137322},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jtbi.2007.06.022},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17686495},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17686495},  day = {21},  doi = {10.1016/j.jtbi.2007.06.022},  issn = {0022-5193},  journal = {Journal of theoretical biology},  keywords = {bacterial-biology},  month = oct,  number = {4},  pages = {736--744},  pmid = {17686495},  posted-at = {2010-10-28 17:37:42},  priority = {2},  title = {{Competing associations in bacterial warfare with two toxins.}},  url = {http://dx.doi.org/10.1016/j.jtbi.2007.06.022},  volume = {248},  year = {2007}  }  @article{citeulike:8131697,  abstract = {{Evolutionary microbiology is a basic science that is increasingly forming the basis for new developments in public-health microbiology. Medical advances might depend on an understanding of the conditions that are required for the emergence and maintenance of human bacterial pathogens. An understanding of the evolutionary engineering rules that lead to virulence or drug resistance — specifically with bacteria in mind — are therefore important and are examined in this article.}},  author = {Baquero, Fernando},  citeulike-article-id = {8131697},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrmicro909},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrmicro909},  day = {01},  doi = {10.1038/nrmicro909},  issn = {1740-1526},  journal = {Nature Reviews Microbiology},  keywords = {bacterial-biology},  month = jun,  number = {6},  pages = {510--518},  posted-at = {2010-10-27 19:59:21},  priority = {2},  publisher = {Nature Publishing Group},  title = {{From pieces to patterns: evolutionary engineering in bacterial pathogens}},  url = {http://dx.doi.org/10.1038/nrmicro909},  volume = {2},  year = {2004}  }  @article{citeulike:419283,  abstract = {{Transformation and conjugation permit the passage of DNA through the bacterial membranes and represent dominant modes for the transfer of genetic information between bacterial cells or between bacterial and eukaryotic cells. As such, they are responsible for the spread of fitness-enhancing traits, including antibiotic resistance. Both processes usually involve the recognition of double-stranded DNA, followed by the transfer of single strands. Elaborate molecular machines are responsible for negotiating the passage of macromolecular DNA through the layers of the cell surface. All or nearly all the machine components involved in transformation and conjugation have been identified, and here we present models for their roles in DNA transport.}},  author = {Chen, In\^{e}s and Christie, Peter J. and Dubnau, David},  citeulike-article-id = {419283},  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1114021},  citeulike-linkout-1 = {http://www.sciencemag.org/cgi/content/abstract/310/5753/1456},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16322448},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16322448},  day = {2},  doi = {10.1126/science.1114021},  issn = {1095-9203},  journal = {Science (New York, N.Y.)},  keywords = {bacterial-biology},  month = dec,  number = {5753},  pages = {1456--1460},  pmid = {16322448},  posted-at = {2010-10-27 19:59:08},  priority = {2},  title = {{The ins and outs of DNA transfer in bacteria.}},  url = {http://dx.doi.org/10.1126/science.1114021},  volume = {310},  year = {2005}  }  @article{citeulike:6930514,  abstract = {{Stochastic profiling, a method to rank heterogeneity of gene expression in a cell population, shows that quantifying cell-to-cell variability has come of age and leads to biological insight.}},  author = {Quaranta, Vito and Garbett, Shawn P.},  citeulike-article-id = {6930514},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nmeth0410-269},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nmeth0410-269},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20354516},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20354516},  day = {01},  doi = {10.1038/nmeth0410-269},  issn = {1548-7105},  journal = {Nature methods},  keywords = {bacterial-biology},  month = apr,  number = {4},  pages = {269--272},  pmid = {20354516},  posted-at = {2010-10-24 10:13:10},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Not all noise is waste.}},  url = {http://dx.doi.org/10.1038/nmeth0410-269},  volume = {7},  year = {2010}  }  @article{citeulike:4546087,  abstract = {{10.1093/bioinformatics/btp274}},  author = {Bateman, Alex and Wood, Matt},  citeulike-article-id = {4546087},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp274},  citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/25/12/1475.abstract},  citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/25/12/1475.full.pdf},  citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/12/1475?etoc},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19435745},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19435745},  day = {15},  doi = {10.1093/bioinformatics/btp274},  issn = {1460-2059},  journal = {Bioinformatics},  keywords = {transversal},  month = jun,  number = {12},  pages = {1475},  pmid = {19435745},  posted-at = {2010-10-24 10:11:18},  priority = {2},  publisher = {Oxford University Press},  title = {{Cloud computing}},  url = {http://dx.doi.org/10.1093/bioinformatics/btp274},  volume = {25},  year = {2009}  }  @article{citeulike:3469180,  author = {Ben-Hur, Asa and Ong, Cheng Soon S. and Sonnenburg, S\"{o}ren and Sch\"{o}lkopf, Bernhard and R\"{a}tsch, Gunnar},  citeulike-article-id = {3469180},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000173},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2547983/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18974822},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18974822},  day = {31},  doi = {10.1371/journal.pcbi.1000173},  issn = {1553-7358},  journal = {PLoS computational biology},  keywords = {transversal},  month = oct,  number = {10},  pages = {e1000173+},  pmcid = {PMC2547983},  pmid = {18974822},  posted-at = {2010-10-24 10:10:54},  priority = {2},  publisher = {Public Library of Science},  title = {{Support vector machines and kernels for computational biology.}},  url = {http://dx.doi.org/10.1371/journal.pcbi.1000173},  volume = {4},  year = {2008}  }  @article{citeulike:6766639,  abstract = {{A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants) are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are used to assign parameter values that minimize some measure of the error between these measurements and the corresponding model prediction. The measurements, which can come from immunoblotting assays, fluorescent markers, etc., tend to be very noisy and taken at a limited number of time points. In this work we present a new approach to the problem of parameter selection of biological models. We show how one can use a dynamic recursive estimator, known as extended Kalman filter, to arrive at estimates of the model parameters. The proposed method follows. First, we use a variation of the Kalman filter that is particularly well suited to biological applications to obtain a first guess for the unknown parameters. Secondly, we employ an a posteriori identifiability test to check the reliability of the estimates. Finally, we solve an optimization problem to refine the first guess in case it should not be accurate enough. The final estimates are guaranteed to be statistically consistent with the measurements. Furthermore, we show how the same tools can be used to discriminate among alternate models of the same biological process. We demonstrate these ideas by applying our methods to two examples, namely a model of the heat shock response in E. coli, and a model of a synthetic gene regulation system. The methods presented are quite general and may be applied to a wide class of biological systems where noisy measurements are used for parameter estimation or model selection. Parameter estimation is a key issue in systems biology, as it represents the crucial step to obtaining predictions from computational models of biological systems. This issue is usually addressed by †fitting†the model simulations to the observed experimental data. Such approach does not take the measurement noise into full consideration. We introduce a new method built on the combination of Kalman filtering, statistical tests, and optimization techniques. The filter is well-known in control and estimation theory and has found application in a wide range of fields, such as inertial guidance systems, weather forecasting, and economics. We show how the statistics of the measurement noise can be optimally exploited and directly incorporated into the design of the estimation algorithm in order to achieve more accurate results, and to validate/invalidate the computed estimates. We also show that a significant advantage of our estimator is that it offers a powerful tool for model selection, allowing rejection or acceptance of competing models based on the available noisy measurements. These results are of immediate practical application in computational biology, and while we demonstrate their use for two specific examples, they can in fact be used to study a wide class of biological systems.}},  author = {Lillacci, Gabriele and Khammash, Mustafa},  citeulike-article-id = {6766639},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000696},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832681/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20221262},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20221262},  day = {5},  doi = {10.1371/journal.pcbi.1000696},  issn = {1553-7358},  journal = {PLoS Comput Biol},  keywords = {system-biology},  month = mar,  number = {3},  pages = {e1000696+},  pmcid = {PMC2832681},  pmid = {20221262},  posted-at = {2010-10-24 10:08:09},  priority = {2},  publisher = {Public Library of Science},  title = {{Parameter Estimation and Model Selection in Computational Biology}},  url = {http://dx.doi.org/10.1371/journal.pcbi.1000696},  volume = {6},  year = {2010}  }  @article{citeulike:523772,  author = {Bourne, Philip E.},  citeulike-article-id = {523772},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.0010057},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1274296/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16261197},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16261197},  day = {28},  doi = {10.1371/journal.pcbi.0010057},  issn = {1553-7358},  journal = {PLoS Comput Biol},  keywords = {transversal},  month = oct,  number = {5},  pages = {e57+},  pmcid = {PMC1274296},  pmid = {16261197},  posted-at = {2010-10-24 10:07:47},  priority = {2},  publisher = {Public Library of Science},  title = {{Ten Simple Rules for Getting Published}},  url = {http://dx.doi.org/10.1371/journal.pcbi.0010057},  volume = {1},  year = {2005}  }  @article{citeulike:7127379,  abstract = {{With DNA sequencing now getting cheaper more quickly than data storage or computation, the time may have come for genome informatics to migrate to the cloud.}},  author = {Stein, Lincoln},  citeulike-article-id = {7127379},  citeulike-linkout-0 = {http://dx.doi.org/10.1186/gb-2010-11-5-207},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898083/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20441614},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20441614},  day = {5},  doi = {10.1186/gb-2010-11-5-207},  issn = {1465-6906},  journal = {Genome Biology},  keywords = {transversal},  month = may,  number = {5},  pages = {207+},  pmcid = {PMC2898083},  pmid = {20441614},  posted-at = {2010-10-24 10:07:38},  priority = {2},  title = {{The case for cloud computing in genome informatics}},  url = {http://dx.doi.org/10.1186/gb-2010-11-5-207},  volume = {11},  year = {2010}  }  @article{citeulike:6775999,  abstract = {{The development of detailed, coherent, models of complex biological systems is recognized as a key requirement for integrating the increasing amount of experimental data. In addition, in-silico simulation of bio-chemical models provides an easy way to test different experimental conditions, helping in the discovery of the dynamics that regulate biological systems. However, the computational power required by these simulations often exceeds that available on common desktop computers and thus expensive high performance computing solutions are required. An emerging alternative is represented by general-purpose scientific computing on graphics processing units (GPGPU), which offers the power of a small computer cluster at a cost of ∼\$400. Computing with a GPU requires the development of specific algorithms, since the programming paradigm substantially differs from traditional CPU-based computing. In this paper, we review some recent efforts in exploiting the processing power of GPUs for the simulation of biological systems.}},  author = {Dematt\'{e}, Lorenzo and Prandi, Davide},  citeulike-article-id = {6775999},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/bib/bbq006},  citeulike-linkout-1 = {http://bib.oxfordjournals.org/content/11/3/323.abstract},  citeulike-linkout-2 = {http://bib.oxfordjournals.org/content/11/3/323.full.pdf},  citeulike-linkout-3 = {http://bib.oxfordjournals.org/cgi/content/abstract/11/3/323},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/20211843},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=20211843},  day = {1},  doi = {10.1093/bib/bbq006},  issn = {1477-4054},  journal = {Briefings in Bioinformatics},  keywords = {transversal},  month = may,  number = {3},  pages = {323--333},  pmid = {20211843},  posted-at = {2010-10-24 10:07:12},  priority = {2},  publisher = {Oxford University Press},  title = {{GPU computing for systems biology}},  url = {http://dx.doi.org/10.1093/bib/bbq006},  volume = {11},  year = {2010}  }  @article{citeulike:4606419,  abstract = {{  Synthetic biology is a research field that combines the investigative nature of biology with the constructive nature of engineering. Efforts in synthetic biology have largely focused on the creation and perfection of genetic devices and small modules that are constructed from these devices. But to view cells as true 'programmable' entities, it is now essential to develop effective strategies for assembling devices and modules into intricate, customizable larger scale systems. The ability to create such systems will result in innovative approaches to a wide range of applications, such as bioremediation, sustainable energy production and biomedical therapies.  }},  author = {Purnick, Priscilla E. M. and Weiss, Ron},  citeulike-article-id = {4606419},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrm2698},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrm2698},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19461664},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19461664},  day = {01},  doi = {10.1038/nrm2698},  issn = {1471-0080},  journal = {Nat Rev Mol Cell Biol},  keywords = {system-biology},  month = jun,  number = {6},  pages = {410--422},  pmid = {19461664},  posted-at = {2010-10-23 18:25:27},  priority = {2},  publisher = {Nature Publishing Group},  title = {{The second wave of synthetic biology: from modules to systems}},  url = {http://dx.doi.org/10.1038/nrm2698},  volume = {10},  year = {2009}  }  @article{citeulike:1387765,  abstract = {{Power-law distributions occur in many situations of scientific interest and  have significant consequences for our understanding of natural and man-made  phenomena. Unfortunately, the detection and characterization of power laws is  complicated by the large fluctuations that occur in the tail of the  distribution -- the part of the distribution representing large but rare events  -- and by the difficulty of identifying the range over which power-law behavior  holds. Commonly used methods for analyzing power-law data, such as  least-squares fitting, can produce substantially inaccurate estimates of  parameters for power-law distributions, and even in cases where such methods  return accurate answers they are still unsatisfactory because they give no  indication of whether the data obey a power law at all. Here we present a  principled statistical framework for discerning and quantifying power-law  behavior in empirical data. Our approach combines maximum-likelihood fitting  methods with goodness-of-fit tests based on the Kolmogorov-Smirnov statistic  and likelihood ratios. We evaluate the effectiveness of the approach with tests  on synthetic data and give critical comparisons to previous approaches. We also  apply the proposed methods to twenty-four real-world data sets from a range of  different disciplines, each of which has been conjectured to follow a power-law  distribution. In some cases we find these conjectures to be consistent with the  data while in others the power law is ruled out.}},  archivePrefix = {arXiv},  author = {Clauset, Aaron and Shalizi, Cosma R. and Newman, M. E. J.},  citeulike-article-id = {1387765},  citeulike-linkout-0 = {http://arxiv.org/abs/0706.1062},  citeulike-linkout-1 = {http://arxiv.org/pdf/0706.1062},  citeulike-linkout-2 = {http://dx.doi.org/10.1137/070710111},  day = {2},  doi = {10.1137/070710111},  eprint = {0706.1062},  issn = {0036-1445},  journal = {SIAM Review},  keywords = {transversal},  month = feb,  number = {4},  pages = {661--703},  posted-at = {2010-10-23 18:25:15},  priority = {2},  title = {{Power-law distributions in empirical data}},  url = {http://dx.doi.org/10.1137/070710111},  volume = {51},  year = {2009}  }  @article{citeulike:5394760,  abstract = {{Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.}},  author = {Novere, Nicolas L. and Hucka, Michael and Mi, Huaiyu and Moodie, Stuart and Schreiber, Falk and Sorokin, Anatoly and Demir, Emek and Wegner, Katja and Aladjem, Mirit I. and Wimalaratne, Sarala M. and Bergman, Frank T. and Gauges, Ralph and Ghazal, Peter and Kawaji, Hideya and Li, Lu and Matsuoka, Yukiko and Villeger, Alice and Boyd, Sarah E. and Calzone, Laurence and Courtot, Melanie and Dogrusoz, Ugur and Freeman, Tom C. and Funahashi, Akira and Ghosh, Samik and Jouraku, Akiya and Kim, Sohyoung and Kolpakov, Fedor and Luna, Augustin and Sahle, Sven and Schmidt, Esther and Watterson, Steven and Wu, Guanming and Goryanin, Igor and Kell, Douglas B. and Sander, Chris and Sauro, Herbert and Snoep, Jacky L. and Kohn, Kurt and Kitano, Hiroaki},  citeulike-article-id = {5394760},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt.1558},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt.1558},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19668183},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19668183},  day = {07},  doi = {10.1038/nbt.1558},  issn = {1087-0156},  journal = {Nature Biotechnology},  keywords = {system-biology},  month = aug,  number = {8},  pages = {735--741},  pmid = {19668183},  posted-at = {2010-10-23 18:24:50},  priority = {2},  publisher = {Nature Publishing Group},  title = {{The Systems Biology Graphical Notation}},  url = {http://dx.doi.org/10.1038/nbt.1558},  volume = {27},  year = {2009}  }  @article{citeulike:5248382,  abstract = {{For decades, we tacitly assumed that the components of such complex systems as the cell, the society, or the Internet are randomly wired together. In the past decade, an avalanche of research has shown that many real networks, independent of their age, function, and scope, converge to similar architectures, a universality that allowed researchers from different disciplines to embrace network theory as a common paradigm. The decade-old discovery of scale-free networks was one of those events that had helped catalyze the emergence of network science, a new research field with its distinct set of challenges and accomplishments.}},  author = {Barab\'{a}si, Albert-L\'{a}szl\'{o}},  citeulike-article-id = {5248382},  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1173299},  citeulike-linkout-1 = {http://www.sciencemag.org/content/325/5939/412.abstract},  citeulike-linkout-2 = {http://www.sciencemag.org/content/325/5939/412.full.pdf},  citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/325/5939/412},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19628854},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19628854},  day = {24},  doi = {10.1126/science.1173299},  issn = {1095-9203},  journal = {Science},  keywords = {transversal},  month = jul,  number = {5939},  pages = {412--413},  pmid = {19628854},  posted-at = {2010-10-23 18:24:40},  priority = {2},  publisher = {American Association for the Advancement of Science},  title = {{Scale-Free Networks: A Decade and Beyond}},  url = {http://dx.doi.org/10.1126/science.1173299},  volume = {325},  year = {2009}  }  @article{citeulike:7203126,  abstract = {{  We report the design, synthesis, and assembly of the 1.08-mega-base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.  }},  author = {Gibson, Daniel G. and Glass, John I. and Lartigue, Carole and Noskov, Vladimir N. and Chuang, Ray-Yuan Y. and Algire, Mikkel A. and Benders, Gwynedd A. and Montague, Michael G. and Ma, Li and Moodie, Monzia M. and Merryman, Chuck and Vashee, Sanjay and Krishnakumar, Radha and Assad-Garcia, Nacyra and Andrews-Pfannkoch, Cynthia and Denisova, Evgeniya A. and Young, Lei and Qi, Zhi-Qing Q. and Segall-Shapiro, Thomas H. and Calvey, Christopher H. and Parmar, Prashanth P. and Hutchison, Clyde A. and Smith, Hamilton O. and Venter, J. Craig},  citeulike-article-id = {7203126},  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1190719},  citeulike-linkout-1 = {http://www.sciencemag.org/content/329/5987/52.abstract},  citeulike-linkout-2 = {http://www.sciencemag.org/content/329/5987/52.full.pdf},  citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/329/5987/52},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/20488990},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=20488990},  day = {2},  doi = {10.1126/science.1190719},  issn = {1095-9203},  journal = {Science (New York, N.Y.)},  keywords = {bacterial-biology},  month = jul,  number = {5987},  pages = {52--56},  pmid = {20488990},  posted-at = {2010-10-22 13:58:18},  priority = {2},  publisher = {American Association for the Advancement of Science},  title = {{Creation of a bacterial cell controlled by a chemically synthesized genome.}},  url = {http://dx.doi.org/10.1126/science.1190719},  volume = {329},  year = {2010}  }  @article{citeulike:593511,  abstract = {{  Bacteria use a variety of means to communicate with one another and with their eukaryotic hosts. In some cases, social interactions allow bacteria to synchronize the behavior of all of the members of the group and thereby act like multicellular organisms. By contrast, some bacterial social engagements promote individuality among members within the group and thereby foster diversity. Here we explore the molecular mechanisms underpinning some recently discovered bacterial communication systems. These include long- and short-range chemical signaling channels; one-way, two-way, and multi-way communication; contact-mediated and contact-inhibited signaling; and the use and spread of misinformation or, more dramatically, even deadly information.  }},  author = {Bassler, Bonnie L. and Losick, Richard},  citeulike-article-id = {593511},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.cell.2006.04.001},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16630813},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16630813},  citeulike-linkout-3 = {http://www.sciencedirect.com/science/article/B6WSN-4JS75DF-C/2/6507e3a0c1f1b21fc4887c3edeb7158e},  day = {21},  doi = {10.1016/j.cell.2006.04.001},  issn = {0092-8674},  journal = {Cell},  keywords = {bacterial-biology},  month = apr,  number = {2},  pages = {237--246},  pmid = {16630813},  posted-at = {2010-10-21 19:00:31},  priority = {2},  title = {{Bacterially speaking.}},  url = {http://dx.doi.org/10.1016/j.cell.2006.04.001},  volume = {125},  year = {2006}  }  @article{citeulike:464384,  abstract = {{Summary: The generic, quantitative, spatially explicit, individual-based model BacSim was developed to simulate growth and behaviour of bacteria. The potential of this approach is in relating the properties of microscopic entities – cells – to the properties of macroscopic, complex systems such as biofilms. Here, the growth of a single Escherichia coli cell into a colony was studied. The object-oriented program BacSim is an extension of Gecko, an ecosystem dynamics model which uses the Swarm toolkit for multi-agent simulations. The model describes bacterial properties including substrate uptake, metabolism, maintenance, cell division and death at the individual cell level. With the aim of making the model easily applicable to various bacteria under different conditions, the model uses as few as eight readily obtainable parameters which can be randomly varied. For substrate diffusion, a two-dimensional diffusion lattice is used. For growth-rate-dependent cell size variation, a conceptual model of cell division proposed by Donachie was examined. A mechanistic version of the Donachie model led to unbalanced growth at higher growth rates, whereas including a minimum period between subsequent replication initiations ensured balanced growth only if this period was unphysiologically long. Only a descriptive version of the Donachie model predicted cell sizes correctly. For maintenance, the Herbert model (constant specific rate of biomass consumption) and for substrate uptake, the Michaelis-Menten or the Best equations were implemented. The simulator output faithfully reproduced all input parameters. Growth characteristics when maintenance and uptake rates were proportional to either cell mass or surface area are compared. The authors propose a new generic measure of growth synchrony to quantify the loss of synchrony due to random variation of cell parameters or spatial heterogeneity. Variation of the maximal uptake rate completely desynchronizes the simulated culture but variation of the volume-at-division does not. A new measure for spatial heterogeneity is introduced: the standard deviation of substrate concentrations as experienced by the cells. Spatial heterogeneity desynchronizes population growth by subdividing the population into parts synchronously growing at different rates. At a high enough spatial heterogeneity, the population appears to grow completely asynchronously.}},  address = {School of Pure and Applied Biology, Cardiff University, UK. [email protected]},  author = {Kreft, Jan-Ulrich and Booth, Ginger and Wimpenny, Julian W. T.},  citeulike-article-id = {464384},  citeulike-linkout-0 = {http://dx.doi.org/10.1099/00221287-144-12-3275},  citeulike-linkout-1 = {http://mic.sgmjournals.org/cgi/content/abstract/144/12/3275},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/9884219},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=9884219},  day = {1},  doi = {10.1099/00221287-144-12-3275},  issn = {1350-0872},  journal = {Microbiology},  keywords = {simulation-and-modeling},  month = dec,  number = {12},  pages = {3275--3287},  pmid = {9884219},  posted-at = {2010-10-21 07:21:02},  priority = {2},  title = {{BacSim, a simulator for individual-based modelling of bacterial colony growth}},  url = {http://dx.doi.org/10.1099/00221287-144-12-3275},  volume = {144},  year = {1998}  }  @article{citeulike:8050122,  abstract = {{Like any form of cooperative behavior, quorum sensing (QS) in bacteria is potentially vulnerable to cheating, the occurrence of individuals that contribute less but still profit from the benefits provided by others. In this paper, we explore the evolutionary stability of QS as a regulatory mechanism of antibiotics production in a spatially structured population, using cellular automaton (CA) modeling. QSg is supposed to regulate the excretion of a bacteriocin (anticompetitor toxin) in a population of bacteria polymorphic for the ability to produce and to be immune to the bacteriocin. Both the social interactions resulting from QS and the competitive interactions resulting from the bacteriocin excretion are supposed to be only effective at the local scale, that is, restricted to the immediately neighboring cells. This implies a rather diffuse kind of group selection. The CA model is contrasted to a model assuming no spatial structure but with otherwise identical assumptions. Our analysis predicts that QS as a regulatory mechanism of bacteriocin excretion is evolutionarily unstable when the competitive interactions between bacteriocin-producing, resistant, and sensitive strains only involve closely related strains which can share the signaling and responding genes involved in QS. However, when the competition is between unrelated strains and the QS alleles can only be carried by the bacteriocin-producing strains, stable QS may evolve provided its costs are small and the critical quorum threshold is neither too low nor too high.}},  author = {Cz\~{A}!`r\~{A}!`n, Tam\~{A}!`s and Hoekstra, Rolf F.},  citeulike-article-id = {8050122},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/beheco/arm061},  citeulike-linkout-1 = {http://beheco.oxfordjournals.org/content/18/5/866.abstract},  citeulike-linkout-2 = {http://beheco.oxfordjournals.org/content/18/5/866.full.pdf},  day = {1},  doi = {10.1093/beheco/arm061},  journal = {Behavioral Ecology},  keywords = {simulation-and-modeling},  month = sep,  number = {5},  pages = {866--873},  posted-at = {2010-10-21 07:20:54},  priority = {2},  title = {{A spatial model of the evolution of quorum sensing regulating bacteriocin production}},  url = {http://dx.doi.org/10.1093/beheco/arm061},  volume = {18},  year = {2007}  }  @article{citeulike:8011561,  abstract = {{Freely provided working code — whatever its quality — improves programming and enables others to engage with your research, says Nick Barnes. I am a professional software engineer and I want to share a trade secret with scientists: most professional computer software isn't very good. The code inside your laptop, television, phone or car is often badly documented, inconsistent and poorly tested.}},  author = {Barnes, Nick},  citeulike-article-id = {8011561},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/467753a},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/467753a},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20944687},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20944687},  day = {14},  doi = {10.1038/467753a},  issn = {0028-0836},  journal = {Nature},  keywords = {transversal},  month = oct,  number = {7317},  pages = {753},  pmid = {20944687},  posted-at = {2010-10-19 10:54:53},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Publish your computer code: it is good enough}},  url = {http://dx.doi.org/10.1038/467753a},  volume = {467},  year = {2010}  }  @article{citeulike:8011567,  abstract = {{…why scientific programming does not compute When hackers leaked thousands of e-mails from the Climatic Research Unit (CRU) at the University of East Anglia in Norwich, UK, last year, global-warming sceptics pored over the documents for signs that researchers had manipulated data. No such evidence emerged, but the e-mails did reveal another problem — one described by a CRU employee named †Harryâ€, who often wrote of his wrestling matches with wonky computer software.}},  author = {Merali, Zeeya},  citeulike-article-id = {8011567},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/467775a},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/467775a},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20944712},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20944712},  day = {14},  doi = {10.1038/467775a},  issn = {0028-0836},  journal = {Nature},  keywords = {transversal},  month = oct,  number = {7317},  pages = {775--777},  pmid = {20944712},  posted-at = {2010-10-19 10:54:21},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Computational science: ...Error}},  url = {http://dx.doi.org/10.1038/467775a},  volume = {467},  year = {2010}  }  @article{citeulike:5277246,  abstract = {{The breadth of genomic diversity found among organisms in nature allows populations to adapt to diverse environments1, 2. However, genomic diversity is difficult to generate in the laboratory and new phenotypes do not easily arise on practical timescales3. Although in vitro and directed evolution methods4, 5, 6, 7, 8, 9 have created genetic variants with usefully altered phenotypes, these methods are limited to laborious and serial manipulation of single genes and are not used for parallel and continuous directed evolution of gene networks or genomes. Here, we describe multiplex automated genome engineering (MAGE) for large-scale programming and evolution of cells. MAGE simultaneously targets many locations on the chromosome for modification in a single cell or across a population of cells, thus producing combinatorial genomic diversity. Because the process is cyclical and scalable, we constructed prototype devices that automate the MAGE technology to facilitate rapid and continuous generation of a diverse set of genetic changes (mismatches, insertions, deletions). We applied MAGE to optimize the 1-deoxy-d-xylulose-5-phosphate (DXP) biosynthesis pathway in Escherichia coli to overproduce the industrially important isoprenoid lycopene. Twenty-four genetic components in the DXP pathway were modified simultaneously using a complex pool of synthetic DNA, creating over 4.3 billion combinatorial genomic variants per day. We isolated variants with more than fivefold increase in lycopene production within 3 days, a significant improvement over existing metabolic engineering techniques. Our multiplex approach embraces engineering in the context of evolution by expediting the design and evolution of organisms with new and improved properties.}},  author = {Wang, Harris H. and Isaacs, Farren J. and Carr, Peter A. and Sun, Zachary Z. and Xu, George and Forest, Craig R. and Church, George M.},  citeulike-article-id = {5277246},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature08187},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature08187},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19633652},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19633652},  day = {13},  doi = {10.1038/nature08187},  issn = {0028-0836},  journal = {Nature},  keywords = {synbio-dna},  month = aug,  number = {7257},  pages = {894--898},  pmid = {19633652},  posted-at = {2010-10-15 21:19:00},  priority = {2},  publisher = {Macmillan Publishers Limited. All rights reserved},  title = {{Programming cells by multiplex genome engineering and accelerated evolution}},  url = {http://dx.doi.org/10.1038/nature08187},  volume = {460},  year = {2009}  }  @article{citeulike:8019944,  abstract = {{In many developmental systems, spatial pattern arises from morphogen gradients, which provide positional information for cells to determine their fate. Typically, diffusion is thought to be the mechanism responsible for building a morphogen gradient. An alternative mechanism is investigated here. Using mathematical modeling, we demonstrate how a non-diffusive morphogen concentration gradient can develop in axially growing tissue systems, where growth is due to cell proliferation only. Two distinct cases are considered: in the first, all cell proliferation occurs in a localized zone where active transcription of a morphogen-producing gene occurs, and in the second, cell proliferation is uniformly distributed throughout the tissue, occurring in both the active transcription zone and beyond. A cell containing morphogen mRNA produces the morphogen protein, hence any gradient in mRNA transcripts translates into a corresponding morphogen protein gradient. Proliferation-driven growth gives rise to both advection (the transport term) and dilution (a reaction term). These two key mechanisms determine the resultant mRNA transcript distribution. Using the full range of uniform initial conditions, we show that advection and dilution due to cell proliferation are, in general, sufficient for morphogen gradient formation for both types of axially growing systems. In particular, mRNA transcript degradation is not necessary for gradient formation; it is only necessary with localized proliferation for one special value of the initial concentration. Furthermore, the morphogen concentration decreases with distance away from the transcription zone, except in the case of localized proliferation with the initial concentration sufficiently large, when the concentration can either increase with distance from the transcription zone or sustain a local minimum. In both localized and uniformly distributed proliferation, in order for a concentration gradient to form across the whole domain, transcription must occur in a zone equal to the initial domain size; otherwise, it will only form across part of the tissue.}},  author = {Chisholm, Rebecca H. and Hughes, Barry D. and Landman, Kerry A.},  citeulike-article-id = {8019944},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0012857},  day = {30},  doi = {10.1371/journal.pone.0012857},  journal = {PLoS ONE},  keywords = {synbio-dna},  month = sep,  number = {9},  pages = {e12857+},  posted-at = {2010-10-15 21:18:36},  priority = {2},  publisher = {Public Library of Science},  title = {{Building a Morphogen Gradient without Diffusion in a Growing Tissue}},  url = {http://dx.doi.org/10.1371/journal.pone.0012857},  volume = {5},  year = {2010}  }  @article{citeulike:8018474,  abstract = {{The field of tissue engineering is moving toward a new concept of "in vitro biomimetics of in vivo tissue development." In Part I of this series, we proposed a theoretical framework integrating the concepts of developmental biology with those of process design to provide the rules for the design of biomimetic processes. We named this methodology "developmental engineering" to emphasize that it is not the tissue but the process of in vitro tissue development that has to be engineered. To formulate the process design rules in a rigorous way that will allow a computational design, we should refer to mathematical methods to model the biological process taking place in vitro. Tissue functions cannot be attributed to individual molecules but rather to complex interactions between the numerous components of a cell and interactions between cells in a tissue that form a network. For tissue engineering to advance to the level of a technologically driven discipline amenable to well-established principles of process engineering, a scientifically rigorous formulation is needed of the general design rules so that the behavior of networks of genes, proteins, or cells that govern the unfolding of developmental processes could be related to the design parameters. Now that sufficient experimental data exist to construct plausible mathematical models of many biological control circuits, explicit hypotheses can be evaluated using computational approaches to facilitate process design. Recent progress in systems biology has shown that the empirical concepts of developmental biology that we used in Part I to extract the rules of biomimetic process design can be expressed in rigorous mathematical terms. This allows the accurate characterization of manufacturing processes in tissue engineering as well as the properties of the artificial tissues themselves. In addition, network science has recently shown that the behavior of biological networks strongly depends on their topology and has developed the necessary concepts and methods to describe it, allowing therefore a deeper understanding of the behavior of networks during biomimetic processes. These advances thus open the door to a transition for tissue engineering from a substantially empirical endeavor to a technology-based discipline comparable to other branches of engineering.}},  author = {Lenas, Petros and Moos, Malcolm and Luyten, Frank P.},  citeulike-article-id = {8018474},  citeulike-linkout-0 = {http://dx.doi.org/10.1089/ten.teb.2009.0461},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19589040},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19589040},  doi = {10.1089/ten.teb.2009.0461},  issn = {1937-3376},  journal = {Tissue engineering. Part B, Reviews},  keywords = {system-biology},  month = dec,  number = {4},  pages = {395--422},  pmid = {19589040},  posted-at = {2010-10-14 19:26:41},  priority = {2},  title = {{Developmental engineering: a new paradigm for the design and manufacturing of cell-based products. Part II: from genes to networks: tissue engineering from the viewpoint of systems biology and network science.}},  url = {http://dx.doi.org/10.1089/ten.teb.2009.0461},  volume = {15},  year = {2009}  }  @article{citeulike:8018476,  abstract = {{Recent advances in developmental biology, systems biology, and network science are converging to poise the heretofore largely empirical field of tissue engineering on the brink of a metamorphosis into a rigorous discipline based on universally accepted engineering principles of quality by design. Failure of more simplistic approaches to the manufacture of cell-based therapies has led to increasing appreciation of the need to imitate, at least to some degree, natural mechanisms that control cell fate and differentiation. The identification of many of these mechanisms, which in general are based on cell signaling pathways, is an important step in this direction. Some well-accepted empirical concepts of developmental biology, such as path-dependence, robustness, modularity, and semiautonomy of intermediate tissue forms, that appear sequentially during tissue development are starting to be incorporated in process design.}},  author = {Lenas, Petros and Moos, Malcolm and Luyten, Frank P.},  citeulike-article-id = {8018476},  citeulike-linkout-0 = {http://dx.doi.org/10.1089/ten.teb.2008.0575},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19505199},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19505199},  doi = {10.1089/ten.teb.2008.0575},  issn = {1937-3376},  journal = {Tissue engineering. Part B, Reviews},  keywords = {system-biology},  month = dec,  number = {4},  pages = {381--394},  pmid = {19505199},  posted-at = {2010-10-14 19:26:01},  priority = {2},  title = {{Developmental engineering: a new paradigm for the design and manufacturing of cell-based products. Part I: from three-dimensional cell growth to biomimetics of in vivo development.}},  url = {http://dx.doi.org/10.1089/ten.teb.2008.0575},  volume = {15},  year = {2009}  }  @incollection{citeulike:8018024,  abstract = {{An Amorphous Computing medium is a highly redundant, massively parallel, asynchronous computing system. Because it makes no assumptions about any precision interconnect or precision geometrical arrangement of the parts, it is an ideal environment for exploring issues of robust design[l]. Recent work in this area has focused on demonstrating that amorphous media can be configured to generate highly complex spatial patterns. Examples of configurable patterns include Euclidean constructions, branching structures, and simple text[3]. In the spirit of robust design, we pose the following question: What happens if these prespecified patterns are later damaged by the external environment, or by defects in the computational units? Under what circumstances can the amorphous computing environment recover from such errors, and what consistency checking strategies might it employ to find them?}},  address = {Berlin, Heidelberg},  author = {Zucker, Jeremy},  booktitle = {Unifying Themes in Complex Systems},  chapter = {32},  citeulike-article-id = {8018024},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-540-35866-4\_32},  citeulike-linkout-1 = {http://www.springerlink.com/content/x7318845170n8413},  doi = {10.1007/978-3-540-35866-4\_32},  editor = {Minai, Ali A. and Bar-Yam, Yaneer},  isbn = {978-3-540-35864-0},  keywords = {amorphous\_computing},  pages = {325--335},  posted-at = {2010-10-14 16:26:24},  priority = {2},  publisher = {Springer Berlin Heidelberg},  title = {{Self-Healing Structures in Amorphous Computing}},  url = {http://dx.doi.org/10.1007/978-3-540-35866-4\_32},  year = {2006}  }  @article{citeulike:6542541,  abstract = {{Nonviral gene therapy vectors are commonly based on recombinant bacterial plasmids or their derivatives. The plasmids are propagated in bacteria, so, in addition to their therapeutic cargo, they necessarily contain a bacterial replication origin and a selection marker, usually a gene conferring antibiotic resistance. Structural and maintenance plasmid stability in bacteria is required for the plasmid DNA production and can be achieved by carefully choosing a combination of the therapeutic DNA sequences, replication origin, selection marker, and bacterial strain. The use of appropriate promoters, other regulatory elements, and mammalian maintenance devices ensures that the therapeutic gene or genes are adequately expressed in target human cells. Optimal immune response to the plasmid vectors can be modulated via inclusion or exclusion of DNA sequences containing immunostimulatory CpG sequence motifs. DNA fragments facilitating construction of plasmid vectors should also be considered for inclusion in the design of plasmid vectors. Techniques relying on site-specific or homologous recombination are preferred for construction of large plasmids (>15 kb), while digestion of DNA by restriction enzymes with subsequent ligation of the resulting DNA fragments continues to be the mainstream approach for generation of small- and medium-size plasmids. Rapid selection of a desired recombinant plasmid against a background of other plasmids continues to be a challenge. In this chapter, the emphasis is placed on efficient and flexible versions of DNA cloning protocols using selection of recombinant plasmids by restriction endonucleases directly in the ligation mixture.}},  author = {Tolmachov, Oleg},  citeulike-article-id = {6542541},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/19565899},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=19565899},  issn = {1064-3745},  journal = {Methods in molecular biology (Clifton, N.J.)},  keywords = {bacterial-biology},  pages = {117--129},  pmid = {19565899},  posted-at = {2010-10-14 16:19:24},  priority = {2},  title = {{Designing plasmid vectors.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/19565899},  volume = {542},  year = {2009}  }  @article{citeulike:6907665,  abstract = {{Enterococcus faecalis has emerged as a prominent healthcare-associated pathogen frequently encountered in bacteremia, endocarditis, urinary tract infection, and as a leading cause of antibiotic-resistant infections. We recently demonstrated a capacity for high-level biofilm formation by a clinical E. faecalis isolate, E99. This high biofilm forming phenotype was attributable to a novel locus, designated bee , specifying a pilus at the bacterial cell surface and localized to a large 80 kb conjugative plasmid. To better understand the origin of the bee locus, as well as to potentially identify additional factors important to the biology and pathogenesis of strain E99, we sequenced the entire plasmid. The nucleotide sequence of the plasmid, designated pBEE99, revealed large regions of identity to the previously characterized conjugative plasmid pCF10. In addition to the bee locus, pBEE99 possesses an open reading frame potentially encoding aggregation substance, as well as open reading frames putatively encoding polypeptides with 60 to 99 \% identity at the amino acid level to proteins involved in regulation of the pheromone response and conjugal transfer of pCF10. However, strain E99 did not respond to the cCF10 pheromone in clumping assays. While pBEE99 was found to be devoid of any readily recognizable antibiotic resistance determinants, it carries two non-identical impB / mucB / samB -type genes, as well as genes potentially encoding a two-component bacteriocin similar to that encoded on pYI14. Although no bacteriocin activity was detected from an OG1RF transconjugant carrying pBEE99 against strain FA2-2, it was approximately an order of magnitude more resistant to ultraviolet radiation. Moreover, curing strain E99 of this plasmid significantly reduced its ability to survive UV exposure. Therefore, pBEE99 represents a novel conjugative plasmid that confers biofilm-forming and enhanced UV resistance traits that might potentially impact the virulence and/or fitness of E. faecalis .}},  author = {Coburn, Phillip S. and Baghdayan, Arto S. and Craig, Nikki and Burroughs, Adam and Tendolkar, Preeti and Miller, Kris and Najar, Fares Z. and Roe, Bruce A. and Shankar, Nathan},  citeulike-article-id = {6907665},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2010.03.001},  day = {20},  doi = {10.1016/j.plasmid.2010.03.001},  issn = {0147619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = mar,  posted-at = {2010-10-14 16:18:26},  priority = {2},  title = {{A novel conjugative plasmid from Enterococcus faecalis E99 enhances resistance to ultraviolet radiation}},  url = {http://dx.doi.org/10.1016/j.plasmid.2010.03.001},  year = {2010}  }  @article{citeulike:551963,  abstract = {{Almost 200 scientists from America, Europe, Asia, Australia, and Africa participated in the Plasmid Biology 2004 meeting, which was organized between 15th and 21st September 2004 in Kanoni (Corfu island), Greece. Various aspects of biology of plasmids and other mobile genetic elements were discussed during the meeting, including problems of replication, transfer, stable inheritance, and evolution. Medical and veterinary aspects of plasmids were highlighted as well as other applications of these replicons. It appears that plasmids and other mobile genetic elements are still excellent models in studies of basic biological problems at the molecular level, and their role in medicine and genetic engineering can be enormous. Moreover, studies on ecology of plasmids provide extremely important data that can be used in environment protection as well as in biotechnology. Understanding the importance of studies on plasmids and other mobile genetic elements, participants of the meeting decided to establish the International Society for Plasmid Biology.}},  address = {Department of Molecular Biology, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland. [email protected]},  author = {Wegrzyn, G.},  citeulike-article-id = {551963},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2004.10.002},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15631950},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15631950},  doi = {10.1016/j.plasmid.2004.10.002},  issn = {0147-619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {14--22},  pmid = {15631950},  posted-at = {2010-10-14 16:17:09},  priority = {2},  title = {{What does "plasmid biology" currently mean? Summary of the Plasmid Biology 2004 Meeting.}},  url = {http://dx.doi.org/10.1016/j.plasmid.2004.10.002},  volume = {53},  year = {2005}  }  @article{citeulike:5184850,  abstract = {{Many bacteria utilize acyl-homoserine lactones as cell to cell signals that can regulate the expression of numerous genes. Structural differences in acyl-homoserine lactones produced by different bacteria, such as acyl side chain length and the presence or absence of an oxy group, make many of the commonly used detection bioassays impractical for broad range detection. Here we present a simple, broad range acyl-homoserine lactone detection bioassay that can be used to detect a wide range of these chemical signals. A plasmid (pEAL01) was constructed and transformed into Pseudomonas aeruginosa strain QSC105 to allow for detection of a broad range of acyl-homoserine lactones through induction of a lasB'–lacZ transcriptional fusion. Monitoring β-galactosidase activity from this bioassay showed that P. aeruginosa strain QSC105 (pEAL01) could detect the presence of eight acyl-homoserine lactones tested at physiological concentrations. This novel strain could also detect acyl-homoserine lactones from the extracts of four different bacteria that produce different acyl-homoserine lactones signals. These data indicate that strain QSC105 (pEAL01) can be used to detect a wide variety of acyl-homoserine lactones by a simple β-galactosidase assay and this bioassay could be a useful and inexpensive tool to quickly identify the presence of these signal molecules.}},  author = {Ling, Elizabeth A. and Ellison, Matthew L. and Pesci, Everett C.},  citeulike-article-id = {5184850},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2009.02.002},  doi = {10.1016/j.plasmid.2009.02.002},  issn = {0147619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = jul,  number = {1},  pages = {16--21},  posted-at = {2010-10-14 16:16:53},  priority = {2},  title = {{A novel plasmid for detection of N-acyl homoserine lactones}},  url = {http://dx.doi.org/10.1016/j.plasmid.2009.02.002},  volume = {62},  year = {2009}  }  @article{citeulike:7491854,  abstract = {{A Francisella tularensis shuttle vector that constitutively expresses the Photorhabdus luminescens lux operon in type A and type B strains of F. tularensis was constructed. The bioluminescence reporter plasmid was introduced into the live vaccine strain of F. tularensis and used to follow F. tularensis growth in a murine intranasal challenge model in real time by bioluminescence imaging. The results show that the new bioluminescence reporter plasmid represents a useful tool for tularemia research that is suitable for following F. tularensis growth in both in vitro and in vivo model systems.}},  author = {Bina, Xiaowen R. and Miller, Mark A. and Bina, James E.},  citeulike-article-id = {7491854},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2010.07.001},  day = {08},  doi = {10.1016/j.plasmid.2010.07.001},  issn = {0147619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = jul,  posted-at = {2010-10-14 16:16:15},  priority = {2},  title = {{Construction of a bioluminescence reporter plasmid for Francisella tularensis}},  url = {http://dx.doi.org/10.1016/j.plasmid.2010.07.001},  year = {2010}  }  @article{citeulike:4833362,  abstract = {{Although plasmid DNA vectors have been extensively applied in biotechnology, there is still a lack of standard plasmid vector classification. Here, we propose a classification method for commonly used plasmid vectors. Plasmid vectors were classified into different classes based on their replication origin, selection marker and promoter information. The replication origins of plasmid vectors were classified as: prokaryotic replication origin, eukaryotic replication origin and viral replication origin. Selection markers of plasmid vectors were mainly classified as ampicillin, kanamycin, neomycin, chloramphenicol, gentamycin, tetracycline, erythromycin, streptomycin, vancomycin and spectinomycin resistance gene markers. Promoter sequences were also classified as prokaryotic, eukaryotic and viral promoters. Finally, the nomenclature of common plasmid vectors has three determinants. We believe that the classification of plasmid vectors can provide useful information for researchers employing molecular cloning procedures. A web service of the plasmid classification was established and it is available from http://www.computationalmedicalbiology.org/plasclas.aspx.}},  author = {Wang, Z. and Jin, L. and Yuan, Z. and Wegrzyn, G. and Wegrzyn, A.},  citeulike-article-id = {4833362},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2008.09.003},  doi = {10.1016/j.plasmid.2008.09.003},  issn = {0147619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {47--51},  posted-at = {2010-10-14 16:15:49},  priority = {2},  title = {{Classification of plasmid vectors using replication origin, selection marker and promoter as criteria}},  url = {http://dx.doi.org/10.1016/j.plasmid.2008.09.003},  volume = {61},  year = {2009}  }  @article{citeulike:7759220,  abstract = {{A cryptic plasmid from Lactobacillus paracasei TXW isolated from koumiss, designated as pTXW, was sequenced and characterized. It is 3178 bp in length with a G+C content of 42.9\%. The plasmid pTXW was predicted to encode 4 putative ORFs. RepB shared high homology with initiator proteins of plasmids from the rolling circle replication (RCR) pMV158 family. copG was predicted to encode a transcriptional repressor, which was involved in plasmid copy number control together with a putative antisense RNA. Mob putatively acts as a relaxase and belongs to the MOB(V) relaxase family. Sequence analysis revealed a double strand origin (dso) located upstream the repB gene, which contained the conserved nick sequence of the pMV158 family. A putative single strand origin (sso-like) consisting of successive inverted repeats was also detected. Mung bean nuclease analysis and Southern hybridization confirmed the presence of single-stranded DNA (ssDNA) intermediates, suggesting that pTXW replicates via the RCR mechanism. Furthermore, the relative copy number of pTXW was estimated to be 73.5±1.2 copies in each cell by real-time PCR. The new RCR plasmid would be valuable to construct vectors for application in food industry.}},  author = {Zhang, Hongxing and Hao, Yanling and Zhang, Dapeng and Luo, Yunbo},  citeulike-article-id = {7759220},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2010.08.002},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20709099},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20709099},  day = {13},  doi = {10.1016/j.plasmid.2010.08.002},  issn = {1095-9890},  journal = {Plasmid},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {1--7},  pmid = {20709099},  posted-at = {2010-10-14 16:15:01},  priority = {2},  title = {{Characterization of the cryptic plasmid pTXW from Lactobacillus paracasei TXW.}},  url = {http://dx.doi.org/10.1016/j.plasmid.2010.08.002},  volume = {65},  year = {2011}  }  @article{citeulike:4131858,  abstract = {{The central elements in the conjugative mobilization of most plasmids are the relaxase and its cognate origin of transfer ( oriT ). The relaxase of the plasmid R1162, together with its oriT , belong to a large and widely distributed family of related relaxase/ oriT pairs. Several of the properties of these elements are considered for R1162 and for other members of this family with a view to understanding how systems for mobilization might have evolved.}},  author = {Parker, C. and Becker, E. and Zhang, X. and Jandle, S. and Meyer, R.},  citeulike-article-id = {4131858},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2004.12.007},  doi = {10.1016/j.plasmid.2004.12.007},  issn = {0147619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = mar,  number = {2},  pages = {113--118},  posted-at = {2010-10-14 16:14:19},  priority = {2},  title = {{Elements in the co-evolution of relaxases and their origins of transfer}},  url = {http://dx.doi.org/10.1016/j.plasmid.2004.12.007},  volume = {53},  year = {2005}  }  @article{citeulike:3805542,  abstract = {{  Entry exclusion is a property of plasmids by which the cells that contain them become bad recipients in additional conjugation rounds. This work reviews entry exclusion essential features and analyzes the mechanisms of action of the best studied systems. We searched for homologs of the proteins responsible for experimentally known exclusion systems. Results were used to classify exclusion systems in families of related elements. We arrive to the conclusion that all conjugative plasmids contain at least one entry exclusion gene. Although entry exclusion genes seem to be part of the plasmid conjugative machinery, they are systematically absent in phylogenetically related type IV protein exporting machines involved in virulence for plants and animals. We infer from this fact that entry exclusion is an essential feature of conjugative plasmid biology. Mathematical models suggest that plasmids expressing entry exclusion selectively eliminate plasmids lacking it, reinforcing its essential character and suggesting that entry exclusion plays a direct role in plasmid survival. Other experimental results confirm that entry exclusion is essential for the stability of a conjugative plasmid. We suggest that entry exclusion limits the damage of lethal zygosis (bacterial death produced by excessive rounds of conjugation). Additionally, it avoids competition in a host among identical plasmid backbones. Conversely, the lack of entry exclusion in conjugative transposons can be understood as a means of generating rapid evolutionary change.  }},  author = {Garcill\'{a}n-Barcia, M. Pilar and de la Cruz, Fernando},  citeulike-article-id = {3805542},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2008.03.002},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18440635},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18440635},  doi = {10.1016/j.plasmid.2008.03.002},  issn = {0147-619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = jul,  number = {1},  pages = {1--18},  pmid = {18440635},  posted-at = {2010-10-14 16:13:31},  priority = {2},  title = {{Why is entry exclusion an essential feature of conjugative plasmids?}},  url = {http://dx.doi.org/10.1016/j.plasmid.2008.03.002},  volume = {60},  year = {2008}  }  @article{citeulike:7355647,  abstract = {{  Networks have become a key approach to understanding systems of interacting objects, unifying the study of diverse phenomena including biological organisms and human society. One crucial step when studying the structure and dynamics of networks is to identify communities: groups of related nodes that correspond to functional subunits such as protein complexes or social spheres. Communities in networks often overlap such that nodes simultaneously belong to several groups. Meanwhile, many networks are known to possess hierarchical organization, where communities are recursively grouped into a hierarchical structure. However, the fact that many real networks have communities with pervasive overlap, where each and every node belongs to more than one group, has the consequence that a global hierarchy of nodes cannot capture the relationships between overlapping groups. Here we reinvent communities as groups of links rather than nodes and show that this unorthodox approach successfully reconciles the antagonistic organizing principles of overlapping communities and hierarchy. In contrast to the existing literature, which has entirely focused on grouping nodes, link communities naturally incorporate overlap while revealing hierarchical organization. We find relevant link communities in many networks, including major biological networks such as protein-protein interaction and metabolic networks, and show that a large social network contains hierarchically organized community structures spanning inner-city to regional scales while maintaining pervasive overlap. Our results imply that link communities are fundamental building blocks that reveal overlap and hierarchical organization in networks to be two aspects of the same phenomenon.  }},  author = {Ahn, Yong-Yeol and Bagrow, James P. and Lehmann, Sune},  citeulike-article-id = {7355647},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature09182},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature09182},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20562860},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20562860},  day = {5},  doi = {10.1038/nature09182},  issn = {0028-0836},  journal = {Nature},  keywords = {system-biology},  month = aug,  number = {7307},  pages = {761--764},  pmid = {20562860},  posted-at = {2010-10-14 16:08:53},  priority = {2},  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},  title = {{Link communities reveal multiscale complexity in networks}},  url = {http://dx.doi.org/10.1038/nature09182},  volume = {466},  year = {2010}  }  @article{2000,  abstract = {{Bayesian statistics have made great strides in recent years, developing a class of methods for estimation and inference via stochastic simulation known as Markov Chain Monte Carlo (MCMC) methods. MCMC constitutes a revolution in statistical practice with effects beginning to be felt in the social sciences: models long consigned to the "too hard" basket are now within reach of quantitative researchers. I review the statistical pedigree of MCMC and the underlying statistical concepts. I demonstrate some of the strengths and weaknesses of MCMC and offer practical suggestions for using MCMC in social-science settings. Simple, illustrative examples include a probit model of voter turnout and a linear regression for time-series data with autoregressive disturbances. I conclude with a more challenging application, a multinomial probit model, to showcase the power of MCMC methods.}},  author = {Jackman, Simon},  citeulike-article-id = {6745199},  citeulike-linkout-0 = {http://www.jstor.org/stable/2669318},  journal = {American Journal of Political Science},  keywords = {simulation-and-modeling},  number = {2},  pages = {375--404},  posted-at = {2010-10-14 16:04:00},  priority = {2},  publisher = {Midwest Political Science Association},  title = {{Estimation and Inference via Bayesian Simulation: An Introduction to Markov Chain Monte Carlo}},  url = {http://www.jstor.org/stable/2669318},  volume = {44},  year = {2000}  }  @article{Davie07,  abstract = {A theory of systems of differential equations of the form dyi = {sum}jfij(y)dxi, where the driving path x(t) is nondifferentiable, has recently been developed by Lyons. I develop an alternative approach to this theory, using (modified) Euler approximations, and investigate its applicability to stochastic differential equations driven by Brownian motion. I also give some other examples showing that the main results are reasonably sharp. 10.1093/amrx/abm009},  author = {Davie, A. M.},  citeulike-article-id = {6768201},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/amrx/abm009},  citeulike-linkout-1 = {http://amrx.oxfordjournals.org/cgi/content/abstract/2007/abm009/abm009},  day = {1},  doi = {10.1093/amrx/abm009},  journal = {Appl Math Res Express},  keywords = {transversal},  month = jan,  number = {abm009},  pages = {abm009--40},  posted-at = {2010-10-14 16:03:39},  priority = {2},  title = {{Differential Equations Driven by Rough Paths: An Approach via Discrete Approximation}},  url = {http://dx.doi.org/10.1093/amrx/abm009},  volume = {2007},  year = {2007}  }  @misc{Baez09,  abstract = {{In physics, Feynman diagrams are used to reason about quantum processes. In  the 1980s, it became clear that underlying these diagrams is a powerful analogy  between quantum physics and topology: namely, a linear operator behaves very  much like a "cobordism". Similar diagrams can be used to reason about logic,  where they represent proofs, and computation, where they represent programs.  With the rise of interest in quantum cryptography and quantum computation, it  became clear that there is extensive network of analogies between physics,  topology, logic and computation. In this expository paper, we make some of  these analogies precise using the concept of "closed symmetric monoidal  category". We assume no prior knowledge of category theory, proof theory or  computer science.}},  archivePrefix = {arXiv},  author = {Baez, John C. and Stay, Mike},  citeulike-article-id = {4121553},  citeulike-linkout-0 = {http://arxiv.org/abs/0903.0340},  citeulike-linkout-1 = {http://arxiv.org/pdf/0903.0340},  citeulike-linkout-2 = {http://adsabs.harvard.edu/cgi-bin/nph-bib\_query?bibcode=2009arXiv0903.0340B},  day = {6},  eprint = {0903.0340},  journal = {ArXiv e-prints},  keywords = {transversal},  month = jun,  posted-at = {2010-10-14 16:03:26},  priority = {2},  title = {{Physics, Topology, Logic and Computation: A Rosetta Stone}},  url = {http://arxiv.org/abs/0903.0340},  year = {2009}  }  @article{Schwartz08,  abstract = {{10.1242/jcs.033340}},  author = {Schwartz, Martin A.},  citeulike-article-id = {3010240},  citeulike-linkout-0 = {http://dx.doi.org/10.1242/jcs.033340},  citeulike-linkout-1 = {http://jcs.biologists.org/content/121/11/1771.abstract},  citeulike-linkout-2 = {http://jcs.biologists.org/content/121/11/1771.full.pdf},  citeulike-linkout-3 = {http://jcs.biologists.org/cgi/content/abstract/121/11/1771},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/18492790},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=18492790},  day = {01},  doi = {10.1242/jcs.033340},  issn = {1477-9137},  journal = {Journal of Cell Science},  keywords = {transversal},  month = jun,  number = {11},  pages = {1771},  pmid = {18492790},  posted-at = {2010-10-14 16:03:18},  priority = {2},  publisher = {The Company of Biologists Ltd},  title = {{The importance of stupidity in scientific research}},  url = {http://dx.doi.org/10.1242/jcs.033340},  volume = {121},  year = {2008}  }  @techreport{Welch95,  abstract = {{In 1960, R.E. Kalman published his famous paper describing a recursive solution  to the discrete-data linear filtering problem. Since that time, due in large part to advances  in digital computing, the Kalman filter has been the subject of extensive research  and application, particularly in the area of autonomous or assisted  navigation.  The Kalman filter is a set of mathematical equations that provides an efficient computational  (recursive) means to estimate the state of a process, in a way that minimizes  the mean of the squared error. The filter is very powerful in several aspects:  it supports estimations of past, present, and even future states, and it can do so even  when the precise nature of the modeled system is unknown.  The purpose of this paper is to provide a practical introduction to the discrete Kalman  filter. This introduction includes a description and some discussion of the basic  discrete Kalman filter, a derivation, description and some discussion of the extended  Kalman filter, and a relatively simple (tangible) example with real numbers \&  results.}},  address = {Chapel Hill, NC, USA},  author = {Welch, Greg and Bishop, Gary},  citeulike-article-id = {4889627},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=897831},  keywords = {transversal},  posted-at = {2010-10-14 16:02:31},  priority = {2},  publisher = {University of North Carolina at Chapel Hill},  title = {{An Introduction to the Kalman Filter}},  url = {http://portal.acm.org/citation.cfm?id=897831},  year = {1995}  }  @article{Gunawardena2010,  abstract = {{10.1126/science.1188974}},  author = {Gunawardena, Jeremy},  citeulike-article-id = {7102630},  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1188974},  citeulike-linkout-1 = {http://www.sciencemag.org/content/328/5978/581.abstract},  citeulike-linkout-2 = {http://www.sciencemag.org/content/328/5978/581.full.pdf},  citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/328/5978/581},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/20431005},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=20431005},  day = {30},  doi = {10.1126/science.1188974},  issn = {1095-9203},  journal = {Science},  keywords = {system-biology},  month = apr,  number = {5978},  pages = {581--582},  pmid = {20431005},  posted-at = {2010-10-14 16:01:49},  priority = {2},  title = {{Biological Systems Theory}},  url = {http://dx.doi.org/10.1126/science.1188974},  volume = {328},  year = {2010}  }  @article{Kohanski2010,  abstract = {{Antibiotic drug-target interactions, and their respective direct effects, are generally well characterized. By contrast, the bacterial responses to antibiotic drug treatments that contribute to cell death are not as well understood and have proven to be complex as they involve many genetic and biochemical pathways. In this Review, we discuss the multilayered effects of drug-target interactions, including the essential cellular processes that are inhibited by bactericidal antibiotics and the associated cellular response mechanisms that contribute to killing. We also discuss new insights into these mechanisms that have been revealed through the study of biological networks, and describe how these insights, together with related developments in synthetic biology, could be exploited to create new antibacterial therapies.}},  author = {Kohanski, Michael A. and Dwyer, Daniel J. and Collins, James J.},  citeulike-article-id = {7122979},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrmicro2333},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrmicro2333},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896384/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/20440275},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=20440275},  day = {04},  doi = {10.1038/nrmicro2333},  issn = {1740-1534},  journal = {Nat Rev Micro},  keywords = {system-biology},  month = jun,  number = {6},  pages = {423--435},  pmcid = {PMC2896384},  pmid = {20440275},  posted-at = {2010-10-14 16:01:40},  priority = {2},  publisher = {Nature Publishing Group},  title = {{How antibiotics kill bacteria: from targets to networks}},  url = {http://dx.doi.org/10.1038/nrmicro2333},  volume = {8},  year = {2010}  }  @article{Meier-Schellersheim09,  abstract = {{Biomedical research frequently involves performing experiments and developing hypotheses that link different scales of biological systems such as, for instance, the scales of intracellular molecular interactions to the scale of cellular behavior and beyond to the behavior of cell populations. Computational modeling efforts that aim at exploring such multiscale systems quantitatively with the help of simulations have to incorporate several different simulation techniques because of the different time and space scales involved. Here, we provide a nontechnical overview of how different scales of experimental research can be combined with the appropriate computational modeling techniques. We also show that current modeling software permits building and simulating multiscale models without having to become involved with the underlying technical details of computational modeling.}},  address = {Program in Systems Immunology and Infectious Disease Modeling (PSIIM), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA},  author = {Meier-Schellersheim, Martin and Fraser, Iain D. and Klauschen, Frederick},  citeulike-article-id = {7145626},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/wsbm.33},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862646/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20448808},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20448808},  citeulike-linkout-4 = {http://www3.interscience.wiley.com/cgi-bin/abstract/122326976/ABSTRACT},  doi = {10.1002/wsbm.33},  issn = {1939-005X},  journal = {Wiley interdisciplinary reviews. Systems biology and medicine},  keywords = {simulation-and-modeling},  month = jul,  number = {1},  pages = {4--14},  pmcid = {PMC2862646},  pmid = {20448808},  posted-at = {2010-10-14 16:01:25},  priority = {2},  title = {{Multiscale modeling for biologists.}},  url = {http://dx.doi.org/10.1002/wsbm.33},  volume = {1},  year = {2009}  }  @article{citeulike:7420983,  abstract = {{Modern single-molecule tools, when applied to enzymes, challenge fundamental concepts of catalysis by uncovering mechanistic pathways, intermediates and heterogeneities hidden in the ensemble average. It is thus reassuring that the Michaelis-Menten formalism, a pillar of enzymology, is upheld, if reinterpreted, even when visualizing single turnover events with a microscope focus. The seminal 1913 discovery of Leonor Michaelis and Maud Menten1 arguably represents the beginning of enzyme kinetics as a systematic field and remains a pillar of enzymology. Thousands of enzymes have been characterized using the Michaelis-Menten formalism, which describes the rate of multiple enzymatic turnovers as a function of substrate concentration (Fig. 1}},  author = {Walter, Nils G.},  citeulike-article-id = {7420983},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nchembio0206-66},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nchembio0206-66},  day = {01},  doi = {10.1038/nchembio0206-66},  issn = {1552-4450},  journal = {Nature Chemical Biology},  keywords = {system-biology},  month = feb,  number = {2},  pages = {66--67},  posted-at = {2010-10-14 16:00:59},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Michaelis-Menten is dead, long live Michaelis-Menten!}},  url = {http://dx.doi.org/10.1038/nchembio0206-66},  volume = {2},  year = {2006}  }  @article{Fitzgerald2009,  abstract = {{Several types of biological networks have recently been shown to be accurately described by a maximum entropy model with pairwise interactions, also known as the Ising model. Here we present an approach for finding the optimal mappings between input signals and network states that allow the network to convey the maximal information about input signals drawn from a given distribution. This mapping also produces a set of linear equations for calculating the optimal Ising-model coupling constants, as well as geometric properties that indicate the applicability of the pairwise Ising model. We show that the optimal pairwise interactions are on average zero for Gaussian and uniformly distributed inputs, whereas they are nonzero for inputs approximating those in natural environments. These nonzero network interactions are predicted to increase in strength as the noise in the response functions of each network node increases. This approach also suggests ways for how interactions with unmeasured parts of the network can be inferred from the parameters of response functions for the measured network nodes.}},  author = {Fitzgerald, Jeffrey D. and Sharpee, Tatyana O.},  citeulike-article-id = {7593530},  citeulike-linkout-0 = {http://dx.doi.org/10.1103/physreve.80.031914},  citeulike-linkout-1 = {http://link.aps.org/abstract/PRE/v80/i3/e031914},  citeulike-linkout-2 = {http://link.aps.org/pdf/PRE/v80/i3/e031914},  doi = {10.1103/physreve.80.031914},  journal = {Physical Review E},  keywords = {transversal},  month = sep,  number = {3},  pages = {031914+},  posted-at = {2010-10-14 16:00:26},  priority = {2},  publisher = {American Physical Society},  title = {{Maximally informative pairwise interactions in networks}},  url = {http://dx.doi.org/10.1103/physreve.80.031914},  volume = {80},  year = {2009}  }  @article{citeulike:7852881,  abstract = {{Systems biology is an interdisciplinary field that aims at understanding complex interactions in cells. Here we demonstrate that linear control theory can provide valuable insight and practical tools for the characterization of complex biological networks. We provide the foundation for such analyses through the study of several case studies including cascade and parallel forms, feedback and feedforward loops. We reproduce experimental results and provide rational analysis of the observed behavior. We demonstrate that methods such as the transfer function (frequency domain) and linear state-space (time domain) can be used to predict reliably the properties and transient behavior of complex network topologies and point to specific design strategies for synthetic networks.}},  author = {Shin, Yong-Jun J. and Bleris, Leonidas},  citeulike-article-id = {7852881},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0012785},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20862288},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20862288},  day = {16},  doi = {10.1371/journal.pone.0012785},  issn = {1932-6203},  journal = {PloS one},  keywords = {system-biology},  month = sep,  number = {9},  pages = {e12785+},  pmid = {20862288},  posted-at = {2010-10-14 15:55:39},  priority = {2},  publisher = {Public Library of Science},  title = {{Linear control theory for gene network modeling.}},  url = {http://dx.doi.org/10.1371/journal.pone.0012785},  volume = {5},  year = {2010}  }  @article{citeulike:5791431,  abstract = {{Systems biology is a rapidly expanding field that integrates diverse areas of science such as physics, engineering, computer science, mathematics, and biology toward the goal of elucidating the underlying principles of hierarchical metabolic and regulatory systems in the cell, and ultimately leading to predictive understanding of cellular response to perturbations. Because post-genomics research is taking place throughout the tree of life, comparative approaches offer a way for combining data from many organisms to shed light on the evolution and function of biological networks from the gene to the organismal level. Therefore, systems biology can build on decades of theoretical work in evolutionary biology, and at the same time evolutionary biology can use the systems biology approach to go in new uncharted directions. In this study, we present a review of how the post-genomics era is adopting comparative approaches and dynamic system methods to understand the underlying design principles of network evolution and to shape the nascent field of evolutionary systems biology. Finally, the application of evolutionary systems biology to robust biological network designs is also discussed from the synthetic biology perspective.}},  author = {Chen, Bor-Sen S. and Wu, Wei-Sheng S.},  citeulike-article-id = {5791431},  citeulike-linkout-0 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684126/},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19468310},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19468310},  issn = {1176-9343},  journal = {Evolutionary bioinformatics online},  keywords = {system-biology},  pages = {245--262},  pmcid = {PMC2684126},  pmid = {19468310},  posted-at = {2010-10-14 15:54:18},  priority = {2},  title = {{Underlying principles of natural selection in network evolution: systems biology approach.}},  url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684126/},  volume = {3},  year = {2007}  }  @article{citeulike:7930541,  abstract = {{Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models, it is not always easy to use published models. Also, since model descriptions are not usually given in mathematical terms, it is difficult to bring mathematical analysis tools to bear, so that models are typically studied through simulation. In order to address this issue, Grimm et al. proposed a protocol for model specification, the so-called ODD protocol, which provides a standard way to describe models. This paper proposes an addition to the ODD protocol which allows the description of an agent-based model as a dynamical system, which provides access to computational and theoretical tools for its analysis. The mathematical framework is that of algebraic models, that is, time-discrete dynamical systems with algebraic structure. It is shown by way of several examples how this mathematical specification can help with model analysis. This mathematical framework can also accommodate other model types such as Boolean networks and the more general logical models, as well as Petri nets.}},  author = {Hinkelmann, Franziska and Murrugarra, David and Jarrah, Abdul Salam S. and Laubenbacher, Reinhard},  citeulike-article-id = {7930541},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s11538-010-9582-8},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20878493},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20878493},  day = {29},  doi = {10.1007/s11538-010-9582-8},  issn = {1522-9602},  journal = {Bulletin of mathematical biology},  keywords = {individual-based-modeling},  month = sep,  pmid = {20878493},  posted-at = {2010-10-14 15:53:48},  priority = {2},  title = {{A Mathematical Framework for Agent Based Models of Complex Biological Networks.}},  url = {http://dx.doi.org/10.1007/s11538-010-9582-8},  year = {2010}  }  @incollection{citeulike:7989967,  abstract = {{This position paper argues that the operational modelling approaches from the formal methods community can be applied fruitfully within the systems biology domain. The results can be complementary to the traditional mathematical descriptive modelling approaches used in systems biology. We discuss one example: a recent Petri net analysis of C. elegans vulval development.}},  address = {Berlin, Heidelberg},  author = {Bonzanni, Nicola and Feenstra, K. and Fokkink, Wan and Krepska, Elzbieta},  booktitle = {FM 2009: Formal Methods},  chapter = {2},  citeulike-article-id = {7989967},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-05089-3\_2},  citeulike-linkout-1 = {http://www.springerlink.com/content/58571w783445q371},  doi = {10.1007/978-3-642-05089-3\_2},  editor = {Cavalcanti,, Ana and Dams,, Dennis},  isbn = {978-3-642-05088-6},  keywords = {system-biology},  pages = {16--22},  posted-at = {2010-10-14 15:52:30},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{What Can Formal Methods Bring to Systems Biology?}},  url = {http://dx.doi.org/10.1007/978-3-642-05089-3\_2},  volume = {5850},  year = {2009}  }  @article{citeulike:7395399,  abstract = {{Why isn't random variation always deleterious? Are there factors that sometimes make adaptation easier? Biological systems are extraordinarily robust to perturbation by mutations, recombination and the environment. It has been proposed that this robustness might make them more evolvable. Robustness to mutation allows genetic variation to accumulate in a cryptic state. Switching mechanisms known as evolutionary capacitors mean that the amount of heritable phenotypic variation available can be correlated to the degree of stress and hence to the novelty of the environment and remaining potential for adaptation. There have been two somewhat separate literatures relating robustness to evolvability. One has focused on molecular phenotypes and new mutations, the other on morphology and cryptic genetic variation. Here, we review both literatures, and show that the true distinction is whether recombination rates are high or low. In both cases, the evidence supports the claim that robustness promotes evolvability. Copyright 2010 Elsevier Ltd. All rights reserved.}},  author = {Masel, Joanna and Trotter, Meredith V.},  citeulike-article-id = {7395399},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.tig.2010.06.002},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198833/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20598394},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20598394},  day = {01},  doi = {10.1016/j.tig.2010.06.002},  issn = {0168-9525},  journal = {Trends in genetics : TIG},  keywords = {system-biology},  month = sep,  number = {9},  pages = {406--414},  pmcid = {PMC3198833},  pmid = {20598394},  posted-at = {2010-10-14 15:51:12},  priority = {2},  title = {{Robustness and evolvability.}},  url = {http://dx.doi.org/10.1016/j.tig.2010.06.002},  volume = {26},  year = {2010}  }  @article{citeulike:6410033,  abstract = {{Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called 'spatial selection': cooperators prevail against defectors by clustering in physical or other spaces.}},  author = {Nowak, Martin A. and Tarnita, Corina E. and Antal, Tibor},  citeulike-article-id = {6410033},  citeulike-linkout-0 = {http://dx.doi.org/10.1098/rstb.2009.0215},  citeulike-linkout-1 = {http://rstb.royalsocietypublishing.org/content/365/1537/19.abstract},  citeulike-linkout-2 = {http://rstb.royalsocietypublishing.org/content/365/1537/19.full.pdf},  citeulike-linkout-3 = {http://rstb.royalsocietypublishing.org/cgi/content/abstract/365/1537/19},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/20008382},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=20008382},  day = {12},  doi = {10.1098/rstb.2009.0215},  journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},  keywords = {game-theory},  month = jan,  number = {1537},  pages = {19--30},  pmid = {20008382},  posted-at = {2010-10-14 15:30:06},  priority = {2},  title = {{Evolutionary dynamics in structured populations}},  url = {http://dx.doi.org/10.1098/rstb.2009.0215},  volume = {365},  year = {2010}  }  @article{citeulike:5984219,  abstract = {{Evolutionary game theory is the study of frequency-dependent selection. The success of an individual depends on the frequencies of strategies that are used in the population. We propose a new model for studying evolutionary dynamics in games with a continuous strategy space. The population size is finite. All members of the population use the same strategy. A mutant strategy is chosen from some distribution over the strategy space. The fixation probability of the mutant strategy in the resident population is calculated. The new mutant takes over the population with this probability. In this case, the mutant becomes the new resident. Otherwise, the existing resident remains. Then, another mutant is generated. These dynamics lead to a stationary distribution over the entire strategy space. Our new approach generalizes classical adaptive dynamics in three ways: (i) the population size is finite; (ii) mutants can be drawn non-locally and (iii) the dynamics are stochastic. We explore reactive strategies in the repeated Prisoner's Dilemma. We perform 'knock-out experiments' to study how various strategies affect the evolution of cooperation. We find that 'tit-for-tat' is a weak catalyst for the emergence of cooperation, while 'always cooperate' is a strong catalyst for the emergence of defection. Our analysis leads to a new understanding of the optimal level of forgiveness that is needed for the evolution of cooperation under direct reciprocity.}},  author = {Imhof, Lorens A. and Nowak, Martin A.},  citeulike-article-id = {5984219},  citeulike-linkout-0 = {http://dx.doi.org/10.1098/rspb.2009.1171},  citeulike-linkout-1 = {http://rspb.royalsocietypublishing.org/content/early/2009/10/20/rspb.2009.1171.abstract},  citeulike-linkout-2 = {http://rspb.royalsocietypublishing.org/content/early/2009/10/20/rspb.2009.1171.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19846456},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19846456},  day = {7},  doi = {10.1098/rspb.2009.1171},  issn = {1471-2954},  journal = {Proceedings of the Royal Society B: Biological Sciences},  keywords = {game-theory},  month = feb,  number = {1680},  pages = {463--468},  pmid = {19846456},  posted-at = {2010-10-14 15:01:00},  priority = {2},  title = {{Stochastic evolutionary dynamics of direct reciprocity}},  url = {http://dx.doi.org/10.1098/rspb.2009.1171},  volume = {277},  year = {2010}  }  @article{citeulike:7615086,  abstract = {{In classical games that have been applied to ecology, individual fitness is either density independent or population density is fixed. This article focuses on the habitat selection game where fitness depends on the population density that evolves over time. This model assumes that changes in animal distribution operate on a fast time scale when compared to demographic processes. Of particular interest is whether it is true, as one might expect, that resident phenotypes who use density-dependent optimal foraging strategies are evolutionarily stable with respect to invasions by mutant strategies. In fact, we show that evolutionary stability does not require that residents use the evolutionarily stable strategy (ESS) at every population density; rather it is the combined resident–mutant system that must be at an evolutionary stable state. That is, the separation of time scales assumption between behavioral and ecological processes does not imply that these processes are independent. When only consumer population dynamics in several habitats are considered (i. e. when resources do not undergo population dynamics), we show that the existence of optimal foragers forces the resident-mutant system to approach carrying capacity in each habitat even though the mutants do not die out. Thus, the ideal free distribution (IFD) for the single-species habitat selection game becomes an evolutionarily stable state that describes a mixture of resident and mutant phenotypes rather than a strategy adopted by all individuals in the system. Also discussed is how these results are affected when animal distribution and demographic processes act on the same time scale.}},  author = {Cressman, R. and K\v{r}ivan, V.},  citeulike-article-id = {7615086},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1600-0706.2010.17845.x},  citeulike-linkout-1 = {http://www.ingentaconnect.com/content/mksg/oki/2010/00000119/00000008/art00004},  doi = {10.1111/j.1600-0706.2010.17845.x},  issn = {0030-1299},  journal = {Oikos},  keywords = {game-theory},  number = {8},  pages = {1231--1242},  posted-at = {2010-10-14 14:58:21},  priority = {2},  publisher = {Blackwell Publishing Ltd},  title = {{The ideal free distribution as an evolutionarily stable state in density-dependent population games}},  url = {http://dx.doi.org/10.1111/j.1600-0706.2010.17845.x},  volume = {119},  year = {2010}  }  @article{citeulike:8017464,  abstract = {{Horizontal gene transfer (HGT) is believed to be a major source of genetic variation, particularly for prokaryotes. It is believed that horizontal gene transfer plays a major role in shaping bacterial genomes and is also believed to be responsible for the relatively rapid dissemination and acquisition of new, adaptive traits across bacterial strains. Despite the importance of horizontal gene transfer as a major source of genetic variation, the bulk of research on theoretical evolutionary dynamics and population genetics has focused on point mutations (sometimes coupled with gene duplication events) as the main engine of genomic change. Here, we seek to specifically model HGT processes in bacterial cells, by developing a mathematical model describing the influence that conjugation-mediated HGT has on the mutation-selection balance in an asexually reproducing population of unicellular, prokaryotic organisms. It is assumed that mutation-selection balance is reached in the presence of a fixed background concentration of antibiotic, to which the population must become resistant to survive. We find that HGT has a nontrivial effect on the mean fitness of the population. However, one of the central results that emerge from our analysis is that, at mutation-selection balance, conjugation-mediated HGT has a slightly deleterious effect on the mean fitness of a population. Therefore, we conclude that HGT does not confer a selection advantage in static environments. Rather, its advantage must lie in its ability to promote faster adaptation in dynamic environments, an interpretation that is consistent with the observation that HGT can be promoted by environmental stresses on a population.}},  author = {Raz, Yoav and Tannenbaum, Emmanuel},  citeulike-article-id = {8017464},  citeulike-linkout-0 = {http://dx.doi.org/10.1534/genetics.109.113613},  citeulike-linkout-1 = {http://www.genetics.org/cgi/content/abstract/185/1/327},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20194966},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20194966},  day = {1},  doi = {10.1534/genetics.109.113613},  journal = {Genetics},  keywords = {bacterial-biology},  month = may,  number = {1},  pages = {327--337},  pmid = {20194966},  posted-at = {2010-10-14 14:49:57},  priority = {2},  title = {{The Influence of Horizontal Gene Transfer on the Mean Fitness of Unicellular Populations in Static Environments}},  url = {http://dx.doi.org/10.1534/genetics.109.113613},  volume = {185},  year = {2010}  }  @article{citeulike:6283653,  abstract = {{Conjugation is an important mechanism involved in the transfer of resistance between bacteria. In this article a stochastic differential equation based model consisting of a continuous time state equation and a discrete time measurement equation is introduced to model growth and conjugation of two Enterococcus faecium strains in a rich exhaustible media. The model contains a new expression for a substrate dependent conjugation rate. A maximum likelihood based method is used to estimate the model parameters. Different models including different noise structure for the system and observations are compared using a likelihood-ratio test and Akaike's information criterion. Experiments indicating conjugation on the agar plates selecting for transconjugants motivates the introduction of an extended model, for which conjugation on the agar plate is described in the measurement equation. This model is compared to the model without plate conjugation. The modelling approach described in this article can be applied generally when modelling dynamical systems.}},  author = {Philipsen, K. R. and Christiansen, L. E. and Hasman, H. and Madsen, H.},  citeulike-article-id = {6283653},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jtbi.2009.11.011},  day = {07},  doi = {10.1016/j.jtbi.2009.11.011},  issn = {00225193},  journal = {Journal of Theoretical Biology},  keywords = {bacterial-biology},  month = mar,  number = {1},  pages = {134--142},  posted-at = {2010-10-14 14:48:57},  priority = {2},  title = {{Modelling conjugation with stochastic differential equations}},  url = {http://dx.doi.org/10.1016/j.jtbi.2009.11.011},  volume = {263},  year = {2010}  }  @article{citeulike:6725288,  abstract = {{All genes critical for plasmid replication regulation are located on the plasmid rather than on the host chromosome. It is possible therefore that there can be copy-up †cheater†mutants. In spite of this possibility, low copy number plasmids appear to exist stably in host populations. We examined this paradox using a multilevel selection model. Simulations showed that, a slightly higher copy number mutant could out-compete the wild type. Consequently, another mutant with still higher copy number could invade the first invader. However, the realized benefit of increasing intra-host fitness was saturating whereas that of inter-host fitness was exponential. As a result, above a threshold, intra-host selection was overcompensated by inter-host selection and the low copy number wild type plasmid could back invade a very high copy number plasmid. This led to a rock-paper-scissor (RPS) like situation that allowed the coexistence of plasmids with varied copy numbers. Furthermore, another type of cheater that had lost the genes required for conjugation but could hitchhike on a conjugal plasmid, could further reduce the advantage of copy-up mutants. These sociobiological interactions may compliment molecular mechanisms of replication regulation in stabilizing the copy numbers.}},  author = {Watve, Mukta M. and Dahanukar, Neelesh and Watve, Milind G.},  citeulike-article-id = {6725288},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0009328},  day = {24},  doi = {10.1371/journal.pone.0009328},  journal = {PLoS ONE},  keywords = {bacterial-biology},  month = feb,  number = {2},  pages = {e9328+},  posted-at = {2010-10-14 13:24:35},  priority = {2},  publisher = {Public Library of Science},  title = {{Sociobiological Control of Plasmid Copy Number in Bacteria}},  url = {http://dx.doi.org/10.1371/journal.pone.0009328},  volume = {5},  year = {2010}  }  @article{citeulike:5110122,  abstract = {{  Comparative whole-genome analyses have demonstrated that horizontal gene transfer (HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of specific prokaryotes is therefore tightly linked to the environment in which they live and the communal pool of genes available within that environment. Here we use the term supergenome to describe the set of all genes that a prokaryotic 'individual' can draw on within a particular environmental setting. Conjugative plasmids can be considered particularly successful entities within the communal pool, which have enabled HGT over large taxonomic distances. These plasmids are collections of discrete regions of genes that function as 'backbone modules' to undertake different aspects of overall plasmid maintenance and propagation. Conjugative plasmids often carry suites of 'accessory elements' that contribute adaptive traits to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized 'private genes'.  }},  author = {Norman, Anders and Hansen, Lars H. and S{\o}rensen, S{\o}ren J.},  citeulike-article-id = {5110122},  citeulike-linkout-0 = {http://dx.doi.org/10.1098/rstb.2009.0037},  citeulike-linkout-1 = {http://rstb.royalsocietypublishing.org/content/364/1527/2275.abstract},  citeulike-linkout-2 = {http://rstb.royalsocietypublishing.org/content/364/1527/2275.full.pdf},  citeulike-linkout-3 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873005/},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19571247},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19571247},  day = {12},  doi = {10.1098/rstb.2009.0037},  issn = {1471-2970},  journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},  keywords = {bacterial-biology},  month = aug,  number = {1527},  pages = {2275--2289},  pmcid = {PMC2873005},  pmid = {19571247},  posted-at = {2010-10-14 13:24:13},  priority = {2},  title = {{Conjugative plasmids: vessels of the communal gene pool.}},  url = {http://dx.doi.org/10.1098/rstb.2009.0037},  volume = {364},  year = {2009}  }  @article{citeulike:7985446,  abstract = {{Although bacteria are unicellular organisms, they have the ability to act in concert by synthesizing and detecting small diffusing autoinducer molecules. The phenomenon, known as quorum sensing, has mainly been proposed to serve as a means for cell-density measurement. Here, we use a cell-based model of growing bacterial microcolonies to investigate a quorum-sensing mechanism at a single cell level. We show that the model indeed predicts a density-dependent behavior, highly dependent on local cell-clustering and the geometry of the space where the colony is evolving. We analyze the molecular network with two positive feedback loops to find the multistability regions and show how the quorum-sensing mechanism depends on different model parameters. Specifically, we show that the switching capability of the network leads to more constraints on parameters in a natural environment where the bacteria themselves produce autoinducer than compared to situations where autoinducer is introduced externally. The cell-based model also allows us to investigate mixed populations, where non-producing cheater cells are shown to have a fitness advantage, but still cannot completely outcompete producer cells. Simulations, therefore, are able to predict the relative fitness of cheater cells from experiments and can also display and account for the paradoxical phenomenon seen in experiments; even though the cheater cells have a fitness advantage in each of the investigated groups, the overall effect is an increase in the fraction of producer cells. The cell-based type of model presented here together with high-resolution experiments will play an integral role in a more explicit and precise comparison of models and experiments, addressing quorum sensing at a cellular resolution. Unicellular organisms have the ability to communicate with each other via signaling molecules, leading to correlated behaviors resembling that of higher organisms. This process, called quorum sensing, allows the cells to monitor the population size or density in a decentralized fashion and perform a common task when these parameters exceed predefined threshold values. The quorum sensing mechanism has been implicated in diverse functions such as producing bioluminescence, virulence factors, and initiating biofilm formation. Complex emergent behaviors, such as quorum sensing, can be hard to analyze and understand without the assistance of mathematical and computational models. Here, we present a cell-based model of proliferating bacterial microcolonies and investigate how population-level responses can emerge from the signaling and mechanical properties of individual cells. We study both signaling variations within homogeneous (homotypic) bacterial populations as well as signaling and competition in mixed heterotypic populations. We investigate in particular how population size, local cell density, and spatial confinement affect colony growth and predict strategies for facilitating quorum sensing. We also show that the interplay between †honest†quorum sensing signal producing bacteria and non-producing †cheaters†can lead to emergent feedback regulation via differentiated growth that provides only a transient benefit for cheating cells.}},  author = {Melke, Pontus and Sahlin, Patrik and Levchenko, Andre and J\"{o}nsson, Henrik},  citeulike-article-id = {7985446},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000819},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20585545},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20585545},  day = {17},  doi = {10.1371/journal.pcbi.1000819},  issn = {1553-7358},  journal = {PLoS Comput Biol},  keywords = {bacterial-biology},  month = jun,  number = {6},  pages = {e1000819+},  pmid = {20585545},  posted-at = {2010-10-11 11:52:58},  priority = {2},  publisher = {Public Library of Science},  title = {{A Cell-Based Model for Quorum Sensing in Heterogeneous Bacterial Colonies}},  url = {http://dx.doi.org/10.1371/journal.pcbi.1000819},  volume = {6},  year = {2010}  }  @article{citeulike:7963183,  abstract = {{  Are plasmids selfish parasitic DNA molecules or an integrated part of the bacterial genome? This chapter reviews the current understanding of the persistence mechanisms of conjugative plasmids harbored by bacterial cells and populations. The diversity and intricacy of mechanisms affecting the successful propagation and long-term continued existence of these extra-chromosomal elements is extensive. Apart from the accessory genetic elements that may provide plasmid-harboring cells a selective advantage, special focus is placed on the mechanisms conjugative plasmids employ to ensure their stable maintenance in the host cell. These importantly include the ability to self-mobilize in a process termed conjugative transfer, which may occur across species barriers. Other plasmid stabilizing mechanisms include the multimer resolution system, active partitioning, and post-segregational-killing of plasmid-free cells. Finally, various molecular adaptations of plasmids to better match the genetic background of their bacterial host cell will be described.  }},  author = {Bahl, Martin Iain I. and Hansen, Lars Hestbjerg H. and S{\o}rensen, S{\o}ren J.},  citeulike-article-id = {7963183},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-1-60327-853-9\_5},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19271180},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19271180},  doi = {10.1007/978-1-60327-853-9\_5},  issn = {1064-3745},  journal = {Methods in molecular biology (Clifton, N.J.)},  keywords = {bacterial-biology},  pages = {73--102},  pmid = {19271180},  posted-at = {2010-10-09 07:39:29},  priority = {2},  title = {{Persistence mechanisms of conjugative plasmids.}},  url = {http://dx.doi.org/10.1007/978-1-60327-853-9\_5},  volume = {532},  year = {2009}  }  @article{citeulike:1700123,  abstract = {{Despite the near-ubiquity of plasmids in bacterial populations and the profound contribution of infectious gene transfer to the adaptation and evolution of bacteria, the mechanisms responsible for the maintenance of plasmids in bacterial populations are poorly understood. In this article, we address the question of how plasmids manage to persist over evolutionary time. Empirical studies suggest that plasmids are not infectiously transmitted at a rate high enough to be maintained as genetic parasites. In PART I, we present a general mathematical proof that if this is the case, then plasmids will not be able to persist indefinitely solely by carrying genes that are beneficial or sometimes beneficial to their host bacteria. Instead, such genes should, in the long run, be incorporated into the bacterial chromosome. If the mobility of host-adaptive genes imposes a cost, that mobility will eventually be lost. In PART II, we illustrate a pair of mechanisms by which plasmids can be maintained indefinitely even when their rates of transmission are too low for them to be genetic parasites. First, plasmids may persist because they can transfer locally adapted genes to newly arriving strains bearing evolutionary innovations, and thereby preserve the local adaptations in the face of background selective sweeps. Second, plasmids may persist because of their ability to shuttle intermittently favored genes back and forth between various (noncompeting) bacterial strains, ecotypes, or even species.}},  author = {Bergstrom, Carl T. and Lipsitch, Marc and Levin, Bruce R.},  citeulike-article-id = {1700123},  citeulike-linkout-0 = {http://www.genetics.org/content/155/4/1505.abstract},  citeulike-linkout-1 = {http://www.genetics.org/content/155/4/1505.full.pdf},  citeulike-linkout-2 = {http://www.genetics.org/cgi/content/abstract/155/4/1505},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/10924453},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=10924453},  day = {1},  issn = {0016-6731},  journal = {Genetics},  keywords = {bacterial-biology},  month = aug,  number = {4},  pages = {1505--1519},  pmid = {10924453},  posted-at = {2010-10-09 07:38:29},  priority = {2},  title = {{Natural Selection, Infectious Transfer and the Existence Conditions for Bacterial Plasmids}},  url = {http://www.genetics.org/content/155/4/1505.abstract},  volume = {155},  year = {2000}  }  @article{citeulike:703736,  abstract = {{This review deals with the prospective, experimental documentation of horizontal gene transfer (HGT) and its role in real-time, local adaptation. We have focused on plasmids and their function as an accessory and/or adaptive gene pool. Studies of the extent of HGT in natural environments have identified certain hot spots, and many of these involve biofilms. Biofilms are uniquely suited for HGT, as they sustain high bacterial density and metabolic activity, even in the harshest environments. Single-cell detection of donor, recipient and transconjugant bacteria in various natural environments, combined with individual-based mathematical models, has provided a new platform for HGT studies.}},  author = {Sorensen, Soren J. and Bailey, Mark and Hansen, Lars H. and Kroer, Niels and Wuertz, Stefan},  citeulike-article-id = {703736},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrmicro1232},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrmicro1232},  day = {01},  doi = {10.1038/nrmicro1232},  issn = {1740-1526},  journal = {Nature Reviews Microbiology},  keywords = {bacterial-biology},  month = sep,  number = {9},  pages = {700--710},  posted-at = {2010-10-03 19:23:20},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Studying plasmid horizontal transfer in situ: a critical review}},  url = {http://dx.doi.org/10.1038/nrmicro1232},  volume = {3},  year = {2005}  }  @article{citeulike:7907527,  abstract = {{Inspired by the recent studies on the analysis of biased random walk behavior of Escherichia coli[Passino, K.M., 2002. Biomimicry of bacterial foraging for distributed optimization and control. IEEE Control Syst. Mag. 22 (3), 52-67; Passino, K.M., 2005. Biomimicry for Optimization, Control and Automation. Springer-Verlag, pp. 768-798; Liu, Y., Passino, K.M., 2002. Biomimicry of social foraging bacteria for distributed optimization: models, principles, and emergent behaviors. J. Optim. Theory Appl. 115 (3), 603-628], we have developed a model describing the motile behavior of E. coli by specifying some simple rules on the chemotaxis. Based on this model, we have analyzed the role of some key parameters involved in the chemotactic behavior to unravel the underlying design principles. By investigating the target tracking capability of E. coli in a maze through computer simulations, we found that E. coli clusters can be controlled as target trackers in a complex micro-scale-environment. In addition, we have explored the dynamical characteristics of this target tracking mechanism through perturbation of parameters under noisy environments. It turns out that the E. coli chemotaxis mechanism might be designed such that it is sensitive enough to efficiently track the target and also robust enough to overcome environmental noises.}},  author = {Kim, Tae-Hwan H. and Jung, Sung Hoon H. and Cho, Kwang-Hyun H.},  citeulike-article-id = {7907527},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.biosystems.2007.08.009},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17923256},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17923256},  doi = {10.1016/j.biosystems.2007.08.009},  issn = {0303-2647},  journal = {Bio Systems},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {171--182},  pmid = {17923256},  posted-at = {2010-09-27 15:42:21},  priority = {2},  title = {{Investigations into the design principles in the chemotactic behavior of Escherichia coli.}},  url = {http://dx.doi.org/10.1016/j.biosystems.2007.08.009},  volume = {91},  year = {2008}  }  @article{citeulike:1110567,  abstract = {{Quorum sensing faces evolutionary problems from non-producing or over-producing cheaters. Such problems are circumvented in diffusion sensing, an alternative explanation for quorum sensing. However, both explanations face the problems of signalling in complex environments such as the rhizosphere where, for example, the spatial distribution of cells can be more important for sensing than cell density, which we show by mathematical modelling. We argue that these conflicting concepts can be unified by a new hypothesis, efficiency sensing, and that some of the problems associated with signalling in complex environments, as well as the problem of maintaining honesty in signalling, can be avoided when the signalling cells grow in microcolonies.}},  author = {Hense, Burkhard A. and Kuttler, Christina and M\"{u}ller, Johannes and Rothballer, Michael and Hartmann, Anton and Ulrich, Jan},  citeulike-article-id = {1110567},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrmicro1600},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrmicro1600},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17304251},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17304251},  day = {01},  doi = {10.1038/nrmicro1600},  issn = {1740-1526},  journal = {Nature Reviews Microbiology},  keywords = {bacterial-biology},  month = mar,  number = {3},  pages = {230--239},  pmid = {17304251},  posted-at = {2010-09-27 15:41:48},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Does efficiency sensing unify diffusion and quorum sensing?}},  url = {http://dx.doi.org/10.1038/nrmicro1600},  volume = {5},  year = {2007}  }  @article{citeulike:789799,  abstract = {{This paper presents an approach to ecological/evolutionary modelling that is inspired by natural bacterial ecosystems and bacterial evolution. An individual-based artificial ecosystem model is proposed, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by rule-based learning classifier systems. The proposed ecosystem model consists of a n-dimensional environmental grid, which can contain different types of artificial resources in arbitrary arrangements. The resources provide the energy that is necessary for the organisms to sustain life, and can trigger different types of behaviour in the organisms, such as movement towards nutrients and away from toxic substances, growth, and the controlled release of signalling resources. The balance between energy and material is modelled carefully to ensure that the ecosystem is dissipative. Those organisms that are able to efficiently exploit the available resources gradually accumulate enough energy to reproduce (by binary fission) and generate copies of themselves in the environment. Organisms are also able to produce their own resources, which can potentially be used as markers to send signals to other organisms (a behaviour known as quorum sensing). The complex relationships between stimuli and actions in the organisms are stochastically altered by means of mutations, thus enabling the organisms to adapt to their environment and maximise their lifespan and reproductive success. In this paper, the proposed bacterial ecosystem model is defined formally and its structure is discussed in detail. This is followed by results from simulation experiments that illustrate the model's operation and how it can be used in evolutionary modelling/computing scenarios.}},  address = {BioComputing and Computational Biology Research Group, Department of Computer Science, The University of Liverpool, Liverpool L69 3BX, UK. [email protected]},  author = {Vlachos, C. and Paton, R. C. and Saunders, J. R. and Wu, Q. H.},  citeulike-article-id = {789799},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.biosystems.2005.06.017},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16386355},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16386355},  doi = {10.1016/j.biosystems.2005.06.017},  issn = {0303-2647},  journal = {Biosystems},  keywords = {simulation-and-modeling},  month = apr,  number = {1},  pages = {49--72},  pmid = {16386355},  posted-at = {2010-09-27 15:41:08},  priority = {2},  title = {{A rule-based approach to the modelling of bacterial ecosystems.}},  url = {http://dx.doi.org/10.1016/j.biosystems.2005.06.017},  volume = {84},  year = {2006}  }  @article{Novak2008Design,  abstract = {{ Cellular rhythms are generated by complex interactions among genes, proteins and metabolites. They are used to control every aspect of cell physiology, from signalling, motility and development to growth, division and death. We consider specific examples of oscillatory processes and discuss four general requirements for biochemical oscillations: negative feedback, time delay, sufficient 'nonlinearity' of the reaction kinetics and proper balancing of the timescales of opposing chemical reactions. Positive feedback is one mechanism to delay the negative-feedback signal. Biological oscillators can be classified according to the topology of the positive- and negative-feedback loops in the underlying regulatory mechanism.}},  author = {Novak, Bela and Tyson, John J.},  citeulike-article-id = {3655691},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nrm2530},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nrm2530},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18971947},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18971947},  day = {30},  doi = {10.1038/nrm2530},  issn = {1471-0072},  journal = {Nature Reviews Molecular Cell Biology},  month = oct,  number = {12},  pages = {981--991},  pmid = {18971947},  posted-at = {2010-09-27 15:11:05},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Design principles of biochemical oscillators}},  url = {http://dx.doi.org/10.1038/nrm2530},  volume = {9},  year = {2008}  }  @incollection{citeulike:7901885,  abstract = {{We propose a novel, generic definition of probabilistic schedulers for population protocols. We then identify the consistent probabilistic schedulers, and prove that any consistent scheduler that assigns a non-zero probability to any transition i\^{a}j, where i and j are configurations satisfying i\^{a}\^{a} \^{a}j, is fair with probability 1. This is a new theoretical framework that aims to simplify proving specific probabilistic schedulers fair. In this paper we propose two new schedulers, the State Scheduler and the Transition Function Scheduler. Both possess the significant capability of being protocol-aware, i.e. they can assign transition probabilities based on information concerning the underlying protocol. By using our framework we prove that the proposed schedulers, and also the Random Scheduler that was defined by Angluin et al. [2], are all fair with probability 1. Finally, we define and study equivalence between schedulers w.r.t. performance and correctness and prove that there exist fair probabilistic schedulers that are not equivalent w.r.t. to performance and others that are not equivalent w.r.t. correctness.}},  address = {Berlin, Heidelberg},  author = {Chatzigiannakis, Ioannis and Dolev, Shlomi and Fekete, S\'{a}ndor and Michail, Othon and Spirakis, Paul},  booktitle = {Principles of Distributed Systems},  chapter = {5},  citeulike-article-id = {7901885},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-10877-8\_5},  citeulike-linkout-1 = {http://www.springerlink.com/content/23p8675874214482},  doi = {10.1007/978-3-642-10877-8\_5},  editor = {Abdelzaher, Tarek and Raynal, Michel and Santoro, Nicola},  isbn = {978-3-642-10876-1},  keywords = {population-protocols},  pages = {33-47--47},  posted-at = {2010-09-26 16:49:16},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Not All Fair Probabilistic Schedulers Are Equivalent}},  url = {http://dx.doi.org/10.1007/978-3-642-10877-8\_5},  volume = {5923},  year = {2009}  }  @article{citeulike:2285571,  abstract = {{Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers.}},  author = {Grimm, Volker and Berger, Uta and Bastiansen, Finn and Eliassen, Sigrunn and Ginot, Vincent and Giske, Jarl and Goss-Custard, John and Grand, Tamara and Heinz, Simone K. and Huse, Geir and Huth, Andreas and Jepsen, Jane U. and J{\o}rgensen, Christian and Mooij, Wolf M. and M\"{u}ller, Birgit and Pe'er, Guy and Piou, Cyril and Railsback, Steven F. and Robbins, Andrew M. and Robbins, Martha M. and Rossmanith, Eva and R\"{u}ger, Nadja and Strand, Espen and Souissi, Sami and Stillman, Richard A. and Vab{\o}, Rune and Visser, Ute and DeAngelis, Donald L.},  citeulike-article-id = {2285571},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ecolmodel.2006.04.023},  citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6VBS-4K606T7-3/2/1dad6192bec683f32fce6dee9d665b51},  day = {15},  doi = {10.1016/j.ecolmodel.2006.04.023},  issn = {03043800},  journal = {Ecological Modelling},  keywords = {individual-based-modeling},  month = sep,  number = {1-2},  pages = {115--126},  posted-at = {2010-09-26 15:37:47},  priority = {2},  title = {{A standard protocol for describing individual-based and agent-based models}},  url = {http://dx.doi.org/10.1016/j.ecolmodel.2006.04.023},  volume = {198},  year = {2006}  }  @incollection{citeulike:7889521,  abstract = {{We introduce a formal model of computation for networks of tiny artifacts, the static synchronous sensor field model (SSSF) which considers that the devices communicate through a fixed communication graph and interact with the environment through input/output data streams. We analyze the performance of SSSFs solving two sensing problems the Average Monitoring and the Alerting problems. For constant memory SSSFs we show that the set of recognized languages is contained in DSPACE(n\^{a}+\^{a}m) where n is the number of nodes of the communication graph and m its number of edges. Finally we explore the capabilities of SSSFs having sensing and additional non-sensing constant memory devices.}},  address = {Berlin, Heidelberg},  author = {\`{A}lvarez, Carme and Duch, Amalia and Gabarro, Joaquim and Serna, Maria},  booktitle = {Algorithmic Aspects of Wireless Sensor Networks},  chapter = {3},  citeulike-article-id = {7889521},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-05434-1\_3},  citeulike-linkout-1 = {http://www.springerlink.com/content/x446744534307m65},  doi = {10.1007/978-3-642-05434-1\_3},  editor = {Dolev, Shlomi},  isbn = {978-3-642-05433-4},  keywords = {population-protocols},  pages = {3-14--14},  posted-at = {2010-09-23 15:04:42},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Sensor Field: A Computational Model}},  url = {http://dx.doi.org/10.1007/978-3-642-05434-1\_3},  volume = {5804},  year = {2009}  }  @incollection{citeulike:7889402,  abstract = {{Two models of distributed computation are described in which the agents are anonymous finite-state sensors interacting through a communication network whose dynamics (in case the agents are mobile) and/or topology they do not control or even know about. These models were recently introduced in a series of papers by Angluin et al. [3,4,2,5].}},  address = {Berlin, Heidelberg},  author = {Peralta, Ren\'{e}},  booktitle = {Secure Mobile Ad-hoc Networks and Sensors},  chapter = {17},  citeulike-article-id = {7889402},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/11801412\_17},  citeulike-linkout-1 = {http://www.springerlink.com/content/r64037u1k923m788},  doi = {10.1007/11801412\_17},  editor = {Burmester, Mike and Yasinsac, Alec},  isbn = {978-3-540-36646-1},  keywords = {population-protocols},  pages = {182-185--185},  posted-at = {2010-09-23 14:42:07},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Dark Encounter Computations}},  url = {http://dx.doi.org/10.1007/11801412\_17},  volume = {4074},  year = {2006}  }  @article{citeulike:7889375,  abstract = {{Abstract 10.1002/cpe.1583.abs This paper studies how to detect anomalies in a distributed manner by using wireless sensor networks (WSNs). We focus on a medical context, where the existing works generally provide large environments to monitor patients using sensors as simple transducers. Those devices forward sensed health parameters to a main base station. This station collects received data and may perform some computations. In this paper, we perform some distributed tasks on the sensors. We propose a distributed algorithm, which allows to raise alarms under some initial rules to alert efficiently medical staff in case of critical situations without needless warnings. Each mote monitors a parameter. When this parameter reaches an abnormal value, the mote communicates with other motes in order to check if it is a 'local' anomaly or if the patient is in an abnormal situation. In such cases an alarm is raised. We implemented our algorithm over a network of micaZ sensors running under TinyOS. The obtained results show promising perspectives. Copyright {\copyright} 2010 John Wiley \& Sons, Ltd.}},  author = {Dessart, N. and Fouchal, H. and Hunel, P.},  citeulike-article-id = {7889375},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/cpe.1583},  doi = {10.1002/cpe.1583},  journal = {Concurrency Computat.: Pract. Exper.},  keywords = {population-protocols},  number = {10},  pages = {1240--1251},  posted-at = {2010-09-23 14:38:17},  priority = {2},  publisher = {John Wiley \& Sons, Ltd.},  title = {{Distributed diagnosis over wireless sensors networks}},  url = {http://dx.doi.org/10.1002/cpe.1583},  volume = {22},  year = {2010}  }  @techreport{BUSNEL:2008:INRIA-00296584:2,  abstract = {{P}opulation protocols provide theoretical foundations for mobile tiny device networks in which global behavior emerges from a set of simple interactions between anonymous agents. {T}he works in this area mostly focus on studying the computational power of the model. {R}esults hold as long as a fair scheduler, ensuring that all reachable system states are endlessly reached, governs the interactions between nodes. {T}his assumption is crucial to ensure that the protocols eventually converge. {T}his paper studies for the first time the impact of the agents? mobility model on the convergence speed of population protocols. {W}e perform our study by considering several mobility models traditionally used in the ad-hoc network community. {W}e propose an augmented population protocol model where each edge of the interaction graph is weighted, representing the probability of two agents to interact. {T}his models the behaviour of the scheduler with respect to various mobility models. {W}e empirically show that mobility models do have a significant impact on the convergence speed of the protocols. {I}n fact, we observe that the uniform distribution always provides the best convergence time. {S}uch a model is representative of the well-known random-way point model used to evaluate most of mobile ad-hoc network protocols. {W}e then formally prove that a uniform distribution of weights provides the lowest bound of average convergence speed for any population protocol.},  author = {{B}usnel, {Y}ann and {B}ertier, {M}arin and {K}ermarrec, {A}nne-{M}arie},  citeulike-article-id = {7889163},  citeulike-linkout-0 = {http://hal.inria.fr/inria-00296584/en/},  institution = {INRIA},  keywords = {population-protocols},  number = {{RR}-6580},  pages = {30},  posted-at = {2010-09-23 14:00:04},  priority = {2},  title = {{O}n the {I}mpact of the {M}obility on {C}onvergence {S}peed of {P}opulation {P}rotocols},  type = {Research Report},  url = {http://hal.inria.fr/inria-00296584/en/},  year = {2008}  }  @incollection{citeulike:7889148,  abstract = {{Developing self-stabilizing solutions is considered to be more challenging and complicated than developing classical solutions, where a proper initialization of the variables can be assumed. This remark holds for a large variety of models. Hence, to ease the task of the developers, some automatic techniques have been proposed to design self-stabilizing algorithms. In this paper, we propose an automatic transformer for algorithms in population protocols model. This model introduced recently for networks with a large number of resource-limited mobile agents. For our purposes, we use a variant of this model. Mainly, we assume agents having characteristics (e.g., moving speed, communication radius) affecting their intercommunication speed and considered through the notion of cover time. The automatic transformer takes as an input an algorithm solving a static problem and outputs a self-stabilizing algorithm for the same problem. We prove that our transformer is correct and we analyze its stabilization complexity.}},  address = {Berlin, Heidelberg},  author = {Beauquier, Joffroy and Burman, Janna and Kutten, Shay},  booktitle = {Stabilization, Safety, and Security of Distributed Systems},  chapter = {7},  citeulike-article-id = {7889148},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-05118-0\_7},  citeulike-linkout-1 = {http://www.springerlink.com/content/k47kl46214v92t4h},  doi = {10.1007/978-3-642-05118-0\_7},  editor = {Guerraoui,, Rachid and Petit,, Franck},  isbn = {978-3-642-05117-3},  keywords = {population-protocols},  pages = {90-104--104},  posted-at = {2010-09-23 13:57:38},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Making Population Protocols Self-stabilizing}},  url = {http://dx.doi.org/10.1007/978-3-642-05118-0\_7},  volume = {5873},  year = {2009}  }  @inproceedings{citeulike:7889130,  abstract = {{The aim of this study is to perform a simulation of large scale Wireless Sensor Networks (WSN) working on medical diagnosis. The main feature of this WSN is its density and the fact that all sensors are in the same radio range. Our approach helps medical staff to diagnose diseases in an automatic way. In this context, each patient is equipped to a set of sensors. Each sensor is connected to a transducer dedicated to measure a specific health parameter. This WSN will perform some computations and run an alarm when some diseases are suspected. This technique is based on the population protocol to handle data exchanged between sensors. This approach is in fact an efficient distributed algorithm which implies that the diagnose may be done by any sensor dealing with the disease detection. The main result of this paper is the approach supports large scalability which proves its practicability for real cases.}},  author = {Dessart, N. and Fouchal, H. and Hunel, P. and Rabat, C.},  citeulike-article-id = {7889130},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/iscc.2010.5546618},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=5546618},  doi = {10.1109/iscc.2010.5546618},  keywords = {population-protocols},  location = {Riccione, Italy},  month = jun,  pages = {1115--1120},  posted-at = {2010-09-23 13:54:53},  priority = {2},  title = {{Simulation of large scale WSN for medical care}},  url = {http://dx.doi.org/10.1109/iscc.2010.5546618},  year = {2010}  }  @techreport{CANEPA:2007:INRIA-00166632:2,  abstract = {{I}n this paper we address the stabilizing leader election problem in the population protocols model augmented with oracles. {P}opulation protocols is a recent model of computation that captures the interactions of biological systems. {I}n this model emergent global behavior is observed while anonymous finite-state agents(nodes) perform local peer interactions. {U}niform self-stabilizing leader election is impossible in such systems without additional assumptions. {T}herefore, the classical model has been augmented with the eventual leader detector, {O}mega?, that eventually detects the presence or absence of a leader. {I}n the augmented model several solutions for leader election in rings and complete networks have been proposed. {I}n this work we extend the study to trees and arbitrary topologies. {W}e propose deterministic and probabilistic solutions. {A}ll the proposed algorithms are memory optimal --- they need only one memory bit per agent. {A}dditionally, we prove the necessity of the eventual leader detector even in environments helped by randomization.},  author = {{C}anepa, {D}avide and {G}radinariu {P}otop {B}utucaru, {M}aria},  citeulike-article-id = {7889125},  citeulike-linkout-0 = {http://hal.inria.fr/inria-00166632/en/},  institution = {INRIA},  keywords = {population-protocols},  number = {{RR}-6269},  pages = {17},  posted-at = {2010-09-23 13:54:07},  priority = {2},  title = {{S}tabilizing leader election in population protocols},  type = {Research Report},  url = {http://hal.inria.fr/inria-00166632/en/},  year = {2007}  }  @inproceedings{citeulike:7889104,  abstract = {{Self-stabilization is a versatile technique to withstand any transient fault in a distributed system. Mobile robots (or agents) are one of the emerging trends in distributed computing as they mimic autonomous biologic entities. The contribution of this paper is threefold. First, we present a new model for studying mobile entities in networks subject to transient faults. Our model differs from the classical robot model because robots have constraints about the paths they are allowed to follow, and from the classical agent model because the number of agents remains fixed throughout the execution of the protocol. Second, in this model, we study the possibility of designing self-stabilizing algorithms when those algorithms are run by mobile robots (or agents) evolving on a graph. We concentrate on the core building blocks of robot and agents problems: naming and leader election. Not surprisingly, when no constraints are given on the network graph topology and local execution model, both problems are impossible to solve. Finally, using minimal hypothesis with respect to impossibility results, we provide deterministic and probabilistic solutions to both problems, and show equivalence of these problems by an algorithmic reduction mechanism.}},  address = {Berlin, Heidelberg},  author = {Blin, L\'{e}lia and Maria Gradinariu Potop Butucaru and Tixeuil, S\'{e}bastien},  booktitle = {OPODIS'07: Proceedings of the 11th international conference on Principles of distributed systems},  citeulike-article-id = {7889104},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1782394.1782416},  isbn = {3-540-77095-X, 978-3-540-77095-4},  keywords = {population-protocols},  location = {Guadeloupe, French West Indies},  pages = {301--314},  posted-at = {2010-09-23 13:50:26},  priority = {2},  publisher = {Springer-Verlag},  title = {{On the self-stabilization of mobile robots in graphs}},  url = {http://portal.acm.org/citation.cfm?id=1782394.1782416},  year = {2007}  }  @unpublished{AngluinAR2009,  author = {Angluin, Dana and Aspnes, James and Reyzin, Lev},  citeulike-article-id = {7889099},  comment = {To appear, ALT 2010},  keywords = {population-protocols},  month = jul,  posted-at = {2010-09-23 13:49:02},  priority = {2},  title = {{Inferring social networks from outbreaks}},  year = {2010}  }  @incollection{citeulike:7217762,  abstract = {{This paper considers the self-stabilizing leader-election problem in a model of interacting anonymous finite-state agents. Leader election is a fundamental problem in distributed systems; many distributed problems are easily solved with the help of a central coordinator. Self-stabilizing algorithms do not require initialization in order to operate correctly and can recover from transient faults that obliterate all state information in the system. Anonymous finite-state agents model systems of identical simple computational nodes such as sensor networks and biological computers. Self-stabilizing leader election is easily shown to be impossible in such systems without additional structure. An eventual leader detector \^{I}{\copyright}? is an oracle that eventually detects the presence or absence of a leader. With the help of \^{I}{\copyright}?, uniform self-stabilizing leader election algorithms are presented for two natural classes of network graphs: complete graphs and rings. The first algorithm works under either a local or global fairness condition, whereas the second requires global fairness. With only local fairness, uniform self-stabilizing leader election in rings is impossible, even with the help of \^{I}{\copyright}?. Keywords: anonymous, failure detector, fairness, finite-state, impossibility result, leader election, population protocols, ring network, self-stabilization, sensor networks.}},  address = {Berlin, Heidelberg},  author = {Fischer, Michael and Jiang, Hong},  booktitle = {Principles of Distributed Systems},  chapter = {28},  citeulike-article-id = {7217762},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/11945529\_28},  citeulike-linkout-1 = {http://www.springerlink.com/content/b6584u0652q7r527},  doi = {10.1007/11945529\_28},  editor = {Shvartsman,, Alexander},  isbn = {978-3-540-49990-9},  keywords = {population-protocols},  pages = {395-409--409},  posted-at = {2010-09-23 13:46:43},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Self-stabilizing Leader Election in Networks of Finite-State Anonymous Agents}},  url = {http://dx.doi.org/10.1007/11945529\_28},  volume = {4305},  year = {2006}  }  @article{citeulike:7889083,  abstract = {{We propose a new theoretical model for passively mobile Wireless Sensor  Networks. We call it the PALOMA model, standing for PAssively mobile  LOgarithmic space MAchines. The main modification w.r.t. the Population  Protocol model is that agents now, instead of being automata, are Turing  Machines whose memory is logarithmic in the population size n. Note that the  new model is still easily implementable with current technology. We focus on  complete communication graphs. We define the complexity class PLM, consisting  of all symmetric predicates on input assignments that are stably computable by  the PALOMA model. We assume that the agents are initially identical.  Surprisingly, it turns out that the PALOMA model can assign unique consecutive  ids to the agents and inform them of the population size! This allows us to  give a direct simulation of a Deterministic Turing Machine of O(nlogn) space,  thus, establishing that any symmetric predicate in SPACE(nlogn) also belongs to  PLM. We next prove that the PALOMA model can simulate the Community Protocol  model, thus, improving the previous lower bound to all symmetric predicates in  NSPACE(nlogn). Going one step further, we generalize the simulation of the  deterministic TM to prove that the PALOMA model can simulate a Nondeterministic  TM of O(nlogn) space. Although providing the same lower bound, the important  remark here is that the bound is now obtained in a direct manner, in the sense  that it does not depend on the simulation of a TM by a Pointer Machine.  Finally, by showing that a Nondeterministic TM of O(nlogn) space decides any  language stably computable by the PALOMA model, we end up with an exact  characterization for PLM: it is precisely the class of all symmetric predicates  in NSPACE(nlogn).}},  archivePrefix = {arXiv},  author = {Chatzigiannakis, Ioannis and Michail, Othon and Nikolaou, Stavros and Pavlogiannis, Andreas and Spirakis, Paul G.},  citeulike-article-id = {7889083},  citeulike-linkout-0 = {http://arxiv.org/abs/1004.3395},  citeulike-linkout-1 = {http://arxiv.org/pdf/1004.3395},  day = {20},  eprint = {1004.3395},  keywords = {population-protocols},  month = apr,  posted-at = {2010-09-23 13:44:29},  priority = {2},  title = {{Passively Mobile Communicating Logarithmic Space Machines}},  url = {http://arxiv.org/abs/1004.3395},  year = {2010}  }  @article{citeulike:7889080,  abstract = {{The computational power of networks of small resource-limited mobile agents is explored. Two new models of computation based on pairwise interactions of finite-state agents in populations of finite but unbounded size are defined. With a fairness condition on interactions, the concept of stable computation of a function or predicate is defined. Protocols are given that stably compute any predicate in the class definable by formulas of Presburger arithmetic, which includes Boolean combinations of threshold-k, majority, and equivalence modulo m. All stably computable predicates are shown to be in NL. Assuming uniform random sampling of interacting pairs yields the model of conjugating automata. Any counter machine with O(1) counters of capacity O(n) can be simulated with high probability by a conjugating automaton in a population of size n. All predicates computable with high probability in this model are shown to be in P; they can also be computed by a randomized logspace machine in exponential time. Several open problems and promising future directions are discussed.}},  author = {Angluin, Dana and Aspnes, James and Diamadi, Zo\"{e} and Fischer, Michael and Peralta, Ren\'{e}},  citeulike-article-id = {7889080},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00446-005-0138-3},  citeulike-linkout-1 = {http://www.springerlink.com/content/p84133033863m083},  day = {4},  doi = {10.1007/s00446-005-0138-3},  issn = {0178-2770},  journal = {Distributed Computing},  keywords = {population-protocols},  month = mar,  number = {4},  pages = {235-253--253},  posted-at = {2010-09-23 13:42:59},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  title = {{Computation in networks of passively mobile finite-state sensors}},  url = {http://dx.doi.org/10.1007/s00446-005-0138-3},  volume = {18},  year = {2006}  }  @inproceedings{citeulike:7889078,  abstract = {{Wireless sensor networks are a new generation of network which needs specific models and algorithms. We are interested specifically to mobile wireless sensor networks which are considered as anonymous asynchronous distributed mobile systems. As broadcast is one of the most important applications for this kind of networks, and as it depends on the communication model used in the network, we tried to find the most adequate one to make a distributed broadcast algorithm. We adopted the model presented by Angluin of pairwise interactions of anonymous finite-state agents to broadcast information: the population protocol. We tried to modify this model to avoid duplication of the information and calculate its complexity. Then, we extended it with the rendezvous one which made the stabilization faster. The implementation, the simulation and the validation of these algorithms and results were done with Visidia.}},  author = {Ouled, Nesrine and Hadj Kacem, Hatem and Mosbah, Mohamed and Zemmari, Akka},  citeulike-article-id = {7889078},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/notere.2010.5536695},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=5536695},  doi = {10.1109/notere.2010.5536695},  keywords = {population-protocols},  location = {Tozeur, Tunisia},  month = may,  pages = {219--226},  posted-at = {2010-09-23 13:42:02},  priority = {2},  title = {{Broadcast in wireless mobile sensor networks with population protocols and extension with the rendezvous model}},  url = {http://dx.doi.org/10.1109/notere.2010.5536695},  year = {2010}  }  @incollection{citeulike:7889075,  abstract = {{Consensus problems occur in many contexts and have therefore been extensively studied in the past. In the original consensus problem, every process initially proposes a value, and the goal is to decide on a single value from all those proposed. We are studying a slight variant of the consensus problem called the stabilizing consensus problem [2]. In this problem, we do not require that each process irrevocably commits to a final value but that eventually they arrive at a common, stable value without necessarily being aware of that. This should work irrespective of the states in which the processes are starting. In other words, we are searching for a self-stabilizing algorithm for the consensus problem. Coming up with such an algorithm is easy without adversarial involvement, but we allow some adversary to continuously change the states of some of the nodes at will. Despite these state changes, we would like the processes to arrive quickly at a common value that will be preserved for as many time steps as possible (in a sense that almost all of the processes will store this value during that period of time). Interestingly, we will demonstrate that there is a simple algorithm for this problem that essentially needs logarithmic time and work with high probability to arrive at such a stable value, even if the adversary can perform arbitrary state changes, as long as it can only do so for a limited number of processes at a time.}},  address = {Berlin, Heidelberg},  author = {Doerr, Benjamin and Goldberg, Leslie and Minder, Lorenz and Sauerwald, Thomas and Scheideler, Christian},  booktitle = {Distributed Computing},  chapter = {50},  citeulike-article-id = {7889075},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-15763-9\_50},  citeulike-linkout-1 = {http://www.springerlink.com/content/n65q748264217128},  doi = {10.1007/978-3-642-15763-9\_50},  editor = {Lynch,, Nancy and Shvartsman,, Alexander},  isbn = {978-3-642-15762-2},  keywords = {population-protocols},  pages = {528-530--530},  posted-at = {2010-09-23 13:40:15},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Brief Announcement: Stabilizing Consensus with the Power of Two Choices}},  url = {http://dx.doi.org/10.1007/978-3-642-15763-9\_50},  volume = {6343},  year = {2010}  }  @incollection{citeulike:7889068,  abstract = {{Recent development on distributed systems has shown that a variety of fairness constraints (some of which are only recently defined) play vital roles in designing self-stabilizing population protocols. Current practice of system analysis is, however, deficient under fairness. In this work, we present PAT, a toolkit for flexible and efficient system analysis under fairness. A unified algorithm is proposed to model check systems with a variety of fairness effectively in two different settings. Empirical evaluation shows that PAT complements existing model checkers in terms of fairness. We report that previously unknown bugs have been revealed using PAT against systems functioning under strong global fairness.}},  address = {Berlin, Heidelberg},  author = {Sun, Jun and Liu, Yang and Dong, JinSong and Pang, Jun},  booktitle = {Computer Aided Verification},  chapter = {59},  citeulike-article-id = {7889068},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-02658-4\_59},  citeulike-linkout-1 = {http://www.springerlink.com/content/0321170v636j1853},  citeulike-linkout-2 = {http://link.springer.com/chapter/10.1007/978-3-642-02658-4\_59},  doi = {10.1007/978-3-642-02658-4\_59},  editor = {Bouajjani, Ahmed and Maler, Oded},  isbn = {978-3-642-02657-7},  keywords = {population-protocols},  pages = {709--714},  posted-at = {2010-09-23 13:39:04},  priority = {2},  publisher = {Springer Berlin Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{PAT: Towards Flexible Verification under Fairness}},  url = {http://dx.doi.org/10.1007/978-3-642-02658-4\_59},  volume = {5643},  year = {2009}  }  @article{citeulike:7889064,  abstract = {{Distributed estimation of global parameters in intermittently connected mobile networks is a challenging research issue. In this paper, we introduce and evaluate different approaches, based on gossiping techniques as well as population protocols. The performance of the mechanisms proposed is shown to depend heavily on the specific features of the underlying mobility patterns. We then present how the various methods proposed can be applied to dynamically tune the parameters characterizing a popular relaying strategy (spray-and-wait) for delay-tolerant networks.}},  author = {Guerrieri, Alessio and Carreras, Iacopo and Pellegrini, Francesco D. and Miorandi, Daniele and Montresor, Alberto},  citeulike-article-id = {7889064},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.comcom.2010.01.019},  day = {16},  doi = {10.1016/j.comcom.2010.01.019},  issn = {01403664},  journal = {Computer Communications},  keywords = {population-protocols},  month = aug,  number = {13},  pages = {1472--1482},  posted-at = {2010-09-23 13:38:14},  priority = {2},  title = {{Distributed estimation of global parameters in delay-tolerant networks}},  url = {http://dx.doi.org/10.1016/j.comcom.2010.01.019},  volume = {33},  year = {2010}  }  @inproceedings{1696833,  address = {Berlin, Heidelberg},  author = {Chatzigiannakis, Ioannis and Dolev, Shlomi and Fekete, S\'{a}ndor P. and Michail, Othon and Spirakis, Paul G.},  booktitle = {OPODIS '09: Proceedings of the 13th International Conference on Principles of Distributed Systems},  citeulike-article-id = {7888933},  location = {N\{\i}mes, France},  pages = {33--47},  posted-at = {2010-09-23 13:13:04},  priority = {2},  publisher = {Springer-Verlag},  title = {{Not All Fair Probabilistic Schedulers Are Equivalent1}},  year = {2009}  }  @incollection{citeulike:7888918,  abstract = {{Synchronization is widely considered as an important service in distributed systems which may simplify protocol design. Phase clock is a general synchronization tool that provides a form of a logical time. This paper presents a self-stabilizing (a tolerating state-corrupting transient faults) phase clock algorithm suited to the model of population protocols with covering. This model has been proposed recently for sensor networks with a very large, possibly unknown number of anonymous mobile agents having small memory. Agents interact in pairs in an asynchronous way subject to the constraints expressed in terms of the cover times of agents. The cover time expresses the frequency of an agent to communicate with all the others and abstracts agent\^{a}€™s communication characteristics (e.g. moving speed/patterns, transmitting/receiving capabilities). We show that a phase clock is impossible in the model with only constant-state agents. Hence, we assume an existence of resource-unlimited agent - the base station. The clock size and duration of each phase of the proposed phase clock tool are adjustable by the user. We provide application examples of this tool and demonstrate how it can simplify the design of protocols. In particular, it yields a solution to Group Mutual Exclusion problem.}},  address = {Berlin, Heidelberg},  author = {Beauquier, Joffroy and Burman, Janna},  booktitle = {Distributed Computing in Sensor Systems},  chapter = {26},  citeulike-article-id = {7888918},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-13651-1\_26},  citeulike-linkout-1 = {http://www.springerlink.com/content/5j871567716584q1},  doi = {10.1007/978-3-642-13651-1\_26},  editor = {Rajaraman,, Rajmohan and Moscibroda,, Thomas and Dunkels,, Adam and Scaglione,, Anna},  isbn = {978-3-642-13650-4},  keywords = {population-protocols},  pages = {362-378--378},  posted-at = {2010-09-23 13:11:09},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Self-stabilizing Synchronization in Mobile Sensor Networks with Covering}},  url = {http://dx.doi.org/10.1007/978-3-642-13651-1\_26},  volume = {6131},  year = {2010}  }  @incollection{citeulike:7888854,  abstract = {{A population protocol is one of distributed computing models for passively-mobile systems, where a number of agents change their states by pairwise interactions between two agents. In this paper, we investigate the solvability of the self-stabilizing leader election in population protocols without any kind of oracles. We identify the necessary and sufficient condition to solve the self-stabilizing leader election in population protocols from the aspects of local memory complexity and fairness assumptions. This paper shows that under the assumption of global fairness, no protocol using only n\^{a}\^{a}\^{a}1 states can solve the self-stabilizing leader election in complete interaction graphs, where n is the number of agents in the system. To prove this impossibility, we introduce a novel proof technique, called closed-set argument. In addition, we propose a self-stabilizing leader election protocol using n states that works even under the unfairness assumption. This protocol requires the exact knowledge about the number of agents in the system. We also show that such knowledge is necessary to construct any self-stabilizing leader election protocol.}},  address = {Berlin, Heidelberg},  author = {Cai, Shukai and Izumi, Taisuke and Wada, Koichi},  booktitle = {Structural Information and Communication Complexity},  chapter = {10},  citeulike-article-id = {7888854},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-11476-2\_10},  citeulike-linkout-1 = {http://www.springerlink.com/content/58g4t72x3264v255},  doi = {10.1007/978-3-642-11476-2\_10},  editor = {Kutten, Shay and \v{Z}erovnik, Janez},  isbn = {978-3-642-11475-5},  keywords = {population-protocols},  pages = {113-125--125},  posted-at = {2010-09-23 13:02:49},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Space Complexity of Self-stabilizing Leader Election in Passively-Mobile Anonymous Agents}},  url = {http://dx.doi.org/10.1007/978-3-642-11476-2\_10},  volume = {5869},  year = {2010}  }  @inproceedings{citeulike:5649672,  abstract = {{In the near future, it is reasonable to expect that new types of systems will appear, of massive scale that will operating in a constantly changing networked environment. We expect that most such systems will have the form of a large society of tiny networked artefacts. Angluin et al. introduced the notion of "probabilistic population protocols" (PPP) in order to model the behavior of such systems where extremely limited agents are represented as finite state machines that interact in pairs under the control of an adversary scheduler. We propose to study the dynamics of probabilistic population protocols, via the differential equations approach. We provide a very general model that allows to examine the continuous dynamics of population protocols and we show that it includes the model of Angluin et al., under certain conditions, with respect to the continuous dynamics of the two models. Our main proposal here is to exploit the powerful tools of continuous nonlinear dynamics in order to examine the behavior of such systems. We also provide a sufficient condition for stability.}},  author = {Chatzigiannakis, Ioannis and Spirakis, Paul G.},  booktitle = {Self-Adaptive and Self-Organizing Systems Workshops, 2008. SASOW 2008. Second IEEE International Conference on},  citeulike-article-id = {5649672},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/sasow.2008.45},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=4800655},  doi = {10.1109/sasow.2008.45},  journal = {Self-Adaptive and Self-Organizing Systems Workshops, 2008. SASOW 2008. Second IEEE International Conference on},  keywords = {population-protocols},  location = {Venice, Italy},  month = oct,  pages = {67--72},  posted-at = {2010-09-23 13:01:21},  priority = {2},  title = {{The Dynamics of Adaptive Networked Societies of Tiny Artefacts}},  url = {http://dx.doi.org/10.1109/sasow.2008.45},  year = {2008}  }  @incollection{citeulike:7888823,  abstract = {{We consider a population of anonymous processes communicating via anonymous message-passing, where the recipient of each message is chosen by an adversary and the sender is not identified to the recipient. Even with unbounded message sizes and process states, such a system can compute only limited predicates on inputs held by the processes. In the finite-state case, we show how the exact strength of the model depends critically on design choices that are irrelevant in the unbounded-state case, such as whether messages are delivered immediately or after a delay, whether a sender can record that it has sent a message, and whether a recipient can queue incoming messages, refusing to accept new messages until it has had a chance to send out messages of its own. These results may have implications for the design of distributed systems where processor power is severely limited, as in sensor networks.}},  address = {Berlin, Heidelberg},  author = {Angluin, Dana and Aspnes, James and Eisenstat, David and Ruppert, Eric},  booktitle = {Principles of Distributed Systems},  chapter = {30},  citeulike-article-id = {7888823},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/11795490\_30},  citeulike-linkout-1 = {http://www.springerlink.com/content/0227m07385136113},  doi = {10.1007/11795490\_30},  editor = {Anderson,, James and Prencipe,, Giuseppe and Wattenhofer,, Roger},  isbn = {978-3-540-36321-7},  keywords = {population-protocols},  pages = {396-411--411},  posted-at = {2010-09-23 12:59:06},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{On the Power of Anonymous One-Way Communication}},  url = {http://dx.doi.org/10.1007/11795490\_30},  volume = {3974},  year = {2006}  }  @incollection{citeulike:7888733,  abstract = {{Gossip protocols are simple, robust and scalable and have been consistently applied to many (mostly wired) distributed systems. Nevertheless, most validation in this area has been empirical so far and there is a lack of a theoretical counterpart to characterize what can and cannot be computed with gossip protocols. Population protocols, on the other hand, benefit from a sound theoretical framework but little empirical evaluation. In this paper, we establish a correlation between population and gossip-based protocols. We propose a classification of gossip-based protocols, based on the nature of the underlying peer sampling service. First, we show that the class of gossip protocols, where each node relies on an arbitrary sample, is equivalent to population protocols. Second, we show that gossip-based protocols, relying on a more powerful peer sampling service providing peers using a clearly identified set of other peers, are equivalent to community protocols, a modern variant of population protocols. Leveraging the resemblances between population and gossip protocols enables to provide a theoretical framework for distributed systems where global behaviors emerge from a set of local interactions, both in wired and wireless settings. The practical validations of gossip-protocols provide empirical evidence of quick convergence times of such algorithms and demonstrate their practical relevance. While existing results in each area can be immediately applied, this also leaves the space to transfer any new results, practical or theoretical, from one domain to the other.}},  address = {Berlin, Heidelberg},  author = {Bertier, Marin and Busnel, Yann and Kermarrec, Anne-Marie},  booktitle = {Structural Information and Communication Complexity},  chapter = {7},  citeulike-article-id = {7888733},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-11476-2\_7},  citeulike-linkout-1 = {http://www.springerlink.com/content/r2081t73652r1rm0},  doi = {10.1007/978-3-642-11476-2\_7},  editor = {Kutten, Shay and \v{Z}erovnik, Janez},  isbn = {978-3-642-11475-5},  keywords = {population-protocols},  pages = {72-86--86},  posted-at = {2010-09-23 12:41:07},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{On Gossip and Populations}},  url = {http://dx.doi.org/10.1007/978-3-642-11476-2\_7},  volume = {5869},  year = {2010}  }  @article{citeulike:7099540,  abstract = {{This article studies self-stabilization in networks of anonymous, asynchronously interacting nodes where the size of the network is unknown. Constant-space protocols are given for Dijkstra-style round-robin token circulation, leader election in rings, two-hop coloring in degree-bounded graphs, and establishing consistent global orientation in an undirected ring. A protocol to construct a spanning tree in regular graphs using O (log D ) memory is also given, where D is the diameter of the graph. A general method for eliminating nondeterministic transitions from the self-stabilizing implementation of a large family of behaviors is used to simplify the constructions, and general conditions under which protocol composition preserves behavior are used in proving their correctness.}},  address = {New York, NY, USA},  author = {Angluin, Dana and Aspnes, James and Fischer, Michael J. and Jiang, Hong},  citeulike-article-id = {7099540},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1452001.1452003},  citeulike-linkout-1 = {http://dx.doi.org/10.1145/1452001.1452003},  doi = {10.1145/1452001.1452003},  issn = {1556-4665},  journal = {ACM Trans. Auton. Adapt. Syst.},  keywords = {population-protocols},  number = {4},  pages = {1--28},  posted-at = {2010-09-23 12:40:00},  priority = {2},  publisher = {ACM},  title = {{Self-stabilizing population protocols}},  url = {http://dx.doi.org/10.1145/1452001.1452003},  volume = {3},  year = {2008}  }  @incollection{citeulike:7888725,  abstract = {{Chandy et al. proposed the methodology of self-similar algorithms for distributed computation in dynamic environments. We further characterize the class of functions computable by such algorithms by showing that self-similarity induces an additive relationship among the level-sets of such functions. Angluin et al. introduced the population protocol model for computation in mobile sensor networks and characterized the class of predicates computable in a standard population. We define and characterize the class of self-similar predicates and show when they are computable by a population protocol.}},  address = {Berlin, Heidelberg},  author = {Bhatia, Swapnil and Barto\v{s}, Radim},  booktitle = {Distributed Computing and Networking},  chapter = {32},  citeulike-article-id = {7888725},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-540-92295-7\_32},  citeulike-linkout-1 = {http://www.springerlink.com/content/18pk75000tw711hx},  doi = {10.1007/978-3-540-92295-7\_32},  editor = {Garg, Vijay and Wattenhofer, Roger and Kothapalli, Kishore},  isbn = {978-3-540-92294-0},  keywords = {population-protocols},  pages = {263-274--274},  posted-at = {2010-09-23 12:38:55},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Self-similar Functions and Population Protocols: A Characterization and a Comparison}},  url = {http://dx.doi.org/10.1007/978-3-540-92295-7\_32},  volume = {5408},  year = {2009}  }  @inproceedings{citeulike:7888716,  abstract = {{Population protocols provide theoretical foundations for mobile tiny device networks in which global behavior emerges from a set of simple interactions between anonymous agents. The works in this area mostly focus on studying the computational power of the model. Results hold as long as a fair scheduler, which governs the interactions between nodes, ensures that all reachable system states may eventually happen. This paper studies for the first time the impact of the agents' mobility model on the convergence speed of population protocols, emphasizing the dynamic of the computation. We propose an augmented population protocol model where each edge of the interaction graph is weighted, representing the probability of two agents to interact. This model enables to define the behavior of the scheduler under various mobility models. We have empirically shown that mobility models have a significant impact on the convergence speed of the protocols. In fact, we observed that the uniform distribution always provides the best convergence time. Such a model is representative of the well-known Random Way Point model used to evaluate most of mobile ad-hoc network protocols. In this paper, we formally prove that a uniform distribution of weights provides the lowest bound of average convergence speed for a large class of population protocols. Therefore, this analysis reveals that the Random Way Point model, following this distribution, provides the best case scenario questioning its relevance as a reference model.}},  author = {Bertier, Marin and Busnel, Yann and Kermarrec, Anne-Marie},  citeulike-article-id = {7888716},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/ictel.2010.5478801},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=5478801},  doi = {10.1109/ictel.2010.5478801},  keywords = {population-protocols},  location = {Doha, Qatar},  month = apr,  pages = {707--714},  posted-at = {2010-09-23 12:37:49},  priority = {2},  title = {{Dynamic computation of population protocols}},  url = {http://dx.doi.org/10.1109/ictel.2010.5478801},  year = {2010}  }  @article{citeulike:3762138,  abstract = {{The population protocol model has emerged as an elegant computation paradigm for describing mobile ad hoc networks, consisting of a number of mobile nodes that interact with each other to carry out a computation. The interactions of nodes are subject to a fairness constraint. One essential property of population protocols is that all nodes must eventually converge to the correct output value (or configuration). In this paper, we aim to automatically verify self-stabilizing population protocols for leader election and token circulation in the Spin model checker. We report our verification results and discuss the issue of modeling strong fairness constraints in Spin.}},  author = {Pang, Jun and Luo, Zhengqin and Deng, Yuxin},  citeulike-article-id = {3762138},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s11704-008-0040-9},  citeulike-linkout-1 = {http://www.springerlink.com/content/m0823437556m5760},  day = {1},  doi = {10.1007/s11704-008-0040-9},  issn = {1673-7350},  journal = {Frontiers of Computer Science in China},  keywords = {population-protocols},  month = dec,  number = {4},  pages = {357-367--367},  posted-at = {2010-09-23 12:34:20},  priority = {2},  publisher = {Higher Education Press, co-published with Springer-Verlag GmbH},  title = {{On automatic verification of self-stabilizing population protocols}},  url = {http://dx.doi.org/10.1007/s11704-008-0040-9},  volume = {2},  year = {2008}  }  @article{citeulike:3127703,  abstract = {{Fast algorithms are presented for performing computations in a probabilistic population model. This is a variant of the standard population protocol model, in which finite-state agents interact in pairs under the control of an adversary scheduler, where all pairs are equally likely to be chosen for each interaction. It is shown that when a unique leader agent is provided in the initial population, the population can simulate a virtual register machine with high probability in which standard arithmetic operations like comparison, addition, subtraction, and multiplication and division by constants can be simulated in O(n log5 n) interactions using a simple register representation or in O(n log2 n) interactions using a more sophisticated representation that requires an extra O(n log O(1) n)-interaction initialization step. The central method is the extensive use of epidemics to propagate information from and to the leader, combined with an epidemic-based phase clock used to detect when these epidemics are likely to be complete. Applications include a reduction of the cost of computing a semilinear predicate to O(n log5 n) interactions from the previously best-known bound of O(n 2 log n) interactions and simulation of a LOGSPACE Turing machine using O(n log2 n) interactions per step after an initial O(n log O(1) n)-interaction startup phase. These bounds on interactions translate into polylogarithmic time per step in a natural parallel model in which each agent participates in an expected \^{I}˜(1) interactions per time unit. Open problems are discussed, together with simulation results that suggest the possibility of removing the initial-leader assumption.}},  author = {Angluin, Dana and Aspnes, James and Eisenstat, David},  citeulike-article-id = {3127703},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00446-008-0067-z},  citeulike-linkout-1 = {http://www.ingentaconnect.com/content/klu/446/2008/00000021/00000003/00000067},  citeulike-linkout-2 = {http://www.springerlink.com/content/396g350166407751},  day = {1},  doi = {10.1007/s00446-008-0067-z},  issn = {0178-2770},  journal = {Distributed Computing},  month = sep,  number = {3},  pages = {183-199--199},  posted-at = {2010-09-23 12:32:25},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  title = {{Fast computation by population protocols with a leader}},  url = {http://dx.doi.org/10.1007/s00446-008-0067-z},  volume = {21},  year = {2008}  }  @inproceedings{citeulike:7888671,  abstract = {{We present a model for asynchronous mobile agent networks that takes into account the notion of speed of the agents. Then, we study the gathering problem (GP), in which an unknown number of anonymous agents have constant values they must deliver (only once) to a non mobile agent, the base station.}},  address = {New York, NY, USA},  author = {Beauquier, Joffroy and Burman, Janna and Clement, Julien and Kutten, Shay},  booktitle = {PODC '09: Proceedings of the 28th ACM symposium on Principles of distributed computing},  citeulike-article-id = {7888671},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1582768},  citeulike-linkout-1 = {http://dx.doi.org/10.1145/1582716.1582768},  doi = {10.1145/1582716.1582768},  isbn = {978-1-60558-396-9},  keywords = {population-protocols},  location = {Calgary, AB, Canada},  pages = {286--287},  posted-at = {2010-09-23 12:31:00},  priority = {2},  publisher = {ACM},  title = {{Brief announcement: non-self-stabilizing and self-stabilizing gathering in networks of mobile agents--the notion of speed}},  url = {http://dx.doi.org/10.1145/1582716.1582768},  year = {2009}  }  @inproceedings{citeulike:7888660,  abstract = {{We review some results about the computational power of several computational models. Considered models have in common to be related to continuous dynamical systems.}},  address = {Berlin, Heidelberg},  author = {Bournez, Olivier and Hainry, Emmanuel},  booktitle = {MCU'07: Proceedings of the 5th international conference on Machines, computations, and universality},  citeulike-article-id = {7888660},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1777097},  isbn = {3-540-74592-0, 978-3-540-74592-1},  keywords = {population-protocols},  location = {Orl\'{e}ans, France},  pages = {12--23},  posted-at = {2010-09-23 12:29:32},  priority = {2},  publisher = {Springer-Verlag},  title = {{On the computational capabilities of several models}},  url = {http://portal.acm.org/citation.cfm?id=1777097},  year = {2007}  }  @incollection{citeulike:6500246,  abstract = {{Fast algorithms are presented for performing computations in a probabilistic population model. This is a variant of the standard population protocol model\^{a}€”in which finite-state agents interact in pairs under the control of an adversary scheduler\^{a}€”where all pairs are equally likely to be chosen for each interaction. It is shown that when a unique leader agent is provided in the initial population, the population can simulate a virtual register machine in which standard arithmetic operations like comparison, addition, subtraction, and multiplication and division by constants can be simulated in O(n log4 n) interactions with high probability. Applications include a reduction of the cost of computing a semilinear predicate to O(n log4 n) interactions from the previously best-known bound of O(n2 logn) interactions and simulation of a LOGSPACE Turing machine using the same O(n log4 n) interactions per step. These bounds on interactions translate into O(log4 n) time per step in a natural parallel model in which each agent participates in an expected \^{I}˜(1) interactions per time unit. The central method is the extensive use of epidemics to propagate information from and to the leader, combined with an epidemic-based phase clock used to detect when these epidemics are likely to be complete.}},  address = {Berlin, Heidelberg},  author = {Angluin, Dana and Aspnes, James and Eisenstat, David},  booktitle = {Distributed Computing},  chapter = {6},  citeulike-article-id = {6500246},  citeulike-linkout-0 = {http://dblp.uni-trier.de/rec/bibtex/conf/wdag/AngluinAE06},  citeulike-linkout-1 = {http://dx.doi.org/10.1007/11864219\_5},  citeulike-linkout-2 = {http://www.springerlink.com/content/7p57452u75286765},  doi = {10.1007/11864219\_5},  editor = {Dolev,, Shlomi},  isbn = {978-3-540-44624-8},  keywords = {population-protocols},  pages = {61-75--75},  posted-at = {2010-09-23 12:28:57},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Fast Computation by Population Protocols with a Leader}},  url = {http://dx.doi.org/10.1007/11864219\_5},  volume = {4167},  year = {2006}  }  @inproceedings{citeulike:7888645,  abstract = {{We consider the model of population protocols introduced by Angluin et al. [2], in which anonymous finite-state agents stably compute a predicate of their inputs via two-way interactions in the all-pairs family of communication networks. We prove that all predicates stably computable in this model (and certain generalizations of it) are semilinear, answering a central open question about the power of the model.}},  address = {New York, NY, USA},  author = {Angluin, Dana and Aspnes, James and Eisenstat, David},  booktitle = {PODC '06: Proceedings of the twenty-fifth annual ACM symposium on Principles of distributed computing},  citeulike-article-id = {7888645},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1146381.1146425},  citeulike-linkout-1 = {http://dx.doi.org/10.1145/1146381.1146425},  doi = {10.1145/1146381.1146425},  isbn = {1-59593-384-0},  keywords = {population-protocols},  location = {Denver, Colorado, USA},  pages = {292--299},  posted-at = {2010-09-23 12:27:11},  priority = {2},  publisher = {ACM},  title = {{Stably computable predicates are semilinear}},  url = {http://dx.doi.org/10.1145/1146381.1146425},  year = {2006}  }  @inproceedings{citeulike:7888639,  abstract = {{The population protocol model has emerged as an elegant computation paradigm for describing mobile ad hoc networks, consisting of a number of mobile nodes that interact with each other to carry out a computation. The interactions of nodes are subject to a fairness constraint. One essential property of population protocols is that all nodes must eventually converge to the correct output value (or configuration). In this paper, we aim to automatically verify self-stabilizing population protocols for leader election and token circulation in the Spin model checker. We report our verification results and discuss the issue of modeling strong fairness constraints in Spin.}},  address = {Washington, DC, USA},  author = {Pang, Jun and Luo, Zhengqin and Deng, Yuxin},  booktitle = {TASE '08: Proceedings of the 2008 2nd IFIP/IEEE International Symposium on Theoretical Aspects of Software Engineering},  citeulike-article-id = {7888639},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1382403},  citeulike-linkout-1 = {http://dx.doi.org/10.1109/tase.2008.8},  doi = {10.1109/tase.2008.8},  isbn = {978-0-7695-3249-3},  pages = {185--192},  posted-at = {2010-09-23 12:26:36},  priority = {2},  publisher = {IEEE Computer Society},  title = {{On Automatic Verification of Self-Stabilizing Population Protocols}},  url = {http://dx.doi.org/10.1109/tase.2008.8},  year = {2008}  }  @incollection{citeulike:6500231,  abstract = {{We introduce a new theoretical model of ad hoc mobile computing in which agents have restricted memory, highly unpredictable movement and no initial knowledge of the system. Each agent\^{a}€™s memory can store O(1) bits, plus a unique identifier, and O(1) other agents\^{a}€™ identifiers. Inputs are distributed across n agents, and all agents must converge to the correct output value. We give a universal construction that proves the model is surprisingly strong: It can solve any decision problem in NSPACE(nlogn). Moreover, the construction is robust with respect to Byzantine failures of a constant number of agents.}},  address = {Berlin, Heidelberg},  author = {Guerraoui, Rachid and Ruppert, Eric},  booktitle = {Automata, Languages and Programming},  chapter = {40},  citeulike-article-id = {6500231},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-02930-1\_40},  citeulike-linkout-1 = {http://www.springerlink.com/content/a00017l71275wuqn},  doi = {10.1007/978-3-642-02930-1\_40},  editor = {Albers,, Susanne and Marchetti-Spaccamela,, Alberto and Matias,, Yossi and Nikoletseas,, Sotiris and Thomas,, Wolfgang},  isbn = {978-3-642-02929-5},  keywords = {population-protocols},  pages = {484-495--495},  posted-at = {2010-09-23 12:24:41},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Names Trump Malice: Tiny Mobile Agents Can Tolerate Byzantine Failures}},  url = {http://dx.doi.org/10.1007/978-3-642-02930-1\_40},  volume = {5556},  year = {2009}  }  @inproceedings{citeulike:7888618,  abstract = {{The population protocol model has emerged as an elegant paradigm for describing mobile ad hoc networks, consisting of a number of nodes that interact with each other to carry out a computation. One essential property of self-stabilizing population protocols is that all nodes must eventually converge to the correct output value, with respect to all possible initial configurations. It has been shown that fairness constraints play a crucial role in designing population protocols. The Process Analysis Toolkit (PAT) has been developed to perform verifications under different fairness constraints efficiently. In particular, it can handle global fairness, which is required for the correctness of most of population protocols. It is an ideal candidate for automatically verifying population protocols. In this paper, we summarize our latest empirical evaluation of PAT on a set of self-stabilizing population protocols for ring networks. We report one previously unknown bug in a protocol for leader election identified using PAT.}},  address = {Washington, DC, USA},  author = {Liu, Yang and Pang, Jun and Sun, Jun and Zhao, Jianhua},  booktitle = {TASE '09: Proceedings of the 2009 Third IEEE International Symposium on Theoretical Aspects of Software Engineering},  citeulike-article-id = {7888618},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1608421},  citeulike-linkout-1 = {http://dx.doi.org/10.1109/tase.2009.51},  doi = {10.1109/tase.2009.51},  isbn = {978-0-7695-3757-3},  keywords = {population-protocols},  pages = {81--89},  posted-at = {2010-09-23 12:23:06},  priority = {2},  publisher = {IEEE Computer Society},  title = {{Verification of Population Ring Protocols in PAT}},  url = {http://dx.doi.org/10.1109/tase.2009.51},  year = {2009}  }  @incollection{citeulike:6500462,  abstract = {{In the population protocol model introduced by Angluin et al. [2], a collection of agents, which are modelled by finite state machines, move around unpredictably and have pairwise interactions. The ability of such systems to compute functions on a multiset of inputs that are initially distributed across all of the agents has been studied in the absence of failures. Here, we show that essentially the same set of functions can be computed in the presence of halting and transient failures, provided preconditions on the inputs are added so that the failures cannot immediately obscure enough of the inputs to change the outcome. We do this by giving a general-purpose transformation that makes any algorithm for the fault-free setting tolerant to failures.}},  address = {Berlin, Heidelberg},  author = {Delporte-Gallet, Carole and Fauconnier, Hugues and Guerraoui, Rachid and Ruppert, Eric},  booktitle = {Distributed Computing in Sensor Systems},  chapter = {4},  citeulike-article-id = {6500462},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/11776178\_4},  citeulike-linkout-1 = {http://www.springerlink.com/content/x616h2827524w3t2},  doi = {10.1007/11776178\_4},  editor = {Gibbons,, Phillip and Abdelzaher,, Tarek and Aspnes,, James and Rao,, Ramesh},  isbn = {978-3-540-35227-3},  keywords = {population-protocols},  pages = {51-66--66},  posted-at = {2010-09-23 12:20:56},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{When Birds Die: Making Population Protocols Fault-Tolerant}},  url = {http://dx.doi.org/10.1007/11776178\_4},  volume = {4026},  year = {2006}  }  @inproceedings{citeulike:7888604,  abstract = {{We work on an extension of the Population Protocol model of Angluin et al. [1] that allows edges of the communication graph, G , to have states that belong to a constant size set. In this extension, the so called Mediated Population Protocol model (MPP) [2,3], both uniformity and anonymity are preserved. We here study a simplified version of MPP, the Graph Decision Mediated Population Protocol model (GDM), in order to capture MPP's ability to decide graph languages. We also prove some first impossibility results both for weakly connected and possibly disconnected communication graphs.}},  address = {Berlin, Heidelberg},  author = {Chatzigiannakis, Ioannis and Michail, Othon and Spirakis, Paul G.},  booktitle = {DISC'09: Proceedings of the 23rd international conference on Distributed computing},  citeulike-article-id = {7888604},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1813164.1813194},  isbn = {3-642-04354-2, 978-3-642-04354-3},  keywords = {population-protocols},  location = {Elche, Spain},  pages = {239--240},  posted-at = {2010-09-23 12:19:30},  priority = {2},  publisher = {Springer-Verlag},  title = {{Brief announcement: decidable graph languages by mediated population protocols}},  url = {http://portal.acm.org/citation.cfm?id=1813164.1813194},  year = {2009}  }  @inproceedings{citeulike:7888600,  abstract = {{We study private computations in a system of tiny mobile agents. We consider the mobile population protocol model of Angluin et al. [2] and ask what can be computed without ever revealing any input to a curious adversary. We show that any computable predicate of the original population model can be made private through an obfuscation procedure that exploits the inherent nondeterminism of the mobility pattern. In short, the idea is for every mobile agent to generate, besides its actual input value, a set of wrong input values to confuse the curious adversary. To converge to the correct result, the procedure has the agents eventually eliminate the wrong values; however, the moment when this happens is hidden from the adversary. This is achieved without jeopardizing the tiny nature of the agents: they still have very small storage size that is independent of the cardinality of the system. We present three variants of this obfuscation procedure that help compute respectively, remainder, threshold, and or predicates which, when composed, cover all those that can be computed in the population protocol model.}},  address = {Berlin, Heidelberg},  author = {Gallet, Carole D. and Fauconnier, Hugues and Guerraoui, Rachid and Ruppert, Eric},  booktitle = {OPODIS'07: Proceedings of the 11th international conference on Principles of distributed systems},  citeulike-article-id = {7888600},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1782394.1782418},  isbn = {3-540-77095-X, 978-3-540-77095-4},  keywords = {population-protocols},  location = {Guadeloupe, French West Indies},  pages = {329--342},  posted-at = {2010-09-23 12:18:42},  priority = {2},  publisher = {Springer-Verlag},  title = {{Secretive birds: privacy in population protocols}},  url = {http://portal.acm.org/citation.cfm?id=1782394.1782418},  year = {2007}  }  @inproceedings{LPD-CONF-2006-035,  abstract = {{In the population protocol model introduced by Angluin et al. [2], a collection of agents, which are modelled by finite state machines, move around unpredictably and have pairwise interactions. The ability of such systems to compute functions on a multiset of inputs that are initially distributed across all of the agents has been studied in the absence of failures. Here, we show that essentially the same set of functions can be computed in the presence of halting and transient failures, provided preconditions on the inputs are added so that the failures cannot immediately obscure enough of the inputs to change the outcome. We do this by giving a general-purpose transformation that makes any algorithm for the fault-free setting tolerant to failures.}},  author = {Delporte-Gallet, Carole and Fauconnier, Hugues and Guerraoui, Rachid and Ruppert, Eric},  booktitle = {Proceedings of the 2006 {I}nternational {C}onference on {D}istributed {C}omputing in {S}ensor {S}ystems ({DCOSS} '06)},  citeulike-article-id = {7888594},  posted-at = {2010-09-23 12:17:14},  priority = {2},  title = {When {B}irds {D}ie: {M}aking {P}opulation {P}rotocols {F}ault-tolerant},  year = {2006}  }  @techreport{LPD-REPORT-2007-006,  abstract = {{Although much research has been devoted to designing and experimenting on ad hoc networks of tiny devices, very little has focussed on devising theoretical models to capture the inherent power and limitations of such networks. A notable exception is the population protocol model of Angluin et al. [2]. This model is simple and elegant but is sometimes considered too restrictive because of its anonymity: mobile agents have no identities and all look the same. We investigate in this paper the inherent power of the population protocol model augmented with the ability of each agent to be uniquely identified as well as store a constant number of other agents\^{a}€™ identifiers. We provide an exact characterization of what can be computed in this new community protocol model: a function can be computed if and only if it is symmetric and in NSPACE(n log n). This is shown using a simulation of pointer machines. We also consider the ability of our community protocol model to handle failures. We describe what can be computed when there are a constant number of benign failures and show that nontrivial computations can be achieved even if agents can be Byzantine.}},  author = {Guerraoui, Rachid and Ruppert, Eric},  citeulike-article-id = {7888590},  keywords = {population-protocols},  posted-at = {2010-09-23 12:15:40},  priority = {2},  title = {Even {S}mall {B}irds are {U}nique: {P}opulation {P}rotocols with {I}dentifiers},  year = {2007}  }  @inproceedings{citeulike:7888589,  abstract = {{Population protocols are a model presented recently for networks with a very large, possibly unknown number of mobile agents having small memory. This model has certain advantages over alternative models (such as DTN) for such networks. However, it was shown that the computational power of this model is limited to semi-linear predicates only. Hence, various extensions were suggested.}},  address = {New York, NY, USA},  author = {Beauquier, Joffroy and Burman, Janna and Clement, Julien and Kutten, Shay},  booktitle = {PODC '10: Proceeding of the 29th ACM SIGACT-SIGOPS symposium on Principles of distributed computing},  citeulike-article-id = {7888589},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1835698.1835775},  citeulike-linkout-1 = {http://dx.doi.org/10.1145/1835698.1835775},  doi = {10.1145/1835698.1835775},  isbn = {978-1-60558-888-9},  keywords = {population-protocols},  location = {Zurich, Switzerland},  pages = {305--314},  posted-at = {2010-09-23 12:14:01},  priority = {2},  publisher = {ACM},  title = {{On utilizing speed in networks of mobile agents}},  url = {http://dx.doi.org/10.1145/1835698.1835775},  year = {2010}  }  @incollection{citeulike:7888562,  abstract = {{A self-stabilizing protocol guarantees that starting from an arbitrary initial configuration, a system eventually comes to satisfy its specification and keeps the specification forever. Although self-stabilizing protocols show excellent fault-tolerance against any transient faults (e.g. memory crash), designing self-stabilizing protocols is difficult and, what is worse, might be impossible due to the severe requirements. To circumvent the difficulty and impossibility, we introduce a novel notion of loose-stabilization, that relaxes the closure requirement of self-stabilization; starting from an arbitrary configuration, a system comes to satisfy its specification in a relatively short time, and it keeps the specification for a long time, though not forever. To show effectiveness and feasibility of this new concept, we present a probabilistic loosely-stabilizing leader election protocol in the Probabilistic Population Protocol (PPP) model of complete networks. Starting from any configuration, the protocol elects a unique leader within O(nNlogn) expected steps and keeps the unique leader for \^{I}{\copyright}(Ne N ) expected steps, where n is the network size (not known to the protocol) and N is a known upper bound of n. This result proves that introduction of the loose-stabilization circumvents the already-known impossibility result; the self-stabilizing leader election problem in the PPP model of complete networks cannot be solved without the knowledge of the exact network size.}},  address = {Berlin, Heidelberg},  author = {Sudo, Yuichi and Nakamura, Junya and Yamauchi, Yukiko and Ooshita, Fukuhito and Kakugawa, Hirotsugu and Masuzawa, Toshimitsu},  booktitle = {Structural Information and Communication Complexity},  chapter = {23},  citeulike-article-id = {7888562},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-11476-2\_23},  citeulike-linkout-1 = {http://www.springerlink.com/content/d2x23227j1111666},  doi = {10.1007/978-3-642-11476-2\_23},  editor = {Kutten, Shay and \v{Z}erovnik, Janez},  isbn = {978-3-642-11475-5},  keywords = {population-protocols},  pages = {295-308--308},  posted-at = {2010-09-23 12:10:21},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Loosely-Stabilizing Leader Election in Population Protocol Model}},  url = {http://dx.doi.org/10.1007/978-3-642-11476-2\_23},  volume = {5869},  year = {2010}  }  @incollection{citeulike:7888555,  abstract = {{This work focuses on the computational power of the Mediated Population Protocol model on complete communication graphs and initially identical edges (SMPP). In particular, we investigate the class MPS of all predicates that are stably computable by the SMPP model. It is already known that MPS is in the symmetric subclass of NSPACE(n 2). Here we prove that this inclusion holds with equality, thus, providing the following exact characterization for MPS: A predicate is in MPS iff it is symmetric and is in NSPACE(n 2).}},  address = {Berlin, Heidelberg},  author = {Chatzigiannakis, Ioannis and Michail, Othon and Nikolaou, Stavros and Pavlogiannis, Andreas and Spirakis, Paul G.},  booktitle = {Mathematical Foundations of Computer Science 2010},  chapter = {25},  citeulike-article-id = {7888555},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-15155-2\_25},  citeulike-linkout-1 = {http://www.springerlink.com/content/v884330571301300},  doi = {10.1007/978-3-642-15155-2\_25},  editor = {Hutchison, David and Kanade, Takeo and Kittler, Josef and Kleinberg, Jon M. and Mattern, Friedemann and Mitchell, John C. and Naor, Moni and Nierstrasz, Oscar and Pandu Rangan, C. and Steffen, Bernhard and Sudan, Madhu and Terzopoulos, Demetri and Tygar, Doug and Vardi, Moshe Y. and Weikum, Gerhard and Hlin\v{e}n\'{y}, Petr and Ku\v{c}era, Anton\'{\i}n},  isbn = {978-3-642-15154-5},  keywords = {population-protocols},  pages = {270-281--281},  posted-at = {2010-09-23 12:08:56},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{All Symmetric Predicates in NSPACE(n2) Are Stably Computable by the Mediated Population Protocol Model}},  url = {http://dx.doi.org/10.1007/978-3-642-15155-2\_25},  volume = {6281},  year = {2010}  }  @article{citeulike:3637701,  abstract = {We describe and analyze a 3-state one-way population protocol to compute approximate majority in the model in which pairs of agents are drawn uniformly at random to interact. Given an initial configuration of x\^{a}€™s, y\^{a}€™s and blanks that contains at least one non-blank, the goal is for the agents to reach consensus on one of the values x or y. Additionally, the value chosen should be the majority non-blank initial value, provided it exceeds the minority by a sufficient margin. We prove that with high probability n agents reach consensus in O(n log n) interactions and the value chosen is the majority provided that its initial margin is at least \$\${\omega(\sqrt{n} \,{\rm log}\, n)}\$\$. This protocol has the additional property of tolerating Byzantine behavior in \$\${o(\sqrt{n})}\$\$ of the agents, making it the first known population protocol that tolerates Byzantine agents.},  author = {Angluin, Dana and Aspnes, James and Eisenstat, David},  citeulike-article-id = {3637701},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00446-008-0059-z},  citeulike-linkout-1 = {http://www.springerlink.com/content/c22112431g64321x},  day = {1},  doi = {10.1007/s00446-008-0059-z},  issn = {0178-2770},  journal = {Distributed Computing},  keywords = {population-protocols},  month = jul,  number = {2},  pages = {87-102--102},  posted-at = {2010-09-23 12:06:48},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  title = {{A simple population protocol for fast robust approximate majority}},  url = {http://dx.doi.org/10.1007/s00446-008-0059-z},  volume = {21},  year = {2008}  }  @article{citeulike:7602361,  abstract = {{ Minimal cells comprise only the genes and biomolecular machinery necessary for basic life. Synthesizing minimal and minimized cells will improve understanding of core biology, enhance development of biotechnology strains of bacteria, and enable evolutionary optimization of natural and unnatural biopolymers. Design and construction of minimal cells is proceeding in two different directions: 'top-down' reduction of bacterial genomes in vivo and 'bottom-up' integration of DNA/RNA/protein/membrane syntheses in vitro . Major progress in the past 5 years has occurred in synthetic genomics, minimization of the Escherichia coli genome, sequencing of minimal bacterial endosymbionts, identification of essential genes, and integration of biochemical systems. }},  author = {Jewett, Michael C. and Forster, Anthony C.},  citeulike-article-id = {7602361},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.copbio.2010.06.008},  day = {16},  doi = {10.1016/j.copbio.2010.06.008},  issn = {09581669},  journal = {Current Opinion in Biotechnology},  keywords = {system-biology},  month = jul,  posted-at = {2010-09-22 15:59:35},  priority = {2},  title = {{Update on designing and building minimal cells}},  url = {http://dx.doi.org/10.1016/j.copbio.2010.06.008},  year = {2010}  }  @article{citeulike:7613028,  abstract = {{A fundamental problem in biology is understanding the evolutionary emergence and maintenance of altruistic behaviors. A well-recognized conceptual insight is provided by a general mathematical relation, Hamilton's rule. This rule can in principle be invoked to explain natural examples of cooperation, but measuring the variables that it involves is a particularly challenging problem and controlling these variables experimentally an even more daunting task. Here, we overcome these difficulties by using a simple synthetic microbial system of producers and nonproducers of an extracellular growth-enhancing molecule, which acts as a 'common good.' For this system, we are able to manipulate the intrinsic growth difference between producers and nonproducers, as well as the impact of the common good on the growth rate of its recipients. Our synthetic system is thus uniquely suited for studying the relation between the parameters entering Hamilton's rule and the quantities governing the systems' behavior. The experimental results highlight a crucial effect of nonlinearities in the response to the common good, which in general tend to limit the predictive value of Hamilton's rule.}},  author = {Chuang, John S. and Rivoire, Olivier and Leibler, Stanislas},  citeulike-article-id = {7613028},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/msb.2010.57},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/msb201057},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20706208},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20706208},  day = {10},  doi = {10.1038/msb.2010.57},  issn = {1744-4292},  journal = {Molecular Systems Biology},  keywords = {system-biology},  month = aug,  pmid = {20706208},  posted-at = {2010-09-22 15:59:02},  priority = {2},  publisher = {Nature Publishing Group},  title = {{Cooperation and Hamilton's rule in a simple synthetic microbial system}},  url = {http://dx.doi.org/10.1038/msb.2010.57},  volume = {6},  year = {2010}  }  @article{citeulike:7750984,  author = {Dos Santos, V\'{\i}tor Martins A. and Damborsky, Jiri},  citeulike-article-id = {7750984},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.copbio.2010.08.001},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20727733},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20727733},  day = {18},  doi = {10.1016/j.copbio.2010.08.001},  issn = {1879-0429},  journal = {Current opinion in biotechnology},  keywords = {system-biology},  month = aug,  pmid = {20727733},  posted-at = {2010-09-22 15:57:42},  priority = {2},  title = {{Systems biology at work.}},  url = {http://dx.doi.org/10.1016/j.copbio.2010.08.001},  year = {2010}  }  @article{citeulike:7846561,  abstract = {{A report of the 3rd International Symposium on Optimization and Systems Biology, 20-22 September 2009, Zhangjiajie, China.}},  author = {Wang, Yong and Zhang, Xiang-Sun S. and Chen, Luonan},  citeulike-article-id = {7846561},  citeulike-linkout-0 = {http://dx.doi.org/10.1186/1752-0509-4-s2-s1},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20840723},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20840723},  doi = {10.1186/1752-0509-4-s2-s1},  issn = {1752-0509},  journal = {BMC systems biology},  keywords = {system-biology},  number = {Suppl 2},  pages = {S1+},  pmid = {20840723},  posted-at = {2010-09-22 15:52:52},  priority = {2},  title = {{Optimization meets systems biology.}},  url = {http://dx.doi.org/10.1186/1752-0509-4-s2-s1},  volume = {4 Suppl 2},  year = {2010}  }  @article{citeulike:7844839,  abstract = {{Comparative analyses, as carried out by comparative genomics and bioinformatics, have proven extremely powerful to obtain insight into the identity of specific genes that underlie differences and similarities across species. The central concept developed in this chapter is that important aspects of the functional differences between organisms derive not only from the differences in genetic components (which underlies comparative genomics) but also from dynamic, molecular (physical) interactions. Approaches that aim at identifying such network-based rather than component-based homologies between species we shall call Comparative Systems Biology. It will be illustrated by a number of examples from metabolic networks from prokaryotes, via yeast, to man. The potential for species comparisons, at the genome-scale using classical approaches and at the more detailed level of dynamic molecular networks will be illustrated. In our opinion, comparative systems biology, as a marriage between bioinformatics and systems biology, will offer new insights into the nature of organisms for the benefit of medicine, biotechnology, and drug design. As dynamic modeling is becoming more mainstream in cell biology, the potential of comparative systems biology will become more evident.}},  author = {Teusink, Bas and Westerhoff, Hans V. and Bruggeman, Frank J.},  citeulike-article-id = {7844839},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/wsbm.74},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20836045},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20836045},  doi = {10.1002/wsbm.74},  issn = {1939-005X},  journal = {Wiley interdisciplinary reviews. Systems biology and medicine},  keywords = {system-biology},  month = sep,  number = {5},  pages = {518--532},  pmid = {20836045},  posted-at = {2010-09-22 15:51:45},  priority = {2},  title = {{Comparative systems biology: from bacteria to man.}},  url = {http://dx.doi.org/10.1002/wsbm.74},  volume = {2},  year = {2010}  }  @incollection{citeulike:7844852,  abstract = {{Interactions among cellular constituents play a crucial role in overall cellular function and organization. These interactions can be viewed as being complementary to the usual parts list of genes and proteins and, in conjunction with the expression states of these parts, are key to a systems level understanding of the cell. Here, we review computational approaches to the understanding of the functional roles of cellular networks, ranging from static models of network topology to dynamical and stochastic simulations.}},  address = {Totowa, NJ},  author = {Vallabhajosyula, Ravishankar R. and Raval, Alpan},  booktitle = {Systems Biology in Drug Discovery and Development},  chapter = {5},  citeulike-article-id = {7844852},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-1-60761-800-3\_5},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20824468},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20824468},  citeulike-linkout-3 = {http://www.springerlink.com/content/gq6743u321n57166},  doi = {10.1007/978-1-60761-800-3\_5},  editor = {Walker, John M. and Yan, Qing},  isbn = {978-1-60761-799-0},  issn = {1940-6029},  journal = {Methods in molecular biology (Clifton, N.J.)},  keywords = {system-biology},  pages = {97--120},  pmid = {20824468},  posted-at = {2010-09-22 15:50:47},  priority = {2},  publisher = {Humana Press},  series = {Methods in Molecular Biologyâ„¢},  title = {{Computational Modeling in Systems Biology}},  url = {http://dx.doi.org/10.1007/978-1-60761-800-3\_5},  volume = {662},  year = {2010}  }  @incollection{citeulike:7844851,  abstract = {{Systems Biology approaches to drug discovery largely focus on the increasing understanding of intracellular and cellular circuits, by computational representation of a molecular system followed by parameter validation against experimental data. This chapter outlines a universal approach to systems biology that allows the linking of intracellular molecular machinery and cellular activity. This procedure is achieved by applying mathematical modeling to molecular modules of a cell in the light of systems biology techniques.}},  address = {Totowa, NJ},  author = {Valeyev, Najl V. and Bates, Declan G. and Umezawa, Yoshinori and Gizatullina, Antonina N. and Kotov, Nikolay V.},  booktitle = {Systems Biology in Drug Discovery and Development},  chapter = {4},  citeulike-article-id = {7844851},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-1-60761-800-3\_4},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20824467},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20824467},  citeulike-linkout-3 = {http://www.springerlink.com/content/n4161mg28287wq12},  doi = {10.1007/978-1-60761-800-3\_4},  editor = {Walker,, John .. and Yan,, Qing},  isbn = {978-1-60761-799-0},  issn = {1940-6029},  journal = {Methods in molecular biology (Clifton, N.J.)},  keywords = {system-biology},  pages = {79-95--95},  pmid = {20824467},  posted-at = {2010-09-22 15:50:27},  priority = {2},  publisher = {Humana Press},  series = {Methods in Molecular Biology},  title = {{Systems Biology of Cell Behavior}},  url = {http://dx.doi.org/10.1007/978-1-60761-800-3\_4},  volume = {662},  year = {2010}  }  @article{citeulike:7844846,  abstract = {{MOTIVATION: The SBML Render Extension enables coloring and shape information of biochemical models to be stored in the Systems Biology Markup Language (SBML). Rendering of this stored graphical information in a portable and well supported system such as T(E)X would be useful for researchers preparing documentation and presentations. In addition, since the Render Extension is not yet supported by many applications, it is helpful for such rendering functionality be extended to the more popular CellDesigner annotation as well. RESULTS: SBML2TikZ supports automatic generation of graphics for biochemical models in the popular T(E)X typesetting system. The library generates a script of T(E)X macro commands for the vector graphics languages PGF/TikZ that can be compiled into scalable vector graphics described in a model. AVAILABILITY: Source code, documentation, and compiled binaries for the SBML2TikZ library can be found at http://www.sbml2tikz.org. In addition, a web application is available at http://www.sys-bio.org/layout. CONTACT: [email protected].}},  author = {Shen, Si Yuan Y. and Bergmann, Frank and Sauro, Herbert M.},  citeulike-article-id = {7844846},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btq512},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20829443},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20829443},  day = {9},  doi = {10.1093/bioinformatics/btq512},  issn = {1367-4811},  journal = {Bioinformatics (Oxford, England)},  keywords = {system-biology},  month = sep,  pmid = {20829443},  posted-at = {2010-09-22 12:19:25},  priority = {2},  title = {{SBML2TikZ: Supporting the SBML Render Extension in LATEX.}},  url = {http://dx.doi.org/10.1093/bioinformatics/btq512},  year = {2010}  }  @incollection{citeulike:7870785,  abstract = {{We extend here the Population Protocol model of Angluin et al. [2] in order to model more powerful networks of very small resource-limited artefacts (agents) that are possibly mobile. The main feature of our extended model is to allow edges of the communication graph, G, to have states that belong to a constant size set. We also allow edges to have readable only costs, whose values also belong to a constant size set. Our protocol specifications are still independent of the population size and do not use agent ids, i.e. they preserve uniformity and anonymity. Our Mediated Population Protocols (MPP) can stably compute graph properties of the communication graph. We show this for the properties of maximal matchings (in undirected communication graphs), also for finding the transitive closure of directed graphs and for finding all edges of small cost. We demonstrate that our mediated protocols are stronger than the classical population protocols, by presenting a MPP for a non-semilinear predicate. To show this fact, we state and prove a general theorem about the composition of two stably computing mediated population protocols. We also show that all predicates stably computable in our model are (non-uniformly) in the class NSPACE(|E(G)|).}},  address = {Berlin, Heidelberg},  author = {Chatzigiannakis, Ioannis and Michail, Othon and Spirakis, Paul},  booktitle = {Automata, Languages and Programming},  chapter = {30},  citeulike-article-id = {7870785},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-02930-1\_30},  citeulike-linkout-1 = {http://www.springerlink.com/content/m42qq47137607kr3},  doi = {10.1007/978-3-642-02930-1\_30},  editor = {Albers,, Susanne and Marchetti-Spaccamela,, Alberto and Matias,, Yossi and Nikoletseas,, Sotiris and Thomas,, Wolfgang},  isbn = {978-3-642-02929-5},  keywords = {population-protocols},  pages = {363-374--374},  posted-at = {2010-09-21 20:01:43},  priority = {0},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Mediated Population Protocols}},  url = {http://dx.doi.org/10.1007/978-3-642-02930-1\_30},  volume = {5556},  year = {2009}  }  @article{citeulike:7358340,  author = {Searls, David B.},  citeulike-article-id = {7358340},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000809},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20589079},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20589079},  day = {24},  doi = {10.1371/journal.pcbi.1000809},  issn = {1553-7358},  journal = {PLoS Comput Biol},  keywords = {transversal},  month = jun,  number = {6},  pages = {e1000809+},  pmid = {20589079},  posted-at = {2010-09-20 18:17:42},  priority = {3},  publisher = {Public Library of Science},  title = {{The Roots of Bioinformatics}},  url = {http://dx.doi.org/10.1371/journal.pcbi.1000809},  volume = {6},  year = {2010}  }  @article{sand-jensen:2009,  abstract = {{Although scientists typically insist that their research is very exciting and adventurous when they talk to laymen and prospective students, the allure of this enthusiasm is too often lost in the predictable, stilted structure and language of their scientific publications. I present here, a top-10 list of recommendations for how to write consistently boring scientific publications. I then discuss why we should and how we could make these contributions more accessible and exciting.}},  author = {Sand-Jensen, Kaj},  citeulike-article-id = {1242600},  citeulike-linkout-0 = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.2007.0030-1299.15674.x},  citeulike-linkout-1 = {http://dx.doi.org/10.1111/j.2007.0030-1299.15674.x},  citeulike-linkout-2 = {http://www.ingentaconnect.com/content/mksg/oki/2007/00000116/00000005/art00001},  doi = {10.1111/j.2007.0030-1299.15674.x},  issn = {0030-1299},  journal = {Oikos},  keywords = {transversal},  month = may,  number = {5},  pages = {723--727},  posted-at = {2010-09-20 18:17:08},  priority = {3},  publisher = {Blackwell Publishing Ltd},  title = {{How to write consistently boring scientific literature}},  url = {http://dx.doi.org/10.1111/j.2007.0030-1299.15674.x},  volume = {116},  year = {2007}  }  @inproceedings{citeulike:3814574,  abstract = {{We describe the use of the social reference management website CiteULike for recommending scientific articles to users, based on their reference library. We test three different collaborative filtering algorithms, and find that user-based filtering performs best. A temporal analysis of the data indexed by CiteULike shows that it takes about two years for the cold-start problem to disappear and recommendation performance to improve.}},  address = {New York, NY, USA},  author = {Bogers, Toine and van den Bosch, Antal},  booktitle = {Proceedings of the 2008 ACM Conference on Recommender Systems},  citeulike-article-id = {3814574},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1454008.1454053},  citeulike-linkout-1 = {http://dx.doi.org/10.1145/1454008.1454053},  doi = {10.1145/1454008.1454053},  isbn = {978-1-60558-093-7},  keywords = {transversal},  location = {Lausanne, Switzerland},  pages = {287--290},  posted-at = {2010-09-20 18:16:50},  priority = {3},  publisher = {ACM},  series = {RecSys '08},  title = {{Recommending Scientific Articles Using Citeulike}},  url = {http://dx.doi.org/10.1145/1454008.1454053},  year = {2008}  }  @book{citeulike:5784887,  author = {Box, George E. P. and Draper, Norman R.},  citeulike-article-id = {5784887},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0471810339},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0471810339},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0471810339},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0471810339},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0471810339/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0471810339},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0471810339},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0471810339},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0471810339\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0471810339},  edition = {1},  howpublished = {Hardcover},  isbn = {0471810339},  keywords = {books},  posted-at = {2010-09-18 23:36:47},  priority = {2},  publisher = {Wiley},  title = {{Empirical Model-Building and Response Surfaces (Wiley Series in Probability and Statistics)}},  url = {http://www.worldcat.org/isbn/0471810339}  }  @book{Srivastava2004,  author = {Srivastava, Sheela},  citeulike-article-id = {7853254},  isbn = {978-1-4020-1633-2},  keywords = {books},  posted-at = {2010-09-18 19:33:18},  priority = {0},  publisher = {Springer},  title = {{Understanding Bacteria}},  year = {2004}  }  @article{citeulike:7853227,  abstract = {{The katF gene of Escherichia coli has been sequenced revealing a 1086 base pair open reading frame from which the sequence of a 362 amino acid protein has been deduced. The direction of transcription of katF was confirmed by expression of the gene cloned in both directions behind a T7 promoter. The KatF protein expressed in vitro migrates with an apparent size of 42 kDa. Comparison of the katF sequence to the sequence of rpoD, which encodes the sigma subunit of RNA polymerase, revealed a 181 bp region with 65\% homology and a 38 bp segment that was 87\% homologous. A 62 amino acid region of the predicted KatF protein sequence was found to be 85\% homologous to the corresponding sequence of sigma 70, including a segment implicated in core polymerase binding. Homology was also observed with the heat shock regulatory protein encoded by htpR.}},  author = {Mulvey, M. R. and Loewen, P. C.},  citeulike-article-id = {7853227},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/2690013},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=2690013},  day = {11},  issn = {0305-1048},  journal = {Nucleic acids research},  keywords = {bacterial-biology},  month = dec,  number = {23},  pages = {9979--9991},  pmid = {2690013},  posted-at = {2010-09-18 18:52:44},  priority = {0},  title = {{Nucleotide sequence of katF of Escherichia coli suggests KatF protein is a novel sigma transcription factor.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/2690013},  volume = {17},  year = {1989}  }  @article{Eiha2002609,  author = {Eiha, Noriko and Komoto, Atsushi and Maenosono, Shinya and Wakano, Joe Y. and Yamamoto, Kenji and Yamaguchi, Yukio},  citeulike-article-id = {7851214},  citeulike-linkout-0 = {http://www.sciencedirect.com/science/article/B6TVG-4645DFW-2/2/085041a38dee3f06721f1ce978339333},  citeulike-linkout-1 = {http://dx.doi.org/10.1016/S0378-4371(02)00983-4},  doi = {10.1016/S0378-4371(02)00983-4},  journal = {Physica A: Statistical Mechanics and its Applications},  keywords = {synbio-bacterial},  number = {3-4},  posted-at = {2010-09-17 20:09:57},  priority = {2},  title = {{The mode transition of the bacterial colony}},  url = {http://www.sciencedirect.com/science/article/B6TVG-4645DFW-2/2/085041a38dee3f06721f1ce978339333},  volume = {313},  year = {2002}  }  @article{citeulike:7835121,  abstract = {{A clear imperative exists to generate radically different antibacterial technologies that will reduce the usage of conventional chemical antibiotics. Here we trace one route into this new frontier of drug discovery, a concept that we call the bacterial conjugation-based technologies (BCBT). One of the objectives of the BCBT is to exploit plasmid biology for combating the rising tide of antibiotic-resistant bacteria. Specifically, the concept utilizes conjugationally delivered plasmids as antimicrobial agents, and it builds on the accumulated work of many scientists dating back to the discoveries of conjugation and plasmids themselves. Each of the individual components that comprise the approach has been demonstrated to be feasible. We discuss the properties of bacterial plasmids to be employed in BCBT.}},  author = {Filutowicz, Marcin and Burgess, Richard and Gamelli, Richard L. and Heinemann, Jack A. and Kurenbach, Brigitta and Rakowski, Sheryl A. and Shankar, Ravi},  citeulike-article-id = {7835121},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.plasmid.2008.03.004},  doi = {10.1016/j.plasmid.2008.03.004},  issn = {0147619X},  journal = {Plasmid},  keywords = {synbio-bacterial},  month = jul,  number = {1},  pages = {38--44},  posted-at = {2010-09-14 17:38:47},  priority = {0},  title = {{Bacterial conjugation-based antimicrobial agents}},  url = {http://dx.doi.org/10.1016/j.plasmid.2008.03.004},  volume = {60},  year = {2008}  }  @inproceedings{4545325,  abstract = {{The application of parallel and distributed simulation techniques is often limited by the amount of parallelism available in the model. This holds true for large-scale cell- biological simulations, afield that has emerged as data and knowledge concerning these systems increases and biologists call for tools to guide wet-lab experimentation. A promising approach to exploit parallelism in this domain is the integration of spatial aspects, which are often crucial to a model's validity. We describe an optimistic, parallel and distributed variant of the Next-Subvolume Method (NSM), a method that augments the well-known Gillespie Stochastic Simulation Algorithm (SSA) with spatial features. We discuss requirements imposed by this application on a parallel discrete event simulation engine to achieve efficient execution. First results of combining NSM and the grid-inspired simulation system AURORA are shown.}},  author = {Jeschke, M. and Park, A. and Ewald, R. and Fujimoto, R. and Uhrmacher, A. M.},  citeulike-article-id = {7804578},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/PADS.2008.20},  doi = {10.1109/PADS.2008.20},  journal = {Principles of Advanced and Distributed Simulation, 2008. PADS '08. 22nd Workshop on},  keywords = {simulation-and-modeling},  month = jun,  posted-at = {2010-09-09 18:53:17},  priority = {2},  title = {{Parallel and Distributed Spatial Simulation of Chemical Reactions}},  url = {http://dx.doi.org/10.1109/PADS.2008.20},  year = {2008}  }  @incollection{citeulike:3206175,  abstract = {{Diverse modelling formalisms are applied in Computational Biology. Some describe the biological system in a continuous manner, others focus on discrete-event systems, or on a combination of continuous and discrete descriptions. Similarly, there are many simulators that support different formalisms and execution types (e.g. sequential, parallel-distributed) of one and the same model. The latter is often done to increase efficiency, sometimes at the cost of accuracy and level of detail. James\^{A} II has been developed to support different modelling formalisms and different simulators and their combinations. It is based on a plug-in concept which enables developers to integrate spatial and non-spatial modelling formalisms (e.g. stochastic \"{I} calculus, Beta binders, Devs, space- \"{I}), simulation algorithms (e.g. variants of Gillespie\^{a}s algorithms (including Tau Leaping and Next Subvolume Method),space- \"{I} simulator, parallel Beta binders simulator) and supporting technologies (e.g. partitioning algorithms, data collection mechanisms, data structures, random number generators) into an existing framework. This eases method development and result evaluation in applied modelling and simulation as well as in modelling and simulation research.}},  address = {Berlin, Heidelberg},  author = {Uhrmacher, Adelinde and Himmelspach, Jan and Jeschke, Matthias and John, Mathias and Leye, Stefan and Maus, Carsten and R\"{o}hl, Mathias and Ewald, Roland},  booktitle = {Formal Methods in Systems Biology},  chapter = {9},  citeulike-article-id = {3206175},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-540-68413-8\_9},  citeulike-linkout-1 = {http://www.springerlink.com/content/4x3873485g404745},  doi = {10.1007/978-3-540-68413-8\_9},  editor = {Fisher, Jasmin},  isbn = {978-3-540-68410-7},  journal = {Formal Methods in Systems Biology},  keywords = {simulation-and-modeling},  pages = {123-138--138},  posted-at = {2010-09-09 18:35:00},  priority = {2},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{One Modelling Formalism \& Simulator Is Not Enough! A Perspective for Computational Biology Based on James II}},  url = {http://dx.doi.org/10.1007/978-3-540-68413-8\_9},  volume = {5054},  year = {2008}  }  @article{citeulike:3478557,  abstract = {{ Interest in the possibility of dynamically simulating complex cellular processes has escalated markedly in recent years. This interest has been fuelled by three factors: the generally accepted value in understanding living processes as integrated systems; the dramatic increase in computational capability; and the availability of new or improved technology for making the quantitative measurements that are needed to drive and validate cellular simulations. Between the extremes of atom-scale and organism-scale simulation is a vast middle-ground requiring simulation strategies that are capable of dealing with a range of spatial, temporal and molecular abundance scales that are crucial for a comprehensive understanding of integrative cell biology. Although at an early stage, methodological improvements and the development of computational platforms provide some hope that simulations will emerge that can bridge the gap between network models and the true operation of the cell as a complex machine. }},  author = {Ridgway, Douglas and Broderick, Gordon and Ellison, Michael J.},  citeulike-article-id = {3478557},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.copbio.2006.08.004},  doi = {10.1016/j.copbio.2006.08.004},  issn = {09581669},  journal = {Current Opinion in Biotechnology},  keywords = {simulation-and-modeling},  month = oct,  number = {5},  pages = {493--498},  posted-at = {2010-09-09 17:32:15},  priority = {0},  title = {{Accommodating space, time and randomness in network simulation}},  url = {http://dx.doi.org/10.1016/j.copbio.2006.08.004},  volume = {17},  year = {2006}  }  @inproceedings{citeulike:5788079,  abstract = {{The application of parallel and distributed simulation techniques is often limited by the amount of parallelism available in the model. This holds true for large-scale cell-biological simulations, a field that has emerged as data and knowledge concerning these systems increases and biologists call for tools to guide wet-lab experimentation. A promising approach to exploit parallelism in this domain is the integration of spatial aspects, which are often crucial to a model's validity. We describe an optimistic, parallel and distributed variant of the Next-Subvolume Method (NSM), a method that augments the well-known Gillespie Stochastic Simulation Algorithm (SSA) with spatial features. We discuss requirements imposed by this application on a parallel discrete event simulation engine to achieve efficient execution. First results of combining NSM and the grid-inspired simulation system Aurora are shown.}},  address = {Washington, DC, USA},  author = {Jeschke, Matthias and Park, Alfred and Ewald, Roland and Fujimoto, Richard and Uhrmacher, Adelinde M.},  booktitle = {Proceedings of the 22nd Workshop on Principles of Advanced and Distributed Simulation},  citeulike-article-id = {5788079},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1381309.1382286},  citeulike-linkout-1 = {http://doi.ieeecomputersociety.org/10.1109/PADS.2008.20},  citeulike-linkout-2 = {http://dx.doi.org/10.1109/pads.2008.20},  citeulike-linkout-3 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=4545325},  day = {6},  doi = {10.1109/pads.2008.20},  isbn = {978-0-7695-3159-5},  issn = {1087-4097},  journal = {Parallel and Distributed Simulation, Workshop on},  keywords = {simulation-and-modeling},  location = {Roma, Italy},  month = jun,  pages = {51--59},  posted-at = {2010-09-09 17:27:40},  priority = {0},  publisher = {IEEE Computer Society},  series = {PADS '08},  title = {{Parallel and Distributed Spatial Simulation of Chemical Reactions}},  url = {http://dx.doi.org/10.1109/pads.2008.20},  volume = {0},  year = {2008}  }  @article{citeulike:7752949,  abstract = {{Bacteria show remarkable adaptability in the face of antibiotic therapeutics. Resistance alleles in drug target-specific sites and general stress responses have been identified in individual end-point isolates. Less is known, however, about the population dynamics during the development of antibiotic-resistant strains. Here we follow a continuous culture of Escherichia coli facing increasing levels of antibiotic and show that the vast majority of isolates are less resistant than the population as a whole. We find that the few highly resistant mutants improve the survival of the population's less resistant constituents, in part by producing indole, a signalling molecule generated by actively growing, unstressed cells. We show, through transcriptional profiling, that indole serves to turn on drug efflux pumps and oxidative-stress protective mechanisms. The indole production comes at a fitness cost to the highly resistant isolates, and whole-genome sequencing reveals that this bacterial altruism is made possible by drug-resistance mutations unrelated to indole production. This work establishes a population-based resistance mechanism constituting a form of kin selection whereby a small number of resistant mutants can, at some cost to themselves, provide protection to other, more vulnerable, cells, enhancing the survival capacity of the overall population in stressful environments.}},  author = {Lee, Henry H. and Molla, Michael N. and Cantor, Charles R. and Collins, James J.},  citeulike-article-id = {7752949},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature09354},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature09354},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936489/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/20811456},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=20811456},  day = {2},  doi = {10.1038/nature09354},  issn = {1476-4687},  journal = {Nature},  keywords = {bacterial-biology},  month = sep,  number = {7311},  pages = {82--85},  pmcid = {PMC2936489},  pmid = {20811456},  posted-at = {2010-09-09 17:26:57},  priority = {0},  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},  title = {{Bacterial charity work leads to population-wide resistance.}},  url = {http://dx.doi.org/10.1038/nature09354},  volume = {467},  year = {2010}  }  @misc{hogg:model,  abstract = {{We go through the many considerations involved in fitting a model to data,  using as an example the fit of a straight line to a set of points in a  two-dimensional plane. Standard weighted least-squares fitting is only  appropriate when there is a dimension along which the data points have  negligible uncertainties, and another along which all the uncertainties can be  described by Gaussians of known variance; these conditions are rarely met in  practice. We consider cases of general, heterogeneous, and arbitrarily  covariant two-dimensional uncertainties, and situations in which there are bad  data (large outliers), unknown uncertainties, and unknown but expected  intrinsic scatter in the linear relationship being fit. Above all we emphasize  the importance of having a "generative model" for the data, even an approximate  one. Once there is a generative model, the subsequent fitting is non-arbitrary  because the model permits direct computation of the likelihood of the  parameters or the posterior probability distribution. Construction of a  posterior probability distribution is indispensible if there are "nuisance  parameters" to marginalize away.}},  archivePrefix = {arXiv},  author = {Hogg, David W. and Bovy, Jo and Lang, Dustin},  citeulike-article-id = {7736929},  citeulike-linkout-0 = {http://arxiv.org/abs/1008.4686},  citeulike-linkout-1 = {http://arxiv.org/pdf/1008.4686},  citeulike-linkout-2 = {http://adsabs.harvard.edu/cgi-bin/nph-bib\_query?bibcode=2010arXiv1008.4686H},  day = {27},  eprint = {1008.4686},  journal = {ArXiv e-prints},  keywords = {simulation-and-modeling},  month = aug,  posted-at = {2010-09-09 17:26:25},  priority = {2},  title = {{Data analysis recipes: Fitting a model to data}},  url = {http://arxiv.org/abs/1008.4686},  year = {2010}  }  @article{citeulike:1224293,  abstract = {{The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis and management in bioinformatics and for systems modelling and simulation in computational and systems biology. The collaborations gave rise to applications and integrated tools that we summarize and discuss in context of the state of the art in this area. We investigate on future challenges and argue that the field should still be explored from many perspectives ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages to be used by information agents, and to the adoption of agents for computational grids.}},  address = {Dipartimento di Matematica e Informatica Via Madonna delle Carceri 9 62032 Camerino, Italy. [email protected]},  author = {Merelli, Emanuela and Armano, Giuliano and Cannata, Nicola and Corradini, Flavio and d'Inverno, Mark and Doms, Andreas and Lord, Phillip and Martin, Andrew and Milanesi, Luciano and M\"{o}ller, Steffen and Schroeder, Michael and Luck, Michael},  citeulike-article-id = {1224293},  citeulike-linkout-0 = {http://dx.doi.org/10.1093/bib/bbl014},  citeulike-linkout-1 = {http://bib.oxfordjournals.org/content/8/1/45.abstract},  citeulike-linkout-2 = {http://bib.oxfordjournals.org/content/8/1/45.full.pdf},  citeulike-linkout-3 = {http://bib.oxfordjournals.org/cgi/content/abstract/8/1/45},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/16772270},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=16772270},  day = {01},  doi = {10.1093/bib/bbl014},  issn = {1477-4054},  journal = {Briefings in Bioinformatics},  keywords = {simulation-and-modeling},  month = jan,  number = {1},  pages = {45--59},  pmid = {16772270},  posted-at = {2010-09-08 16:09:12},  priority = {0},  publisher = {Oxford University Press},  title = {{Agents in bioinformatics, computational and systems biology}},  url = {http://dx.doi.org/10.1093/bib/bbl014},  volume = {8},  year = {2007}  }  @inproceedings{citeulike:2443758,  abstract = {{We apply the multi-agent system (MAS) platform to the task of biological network simulation. In this paper, we describe the simulation of signal transduction (ST) networks using the DECAF [9] MAS architecture. Unlike previous approaches that relied on systems of differential equations (DE), the distributed framework of MAS scales well and allows us to model large, highly interconnected ST pathways. This scalability is achieved by adopting a hybrid strategy that factors macro-level measures, such as reaction rateconstants, to calculate the stochastic kinetics at the level of individual molecules. Thus, by capturing the ST domain at an intermediate level of abstraction, we are able to retain much of the granularity afforded by a purely individual-based approach. The task distribution within a MAS enables us to model certain physical properies, such as diffusion and subcellular compartmentalization, which have proven to be difficult for DE systems. We demonstrate that large-grained agents are well suited to maintaining interal state representations and efficient in computing reactant concentration, both of which are vital considerations in modeling the ST domain. In our system, a molecular species is modeled as an individual agent with hierarchical task network structures to represent self- and externally-initiated reactions. An agent's identity is determined by a rule file (one for every participating molecular species) that specifies the reactions it may participate in, as well as its initial concentration. Reactions within the system are actuated by inter-agent communication. We present results from modeling the well-studied epidermal growth factor (EGF) pathway, demonstrating the viability of MAS technologies as a simulation platform for biological networks.}},  address = {New York, NY, USA},  author = {Khan, Salim and Makkena, Ravi and McGeary, Foster and Decker, Keith and Gillis, William and Schmidt, Carl},  booktitle = {Proceedings of the second international joint conference on Autonomous agents and multiagent systems},  citeulike-article-id = {2443758},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=860575.860637},  citeulike-linkout-1 = {http://dx.doi.org/10.1145/860575.860637},  doi = {10.1145/860575.860637},  isbn = {1-58113-683-8},  keywords = {simulation-and-modeling},  location = {Melbourne, Australia},  pages = {385--392},  posted-at = {2010-09-08 15:18:36},  priority = {0},  publisher = {ACM},  series = {AAMAS '03},  title = {{A multi-agent system for the quantitative simulation of biological networks}},  url = {http://dx.doi.org/10.1145/860575.860637},  year = {2003}  }  @book{Hopcroft79,  abstract = {{This book is a rigorous exposition of formal languages and models ofcomputation, with an introduction to computational complexity. The authorspresent the theory in a concise and straightforward manner, with an eye outfor the practical applications. Exercises at the end of each chapter,including some that have been solved, help readers confirm and enhance theirunderstanding of the material. This book is appropriate for upper-levelcomputer science undergraduates who are comfortable with mathematicalarguments.}},  author = {Hopcroft, John E. and Ullman, Jeffrey D.},  citeulike-article-id = {4680992},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/020102988X},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/020102988X},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/020102988X},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/020102988X},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/020102988X/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/020102988X},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/020102988X},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN020102988X},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=020102988X\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/020102988X},  howpublished = {ãƒãƒ¼ãƒ‰ã‚«ãƒãƒ¼},  isbn = {020102988X},  keywords = {books},  posted-at = {2010-09-07 21:51:56},  priority = {2},  publisher = {Addison Wesley Publishing Company},  title = {{Introduction to Automata Theory, Languages, and Computation}},  url = {http://www.worldcat.org/isbn/020102988X},  year = {1979}  }  @article{citeulike:3653185,  abstract = {{We demonstrate how a single-celled organism could undertake associative learning. Although to date only one previous study has found experimental evidence for such learning, there is no reason in principle why it should not occur. We propose a gene regulatory network that is capable of associative learning between any pre-specified set of chemical signals, in a Hebbian manner, within a single cell. A mathematical model is developed, and simulations show a clear learned response. A preliminary design for implementing this model using plasmids within Escherichia coli is presented, along with an alternative approach, based on double-phosphorylated protein kinases.}},  author = {Fernando, Chrisantha T. and Liekens, Anthony M. L. and Bingle, Lewis E. H. and Beck, Christian and Lenser, Thorsten and Stekel, Dov J. and Rowe, Jonathan E.},  citeulike-article-id = {3653185},  citeulike-linkout-0 = {http://dx.doi.org/10.1098/rsif.2008.0344},  citeulike-linkout-1 = {http://rsif.royalsocietypublishing.org/content/6/34/463.abstract},  citeulike-linkout-2 = {http://rsif.royalsocietypublishing.org/content/6/34/463.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18835803},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18835803},  citeulike-linkout-5 = {http://journals.royalsociety.org/content/81252g53k2310525},  day = {6},  doi = {10.1098/rsif.2008.0344},  journal = {Journal of The Royal Society Interface},  keywords = {synbio-bacterial},  month = may,  number = {34},  pages = {463--469},  pmid = {18835803},  posted-at = {2010-09-07 19:47:34},  priority = {2},  title = {{Molecular circuits for associative learning in single-celled organisms}},  url = {http://dx.doi.org/10.1098/rsif.2008.0344},  volume = {6},  year = {2009}  }  @phdthesis{citeulike:7794971,  author = {Weiss, Ron},  citeulike-article-id = {7794971},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=935268},  keywords = {synbio-dna},  posted-at = {2010-09-07 07:46:56},  priority = {0},  publisher = {Massachusetts Institute of Technology},  title = {{Cellular computation and communications using engineered genetic regulatory networks}},  url = {http://portal.acm.org/citation.cfm?id=935268},  year = {2001}  }  @article{citeulike:1297109,  abstract = {{Advances in biology and engineering have enabled the reprogramming of cells with well-defined functions, leading to the emergence of synthetic biology. Early successes in this nascent field suggest its potential to impact diverse areas. Here, we examine the feasibility of engineering circuits for cell-based computation. We illustrate the basic concepts by describing the mapping of several computational problems to engineered gene circuits. Revolving around these examples and past studies, we discuss technologies and computational methods available to design, test, and optimize gene circuits. We conclude with discussion of challenges involved in a typical design cycle, as well as those specific to cellular computation.}},  address = {Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.},  author = {Tan, Cheemeng and Song, Hao and Niemi, Jarad and You, Lingchong},  citeulike-article-id = {1297109},  citeulike-linkout-0 = {http://dx.doi.org/10.1039/b618473c},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17460793},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17460793},  citeulike-linkout-3 = {http://www.rsc.org/Publishing/Journals/article.asp?doi=b618473c},  doi = {10.1039/b618473c},  issn = {1742-206X},  journal = {Molecular bioSystems},  keywords = {synbio-bacterial},  month = may,  number = {5},  pages = {343--353},  pmid = {17460793},  posted-at = {2010-09-07 07:41:50},  priority = {2},  title = {{A synthetic biology challenge: making cells compute.}},  url = {http://dx.doi.org/10.1039/b618473c},  volume = {3},  year = {2007}  }  @article{citeulike:3920676,  abstract = {{  Microbial consortia are ubiquitous in nature and are implicated in processes of great importance to humans, from environmental remediation and wastewater treatment to assistance in food digestion. Synthetic biologists are honing their ability to program the behavior of individual microbial populations, forcing the microbes to focus on specific applications, such as the production of drugs and fuels. Given that microbial consortia can perform even more complicated tasks and endure more changeable environments than monocultures can, they represent an important new frontier for synthetic biology. Here, we review recent efforts to engineer synthetic microbial consortia, and we suggest future applications.  }},  author = {Brenner, Katie and You, Lingchong and Arnold, Frances H.},  citeulike-article-id = {3920676},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.tibtech.2008.05.004},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18675483},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18675483},  doi = {10.1016/j.tibtech.2008.05.004},  issn = {0167-7799},  journal = {Trends in biotechnology},  keywords = {synbio-bacterial},  month = sep,  number = {9},  pages = {483--489},  pmid = {18675483},  posted-at = {2010-09-07 07:40:04},  priority = {0},  title = {{Engineering microbial consortia: a new frontier in synthetic biology.}},  url = {http://dx.doi.org/10.1016/j.tibtech.2008.05.004},  volume = {26},  year = {2008}  }  @article{citeulike:6194142,  abstract = {{Stochasticity pervades life at the cellular level. Cells receive stochastic signals, perform detection and transduction with stochastic biochemistry, and grow and die in stochastic environments. Here we review progress in going from the molecular details to the information-processing strategies cells use in their decision-making. Such strategies are fundamentally influenced by stochasticity. We argue that the cellular decision-making can only be probabilistic and occurs at three levels. First, cells must infer from noisy signals the probable current and anticipated future state of their environment. Second, they must weigh the costs and benefits of each potential response, given that future. Third, cells must decide in the presence of other, potentially competitive, decision-makers. In this context, we discuss cooperative responses where some individuals can appear to sacrifice for the common good. We believe that decision-making strategies will be conserved, with comparatively few strategies being implemented by different biochemical mechanisms in many organisms. Determining the strategy of a decision-making network provides a potentially powerful coarse-graining that links systems and evolutionary biology to understand biological design.}},  author = {Perkins, Theodore J. and Swain, Peter S.},  booktitle = {Mol Syst Biol},  citeulike-article-id = {6194142},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/msb.2009.83},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/msb200983},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19920811},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19920811},  day = {17},  doi = {10.1038/msb.2009.83},  issn = {1744-4292},  journal = {Molecular Systems Biology},  keywords = {game-theory},  month = nov,  number = {1},  pmid = {19920811},  posted-at = {2010-09-06 15:01:04},  priority = {0},  publisher = {Nature Publishing Group},  title = {{Strategies for cellular decision-making}},  url = {http://dx.doi.org/10.1038/msb.2009.83},  volume = {5},  year = {2009}  }  @incollection{citeulike:7790609,  abstract = {{Traditional centralized and rigid control structures are becoming inflexible to face the requirements of reconfigurability, responsiveness and robustness, imposed by customer demands in the current global economy. The Holonic Manufacturing Systems (HMS) paradigm, which was pointed out as a suitable solution to face these requirements, translates the concepts inherited from social organizations and biology to the manufacturing world. It offers an alternative way of designing adaptive systems where the traditional centralized control is replaced by decentralization over distributed and autonomous entities organized in hierarchical structures formed by intermediate stable forms. In spite of its enormous potential, methods regarding the self-adaptation and self-organization of complex systems are still missing. This paper discusses how the insights from biology in connection with new fields of computer science can be useful to enhance the holonic design aiming to achieve more self-adaptive and evolvable systems. Special attention is devoted to the discussion of emergent behavior and self-organization concepts, and the way they can be combined with the holonic rationale.}},  address = {Berlin, Heidelberg},  author = {Leitao, Paulo},  booktitle = {Transactions on Large-Scale Data- and Knowledge-Centered Systems I},  chapter = {10},  citeulike-article-id = {7790609},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-03722-1\_10},  citeulike-linkout-1 = {http://www.springerlink.com/content/t28270742t5p254k},  doi = {10.1007/978-3-642-03722-1\_10},  editor = {Hameurlain, Abdelkader and K\"{u}ng, Josef and Wagner, Roland},  isbn = {978-3-642-03721-4},  pages = {243-266--266},  posted-at = {2010-09-06 13:07:04},  priority = {0},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Holonic Rationale and Bio-inspiration on Design of Complex Emergent and Evolvable Systems}},  url = {http://dx.doi.org/10.1007/978-3-642-03722-1\_10},  volume = {5740},  year = {2009}  }  @article{citeulike:7790525,  abstract = {{The spread of the Internet and the evolution of mobile communication, have created new possibilities for software applications such as ubiquitous computing, dynamic supply chains and medical home care. Such systems need to operate in dynamic, heterogeneous environments and face the challenge of handling frequently changing requirements; therefore they must be flexible, robust and capable of adapting to the circumstances. It is widely believed that multi-agent systems coordinated by selforganisation and emergence mechanisms are an effective way to design these systems. This paper aims to define the concepts of self-organisation and emergence and to provide a state of the art survey about the different classes of self-organisation mechanisms applied in the multi-agent systems domain. Furthermore, the strengths and limits of these approaches are examined and research issues are provided. Povzetek: \v{C}lanek opisuje pregled samoorganizacije v MAS. 1}},  author = {Di, Giovanna and Serugendo, Marzo and Gleizes, Marie-pierre and Karageorgos, Anthony},  citeulike-article-id = {7790525},  citeulike-linkout-0 = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.114.2904},  journal = {In this volume},  pages = {45--54},  posted-at = {2010-09-06 11:51:39},  priority = {0},  title = {{Self-organisation and emergence in mas: An overview}},  url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.114.2904},  volume = {30},  year = {2006}  }  @article{citeulike:3372592,  abstract = {{Natural computing builds a bridge between computer science and natural sciences.}},  address = {New York, NY, USA},  author = {Kari, Lila and Rozenberg, Grzegorz},  citeulike-article-id = {3372592},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1400181.1400200},  citeulike-linkout-1 = {http://dx.doi.org/10.1145/1400181.1400200},  doi = {10.1145/1400181.1400200},  issn = {0001-0782},  journal = {Commun. ACM},  number = {10},  pages = {72--83},  posted-at = {2010-09-06 07:39:33},  priority = {0},  publisher = {ACM},  title = {{The many facets of natural computing}},  url = {http://dx.doi.org/10.1145/1400181.1400200},  volume = {51},  year = {2008}  }  @article{citeulike:3975313,  abstract = {{Amorphous computing differs from the classical ideas about computations almost in every aspect. The architecture of amorphous computers is random, since they consist of a plethora of identical computational units spread randomly over a given area. Within a limited radius the units can communicate wirelessly with their neighbors via a single-channel radio. We consider a model whose assumptions on the underlying computing and communication abilities are among the weakest possible: all computational units are finite state probabilistic automata working asynchronously, there is no broadcasting collision detection mechanism and no network addresses. We show that under reasonable probabilistic assumptions such amorphous computing systems can possess universal computing power with a high probability. The underlying theory makes use of properties of random graphs and that of probabilistic analysis of algorithms. To the best of our knowledge this is the first result showing the universality of such computing systems.}},  author = {Wiedermann, Ji\v{r}\'{\i} and Petr\r{u}, Luk\'{a}\v{s}},  citeulike-article-id = {3975313},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00224-009-9178-6},  citeulike-linkout-1 = {http://www.springerlink.com/content/k2x6266k78274m05},  day = {1},  doi = {10.1007/s00224-009-9178-6},  issn = {1432-4350},  journal = {Theory of Computing Systems},  keywords = {amorphous\_computing},  month = nov,  number = {4},  pages = {995-1010--1010},  posted-at = {2010-09-06 07:29:28},  priority = {0},  publisher = {Springer New York},  title = {{On the Universal Computing Power of Amorphous Computing Systems}},  url = {http://dx.doi.org/10.1007/s00224-009-9178-6},  volume = {45},  year = {2009}  }  @article{citeulike:875640,  abstract = {{Note: OCR errors may be found in this Reference List extracted from the full text article. ACM has opted to expose the complete List rather than only correct and linked references.}},  address = {New York, NY, USA},  author = {Abelson, Harold and Allen, Don and Coore, Daniel and Hanson, Chris and Homsy, George and Knight, Thomas F. and Nagpal, Radhika and Rauch, Erik and Sussman, Gerald J. and Weiss, Ron},  citeulike-article-id = {875640},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=332842},  citeulike-linkout-1 = {http://dx.doi.org/10.1145/332833.332842},  doi = {10.1145/332833.332842},  issn = {0001-0782},  journal = {Commun. ACM},  keywords = {amorphous\_computing},  month = may,  number = {5},  pages = {74--82},  posted-at = {2010-09-06 07:27:28},  priority = {0},  publisher = {ACM},  title = {{Amorphous computing}},  url = {http://dx.doi.org/10.1145/332833.332842},  volume = {43},  year = {2000}  }  @article{citeulike:3789174,  abstract = {{In vitro selection, or SELEX, is a technique that allows the simultaneous screening of highly diverse pools of different RNA or DNA (dsDNA or ssDNA) molecules for a particular feature. Different examples from a great variety of applications ofin vitro selection experiments are described and a detailed overview of the method and its variations will be given. Some especially conclusivein vitro selection experiments are discussed in detail to illustrate the potential power and diversity of this method. Potential restrictions of the methods and possible ways to overcome them are pointed out.}},  author = {Klug, Stefanie J. and Famulok, Michael},  citeulike-article-id = {3789174},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/bf00996358},  citeulike-linkout-1 = {http://www.springerlink.com/content/l4206618t11009rx},  day = {1},  doi = {10.1007/bf00996358},  issn = {0301-4851},  journal = {Molecular Biology Reports},  month = jun,  number = {2},  pages = {97-107--107},  posted-at = {2010-09-04 18:27:31},  priority = {2},  publisher = {Springer Netherlands},  title = {{All you wanted to know about SELEX}},  url = {http://dx.doi.org/10.1007/bf00996358},  volume = {20},  year = {1994}  }  @article{citeulike:1230234,  abstract = {{Natural and engineered RNA 'parts' can perform a variety of functions, including hybridizing to targets, binding ligands and undergoing programmed conformational changes, and catalyzing reactions. These RNA parts can in turn be assembled into synthetic genetic circuits that regulate gene expression by acting either in cis or in trans on mRNAs. As more parts are discovered and engineered, it should be increasingly possible to create synthetic RNA circuits that are able to carry out complex logical operations in cells, either superimposed on or autonomous to extant gene regulation.}},  author = {Davidson, Eric A. and Ellington, Andrew D.},  citeulike-article-id = {1230234},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nchembio846},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nchembio846},  day = {15},  doi = {10.1038/nchembio846},  issn = {1552-4450},  journal = {Nature Chemical Biology},  keywords = {synbio-dna},  month = dec,  number = {1},  pages = {23--28},  posted-at = {2010-09-04 18:25:04},  priority = {0},  publisher = {Nature Publishing Group},  title = {{Synthetic RNA circuits}},  url = {http://dx.doi.org/10.1038/nchembio846},  volume = {3},  year = {2006}  }  @article{citeulike:1073636,  abstract = {{Genetic engineering is entering a new era, where microorganisms can be programmed using synthetic constructs of DNA encoding logic and operational commands. A toolbox of modular genetic parts is being developed, comprised of cell-based environmental sensors and genetic circuits. Systems have already been designed to be interconnected with each other and interfaced with the control of cellular processes. Engineering theory will provide a predictive framework to design operational multicomponent systems. On the basis of these developments, increasingly complex cellular machines are being constructed to build specialty chemicals, weave biomaterials, and to deliver therapeutics.}},  address = {Biophysics and Chemistry \& Chemical Biology, Department of Pharmaceutical Chemistry, University of California San Francisco, QB3 Box 2540, 1700 4th Street, San Francisco, CA 94158, USA. [email protected]},  author = {Voigt, Christopher A.},  citeulike-article-id = {1073636},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.copbio.2006.09.001},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16978856},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16978856},  citeulike-linkout-3 = {http://www.sciencedirect.com/science/article/B6VRV-4KWTFBB-3/2/ca79719d3ae2228f32e5122d8cff62a8},  doi = {10.1016/j.copbio.2006.09.001},  issn = {09581669},  journal = {Current Opinion in Biotechnology},  keywords = {synbio-bacterial},  month = oct,  number = {5},  pages = {548--557},  pmid = {16978856},  posted-at = {2010-09-04 18:23:51},  priority = {0},  title = {{Genetic parts to program bacteria}},  url = {http://dx.doi.org/10.1016/j.copbio.2006.09.001},  volume = {17},  year = {2006}  }  @book{1481388,  author = {Shonkwiler, Ronald W.},  citeulike-article-id = {7766737},  keywords = {simulation-and-modeling},  posted-at = {2010-09-03 20:29:51},  priority = {2},  publisher = {Springer Publishing Company, Incorporated},  title = {{Mathematical Biology: An Introduction with Maple and Matlab}},  year = {2008}  }  @book{smut-holi,  address = {London},  author = {Smuts, Jan C.},  citeulike-article-id = {7766718},  keywords = {books},  posted-at = {2010-09-03 20:25:06},  priority = {0},  publisher = {Macmillan and Co.},  title = {{Holism and Evolution}},  year = {1926}  }  @article{citeulike:2329240,  abstract = {{Abstract\ \ A highly desired part of the synthetic biology toolbox is an embedded chemical microcontroller, capable of autonomously following a logic program specified by a set of instructions, and interacting with its cellular environment. Strategies for incorporating logic in aqueous chemistry have focused primarily on implementing components, such as logic gates, that are composed into larger circuits, with each logic gate in the circuit corresponding to one or more molecular species. With this paradigm, designing and producing new molecular species is necessary to perform larger computations. An alternative approach begins by noticing that chemical systems on the small scale are fundamentally discrete and stochastic. In particular, the exact molecular counts of each molecular species present, is an intrinsically available form of information. This might appear to be a very weak form of information, perhaps quite difficult for computations to utilize. Indeed, it has been shown that error-free Turing universal computation is impossible in this setting. Nevertheless, we show a design of a chemical computer that achieves fast and reliable Turing-universal computation using molecular counts. Our scheme uses only a small number of different molecular species to do computation of arbitrary complexity. The total probability of error of the computation can be made arbitrarily small (but not zero) by adjusting the initial molecular counts of certain species. While physical implementations would be difficult, these results demonstrate that molecular counts can be a useful form of information for small molecular systems such as those operating within cellular environments.}},  author = {Soloveichik, David and Cook, Matthew and Winfree, Erik and Bruck, Jehoshua},  citeulike-article-id = {2329240},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s11047-008-9067-y},  doi = {10.1007/s11047-008-9067-y},  journal = {Natural Computing},  posted-at = {2010-09-03 20:22:39},  priority = {2},  title = {{Computation with finite stochastic chemical reaction networks}},  url = {http://dx.doi.org/10.1007/s11047-008-9067-y}  }  @article{citeulike:7761130,  abstract = { },  author = {Aguilar, C. and Vlamakis, H. and Losick, R. and Kolter, R.},  citeulike-article-id = {7761130},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.mib.2007.09.006},  doi = {10.1016/j.mib.2007.09.006},  issn = {13695274},  journal = {Current Opinion in Microbiology},  keywords = {bacterial-biology},  month = dec,  number = {6},  pages = {638--643},  posted-at = {2010-09-03 07:19:21},  priority = {0},  title = {{Thinking about Bacillus subtilis as a multicellular organism}},  url = {http://dx.doi.org/10.1016/j.mib.2007.09.006},  volume = {10},  year = {2007}  }  @article{Shapiro1998,  abstract = {{It has been a decade since multicellularity was proposed as a general bacterial trait. Intercellular communication and multicellular coordination are now known to be widespread among prokaryotes and to affect multiple phenotypes. Many different classes of signaling molecules have been identified in both Gram-positive and Gram-negative species. Bacteria have sophisticated signal transduction networks for integrating intercellular signals with other information to make decisions about gene expression and cellular differentiation. Coordinated multicellular behavior can be observed in a variety of situations, including development of E. coli and B. subtilis colonies, swarming by Proteus and Serratia, and spatially organized interspecific metabolic cooperation in anaerobic bioreactor granules. Bacteria benefit from multicellular cooperation by using cellular division of labor, accessing resources that cannot effectively be utilized by single cells, collectively defending against antagonists, and optimizing population survival by differentiating into distinct cell types.}},  address = {Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, USA. [email protected]},  author = {Shapiro, J. A.},  citeulike-article-id = {581095},  citeulike-linkout-0 = {http://www.annualreviews.org/doi/abs/10.1146/annurev.micro.52.1.81},  citeulike-linkout-1 = {http://dx.doi.org/10.1146/annurev.micro.52.1.81},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/9891794},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=9891794},  doi = {10.1146/annurev.micro.52.1.81},  issn = {0066-4227},  journal = {Annual review of microbiology},  keywords = {bacterial-biology},  number = {1},  pages = {81--104},  pmid = {9891794},  posted-at = {2010-09-02 18:03:26},  priority = {2},  title = {{Thinking about bacterial populations as multicellular organisms.}},  url = {http://dx.doi.org/10.1146/annurev.micro.52.1.81},  volume = {52},  year = {1998}  }  @incollection{citeulike:7753769,  abstract = {{The population protocol model (PP) proposed by Angluin et al. [2] describes sensor networks consisting of passively mobile finite-state agents. The agents sense their environment and communicate in pairs to carry out some computation on the sensed values. The mediated population protocol model (MPP) [13] extended the PP model by communication links equipped with a constant size buffer. The MPP model was proved in [13] to be stronger than the PP model. However, its most important contribution is that it provides us with the ability to devise optimizing protocols, approximation protocols and protocols that decide properties of the communication graph on which they run. The latter case, suggests a simplified model, the GDM model, that was formally defined and studied in [11]. GDM is a special case of MPP that captures MPP\^{a}s ability to decide properties of the communication graph. Here we survey recent advances in the area initiated by the proposal of the PP model and at the same time we provide new protocols, novel ideas and results.}},  address = {Berlin, Heidelberg},  author = {Chatzigiannakis, Ioannis and Michail, Othon and Spirakis, Paul G.},  booktitle = {Mathematical Foundations of Computer Science 2009},  chapter = {6},  citeulike-article-id = {7753769},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-642-03816-7\_6},  citeulike-linkout-1 = {http://www.springerlink.com/content/04357n3084x10071},  doi = {10.1007/978-3-642-03816-7\_6},  editor = {Hutchison, David and Kanade, Takeo and Kittler, Josef and Kleinberg, Jon M. and Mattern, Friedemann and Mitchell, John C. and Naor, Moni and Nierstrasz, Oscar and Pandu Rangan, C. and Steffen, Bernhard and Sudan, Madhu and Terzopoulos, Demetri and Tygar, Doug and Vardi, Moshe Y. and Weikum, Gerhard and Kr\'{a}lovi\v{c}, Rastislav and Niwi\'{n}ski, Damian},  isbn = {978-3-642-03815-0},  keywords = {population-protocols},  pages = {56-76--76},  posted-at = {2010-09-01 22:40:49},  priority = {0},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{Recent Advances in Population Protocols}},  url = {http://dx.doi.org/10.1007/978-3-642-03816-7\_6},  volume = {5734},  year = {2009}  }  @article{citeulike:7219977,  abstract = {{Evolutionary optimization has been successfully used to increase our understanding of key properties of biochemical systems. Traditional optimization is, however, often insufficient for gaining deeper insights into the evolution of such systems because usually there is a mutual relationship between the properties optimized by evolution and the properties of the environment. Thus, by evolving towards optimal properties, organisms change their environment, which in turn alters the optimum. Evolutionary game theory provides an appropriate framework for analyzing evolution in such 'dynamic fitness landscapes'. We therefore argue that it is a promising approach to studying the evolution of biochemical systems. Indeed, recent studies have applied evolutionary game theory to key issues in the evolution of energy metabolism.}},  author = {Pfeiffer, Thomas and Schuster, Stefan},  citeulike-article-id = {7219977},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.tibs.2004.11.006},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15653322},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15653322},  doi = {10.1016/j.tibs.2004.11.006},  issn = {0968-0004},  journal = {Trends in biochemical sciences},  keywords = {game-theory},  month = jan,  number = {1},  pages = {20--25},  pmid = {15653322},  posted-at = {2010-09-01 19:06:10},  priority = {0},  title = {{Game-theoretical approaches to studying the evolution of biochemical systems.}},  url = {http://dx.doi.org/10.1016/j.tibs.2004.11.006},  volume = {30},  year = {2005}  }  @article{citeulike:7751822,  abstract = {{Developing dental bacterial plaques formed in vivo on enamel surfaces were examined in specimens from 18 adult volunteers during the first day of plaque formation. An intraoral model placing enamel pieces onto teeth was used to study bacterial plaque populations developing naturally to various cell densities per square millimeter of surface area of the enamel (W. F. Liljemark, C. G. Bloomquist, C. L. Bandt, B. L. Philstrom, J. E. Hinrichs, and L. F. Wolff, Oral Microbiol. Immunol. 8:5-15, 1993). Radiolabeled nucleoside incorporation was used to measure DNA synthesis concurrent with the taking of standard viable cell counts of the plaque samples. Results showed that in vivo plaque formation began with the rapid adherence of bacteria until ca. 12 to 32\% of the enamel's salivary pellicle was saturated (ca. 2.5 x 10(5) to 6.3 x 10(5) cells per mm2). The pioneer adherent species were predominantly those of the "sanguis streptococci." At the above-noted density, the bacteria present on the salivary pellicle incorporated low levels of radiolabeled nucleoside per viable cell. As bacterial numbers reached densities between 8.0 x 10(5) and 2.0 x 10(6) cells per mm2, there was a small increase in the incorporation of radiolabeled nucleosides per cell. At 2.5 x 10(6) to 4.0 x 10(6) cells per mm2 of enamel surface, there was a marked increase in the incorporation of radiolabeled nucleosides per cell which appeared to be cell-density dependent. The predominant species group in developing dental plaque films during density-dependent growth was the sanguis streptococci; however, most other species present showed similar patterns of increased DNA synthesis as the density noted above approached 2.5 x 10(6) to 4.0 x 10(6) cells per mm2.}},  author = {Bloomquist, C. G. and Reilly, B. E. and Liljemark, W. F.},  citeulike-article-id = {7751822},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/8576054},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=8576054},  issn = {0021-9193},  journal = {Journal of bacteriology},  keywords = {bacterial-biology},  month = feb,  number = {4},  pages = {1172--1177},  pmid = {8576054},  posted-at = {2010-09-01 15:59:11},  priority = {0},  title = {{Adherence, accumulation, and cell division of a natural adherent bacterial population.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/8576054},  volume = {178},  year = {1996}  }  @article{citeulike:7751682,  abstract = {{A mass action model for the infectious transmission of conjugative plasmids and procedures to estimate its parameters are presented. The suitability of this model as an analog of the kinetics of conjugative plasmid transmission is examined with batch and chemostat populations of Escherichia coli K-12 and three of its plasmids, F-lac-pro, R1 (Km-Cm-Ap), and R1-drd-19 (Km-Cm-Ap). Evidence is presented that this mass action model, with a unique and constant rate parameter, represents a reasonable analog of the kinetics of plasmid transfer for bacterial populations dividing at a constant rate in either exponentially growing cultures or at equilibrium in chemostats. As anticipated from this model magnitudes of the transfer rate constant for these plasmids appear to be relatively insensitive to both total cell density and the donor-recipient ratio. For all plasmids, the value of the transfer rate constant in rapidly dividing (exponentially growing) cultures is considerably greater than its corresponding value in slowly dividing, chemostat equilibrium cultures and the values of the transfer rate constant of the permanently derepressed plasmids F-lac-pro and R1-drd-19 are considerably greater than that of the wild-type, repressed transfer plasmid R1. The implications of this apparent fit to a mass action model are discussed and a recommendation is made to use the transfer rate constant as the measure of the fertility of conjugative plasmids.}},  author = {Levin, B.},  citeulike-article-id = {7751682},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/0147-619x(79)90043-x},  doi = {10.1016/0147-619x(79)90043-x},  issn = {0147619X},  journal = {Plasmid},  keywords = {bacterial-biology},  month = apr,  number = {2},  pages = {247--260},  posted-at = {2010-09-01 14:31:31},  priority = {2},  title = {{The kinetics of conjugative plasmid transmission: Fit of a simple mass action model}},  url = {http://dx.doi.org/10.1016/0147-619x(79)90043-x},  volume = {2},  year = {1979}  }  @article{citeulike:7751678,  abstract = {Quantitative measurements of horizontal DNA transfer are critical if one wishes to address questions relating to ecology, evolution and the safe use of recombinant bacteria. Traditionally, the efficiency of a conjugation system has been described by its transfer frequency. However, transfer frequencies can be determined in many ways and may be sensitive to physical, chemical and biological conditions. In this study the authors have used the mechanistic similarity between bacterial conjugation and simple enzyme catalysis in order to calculate the maximal conjugation rate (Vmax) and the recipient concentration (Km) at which the conjugation rate is half its maximal value, for two different conjugation systems: the F plasmid from Escherichia coli and plasmid pCF10 from Enterococcus faecalis. The results are compared with the data obtained from the aggregation-mediated conjugation system encoded on pXO16 from Bacillus thuringiensis. The conjugation systems analysed are fundamentally different; however, they have some characteristics in common: they are able to sustain conjugative transfer in liquid medium and the transfer efficiencies are very high. Conjugation encoded by the F plasmid in E. coli involves the formation of small aggregates (2-20 cells), established by sex pili, and the plasmid's maximal conjugation rate was estimated to be approximately 0{middle dot}15 transconjugants per donor per minute. Pheromone-induced conjugation in Ent. faecalis, which involves the formation of large aggregates, was found to proceed at a maximal conjugation rate of 0{middle dot}29 transconjugants per donor per minute. Also, the Km value differed significantly between these conjugation systems; this may reflect the inherent differences in mating pair formation and transfer mechanisms. In these conjugation systems, the donors underwent a recovery period' between rounds of conjugative transfer and newly formed transconjugants required a period of about 40-80 min to mature into proficient donors. 10.1099/13500872-145-8-2001},  author = {Andrup, Lars and Andersen, Katja},  citeulike-article-id = {7751678},  citeulike-linkout-0 = {http://dx.doi.org/10.1099/13500872-145-8-2001},  citeulike-linkout-1 = {http://mic.sgmjournals.org/cgi/content/abstract/145/8/2001},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/10463166},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=10463166},  day = {1},  doi = {10.1099/13500872-145-8-2001},  journal = {Microbiology},  keywords = {bacterial-biology},  month = aug,  number = {8},  pages = {2001--2009},  pmid = {10463166},  posted-at = {2010-09-01 14:29:14},  priority = {0},  title = {{A comparison of the kinetics of plasmid transfer in the conjugation systems encoded by the F plasmid from Escherichia coli and plasmid pCF10 from Enterococcus faecalis}},  url = {http://dx.doi.org/10.1099/13500872-145-8-2001},  volume = {145},  year = {1999}  }  @article{citeulike:7751630,  author = {ADELBERG, E. A. and PITTARD, J.},  citeulike-article-id = {7751630},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/14310189},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=14310189},  issn = {0005-3678},  journal = {Bacteriological reviews},  keywords = {bacterial-biology},  month = jun,  pages = {161--172},  pmid = {14310189},  posted-at = {2010-09-01 14:03:57},  priority = {0},  title = {CHROMOSOME TRANSFER IN BACTERIAL CONJUGATION.},  url = {http://view.ncbi.nlm.nih.gov/pubmed/14310189},  volume = {29},  year = {1965}  }  @article{citeulike:7751309,  abstract = {{An automaton built with DNA enzymes plays tic-tac-toe against human players. Adleman's1 seminal 1994 insight that computation could be encoded in DNA set off a raft of speculation on such topics as whether massively parallel DNA computations might one day break the data encryption standard2, 3. However, the utility of DNA computation can be evaluated to some extent by the level of its adoption, and in the years following Adleman's brilliant insights, few if any applications for DNA computing have been realized.}},  author = {Tabor, Jeffrey J. and Ellington, Andrew D.},  citeulike-article-id = {7751309},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt0903-1013},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt0903-1013},  day = {01},  doi = {10.1038/nbt0903-1013},  issn = {1087-0156},  journal = {Nature Biotechnology},  keywords = {synbio-dna},  month = sep,  number = {9},  pages = {1013--1015},  posted-at = {2010-09-01 13:14:47},  priority = {0},  publisher = {Nature Publishing Group},  title = {{Playing to win at DNA computation}},  url = {http://dx.doi.org/10.1038/nbt0903-1013},  volume = {21},  year = {2003}  }  @article{citeulike:1181,  abstract = {{We describe a molecular automaton, called MAYA, which encodes a version of the game of tic-tac-toe and interactively competes against a human opponent. The automaton is a Boolean network of deoxyribozymes that incorporates 23 molecular-scale logic gates and one constitutively active deoxyribozyme arrayed in nine wells (3×3) corresponding to the game board. To make a move, MAYA carries out an analysis of the input oligonucleotide keyed to a particular move by the human opponent and indicates a move by fluorescence signaling in a response well. The cycle of human player input and automaton response continues until there is a draw or a victory for the automaton. The automaton cannot be defeated because it implements a perfect strategy.}},  address = {Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, Box 84, 650W 168th Street, New York, New York 10032, USA. [email protected]},  author = {Stojanovic, Milan N. and Stefanovic, Darko},  citeulike-article-id = {1181},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt862},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt862},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/12923549},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=12923549},  day = {17},  doi = {10.1038/nbt862},  issn = {1087-0156},  journal = {Nat Biotech},  keywords = {synbio-dna},  month = sep,  number = {9},  pages = {1069--1074},  pmid = {12923549},  posted-at = {2010-09-01 13:14:09},  priority = {0},  publisher = {Nature Publishing Group},  title = {{A deoxyribozyme-based molecular automaton}},  url = {http://dx.doi.org/10.1038/nbt862},  volume = {21},  year = {2003}  }  @article{citeulike:7749684,  abstract = {{DNA ligases join breaks in the phosphodiester backbone of DNA molecules and are used in many essential reactions within the cell. All DNA ligases follow the same reaction mechanism, but they may use either ATP or NAD+ as a cofactor. All Bacteria (eubacteria) contain NAD+-dependent DNA ligases, and the uniqueness of these enzymes to Bacteria makes them an attractive target for novel antibiotics. In addition to their NAD+-dependent enzymes, some Bacteria contain genes for putative ATP-dependent DNA ligases. The requirement for these different isozymes in Bacteria is unknown, but may be related to their utilization in different aspects of DNA metabolism. The putative ATP-dependent DNA ligases found in Bacteria are most closely related to proteins from Archaea and viruses. Phylogenetic analysis suggests that all NAD+-dependent DNA ligases are closely related, but the ATP-dependent enzymes have been acquired by Bacterial genomes on a number of separate occasions.}},  author = {Wilkinson, A. and Day, J. and Bowater, R.},  citeulike-article-id = {7749684},  citeulike-linkout-0 = {http://dx.doi.org/10.1046/j.1365-2958.2001.02479.x},  doi = {10.1046/j.1365-2958.2001.02479.x},  journal = {Molecular Microbiology},  keywords = {bacterial-biology},  number = {6},  pages = {1241--1248},  posted-at = {2010-08-31 12:49:41},  priority = {0},  publisher = {Blackwell Science, Ltd},  title = {{Bacterial DNA ligases}},  url = {http://dx.doi.org/10.1046/j.1365-2958.2001.02479.x},  volume = {40},  year = {2001}  }  @article{citeulike:2906392,  abstract = {{The construction of new plasmid DNA species by in vitro joining of restriction endonuclease-generated fragments of separate plasmids is described. Newly constructed plasmids that are inserted into Escherichia coli by transformation are shown to be biologically functional replicons that possess genetic properties and nucleotide base sequences from both of the parent DNA molecules. Functional plasmids can be obtained by reassociation of endonuclease-generated fragments of larger replicons, as well as by joining of plasmid DNA molecules of entirely different origins.}},  author = {Cohen, Stanley N. and Chang, Annie C. Y. and Boyer, Herbert W. and Helling, Robert B.},  citeulike-article-id = {2906392},  citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.70.11.3240},  citeulike-linkout-1 = {http://www.pnas.org/content/70/11/3240.abstract},  citeulike-linkout-2 = {http://www.pnas.org/content/70/11/3240.full.pdf},  citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/70/11/3240},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/4594039},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=4594039},  day = {1},  doi = {10.1073/pnas.70.11.3240},  journal = {Proceedings of the National Academy of Sciences},  month = nov,  number = {11},  pages = {3240--3244},  pmid = {4594039},  posted-at = {2010-08-30 16:30:47},  priority = {0},  title = {{Construction of Biologically Functional Bacterial Plasmids In Vitro}},  url = {http://dx.doi.org/10.1073/pnas.70.11.3240},  volume = {70},  year = {1973}  }  @article{citeulike:2528626,  abstract = {{The tools of molecular biology were used to solve an instance of the directed Hamiltonian path problem. A small graph was encoded in molecules of DNA, and the "operations" of the computation were performed with standard protocols and enzymes. This experiment demonstrates the feasibility of carrying out computations at the molecular level.}},  address = {Department of Computer Science, University of Southern California, Los Angeles 90089.},  author = {Adleman, L. M.},  citeulike-article-id = {2528626},  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.7973651},  citeulike-linkout-1 = {http://www.sciencemag.org/content/266/5187/1021.abstract},  citeulike-linkout-2 = {http://www.sciencemag.org/content/266/5187/1021.full.pdf},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/7973651},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=7973651},  day = {11},  doi = {10.1126/science.7973651},  issn = {1095-9203},  journal = {Science},  keywords = {synbio-dna},  month = nov,  number = {5187},  pages = {1021--1024},  pmid = {7973651},  posted-at = {2010-08-30 13:29:53},  priority = {0},  publisher = {American Association for the Advancement of Science},  title = {{Molecular computation of solutions to combinatorial problems}},  url = {http://dx.doi.org/10.1126/science.7973651},  volume = {266},  year = {1994}  }  @article{citeulike:6346105,  abstract = {{Synthetic biology is focused on the rational construction of biological systems based on engineering principles. During the field's first decade of development, significant progress has been made in designing biological parts and assembling them into genetic circuits to achieve basic functionalities. These circuits have been used to construct proof-of-principle systems with promising results in industrial and medical applications. However, advances in synthetic biology have been limited by a lack of interoperable parts, techniques for dynamically probing biological systems and frameworks for the reliable construction and operation of complex, higher-order networks. As these challenges are addressed, synthetic biologists will be able to construct useful next-generation synthetic gene networks with real-world applications in medicine, biotechnology, bioremediation and bioenergy.}},  author = {Lu, Timothy K. and Khalil, Ahmad S. and Collins, James J.},  booktitle = {Nat Biotech},  citeulike-article-id = {6346105},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt.1591},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt.1591},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796205/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/20010597},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=20010597},  day = {09},  doi = {10.1038/nbt.1591},  issn = {1087-0156},  journal = {Nature Biotechnology},  keywords = {synbio-dna},  month = dec,  number = {12},  pages = {1139--1150},  pmcid = {PMC2796205},  pmid = {20010597},  posted-at = {2010-08-29 10:46:25},  priority = {0},  publisher = {Nature Publishing Group},  title = {{Next-generation synthetic gene networks}},  url = {http://dx.doi.org/10.1038/nbt.1591},  volume = {27},  year = {2009}  }  @article{citeulike:7577548,  abstract = {{A living organism must not only organize itself from within; it must also maintain its organization in the face of changes in its environment and degradation of its components. We show here that a simple (M,R)-system consisting of three interlocking catalytic cycles, with every catalyst produced by the system itself, can both establish a non-trivial steady state and maintain this despite continuous loss of the catalysts by irreversible degradation. As long as at least one catalyst is present at a sufficient concentration in the initial state, the others can be produced and maintained. The system shows bistability, because if the amount of catalyst in the initial state is insufficient to reach the non-trivial steady state the system collapses to a trivial steady state in which all fluxes are zero. It is also robust, because if one catalyst is catastrophically lost when the system is in steady state it can recreate the same state. There are three elementary flux modes, but none of them is an enzyme-maintaining mode, the entire network being necessary to maintain the two catalysts. The question of whether a whole organism (as opposed to particular properties of an organism) can be modeled in the computer has been controversial. As a step towards resolving it, we have studied the feasibility of simulating the behavior of a simple theoretical model in which all the catalysts needed for the metabolism of a system are themselves products of the metabolism itself, and in which there is a continuous loss of catalysts in unavoidable degradation reactions. In addition to a trivial ( †deadâ€) steady state in which all rates are zero, the model is capable of establishing a stable non-trivial steady state with finite and reproducible fluxes. This can be achieved by †seeding†it with a sufficient quantity of at least one of the catalysts needed for functioning. It is also robust, because it can recover from a catastrophic disappearance of a catalyst.}},  author = {Piedrafita, Gabriel and Montero, Francisco and Mor\'{a}n, Federico and C\'{a}rdenas, Mar\'{\i}a L. and Cornish-Bowden, Athel},  citeulike-article-id = {7577548},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000872},  day = {5},  doi = {10.1371/journal.pcbi.1000872},  journal = {PLoS Comput Biol},  month = aug,  number = {8},  pages = {e1000872+},  posted-at = {2010-08-27 16:31:03},  priority = {2},  publisher = {Public Library of Science},  title = {{A Simple Self-Maintaining Metabolic System: Robustness, Autocatalysis, Bistability}},  url = {http://dx.doi.org/10.1371/journal.pcbi.1000872},  volume = {6},  year = {2010}  }  @article{citeulike:7424482,  abstract = {{Cooperative behavior that increases the fitness of others at a cost to oneself can be promoted by natural selection only in the presence of an additional mechanism. One such mechanism is based on population structure, which can lead to clustering of cooperating agents. Recently, the focus has turned to complex dynamical population structures such as social networks, where the nodes represent individuals and links represent social relationships. We investigate how the dynamics of a social network can change the level of cooperation in the network. Individuals either update their strategies by imitating their partners or adjust their social ties. For the dynamics of the network structure, a random link is selected and breaks with a probability determined by the adjacent individuals. Once it is broken, a new one is established. This linking dynamics can be conveniently characterized by a Markov chain in the configuration space of an ever-changing network of interacting agents. Our model can be analytically solved provided the dynamics of links proceeds much faster than the dynamics of strategies. This leads to a simple rule for the evolution of cooperation: The more fragile links between cooperating players and non-cooperating players are (or the more robust links between cooperators are), the more likely cooperation prevails. Our approach may pave the way for analytically investigating coevolution of strategy and structure.}},  author = {Wu, Bin and Zhou, Da and Fu, Feng and Luo, Qingjun and Wang, Long and Traulsen, Arne},  citeulike-article-id = {7424482},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0011187},  day = {30},  doi = {10.1371/journal.pone.0011187},  journal = {PLoS ONE},  month = jun,  number = {6},  pages = {e11187+},  posted-at = {2010-08-27 16:30:56},  priority = {2},  publisher = {Public Library of Science},  title = {{Evolution of Cooperation on Stochastic Dynamical Networks}},  url = {http://dx.doi.org/10.1371/journal.pone.0011187},  volume = {5},  year = {2010}  }  @article{citeulike:7709398,  abstract = {{Eusociality, in which some individuals reduce their own lifetime reproductive potential to raise the offspring of others, underlies the most advanced forms of social organization and the ecologically dominant role of social insects and humans. For the past four decades kin selection theory, based on the concept of inclusive fitness, has been the major theoretical attempt to explain the evolution of eusociality. Here we show the limitations of this approach. We argue that standard natural selection theory in the context of precise models of population structure represents a simpler and superior approach, allows the evaluation of multiple competing hypotheses, and provides an exact framework for interpreting empirical observations.}},  author = {Nowak, Martin A. and Tarnita, Corina E. and Wilson, Edward O.},  citeulike-article-id = {7709398},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature09205},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature09205},  day = {26},  doi = {10.1038/nature09205},  issn = {0028-0836},  journal = {Nature},  keywords = {game-theory},  month = aug,  number = {7310},  pages = {1057--1062},  posted-at = {2010-08-27 16:30:39},  priority = {2},  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},  title = {{The evolution of eusociality}},  url = {http://dx.doi.org/10.1038/nature09205},  volume = {466},  year = {2010}  }  @article{citeulike:4202,  abstract = {{  The rapid accumulation of genetic information and advancement of experimental techniques have opened a new frontier in biomedical engineering. With the availability of well-characterized components from natural gene networks, the stage has been set for the engineering of artificial gene regulatory networks with sophisticated computational and functional capabilities. In these efforts, the ability to construct, analyze, and interpret qualitative and quantitative models is becoming increasingly important. In this review, we consider the current state of gene network engineering from a combined experimental and modeling perspective. We discuss how networks with increased complexity are being constructed from simple modular components and how quantitative deterministic and stochastic modeling of these modules may provide the foundation for accurate in silico representations of gene regulatory network function in vivo.  }},  address = {Center for BioDynamics, Department of Biomedical Engineering, and Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA. [email protected]},  author = {Kaern, Mads and Blake, William J. and Collins, J. J.},  citeulike-article-id = {4202},  citeulike-linkout-0 = {http://www.annualreviews.org/doi/abs/10.1146/annurev.bioeng.5.040202.121553},  citeulike-linkout-1 = {http://dx.doi.org/10.1146/annurev.bioeng.5.040202.121553},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/14527313},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=14527313},  doi = {10.1146/annurev.bioeng.5.040202.121553},  issn = {1523-9829},  journal = {Annual review of biomedical engineering},  keywords = {synbio-dna},  number = {1},  pages = {179--206},  pmid = {14527313},  posted-at = {2010-08-25 18:19:36},  priority = {0},  title = {{The engineering of gene regulatory networks.}},  url = {http://dx.doi.org/10.1146/annurev.bioeng.5.040202.121553},  volume = {5},  year = {2003}  }  @article{citeulike:812615,  abstract = {{Construction of a chemical system capable of replication and evolution, fed only by small molecule nutrients, is now conceivable. This could be achieved by stepwise integration of decades of work on the reconstitution of DNA, RNA and protein syntheses from pure components. Such a minimal cell project would initially define the components sufficient for each subsystem, allow detailed kinetic analyses and lead to improved in vitro methods for synthesis of biopolymers, therapeutics and biosensors. Completion would yield a functionally and structurally understood self-replicating biosystem. Safety concerns for synthetic life will be alleviated by extreme dependence on elaborate laboratory reagents and conditions for viability. Our proposed minimal genome is 113 kbp long and contains 151 genes. We detail building blocks already in place and major hurdles to overcome for completion.}},  author = {Forster, Anthony C. and Church, George M.},  citeulike-article-id = {812615},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/msb4100090},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/msb4100090},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16924266},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16924266},  day = {22},  doi = {10.1038/msb4100090},  issn = {1744-4292},  journal = {Molecular Systems Biology},  month = aug,  pmid = {16924266},  posted-at = {2010-08-24 18:38:28},  priority = {0},  publisher = {Nature Publishing Group},  title = {{Towards synthesis of a minimal cell}},  url = {http://dx.doi.org/10.1038/msb4100090},  volume = {2},  year = {2006}  }  @article{citeulike:553506,  abstract = {{'Bottom-up fabrication', which exploits the intrinsic properties of atoms and molecules to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of DNA molecules provides an attractive route towards this goal. Here I describe a simple method for folding long, single-stranded DNA molecules into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diameter and approximate desired shapes such as squares, disks and five-pointed stars with a spatial resolution of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex).}},  author = {Rothemund, Paul W. K.},  citeulike-article-id = {553506},  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature04586},  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature04586},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16541064},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16541064},  day = {16},  doi = {10.1038/nature04586},  issn = {0028-0836},  journal = {Nature},  month = mar,  number = {7082},  pages = {297--302},  pmid = {16541064},  posted-at = {2010-08-22 17:17:01},  priority = {0},  publisher = {Nature Publishing Group},  title = {{Folding DNA to create nanoscale shapes and patterns}},  url = {http://dx.doi.org/10.1038/nature04586},  volume = {440},  year = {2006}  }  @article{citeulike:7686290,  abstract = {{Bacterial conjugation is a mechanism for horizontal DNA transfer with potential for universal DNA delivery. The conjugal machinery can be separated into three functional modules: the relaxosome, the coupling protein, and a type IV protein secretion system. Module interchangeability among different conjugative systems opens up the possibility of "a la carte" engineering of DNA delivery into virtually any cell type.}},  author = {Llosa, Matxalen and de la Cruz, Fernando},  citeulike-article-id = {7686290},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.resmic.2004.07.008},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15636742},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15636742},  doi = {10.1016/j.resmic.2004.07.008},  issn = {0923-2508},  journal = {Research in microbiology},  keywords = {synbio-bacterial},  month = feb,  number = {1},  pages = {1--6},  pmid = {15636742},  posted-at = {2010-08-21 19:42:09},  priority = {0},  title = {{Bacterial conjugation: a potential tool for genomic engineering.}},  url = {http://dx.doi.org/10.1016/j.resmic.2004.07.008},  volume = {156},  year = {2005}  }  @article{citeulike:7681242,  abstract = {{The transfer of genetic material among bacteria in the environment can occur both in the planktonic and attached state. Given the propensity of organisms to exist in sessile microbial communities in oligotrophic subsurface conditions, and that such conditions typify the subsurface, this study focuses on exploratory modeling of horizontal gene transfer among surface-associated Escherichia coli in the subsurface. The mathematics so far used to describe the kinetics of conjugation in biofilms are developed largely from experimental observations of planktonic gene transfer, and are absent of lags or plasmid stability that appear experimentally. We develop a model and experimental system to quantify bacterial filtration and gene transfer in the attached state, on granular porous media. We include attachment kinetics described in Nelson et al. (2007) using the filtration theory approach of Nelson and Ginn (2001, 2005) with motility of E. coli described according to Biondi et al. (1998).}},  author = {Massoudieh, A. and Crain, C. and Lambertini, E. and Nelson, K. E. and Barkouki, T. and L'Amoreaux, P. and Loge, F. J. and Ginn, T. R.},  booktitle = {Frontiers in Reactive Transport: Microbial Dynamics nad Redox Zonation in the Subsurface},  citeulike-article-id = {7681242},  citeulike-linkout-0 = {http://www.sciencedirect.com/science/article/B6V94-4XP37M5-1/2/dfac99ff517ceb9043febaccda2ee003},  citeulike-linkout-1 = {http://dx.doi.org/10.1016/j.jconhyd.2009.10.009},  day = {1},  doi = {10.1016/j.jconhyd.2009.10.009},  issn = {0169-7722},  journal = {Journal of Contaminant Hydrology},  keywords = {bacterial-biology},  month = mar,  number = {1-4},  pages = {91--102},  posted-at = {2010-08-20 11:45:18},  priority = {0},  title = {{Kinetics of conjugative gene transfer on surfaces in granular porous media}},  url = {http://www.sciencedirect.com/science/article/B6V94-4XP37M5-1/2/dfac99ff517ceb9043febaccda2ee003},  volume = {112},  year = {2010}  }  @article{citeulike:3567840,  abstract = {{  Bacterial plasmids are extra-chromosomal genetic elements that code for a wide variety of phenotypes in their bacterial hosts and are maintained in bacterial communities through both vertical and horizontal transfer. Current mathematical models of plasmid-bacteria dynamics, based almost exclusively on mass-action differential equations that describe these interactions in completely mixed environments, fail to adequately explain phenomena such as the long-term persistence of plasmids in natural and clinical bacterial communities. This failure is, at least in part, due to the absence of any spatial structure in these models, whereas most bacterial populations are spatially structured in microcolonies and biofilms. To help bridge the gap between theoretical predictions and observed patterns of plasmid spread and persistence, an individual-based lattice model (interacting particle system) that provides a predictive framework for understanding the dynamics of plasmid-bacteria interactions in spatially structured populations is presented here. To assess the accuracy and flexibility of the model, a series of experiments that monitored plasmid loss and horizontal transfer of the IncP-1beta plasmid pB10 : : rfp in Escherichia coli K12 and other bacterial populations grown on agar surfaces were performed. The model-based visual patterns of plasmid loss and spread, as well as quantitative predictions of the effects of different initial parental strain densities and incubation time on densities of transconjugants formed on a 2D grid, were in agreement with this and previously published empirical data. These results include features of spatially structured populations that are not predicted by mass-action differential equation models.  }},  author = {Krone, Stephen M. and Lu, Ruinan and Fox, Randal and Suzuki, Haruo and Top, Eva M.},  citeulike-article-id = {3567840},  citeulike-linkout-0 = {http://dx.doi.org/10.1099/mic.0.2006/004531-0},  citeulike-linkout-1 = {http://mic.sgmjournals.org/cgi/content/abstract/153/8/2803},  citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613009/},  citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/17660444},  citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=17660444},  day = {1},  doi = {10.1099/mic.0.2006/004531-0},  issn = {1350-0872},  journal = {Microbiology (Reading, England)},  keywords = {bacterial-biology},  month = aug,  number = {Pt 8},  pages = {2803--2816},  pmcid = {PMC2613009},  pmid = {17660444},  posted-at = {2010-08-20 11:42:18},  priority = {0},  title = {{Modelling the spatial dynamics of plasmid transfer and persistence.}},  url = {http://dx.doi.org/10.1099/mic.0.2006/004531-0},  volume = {153},  year = {2007}  }  @incollection{citeulike:7681224,  abstract = {{Plasmids have established themselves in all three domains of life but they appear to be especially adept at finding homes in bacteria. Like living organisms, plasmids must reproduce to survive, and successful long-term proliferation requires their replication rate to be responsive to environmental factors. In this article, the maintenance and spread of bacterial plasmids is discussed. The [`]basics' of plasmid maintenance focuses on functional units, called replicons, with their requisite ori sequences from which replication originates. A variety of plasmid- and host-encoded proteins are recruited to the ori leading to initiation of DNA replication, and this is only the beginning of the story. Replicated plasmids must be distributed to [`]daughter' cells, which require partitioning machines. But first, individual ([`]unit') plasmids must be separated from one another, a process requiring its own set of enzymatic machinery. After tackling the complexities of plasmid maintenance, the broader and interrelated ecological issues of how plasmids spread and evolve are discussed. As selfish DNA elements, the survival of plasmids is nonetheless enhanced by genes that benefit their hosts (e.g., antibiotic resistance and virulence). As a result, the growing emphasis on plasmid ecology studies will likely lead to rapid advances in our understanding of microbial evolution.}},  author = {Filutowicz, M.},  booktitle = {Encyclopedia of Microbiology},  citeulike-article-id = {7681224},  citeulike-linkout-0 = {http://www.sciencedirect.com/science/article/B9BCD-4VMRTVG-5J/2/3f95ede25345a0feb5ff18bd1d89ad99},  citeulike-linkout-1 = {http://dx.doi.org/10.1016/B978-012373944-5.00014-6},  doi = {10.1016/B978-012373944-5.00014-6},  editor = {Schaechter, Moselio},  isbn = {978-0-12-373944-5},  keywords = {bacterial-biology},  location = {Oxford},  pages = {644--665},  posted-at = {2010-08-20 11:37:04},  priority = {0},  publisher = {Academic Press},  title = {{Plasmids, Bacterial}},  url = {http://www.sciencedirect.com/science/article/B9BCD-4VMRTVG-5J/2/3f95ede25345a0feb5ff18bd1d89ad99},  year = {2009}  }  @article{citeulike:7681220,  abstract = {{Plasmids are important vehicles for horizontal gene transfer and rapid adaptation in bacteria, including the spread of antibiotic resistance genes. Conjugative transfer of a plasmid from a plasmid-bearing to a plasmid-free bacterial cell requires contact and attachment of the cells followed by plasmid DNA transfer prior to detachment. We introduce a system of differential equations for plasmid transfer in well-mixed populations that accounts for attachment, DNA transfer, and detachment dynamics. These equations offer advantages over classical mass-action models that combine these three processes into a single "bulk" conjugation rate. By decomposing the process of plasmid transfer into its constituent parts, this new model provides a framework that facilitates meaningful comparisons of plasmid transfer rates in surface and liquid environments. The model also allows one to account for experimental and environmental effects such as mixing intensity. To test the adequacy of the model and further explore the effects of mixing on plasmid transfer, we performed batch culture experiments using three different plasmids and a range of different mixing intensities. The results show that plasmid transfer is optimized at low to moderate shaking speeds and that vigorous shaking negatively affects plasmid transfer. Using reasonable assumptions on attachment and detachment rates, the mathematical model predicts the same behavior.}},  author = {Zhong, Xue and Kro[dot above]l, JarosLaw E. and Top, Eva M. and Krone, Stephen M.},  citeulike-article-id = {7681220},  citeulike-linkout-0 = {http://www.sciencedirect.com/science/article/B6WMD-4XFPR7C-4/2/156ed3794273f1427ca2bccea49512a5},  citeulike-linkout-1 = {http://dx.doi.org/10.1016/j.jtbi.2009.10.013},  day = {21},  doi = {10.1016/j.jtbi.2009.10.013},  issn = {0022-5193},  journal = {Journal of Theoretical Biology},  keywords = {bacterial-biology},  month = feb,  number = {4},  pages = {711--719},  posted-at = {2010-08-20 11:34:29},  priority = {0},  title = {{Accounting for mating pair formation in plasmid population dynamics}},  url = {http://www.sciencedirect.com/science/article/B6WMD-4XFPR7C-4/2/156ed3794273f1427ca2bccea49512a5},  volume = {262},  year = {2010}  }  @article{citeulike:7678332,  abstract = {{This paper presents two approaches to the individual-based modelling of bacterial ecologies and evolution using computational tools. The first approach is a fine-grained model that is based on networks of interactivity between computational objects representing genes and proteins. The second approach is a coarser-grained, agent-based model, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of these computational models is discussed, and some results from simulation experiments are presented. Finally, the potential applications of the proposed models to the solution of real-world computational problems, and their use in improving our understanding of the mechanisms of evolution, are briefly outlined.}},  author = {Vlachos, C. and Gregory, R. and Paton, R. C. and Saunders, J. R. and Wu, Q. H.},  citeulike-article-id = {7678332},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/cfg.368},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18629041},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18629041},  doi = {10.1002/cfg.368},  issn = {1531-6912},  journal = {Comparative and functional genomics},  keywords = {individual-based-modeling},  number = {1},  pages = {100--104},  pmid = {18629041},  posted-at = {2010-08-18 21:16:18},  priority = {0},  publisher = {John Wiley \& Sons, Ltd.},  title = {{Individual-based modelling of bacterial ecologies and evolution.}},  url = {http://dx.doi.org/10.1002/cfg.368},  volume = {5},  year = {2004}  }  @incollection{citeulike:7678312,  abstract = {{Modeling, designing and analyzing large scale multi-agent systems (MAS) with anywhere from tens of thousands to millions of autonomous agents will require mathematical and computational theories and models substantially different from those underlying the study of small- to medium-scale MAS made of only dozens, or perhaps hundreds, of agents. In this paper, we study certain aspects of the global behavior of large ensembles of simple reactive agents. We do so by analyzing the collective dynamics of several related models of discrete complex systems based on cellular automata. We survey our recent results on dynamical properties of the complex systems of interest, and discuss some useful ways forward in modeling and analysis of large-scale MAS via appropriately modified versions of the classical cellular automata.}},  address = {Berlin, Heidelberg},  author = {To\AA{}!`i\"{A}‡, Predrag},  booktitle = {Computational Science \^{a}€“ ICCS 2006},  chapter = {38},  citeulike-article-id = {7678312},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/11758532\_38},  citeulike-linkout-1 = {http://www.springerlink.com/content/030p15608414546h},  doi = {10.1007/11758532\_38},  editor = {Alexandrov,, Vassil and van, Albada, e. e. r. t. and Sloot,, Peter and Dongarra,, Jack},  isbn = {978-3-540-34383-7},  keywords = {simulation-and-modeling},  pages = {272-280--280},  posted-at = {2010-08-18 21:03:26},  priority = {0},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{On Modeling and Analyzing Sparsely Networked Large-Scale Multi-agent Systems with Cellular and Graph Automata}},  url = {http://dx.doi.org/10.1007/11758532\_38},  volume = {3993},  year = {2006}  }  @inproceedings{citeulike:7678276,  abstract = {{Simulating large scale, distributed systems of autonomous decision-makers, e.g. global logistics supply networks, is a huge challenge for hardware and software infrastructure as well as managing the process of simulation. Facing this challenge, we are going to introduce an architecture for large scale grid-based simulation infrastructure to enable high performance multiagent simulation experiments that deal with a huge amount of software agents, i.e. more than ten thousands of agents.}},  author = {Timm, I. J. and Pawlaszczyk, D.},  booktitle = {CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.},  citeulike-article-id = {7678276},  citeulike-linkout-0 = {http://dx.doi.org/10.1109/ccgrid.2005.1558574},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=1558574},  doi = {10.1109/ccgrid.2005.1558574},  isbn = {0-7803-9074-1},  keywords = {simulation-and-modeling},  location = {Cardiff, Wales, UK},  pages = {334--341},  posted-at = {2010-08-18 20:48:48},  priority = {0},  publisher = {IEEE},  title = {{Large scale multiagent simulation on the grid}},  url = {http://dx.doi.org/10.1109/ccgrid.2005.1558574},  year = {2005}  }  @incollection{citeulike:7675124,  author = {Lingchong, You and Dennis, Tu and Jiwon, Lee and Taylan, Ozdere and Tae, Jun L.},  booktitle = {Nanotechnology in Biology and Medicine},  citeulike-article-id = {7675124},  citeulike-linkout-0 = {http://dx.doi.org/10.1201/9781420004441.ch24},  comment = {doi:10.1201/9781420004441.ch24},  day = {17},  doi = {10.1201/9781420004441.ch24},  isbn = {978-0-8493-2949-4},  keywords = {synbio-dna},  month = aug,  posted-at = {2010-08-17 22:17:18},  priority = {0},  publisher = {CRC Press},  title = {{Engineering Gene Circuits}},  url = {http://dx.doi.org/10.1201/9781420004441.ch24},  volume = {null},  year = {2010}  }  @article{citeulike:693838,  abstract = {{Abstract Bacteria communicate with one another using chemical signal molecules. As in higher organisms, the information supplied by these molecules is critical for synchronizing the activities of large groups of cells. In bacteria, chemical communication involves producing, releasing, detecting, and responding to small hormone-like molecules termed autoinducers. This process, termed quorum sensing, allows bacteria to monitor the environment for other bacteria and to alter behavior on a population-wide scale in response to changes in the number and/or species present in a community. Most quorum-sensing-controlled processes are unproductive when undertaken by an individual bacterium acting alone but become beneficial when carried out simultaneously by a large number of cells. Thus, quorum sensing confuses the distinction between prokaryotes and eukaryotes because it enables bacteria to act as multicellular organisms. This review focuses on the architectures of bacterial chemical communication networks; how chemical information is integrated, processed, and transduced to control gene expression; how intra- and interspecies cell-cell communication is accomplished; and the intriguing possibility of prokaryote-eukaryote cross-communication.}},  address = {Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544-1014, USA. [email protected]},  author = {Waters, Christopher M. and Bassler, Bonnie L.},  citeulike-article-id = {693838},  citeulike-linkout-0 = {http://www.annualreviews.org/doi/abs/10.1146/annurev.cellbio.21.012704.131001},  citeulike-linkout-1 = {http://dx.doi.org/10.1146/annurev.cellbio.21.012704.131001},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16212498},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16212498},  doi = {10.1146/annurev.cellbio.21.012704.131001},  issn = {1081-0706},  journal = {Annual Review of Cell and Developmental Biology},  keywords = {synbio-bacterial},  number = {1},  pages = {319--346},  pmid = {16212498},  posted-at = {2010-08-16 09:06:01},  priority = {0},  title = {{QUORUM SENSING: Cell-to-Cell Communication in Bacteria}},  url = {http://dx.doi.org/10.1146/annurev.cellbio.21.012704.131001},  volume = {21},  year = {2005}  }  @article{citeulike:7606662,  author = {Willetts, N. and Wilkins, B.},  citeulike-article-id = {7606662},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/6201705},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=6201705},  issn = {0146-0749},  journal = {Microbiological reviews},  keywords = {bacterial-biology},  month = mar,  number = {1},  pages = {24--41},  pmid = {6201705},  posted-at = {2010-08-10 12:42:49},  priority = {0},  title = {{Processing of plasmid DNA during bacterial conjugation.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/6201705},  volume = {48},  year = {1984}  }  @article{citeulike:7598248,  abstract = {{We present two approaches to the individual-based modeling (IbM) of bacterial ecologies and evolution using computational tools. The IbM approach is introduced, and its important complementary role to biosystems modeling is discussed. A fine-grained model of bacterial evolution is then presented that is based on networks of interactivity between computational objects representing genes and proteins. This is followed by a coarser grained agent-based model, which is designed to explore the evolvability of adaptive behavioral strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of the two proposed individual-based bacterial models are discussed, and some results from simulation experiments are presented, illustrating their adaptive properties.}},  author = {Paton, Ray and Gregory, Richard and Vlachos, Costas and Saunders, Jon and Wu, Henry},  citeulike-article-id = {7598248},  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/15473073},  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=15473073},  issn = {1536-1241},  journal = {IEEE transactions on nanobioscience},  keywords = {simulation-and-modeling},  month = sep,  number = {3},  pages = {208--216},  pmid = {15473073},  posted-at = {2010-08-09 16:21:29},  priority = {2},  title = {{Evolvable social agents for bacterial systems modeling.}},  url = {http://view.ncbi.nlm.nih.gov/pubmed/15473073},  volume = {3},  year = {2004}  }  @inproceedings{citeulike:7598093,  abstract = {{We present a hybrid model of the interactions within (multiple-species) populations of bacteria in a developing biofilm which integrates continuum models of population processes (e.g., diffusion of substrates and signalling molecules) with individual-based models of cellular processes (notably growth, division, displacement, and up-regulation). The cell level models combine both aggregated models of continuous processes (growth, division and displacement) for small collections of cells and individual-cell level models of quorum sensing molecule (QSM) sensing, production and up-regulation which encompass both stochastic and discrete processes. The use of both aggregated and individual models of cellular processes allows the resolution of the model to be tailored for a particular modelling problem, while at the same time remaining computationally tractable.}},  address = {Piscataway, NJ, USA},  author = {Lees, Michael and Logan, Brian and King, John},  booktitle = {WSC '07: Proceedings of the 39th conference on Winter simulation},  citeulike-article-id = {7598093},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1351699},  isbn = {1-4244-1306-0},  keywords = {simulation-and-modeling},  location = {Washington D.C.},  pages = {881--890},  posted-at = {2010-08-09 15:56:54},  priority = {2},  publisher = {IEEE Press},  title = {{Multiscale models of bacterial populations}},  url = {http://portal.acm.org/citation.cfm?id=1351699},  year = {2007}  }  @article{citeulike:7592286,  abstract = {{Abstract 10.1002/cbic.200700180.abs The main advantage of autonomous biomolecular computing devices over electronic computers is their ability to interact directly with biological systems. No interface is required since all components of molecular computers, including hardware, software, input, and output are molecules that interact in solution along a cascade of programmable chemical events. Here, we demonstrate for the first time that the output of a computation preduced by a molecular finite automaton can be a visible bacterial phenotype. Our 2-symbol-2-state finite automaton utilized linear double-stranded DNA inputs that were prepared by inserting a string of six base pair symbols into the lacZ gene on the pUC18 plasmid. The computation resulted in a circular plasmid that differed from the original pUC18 by either a 9 base pair (accepting state) or 11 base pair insert (unaccepting state) within the lacZ α region gene. Upon transformation and expression of the resultant plasmids in E. coli, the accepting state was represented by production of functional β-galactosidase and formation of blue colonies on X-gal medium. In contrast, the unaccepting state was represented by white colonies due to a shift in the open reading frame of lacZ.}},  author = {Kossoy, E. and Lavid, N. and Soreni-Harari, M. and Shoham, Y. and Keinan, E.},  citeulike-article-id = {7592286},  citeulike-linkout-0 = {http://dx.doi.org/10.1002/cbic.200700180},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17562552},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17562552},  day = {23},  doi = {10.1002/cbic.200700180},  issn = {1439-4227},  journal = {Chem. Eur. J. of Chem. Bio.},  keywords = {synbio-bacterial},  month = jul,  number = {11},  pages = {1255--1260},  pmid = {17562552},  posted-at = {2010-08-09 07:07:11},  priority = {0},  publisher = {WILEY-VCH Verlag},  title = {{A Programmable Biomolecular Computing Machine with Bacterial Phenotype Output}},  url = {http://dx.doi.org/10.1002/cbic.200700180},  volume = {8},  year = {2007}  }  @article{citeulike:7592197,  abstract = {{Molecular communication has been recently proposed for interconnected nano-scale devices as an alternative to classical communication paradigms such as electromagnetic waves, acoustic or optical communication. In this novel approach, the information is encoded as molecules that are transported between nano-scale devices within different distances. For short distances (nm-mm ranges) there exist molecular motors and calcium signaling techniques to realize the communication. For long distances (mm-m ranges), pheromones are used to transport information. In this work, the medium-range is explored to cover distances from \&\#181;m to mm and a molecular network architecture is proposed to realize the communication between nano-machines that can be deployed over different (short, medium and long) distances. In addition, two new communication techniques, flagellated bacteria and catalytic nanomotors, are proposed to cover the medium-range. Both techniques are based on the transport of DNA encoded information between emitters and receivers by means of a physical carrier. Finally, a qualitative comparison of both communication techniques is carried out and some future research topics are pointed out.}},  address = {Piscataway, NJ, USA},  author = {Gregori, Maria and Akyildiz, Ian F.},  citeulike-article-id = {7592197},  citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1821424},  citeulike-linkout-1 = {http://dx.doi.org/10.1109/jsac.2010.100510},  doi = {10.1109/jsac.2010.100510},  issn = {0733-8716},  journal = {IEEE J.Sel. A. Commun.},  keywords = {bacterial-biology},  number = {4},  pages = {612--619},  posted-at = {2010-08-09 06:52:43},  priority = {0},  publisher = {IEEE Press},  title = {{A new nanonetwork architecture using flagellated bacteria and catalytic nanomotors}},  url = {http://dx.doi.org/10.1109/jsac.2010.100510},  volume = {28},  year = {2010}  }  @article{citeulike:1069168,  abstract = {{Genetic surveys reveal the diversity of bacteria and lead to the questioning of species concepts used to categorize bacteria. One difficulty in defining bacterial species arises from the high rates of recombination that results in the transfer of DNA between relatively distantly related bacteria. Barriers to this process, which could be used to define species naturally, are not apparent. Here, we review conceptual models of bacterial speciation and describe our computer simulations of speciation. Our findings suggest that the rate of recombination and its relation to genetic divergence have a strong influence on outcomes. We propose that a distinction be made between clonal divergence and sexual speciation. Hence, to make sense of bacterial diversity, we need data not only from genetic surveys but also from experimental determination of selection pressures and recombination rates and from theoretical models.}},  author = {Fraser, Christophe and Hanage, William P. and Spratt, Brian G.},  citeulike-article-id = {1069168},  citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1127573},  citeulike-linkout-1 = {http://www.sciencemag.org/content/315/5811/476.abstract},  citeulike-linkout-2 = {http://www.sciencemag.org/content/315/5811/476.full.pdf},  citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/315/5811/476},  citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/17255503},  citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=17255503},  day = {26},  doi = {10.1126/science.1127573},  issn = {1095-9203},  journal = {Science},  keywords = {bacterial-biology},  month = jan,  number = {5811},  pages = {476--480},  pmid = {17255503},  posted-at = {2010-08-09 06:50:42},  priority = {0},  publisher = {American Association for the Advancement of Science},  title = {{Recombination and the Nature of Bacterial Speciation}},  url = {http://dx.doi.org/10.1126/science.1127573},  volume = {315},  year = {2007}  }  @article{citeulike:5774572,  abstract = {{  Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments.  }},  address = {Gntique des Gnomes Bactriens, Institut Pasteur, Paris, France},  author = {Danchin, Antoine},  citeulike-article-id = {5774572},  citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1574-6976.2008.00137.x},  citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704931/},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19016882},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19016882},  citeulike-linkout-4 = {http://www3.interscience.wiley.com/cgi-bin/abstract/121510564/ABSTRACT},  doi = {10.1111/j.1574-6976.2008.00137.x},  issn = {0168-6445},  journal = {FEMS microbiology reviews},  keywords = {bacterial-biology},  month = jan,  number = {1},  pages = {3--26},  pmcid = {PMC2704931},  pmid = {19016882},  posted-at = {2010-08-09 06:47:30},  priority = {0},  publisher = {Blackwell Publishing Ltd},  title = {{Bacteria as computers making computers.}},  url = {http://dx.doi.org/10.1111/j.1574-6976.2008.00137.x},  volume = {33},  year = {2009}  }  @book{citeulike:4505950,  abstract = {{Based on the author's 27 years of teaching experience, \_Genetics: A Conceptual  Approach, Third Edition\_, builds upon features that have made past editions so  successful:  an engaging writing style; relevant applications; an accessible  and instructive art program; an emphasis on problem-solving; and, most  importantly, a strong focus on concepts and connections.  To bring these key  concepts into sharper focus, Ben Pierce has selectively reduced the amount of  detail and has streamlined coverage to focus on essential concepts.}},  author = {Pierce, Benjamin},  citeulike-article-id = {4505950},  citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0716779285},  citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0716779285},  citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0716779285},  citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0716779285},  citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0716779285/citeulike00-21},  citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0716779285},  citeulike-linkout-6 = {http://www.worldcat.org/isbn/0716779285},  citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0716779285},  citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0716779285\&index=books\&linkCode=qs},  citeulike-linkout-9 = {http://www.librarything.com/isbn/0716779285},  day = {17},  edition = {Third Edition},  howpublished = {Hardcover},  isbn = {0716779285},  keywords = {books},  month = dec,  posted-at = {2010-08-05 17:38:22},  priority = {0},  publisher = {W. H. Freeman},  title = {{Genetics: A Conceptual Approach}},  url = {http://www.worldcat.org/isbn/0716779285},  year = {2007}  }  @article{citeulike:3857588,  abstract = {{The Virtual Cell (VCell; http://vcell.org/) is a problem solving environment, built on a central database, for analysis, modelling and simulation of cell biological processes. VCell integrates a growing range of molecular mechanisms, including reaction kinetics, diffusion, flow, membrane transport, lateral membrane diffusion and electrophysiology, and can associate these with geometries derived from experimental microscope images. It has been developed and deployed as a web-based, distributed, client-server system, with more than a thousand world-wide users. VCell provides a separation of layers (core technologies and abstractions) representing biological models, physical mechanisms, geometry, mathematical models and numerical methods. This separation clarifies the impact of modelling decisions, assumptions and approximations. The result is a physically consistent, mathematically rigorous, spatial modelling and simulation framework. Users create biological models and VCell will automatically (i) generate the appropriate mathematical encoding for running a simulation and (ii) generate and compile the appropriate computer code. Both deterministic and stochastic algorithms are supported for describing and running non-spatial simulations; a full partial differential equation solver using the finite volume numerical algorithm is available for reaction-diffusion-advection simulations in complex cell geometries including 3D geometries derived from microscope images. Using the VCell database, models and model components can be reused and updated, as well as privately shared among collaborating groups, or published. Exchange of models with other tools is possible via import/export of SBML, CellML and MatLab formats. Furthermore, curation of models is facilitated by external database binding mechanisms for unique identification of components and by standardised annotations compliant with the MIRIAM standard. VCell is now open source, with its native model encoding language (V-  -  CML) being a public specification, which stands as the basis for a new generation of more customised, experiment-centric modelling tools using a new plug-in based platform.}},  author = {Moraru, I. I. and Schaff, J. C. and Slepchenko, B. M. and Blinov, M. L. and Morgan, F. and Lakshminarayana, A. and Gao, F. and Li, Y. and Loew, L. M.},  citeulike-article-id = {3857588},  citeulike-linkout-0 = {http://dx.doi.org/10.1049/iet-syb:20080102},  citeulike-linkout-1 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=4648916},  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19045830},  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19045830},  doi = {10.1049/iet-syb:20080102},  issn = {17518849},  journal = {IET Systems Biology},  keywords = {simulation-and-modeling},  month = sep,  number = {5},  pages = {352--362},  pmid = {19045830},  posted-at = {2010-08-04 23:01:15},  priority = {0},  title = {{Virtual Cell modelling and simulation software environment}},  url = {http://dx.doi.org/10.1049/iet-syb:20080102},  volume = {2},  year = {2008}  }  @article{citeulike:7562796,  abstract = {{Recombinant-DNA technology is now commonly used in virtually every aspect of the biological sciences. The purpose of this brief exposition is to provide an outline of the approaches used to identify genes, to isolate the gene of interest, to amplify the gene if necessary, and to clone genes. A short introduction to the principles of separating very large genes is provided, along with a description of an approach to propagating and cloning these large genes.}},  author = {Carroll, W. L.},  citeulike-article-id = {7562796},  citeulike-linkout-0 = {http://www.ajcn.org/cgi/content/abstract/58/2/249S},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/8392284},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=8392284},  day = {1},  journal = {The American Journal of Clinical Nutrition},  month = aug,  number = {2},  pages = {249S--258S},  pmid = {8392284},  posted-at = {2010-08-03 18:35:13},  priority = {0},  title = {{Introduction to recombinant-DNA technology.}},  url = {http://www.ajcn.org/cgi/content/abstract/58/2/249S},  volume = {58},  year = {1993}  }  @article{Nadell2010a,  abstract = {{On its own, a single cell cannot exert more than a microscopic influence on its immediate surroundings. However, via strength in numbers and the expression of cooperative phenotypes, such cells can enormously impact their environments. Simple cooperative phenotypes appear to abound in the microbial world, but explaining their evolution is challenging because they are often subject to exploitation by rapidly growing, non-cooperative cell lines. Population spatial structure may be critical for this problem because it influences the extent of interaction between cooperative and non-cooperative individuals. It is difficult for cooperative cells to succeed in competition if they become mixed with non-cooperative cells, which can exploit the public good without themselves paying a cost. However, if cooperative cells are segregated in space and preferentially interact with each other, they may prevail. Here we use a multi-agent computational model to study the origin of spatial structure within growing cell groups. Our simulations reveal that the spatial distribution of genetic lineages within these groups is linked to a small number of physical and biological parameters, including cell growth rate, nutrient availability, and nutrient diffusivity. Realistic changes in these parameters qualitatively alter the emergent structure of cell groups, and thereby determine whether cells with cooperative phenotypes can locally and globally outcompete exploitative cells. We argue that cooperative and exploitative cell lineages will spontaneously segregate in space under a wide range of conditions and, therefore, that cellular cooperation may evolve more readily than naively expected. Cooperation is a fundamental and widespread phenomenon in nature, yet explaining the evolution of cooperation is difficult. Natural selection typically favors individuals that maximize their own reproduction, so how is it that many diverse organisms, from bacteria to humans, have evolved to help others at a cost to themselves? Research has shown that cooperation can most readily evolve when cooperative individuals preferentially help each other, but this leaves open another critical question: How do cooperators achieve selective interaction with one another? We focus on this question in the context of unicellular organisms, such as bacteria, which exhibit simple forms of cooperation that play roles in nutrient acquisition and pathogenesis. We use a realistic simulation framework to model large cell groups, and observe that cell lines can spontaneously segregate from each other in space as the group expands. Finally, we demonstrate that lineage segregation allows cooperative cell types to preferentially benefit each other, thereby favoring the evolution of cooperation.}},  author = {Nadell, Carey D. and Foster, Kevin R. and Xavier, Jo\~{a}o B.},  citeulike-article-id = {6895658},  citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000716},  citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20333237},  citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20333237},  day = {19},  doi = {10.1371/journal.pcbi.1000716},  issn = {1553-7358},  journal = {PLoS Comput Biol},  keywords = {simulation-and-modeling},  month = mar,  number = {3},  pages = {e1000716+},  pmid = {20333237},  posted-at = {2010-07-28 10:00:10},  priority = {0},  publisher = {Public Library of Science},  title = {{Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation}},  url = {http://dx.doi.org/10.1371/journal.pcbi.1000716},  volume = {6},  year = {2010}  }  @article{Andrews2004a,  abstract = {{Methods are presented for simulating chemical reaction networks with a spatial resolution that is accurate to nearly the size scale of individual molecules. Using an intuitive picture of chemical reaction systems, each molecule is treated as a point-like particle that diffuses freely in three-dimensional space. When a pair of reactive molecules collide, such as an enzyme and its substrate, a reaction occurs and the simulated reactants are replaced by products. Achieving accurate bimolecular reaction kinetics is surprisingly difficult, requiring a careful consideration of reaction processes that are often overlooked. This includes whether the rate of a reaction is at steady-state and the probability that multiple reaction products collide with each other to yield a back reaction. Inputs to the simulation are experimental reaction rates, diffusion coefficients and the simulation time step. From these are calculated the simulation parameters, including the 'binding radius' and the 'unbinding radius', where the former defines the separation for a molecular collision and the latter is the initial separation between a pair of reaction products. Analytic solutions are presented for some simulation parameters while others are calculated using look-up tables. Capabilities of these methods are demonstrated with simulations of a simple bimolecular reaction and the Lotka–Volterra system.}},  author = {Andrews, Steven S. and Bray, Dennis},  citeulike-article-id = {2817971},  citeulike-linkout-0 = {http://dx.doi.org/10.1088/1478-3967/1/3/001},  citeulike-linkout-1 = {http://iopscience.iop.org/1478-3967/1/3/001},  day = {01},  doi = {10.1088/1478-3967/1/3/001},  issn = {1478-3967},  journal = {Physical Biology},  keywords = {simulation-and-modeling},  month = sep,  number = {3},  pages = {137--151},  posted-at = {2010-07-27 20:16:08},  priority = {0},  title = {{Stochastic simulation of chemical reactions with spatial resolution and single molecule detail}},  url = {http://dx.doi.org/10.1088/1478-3967/1/3/001},  volume = {1},  year = {2004}  }  @article{Tolle2006a,  abstract = {{Computational modeling and simulation have become invaluable tools for the biological sciences. Both aid in the formulation of new hypothesis and supplement traditional experimental research. Many different types of models using various mathematical formalisms can be created to represent any given biological system. Here we review a class of modeling techniques based on particle-based stochastic approaches. In these models, every reacting molecule is represented individually. Reactions between molecules occur in a probabilistic manner. Modeling problems caused by spatial heterogeneity and combinatorial complexity, features common to biochemical and cellular systems, are best addressed using Monte-Carlo single-particle methods. Several software tools implementing single-particle based modeling techniques are introduced and their various advantages and pitfalls discussed.}},  author = {Tolle, Dominic P. and Le Novere, Nicolas},  citeulike-article-id = {746930},  citeulike-linkout-0 = {http://dx.doi.org/10.2174/157489306777827964},  citeulike-linkout-1 = {http://www.ingentaconnect.com/content/ben/cbio/2006/00000001/00000003/art00005},  doi = {10.2174/157489306777827964},  issn = {1574-8936},  journal = {Current Bioinformatics},  keywords = {simulation-and-modeling},  month = aug,  number = {3},  pages = {315--320},  posted-at = {2010-07-27 14:11:07},  priority = {0},  publisher = {Bentham Science Publishers},  title = {{Particle-Based Stochastic Simulation in Systems Biology}},  url = {http://dx.doi.org/10.2174/157489306777827964},  volume = {1},  year = {2006}  }  @article{Bournez2009b,  abstract = {{Population protocols have been introduced as a model of sensor networks  consisting of very limited mobile agents with no control over their own  movement: A collection of anonymous agents, modeled by finite automata,  interact in pairs according to some rules.  Predicates on the initial configurations that can be computed by such  protocols have been characterized under several hypotheses.  We discuss here whether and when the rules of interactions between agents can  be seen as a game from game theory. We do so by discussing several basic  protocols.}},  archivePrefix = {arXiv},  author = {Bournez, Olivier and Chalopin, J\'{e}r\'{e}mie and Cohen, Johanne and Koegler, Xavier},  citeulike-article-id = {7537987},  citeulike-linkout-0 = {http://arxiv.org/abs/0906.3256},  citeulike-linkout-1 = {http://arxiv.org/pdf/0906.3256},  day = {17},  eprint = {0906.3256},  keywords = {population-protocols},  month = jun,  posted-at = {2010-07-25 16:34:27},  priority = {0},  title = {{Playing With Population Protocols}},  url = {http://arxiv.org/abs/0906.3256},  year = {2009}  }  @techreport{BUSNEL:2008:INRIA-00338098:1,  abstract = {{G}ossip-based protocols are simple, robust and scalable and have been consistently applied in many distributed, mostly wired, settings. {M}ost validation in this area has been so far empirical and there is a clear lack of a theoretical counterpart clearly defining what can and cannot be computed with gossip-based protocols. {P}opulation protocols, on the other hand, provide a clear and formal model for mobile sensor networks, capturing their power and limitations. {I}n this paper, we establish a correlation between population and gossip-based protocols. {S}tudying the equivalence between them, we propose a classification of gossip-based protocols, based on the nature of the underlying peer sampling service. {F}irst, we show that the class of gossip protocols, where each node relies on an arbitrary sample, is equivalent to population protocols. {S}econd, we show that gossip-based protocols, relying on a more powerful peer sampling providing peers using a clearly identified set of other peers, are equivalent to community protocols, a variant of population protocols. {L}everaging the resemblances between these areas enables to provide a theoretical framework for distributed systems where global behaviours emerge from a set of local interactions, both in wired and wireless settings. {L}ikewise, the practical validations of gossip-protocols provide empirical evidence of quick convergence times of such algorithms and demonstrate their practical relevance. {W}hile existing results in each area can be immediately applied, this also leaves the space to transfer any new results, practical or theoretical, from one domain to the other. {A}s an application of this possibility, we also propose a new result in the area of population protocols and show that a uniform distribution of interactions is optimal for population and community protocols with respect to convergence time. {C}onsequently, we can conclude that the gossip-based random peer sampling service provides such an optimal sampling for gossip-based protocols, corroborating practical evidences.},  author = {{B}usnel, {Y}ann and {B}ertier, {M}arin and {K}ermarrec, {A}nne-{M}arie},  citeulike-article-id = {7537985},  citeulike-linkout-0 = {http://hal.inria.fr/inria-00338098/en/},  institution = {INRIA},  keywords = {population-protocols},  number = {{RR}-6720},  pages = {26},  posted-at = {2010-07-25 16:32:10},  priority = {0},  title = {{B}ridging the {G}ap between {P}opulation and {G}ossip-based {P}rotocols},  type = {Research Report},  url = {http://hal.inria.fr/inria-00338098/en/},  year = {2008}  }  @article{Bournez2009a,  abstract = {{Population protocols have been introduced as a model of sensor networks consisting of very limited mobile agents with no control over their own movement. A population protocol corresponds to a collection of anonymous agents, modeled by finite automata, that interact with one another to carry out computations, by updating their states, using some rules. Their computational power has been investigated under several hypotheses but always when restricted to finite size populations. In particular, predicates stably computable in the original model have been characterized as those definable in Presburger arithmetic. We study mathematically the convergence of population protocols when the size of the population goes to infinity. We do so by giving general results, that we illustrate through the example of a particular population protocol for which we even obtain an asymptotic development. This example shows in particular that these protocols seem to have a rather different computational power when a huge population hypothesis is considered.}},  author = {Bournez, Olivier and Chassaing, Philippe and Cohen, Johanne and Gerin, Lucas and Koegler, Xavier},  citeulike-article-id = {7537983},  citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.amc.2009.04.056},  day = {15},  doi = {10.1016/j.amc.2009.04.056},  issn = {00963003},  journal = {Applied Mathematics and Computation},  keywords = {population-protocols},  month = oct,  number = {4},  pages = {1340--1350},  posted-at = {2010-07-25 16:22:33},  priority = {0},  title = {{On the convergence of population protocols when population goes to infinity}},  url = {http://dx.doi.org/10.1016/j.amc.2009.04.056},  volume = {215},  year = {2009}  }  @incollection{Chatzigiannakis2008a,  abstract = {{Angluin et al. [1] introduced the notion of Probabilistic Population Protocols (PPP) where extremely limited agents are represented as finite state machines that interact in pairs under the control of an adversary scheduler. We provide a very general model that allows to examine the continuous dynamics of population protocols and we show that it includes the model of [1], under certain conditions, with respect to the continuous dynamics of the two models.}},  address = {Berlin, Heidelberg},  author = {Chatzigiannakis, Ioannis and Spirakis, Paul},  booktitle = {Distributed Computing},  chapter = {35},  citeulike-article-id = {7537792},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-540-87779-0\_35},  citeulike-linkout-1 = {http://www.springerlink.com/content/d581n70624h368k2},  doi = {10.1007/978-3-540-87779-0\_35},  editor = {Taubenfeld,, Gadi},  isbn = {978-3-540-87778-3},  issn = {0302-9743},  keywords = {population-protocols},  pages = {498-499--499},  posted-at = {2010-07-25 11:08:00},  priority = {0},  publisher = {Springer Berlin / Heidelberg},  series = {Lecture Notes in Computer Science},  title = {{The Dynamics of Probabilistic Population Protocols}},  url = {http://dx.doi.org/10.1007/978-3-540-87779-0\_35},  volume = {5218},  year = {2008}  }  @article{Angluin2007a,  abstract = {{Abstract\ \ We consider the model of population protocols introduced by Angluin et\ al. (Computation in networks of passively mobile finite-state sensors, pp. 290–299. ACM, New York, 2004), in which anonymous finite-state agents stably compute a predicate of the multiset of their inputs via two-way interactions in the family of all-pairs communication networks. We prove that all predicates stably computable in this model (and certain generalizations of it) are semilinear, answering a central open question about the power of the model. Removing the assumption of two-way interaction, we also consider several variants of the model in which agents communicate by anonymous message-passing where the recipient of each message is chosen by an adversary and the sender is not identified to the recipient. These one-way models are distinguished by whether messages are delivered immediately or after a delay, whether a sender can record that it has sent a message, and whether a recipient can queue incoming messages, refusing to accept new messages until it has had a chance to send out messages of its own. We characterize the classes of predicates stably computable in each of these one-way models using natural subclasses of the semilinear predicates.}},  author = {Angluin, Dana and Aspnes, James and Eisenstat, David and Ruppert, Eric},  citeulike-article-id = {6926758},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00446-007-0040-2},  citeulike-linkout-1 = {http://www.springerlink.com/content/1227gmx720257372},  day = {24},  doi = {10.1007/s00446-007-0040-2},  issn = {0178-2770},  journal = {Distributed Computing},  keywords = {population-protocols},  month = nov,  number = {4},  pages = {279--304},  posted-at = {2010-07-25 11:05:10},  priority = {0},  title = {{The computational power of population protocols}},  url = {http://dx.doi.org/10.1007/s00446-007-0040-2},  volume = {20},  year = {2007}  }  @incollection{Aspnes2009a,  abstract = {{Population protocols are used as a theoretical model for a collection (or population) of tiny mobile agents that interact with one another to carry out a computation. The agents are identically programmed finite state machines. Input values are initially distributed to the agents, and pairs of agents can exchange state information with other agents when they are close together. The movement pattern of the agents is unpredictable, but subject to some fairness constraints, and computations must eventually converge to the correct output value in any schedule that results from that movement. This framework can be used to model mobile ad hoc networks of tiny devices or collections of molecules undergoing chemical reactions. This chapter surveys results that describe what can be computed in various versions of the population protocol model.}},  address = {Berlin, Heidelberg},  author = {Aspnes, James and Ruppert, Eric},  booktitle = {Middleware for Network Eccentric and Mobile Applications },  chapter = {5},  citeulike-article-id = {7537788},  citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-3-540-89707-1\_5},  citeulike-linkout-1 = {http://www.springerlink.com/content/k33574570p42g328},  doi = {10.1007/978-3-540-89707-1\_5},  editor = {Garbinato, Beno\^{i}t and Miranda, Hugo and Rodrigues, Lu\'{\i}s},  isbn = {978-3-540-89706-4},  keywords = {population-protocols},  pages = {97--120},  posted-at = {2010-07-25 11:03:30},  priority = {0},  publisher = {Springer Berlin Heidelberg},  title = {{An Introduction to Population Protocols}},  url = {http://dx.doi.org/10.1007/978-3-540-89707-1\_5},  year = {2009}  }