% bmc_article.bib % % An example of bibtex entries. % Entries taken from BMC instructions for authors page. @article{MHCLam, author = {Lam, E T and Hastie, A and Lin, C and Ehrlich, D and Das, S K and Austin, M D and Deshpande, P and Cao, H and Nagarajan, N and Xiao, M and Kwok, P}, title = {Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly}, journal = {Nature Biotechnology}, year = {2012}, month = {AUGUST}, volume= {30}, number= {8}, pages = {}, note = {doi:10.1038/nbt.2303}, } @article{Beetle2008, author = {Richards, S and Gibbs, R A and Weinstock, G M and Brown, S J and Denell, R and Beeman, R W and Gibbs, R and Bucher, G and Friedrich, M and Grimmelikhuijzen, C J et al.}, title = {The genome of the model beetle and pest Tribolium castaneum}, journal = {Nature}, year = {2008}, month = {APRIL}, volume= {452}, number= {}, pages = {949-955}, note = {http://dx.doi.org/10.1038/nature06784}, } @article{BeetleGenMap2005, author = {Lorenzen, M D and Doyungan, Z and Savard, J and Snow, K and Crumly, L R and Shippy, T D and Stuart, J J and Brown, S J and Beeman, R W}, title = {Genetic linkage maps of the red flour beetle, Tribolium castaneum, based on bacterial artificial chromosomes and expressed sequence tags.}, journal = {Genetics}, year = {2005}, month = {APRIL}, volume= {170}, number= {2}, pages = {741-747}, note = {doi: 10.1534/genetics.104.032227}, } @article{Assem22013, author = {Bradnam, K and Faas, J and Alexandrov, A and Baranay, P and Bechner, M and Birol, I and Boisvert, S and Chapman, J and Chapuis, G and Chikhi, R and Chitsaz, H and Chou, W and Corbeil, J and Del Fabbro, C and Docking, T R and Durbin, R and Earl, D E and Emrich, S and Fedotov, P and Fonseca, N A and Ganapathy, G and Gibbs, R A and Gnerre, S and Godzaridis, E and Goldstein, S and Haimel, M and Hall, G and Haussler, D and Hiatt, J B and Ho, I Y and Howard, J and Hunt, M and Jackman, S D and Jaffe, D B and Jarvis, E and Jiang, H et al.}, title = {Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species}, journal = {GigaScience}, year = {2013}, month = {JUNE}, volume= {2}, number= {10}, pages = {}, note = {10.1186/2047-217X-2-10}, } @article{Moleculo2014, author = {McCoy, R C and Taylor, R W and Blauwkamp, T A and Kelley, J L and Kertesz, M and Pushkarev, D and Petrov, D A and Fiston-Lavier A}, title = {Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements}, journal = {PLoS ONE}, year = {2014}, month = {SEPTEMBER}, volume= {9}, number= {9}, pages = {}, note = {DOI: 10.1371/journal.pone.0106689}, } @article{Nanopore2014, author = {Quick, J and Quinlan, A R and Loman N J}, title = {A reference bacterial genome dataset generated on the MinION portable single-molecule nanopore sequencer}, journal = {GigaScience}, year = {2014}, month = {SEPTEMBER}, volume= {3}, number= {22}, pages = {}, note = {doi:10.1186/2047-217X-3-22}, } @article{Gage2012, author = {Salzberg, S L and Phillippy, A M and Zimin, A and Puiu, D and Magoc, T and Koren, S and Treangen, T J and Schatz, M C and Delcher, A L and Roberts, M and Marçais, G and Pop, M and Yorke J A}, title = {GAGE: A critical evaluation of genome assemblies and assembly algorithms}, journal = {Genome Research}, year = {2012}, month = {JUNE}, volume= {22}, number= {6}, pages = {}, note = {doi: 10.1101/gr.131383.111}, } @article{Feature-by-F2012, author = {Vezzi, F and Narzisi, G and Mishra, B}, title = {Feature-by-Feature – Evaluating De Novo Sequence Assembly}, journal = {PLoS ONE}, year = {2012}, month = {FEB}, volume= {7}, number= {2}, pages = {}, note = {DOI: 10.1371/journal.pone.0031002}, } @article{Argos2009, author = {Teague, B and Waterman, M S and Goldstein, S and Potamousis, K and Zhou, S and Reslewic, S and Sarkar, D and Valouev, A and Churas, C and Kidd, J M and Kohn, S and Runnheim, R and Lamers, C and Forrest, D and Newton, M A and Eichler, E E and Kent-First, M and Surti, U and Livny, M and Schwartz, D C}, title = {High-resolution human genome structure by single-molecule analysis}, journal = {PNAS}, year = {2012}, month = {DEC}, volume= {107}, number= {24}, pages = {}, note = {doi: 10.1073/pnas.0914638107}, } @article{OpGenAnalysis2014, author = {Mendelowitz, L and Pop, M}, title = {Computational methods for optical mapping}, journal = {GigaScience}, year = {2014}, month = {DEC}, volume= {3}, number= {33}, pages = {}, note = {doi:10.1186/2047-217X-3-33}, } @article{SeqBias2013, author = {Ross, M G and Russ, C and Costello, M and Hollinger, A and Lennon, N J and Hegarty, R and Nusbaum, C and Jaffe, D B}, title = {Characterizing and measuring bias in sequence data}, journal = {Genome Biology}, year = {2013}, month = {MAY}, volume= {14}, number= {R51}, pages = {}, note = {doi:10.1186/gb-2013-14-5-r51}, } @article{BioNano2010, author = {Das, S K and Austin, M D and Akana, M C and Deshpande, P and Cao, H and Xiao, M}, title = {Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes.}, journal = {Nucleic Acids Research}, year = {2010}, month = {JUL}, volume= {38}, number= {e177}, pages = {}, note = {doi: 10.1093/nar/gkq673}, } @article{BioNanoSV2014, author = {Cao, H and Hastie, A R and Cao, D and Lam, E T and Sun, Y and Huang, H and Liu, X and Lin, L and Andrews, W and Chan, S and Huang, S and Tong, X and Requa, M and Anantharaman, T and Krogh, A and Yang, H and Cao, H and Xu, X}, title = {Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology}, journal = {GigaScience}, year = {2014}, month = {DEC}, volume= {3}, number= {34}, pages = {}, note = {doi:10.1186/2047-217X-3-34}, } @article{blank, author = {}, title = {}, journal = {}, year = {}, month = {}, volume= {}, number= {}, pages = {}, note = {}, } % Article within a journal @ARTICLE{koon, author = {Koonin, E V and Altschul, S F and P Bork}, title = {BRCA1 protein products: functional motifs}, journal = {Nat Genet}, year = {1996}, volume = {13}, pages = {266-267} } % Article within a journal supplement @ARTICLE{oreg, author = {Orengo, C A and Bray, J E and Hubbard, T and LoConte, L and Sillitoe, I}, title = {Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction}, journal = {Proteins}, year = {1999}, volume = {Suppl 3}, pages = {149-170} } % In press article @inpress{khar, author = {Kharitonov, S A and Barnes, P J}, title = {Clinical aspects of exhaled nitric oxide}, journal = {Eur Respir J}, note = {in press} } % % Published abstract % @ARTICLE{zvai, author = {Zvaifler, N J and Burger, J A and Marinova-Mutafchieva, L and Taylor, P and Maini, R N}, title = {Mesenchymal cells, stromal derived factor-1 and rheumatoid arthritis [abstract]}, journal = {Arthritis Rheum}, year = {1999}, volume = {42}, pages = {s250}, } % % Article within conference proceedings % @Inproceedings{check, author = {X Jones}, title = {Zeolites and synthetic mechanisms}, booktitle = {Proceedings of the First National Conference on Porous Sieves: 27-30 June 1996; Baltimore}, year = {1996}, editor = {Y Smith}, pages = {16-27}, organization = {Stoneham: Butterworth-Heinemann} } @Inproceedings{ProbFP, author = {Anantharaman, T and Mishra, B}, title = {A Probabilistic Analysis of False Positives in Optical Map Alignment and Validation}, journal = {WABI2001}, year = {2001}, month = {AUGUST}, note = {https://cs.nyu.edu/mishra/PUBLICATIONS/01.falsepos.ps} } %%%%%%%% % Book chapter, or article within a book % @incollection{schn, author = {E Schnepf}, title = {From prey via endosymbiont to plastids: comparative studies in dinoflagellates}, booktitle = {Origins of Plastids}, editor = {R A Lewin}, publisher = {Chapman and Hall}, pages = {53-76}, year = {1993}, address = {New York}, volume = {2}, edition = {2nd} } %%%%%%%% % Whole issue of journal % @wholejournal{pond, editor = {B Ponder and S Johnston and L Chodosh}, title = {Innovative oncology}, journal = {Breast Cancer Res}, year = {1998}, volume= {10}, pages = {1-72} } %%%%%%%% % Whole conference proceedings % @proceedings{smith, editor = {Y Smith}, title = {Proceedings of the First National Conference on Porous Sieves: 27-30 June 1996; Baltimore}, year = 1996, address= {Stoneham}, publisher = {Butterworth-Heinemann}, } %%%%%%%% % Complete book % @book{marg, author = {L Margulis}, title = {Origin of Eukaryotic Cells}, publisher = {Yale University Press}, year = {1970}, address = {New Haven} } %%%%%%%% % Monograph or book in series % @incollection{hunn, author = {G W Hunninghake and J E Gadek}, title = {The alveloar macrophage}, booktitle = {Cultured Human Cells and Tissues}, publisher = {Academic Press}, year = {1995}, pages = {54-56}, editor = {T J R Harris}, address = {New York}, note = {Stoner G (Series Editor): Methods and Perspectives in Cell Biology, vol 1} } %%%%%%%% % Book with institutional author @manual{advi, title = {Annual Report}, organization = {Advisory Committee on Genetic Modification}, address = {London}, year = {1999} } %%%%%%%% % PHD Thesis % @phdthesis{koha, author = {R Kohavi}, title = {Wrappers for performance enhancement and obvious decision graphs}, school = {Stanford University, Computer Science Department}, year = {1995} } %%%%%%%% % Webpage Link / URL % @webpage{mouse, title = {The Mouse Tumor Biology Database}, url = {http://tumor.informatics.jax.org/cancer\_links.html} } %%%%%%%% % Webpage Link / URL % @webpage{BioNanoSpecs, key = {BioNano IrysChips specifications}, title = {BioNano IrysChips specifications}, url = {http://www.bionanogenomics.com/wp-content/uploads/2015/01/datasheet-web.pdf} } %%%%%%%% % Webpage Link / URL % @webpage{PacBioSpecs, key = {PacBio P6-C4 chemistry specifications}, title = {PacBio P6-C4 chemistry specifications}, url = {http://investor.pacificbiosciences.com/releasedetail.cfm?ReleaseID=876252} } %%%%%%%% % Webpage Link / URL % @webpage{OpgenSpecs, key = {Opgen Argus MapCard specifications}, title = {Opgen Argus MapCard specifications}, url = {http://www.tgac.ac.uk/sequencing-platforms/} } %%%%%%%% % Webpage Link / URL % @webpage{MoleculoSpecs, key = {Illumina TruSeq synthetic long-read specifications}, title = {Illumina TruSeq synthetic long-read specifications}, url = {http://investor.pacificbiosciences.com/releasedetail.cfm?ReleaseID=876252} } %%%%%%%% % Webpage Link / URL % @webpage{LDJSpecs, key = {Illumina Long Distance Jump Library specifications}, title = {Illumina Long Distance Jump Library specifications}, url = {http://www.operon.com/services/next-generation-sequencing/illumina/libraries.aspx} }