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Antonino Ingargiola Track bibliography
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@article{Stephens1974,
author = {Stephens, M. A.},
doi = {10.2307/2286009},
issn = {01621459},
journal = {Journal of the American Statistical Association},
keywords = {EDF,statistics},
language = {en},
mendeley-tags = {EDF,statistics},
month = {sep},
number = {347},
pages = {730},
publisher = {Taylor {\&} Francis Group},
title = {{EDF Statistics for Goodness of Fit and Some Comparisons}},
url = {http://www.tandfonline.com/doi/abs/10.1080/01621459.1974.10480196{\#}.VraD-DYrJME http://www.jstor.org/stable/2286009 http://www.jstor.org/stable/2286009?origin=crossref},
volume = {69},
year = {1974},
}
@article{Parr1980,
author = {Parr, William C. and Schucany, William R.},
doi = {10.2307/2287658},
issn = {01621459},
journal = {Journal of the American Statistical Association},
keywords = {EDF,Influence curve,Minimum distance,Non-location and scale problems,Robust estimation,Swindle,statistics},
language = {en},
mendeley-tags = {EDF,statistics},
month = {sep},
number = {371},
pages = {616},
publisher = {Taylor {\&} Francis Group},
title = {{Minimum Distance and Robust Estimation}},
url = {http://www.tandfonline.com/doi/abs/10.1080/01621459.1980.10477522 http://www.jstor.org/stable/2287658?origin=crossref},
volume = {75},
year = {1980},
}
@article{Ingargiola2016,
author = {Ingargiola, Antonino and Laurence, Ted and Boutelle, Robert and Weiss, Shimon and Michalet, Xavier},
doi = {10.1016/j.bpj.2015.11.013},
issn = {00063495},
journal = {Biophysical Journal},
keywords = {HDF5,file format},
month = {jan},
number = {1},
pages = {26--33},
publisher = {Elsevier},
title = {{Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments}},
url = {http://www.cell.com/article/S0006349515011704/fulltext},
volume = {110},
year = {2016},
}
@article{Antonik2006,
author = {Antonik, Matthew and Felekyan, Suren and Gaiduk, Alexander and Seidel, Claus A M},
doi = {10.1021/jp057257+},
file = {:Users/anto/Documents/Mendeley Desktop/Antonik et al. - 2006 - Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distr.pdf:pdf},
isbn = {1520-6106},
issn = {15206106},
journal = {Journal of Physical Chemistry B},
keywords = {DNA,DNA: chemistry,Fluorescence Resonance Energy Transfer,PDA,Photons,Probability,Stochastic Processes,smFRET,smFRET analysis},
mendeley-tags = {PDA,smFRET,smFRET analysis},
month = {apr},
number = {13},
pages = {6970--6978},
pmid = {16571010},
publisher = {American Chemical Society},
title = {{Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distributions via photon distribution analysis}},
url = {http://dx.doi.org/10.1021/jp057257+},
volume = {110},
year = {2006},
}
@article{Kapanidis_2006,
doi = {10.1126/science.1131399},
url = {http://dx.doi.org/10.1126/science.1131399},
year = {2006},
month = {nov},
publisher = {American Association for the Advancement of Science ({AAAS})},
volume = {314},
number = {5802},
pages = {1144--1147},
author = {A. N. Kapanidis and E. Margeat and S. O. Ho and E. Kortkhonjia and S. Weiss and R. H. Ebright},
title = {{Initial Transcription by {RNA} Polymerase Proceeds Through a {DNA}-Scrunching Mechanism}},
journal = {Science},
}
@article{Shen_2014,
doi = {10.1038/515151a},
url = {http://dx.doi.org/10.1038/515151a},
year = {2014},
month = {nov},
publisher = {Nature Publishing Group},
volume = {515},
number = {7525},
pages = {151--152},
author = {Helen Shen},
title = {{Interactive notebooks: Sharing the code}},
journal = {Nature},
}
@article{Lee_2005,
doi = {10.1529/biophysj.104.054114},
url = {http://dx.doi.org/10.1529/biophysj.104.054114},
year = {2005},
month = {apr},
publisher = {Elsevier {BV}},
volume = {88},
number = {4},
pages = {2939--2953},
author = {Nam Ki Lee and Achillefs N. Kapanidis and You Wang and Xavier Michalet and Jayanta Mukhopadhyay and Richard H. Ebright and Shimon Weiss},
title = {{Accurate {FRET} Measurements within Single Diffusing Biomolecules Using Alternating-Laser Excitation}},
journal = {Biophysical Journal},
}
@article{Eggeling_1998,
doi = {10.1073/pnas.95.4.1556},
url = {http://dx.doi.org/10.1073/pnas.95.4.1556},
year = {1998},
month = {feb},
publisher = {Proceedings of the National Academy of Sciences},
volume = {95},
number = {4},
pages = {1556--1561},
author = {C. Eggeling and J. R. Fries and L. Brand and R. Gunther and C. A. M. Seidel},
title = {{Monitoring conformational dynamics of a single molecule by selective fluorescence spectroscopy}},
journal = {Proceedings of the National Academy of Sciences},
}
@article{Michalet_2012,
doi = {10.1098/rstb.2012.0035},
url = {http://dx.doi.org/10.1098/rstb.2012.0035},
year = {2012},
month = {dec},
publisher = {The Royal Society},
volume = {368},
number = {1611},
pages = {20120035--20120035},
author = {X. Michalet and R. A. Colyer and G. Scalia and A. Ingargiola and R. Lin and J. E. Millaud and S. Weiss and O. H. W. Siegmund and A. S. Tremsin and J. V. Vallerga and A. Cheng and M. Levi and D. Aharoni and K. Arisaka and F. Villa and F. Guerrieri and F. Panzeri and I. Rech and A. Gulinatti and F. Zappa and M. Ghioni and S. Cova},
title = {{Development of new photon-counting detectors for single-molecule fluorescence microscopy}},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
}
@article{Nir_2006,
doi = {10.1021/jp063483n},
url = {http://dx.doi.org/10.1021/jp063483n},
year = {2006},
month = {nov},
publisher = {American Chemical Society ({ACS})},
volume = {110},
number = {44},
pages = {22103--22124},
author = {Eyal Nir and Xavier Michalet and Kambiz M. Hamadani and Ted A. Laurence and Daniel Neuhauser and Yevgeniy Kovchegov and Shimon Weiss},
title = {{Shot-Noise Limited Single-Molecule {FRET} Histograms:~ Comparison between Theory and Experiments {\textdagger}}},
journal = {J. Phys. Chem. B},
}
@article{Gopich_2008,
doi = {10.1021/jp0764182},
url = {http://dx.doi.org/10.1021/jp0764182},
year = {2008},
month = {may},
publisher = {American Chemical Society ({ACS})},
volume = {112},
number = {19},
pages = {6214--6220},
author = {Irina V. Gopich},
title = {{Concentration Effects in {\textquotedblleft}Single-Molecule{\textquotedblright} Spectroscopy {\textdagger}}},
journal = {J. Phys. Chem. B},
}
@article{Prli__2012,
doi = {10.1371/journal.pcbi.1002802},
url = {http://dx.doi.org/10.1371/journal.pcbi.1002802},
year = {2012},
month = {dec},
publisher = {Public Library of Science ({PLoS})},
volume = {8},
number = {12},
pages = {e1002802},
author = {Andreas Prli{\'{c}} and James B. Procter},
title = {{Ten Simple Rules for the Open Development of Scientific Software}},
journal = {{PLoS} Computational Biology},
}
@inproceedings{Ingargiola_2013,
author = {Ingargiola, Antonino and Panzeri, Francesco and Sarkhosh, Niusha and Gulinatti, Angelo and Rech, Ivan and Ghioni, Massimo and Weiss, Shimon and Michalet, Xavier},
title = {{8-spot smFRET analysis using two 8-pixel SPAD arrays}},
publisher = {{SPIE}},
volume = {8590},
pages = {85900E-85900E-11},
year = {2013},
doi = {10.1117/12.2003704},
url = {http://dx.doi.org/10.1117/12.2003704},
booktitle = {{Single Molecule Spectroscopy and Superresolution Imaging VI}},
note = {doi:\href{http://dx.doi.org/10.1117/12.2003704}{10.1117/12.2003704}},
}
@article{M_ller_2005,
doi = {10.1529/biophysj.105.064766},
url = {http://dx.doi.org/10.1529/biophysj.105.064766},
year = {2005},
month = {nov},
publisher = {Elsevier {BV}},
volume = {89},
number = {5},
pages = {3508--3522},
author = {Barbara K. Müller and Evgeny Zaychikov and Christoph Bräuchle and Don C. Lamb},
title = {{Pulsed Interleaved Excitation}},
journal = {Biophysical Journal},
}
@article{Kapanidis_2005,
doi = {10.1021/ar0401348},
url = {http://dx.doi.org/10.1021/ar0401348},
year = {2005},
month = {jul},
publisher = {American Chemical Society ({ACS})},
volume = {38},
number = {7},
pages = {523--533},
author = {Achillefs N. Kapanidis and Ted A. Laurence and Nam Ki Lee and Emmanuel Margeat and Xiangxu Kong and Shimon Weiss},
title = {{Alternating-Laser Excitation of Single Molecules}},
journal = {Acc. Chem. Res.},
}
@article{Laurence_2005,
author = {Laurence, Ted A. and Kong, Xiangxu and Jäger, Marcus and Weiss, Shimon},
title = {{Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins}},
journal = {Proceedings of the National Academy of Sciences},
volume = {102},
number = {48},
pages = {17348-17353},
year = {2005},
doi = {10.1073/pnas.0508584102},
}
@article{Wilson_2014,
doi = {10.1371/journal.pbio.1001745},
url = {http://dx.doi.org/10.1371/journal.pbio.1001745},
year = {2014},
month = {jan},
publisher = {Public Library of Science ({PLoS})},
volume = {12},
number = {1},
pages = {e1001745},
author = {Greg Wilson and D. A. Aruliah and C. Titus Brown and Neil P. Chue Hong and Matt Davis and Richard T. Guy and Steven H. D. Haddock and Kathryn D. Huff and Ian M. Mitchell and Mark D. Plumbley and Ben Waugh and Ethan P. White and Paul Wilson},
editor = {Jonathan A. Eisen},
title = {{Best Practices for Scientific Computing}},
journal = {{PLoS} Biology},
}
@article{Fries_1998,
doi = {10.1021/jp980965t},
url = {http://dx.doi.org/10.1021/jp980965t},
year = {1998},
month = {aug},
publisher = {American Chemical Society ({ACS})},
volume = {102},
number = {33},
pages = {6601--6613},
author = {Joachim R. Fries and Leif Brand and Christian Eggeling and Malte Köllner and Claus A. M. Seidel},
title = {{Quantitative Identification of Different Single Molecules by Selective Time-Resolved Confocal Fluorescence Spectroscopy}},
journal = {J. Phys. Chem. A},
}
@article{Weiss_1999,
doi = {10.1126/science.283.5408.1676},
url = {http://dx.doi.org/10.1126/science.283.5408.1676},
year = {1999},
month = {mar},
publisher = {American Association for the Advancement of Science ({AAAS})},
volume = {283},
number = {5408},
pages = {1676--1683},
author = {S. Weiss},
title = {{Fluorescence Spectroscopy of Single Biomolecules}},
journal = {Science},
}
@article{Dahan_1999,
doi = {10.1016/s0301-0104(99)00132-9},
url = {http://dx.doi.org/10.1016/S0301-0104(99)00132-9},
year = {1999},
month = {aug},
publisher = {Elsevier {BV}},
volume = {247},
number = {1},
pages = {85--106},
author = {Maxime Dahan and Ashok A. Deniz and Taekjip Ha and Daniel S. Chemla and Peter G. Schultz and Shimon Weiss},
title = {{Ratiometric measurement and identification of single diffusing molecules}},
journal = {Chemical Physics},
}
@article{Hohlbein_2014,
doi = {10.1039/c3cs60233h},
url = {http://dx.doi.org/10.1039/c3cs60233h},
year = {2014},
publisher = {Royal Society of Chemistry ({RSC})},
volume = {43},
number = {4},
pages = {1156--1171},
author = {Johannes Hohlbein and Timothy D. Craggs and Thorben Cordes},
title = {{Alternating-laser excitation: single-molecule {FRET} and beyond}},
journal = {Chem. Soc. Rev.},
}
@article{Eggeling_2001,
doi = {10.1016/s0168-1656(00)00412-0},
url = {http://dx.doi.org/10.1016/S0168-1656(00)00412-0},
year = {2001},
month = {apr},
publisher = {Elsevier {BV}},
volume = {86},
number = {3},
pages = {163--180},
author = {C. Eggeling and S. Berger and L. Brand and J.R. Fries and J. Schaffer and A. Volkmer and C.A.M. Seidel},
title = {{Data registration and selective single-molecule analysis using multi-parameter fluorescence detection}},
journal = {Journal of Biotechnology},
}
@article{Torella_2011,
doi = {10.1016/j.bpj.2011.01.066},
url = {http://dx.doi.org/10.1016/j.bpj.2011.01.066},
year = {2011},
month = {mar},
publisher = {Elsevier {BV}},
volume = {100},
number = {6},
pages = {1568--1577},
author = {Joseph~P. Torella and Seamus~J. Holden and Yusdi Santoso and Johannes Hohlbein and Achillefs~N. Kapanidis},
title = {{Identifying Molecular Dynamics in Single-Molecule {FRET} Experiments with Burst Variance Analysis}},
journal = {Biophysical Journal},
}
@article{Tomov_2012,
doi = {10.1016/j.bpj.2011.11.4025},
url = {http://dx.doi.org/10.1016/j.bpj.2011.11.4025},
year = {2012},
month = {mar},
publisher = {Elsevier {BV}},
volume = {102},
number = {5},
pages = {1163--1173},
author = {Toma~E. Tomov and Roman Tsukanov and Rula Masoud and Miran Liber and Noa Plavner and Eyal Nir},
title = {{Disentangling Subpopulations in Single-Molecule {FRET} and {ALEX} Experiments with Photon Distribution Analysis}},
journal = {Biophysical Journal},
}
@article{Santoso_2010,
doi = {10.1002/cphc.201000129},
url = {http://dx.doi.org/10.1002/cphc.201000129},
year = {2010},
month = {jun},
publisher = {Wiley-Blackwell},
volume = {11},
number = {10},
pages = {2209--2219},
author = {Yusdi Santoso and Joseph P. Torella and Achillefs N. Kapanidis},
title = {{Characterizing Single-Molecule {FRET} Dynamics with Probability Distribution Analysis}},
journal = {{ChemPhysChem}},
}
@article{Lerner_2014,
annote = {cited in FRETBursts paper},
author = {Lerner, E and Orevi, T and {Ben Ishay}, E and Amir, D and Haas, E},
doi = {10.1016/j.bpj.2013.11.4500},
file = {:Users/anto/Documents/Mendeley Desktop/Lerner et al. - 2014 - Kinetics of fast changing intramolecular distance distributions obtained by combined analysis of FRET efficiency.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
keywords = {Adenylate Kinase,Adenylate Kinase: chemistry,Adenylate Kinase: genetics,Amino Acid Sequence,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: genetics,Escherichia coli,Escherichia coli: enzymology,Fluorescence Resonance Energy Transfer,Fluorescence Resonance Energy Transfer: methods,Molecular Sequence Data,Mutation,Protein Folding,Protein Structure, Tertiary},
month = {feb},
number = {3},
pages = {667--76},
pmid = {24507607},
title = {{Kinetics of fast changing intramolecular distance distributions obtained by combined analysis of FRET efficiency kinetics and time-resolved FRET equilibrium measurements.}},
url = {http://www.sciencedirect.com/science/article/pii/S0006349513057974},
volume = {106},
year = {2014},
}
@article{Rahamim_2015,
annote = {cited in FRETBursts paper},
author = {Rahamim, Gil and Chemerovski-Glikman, Marina and Rahimipour, Shai and Amir, Dan and Haas, Elisha},
doi = {10.1371/journal.pone.0143732},
file = {:Users/anto/Documents/Mendeley Desktop/Rahamim et al. - 2015 - Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FR.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
month = {jan},
number = {12},
pages = {e0143732},
pmid = {26699718},
publisher = {Public Library of Science},
title = {{Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FRET Measurements.}},
url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143732},
volume = {10},
year = {2015},
}
@article{Gopich_2007,
doi = {10.1021/jp075255e},
url = {http://dx.doi.org/10.1021/jp075255e},
year = {2007},
month = {nov},
publisher = {American Chemical Society ({ACS})},
volume = {111},
number = {44},
pages = {12925--12932},
author = {Irina V. Gopich and Attila Szabo},
title = {{Single-Molecule {FRET} with Diffusion and Conformational Dynamics}},
journal = {J. Phys. Chem. B},
}
@article{Camley_2009,
doi = {10.1063/1.3230974},
url = {http://dx.doi.org/10.1063/1.3230974},
year = {2009},
publisher = {{AIP} Publishing},
volume = {131},
number = {10},
pages = {104509},
author = {Brian A. Camley and Frank L. H. Brown and Everett A. Lipman},
title = {{F\"{o}rster transfer outside the weak-excitation limit}},
journal = {J. Chem. Phys.},
}
@article{Zhang_2005,
doi = {10.1021/jp0546047},
url = {http://dx.doi.org/10.1021/jp0546047},
year = {2005},
month = {nov},
publisher = {American Chemical Society ({ACS})},
volume = {109},
number = {46},
pages = {21930--21937},
author = {Kai Zhang and Haw Yang},
title = {{Photon-by-Photon Determination of Emission Bursts from Diffusing Single Chromophores}},
journal = {J. Phys. Chem. B},
}
@article{Gopich_2005,
doi = {10.1063/1.1812746},
url = {http://dx.doi.org/10.1063/1.1812746},
year = {2005},
publisher = {{AIP} Publishing},
volume = {122},
number = {1},
pages = {014707},
author = {Irina Gopich and Attila Szabo},
title = {{Theory of photon statistics in single-molecule F\"{o}rster resonance energy transfer}},
journal = {J. Chem. Phys.},
}
@incollection{Buckheit_1995,
doi = {10.1007/978-1-4612-2544-7_5},
url = {http://dx.doi.org/10.1007/978-1-4612-2544-7_5},
year = {1995},
publisher = {Springer Science $+$ Business Media},
volume = {103},
pages = {55--81},
author = {Jonathan B. Buckheit and David L. Donoho},
title = {{{WaveLab} and Reproducible Research}},
booktitle = {Wavelets and Statistics},
note = {\href{http://dx.doi.org/10.1007/978-1-4612-2544-7_5}{doi:10.1007/978-1-4612-2544-7\_5}},
}
@article{Pradal_2013,
doi = {10.1016/j.jocs.2013.08.001},
url = {http://dx.doi.org/10.1016/j.jocs.2013.08.001},
year = {2013},
month = {sep},
publisher = {Elsevier {BV}},
volume = {4},
number = {5},
pages = {311--312},
author = {Christophe Pradal and Gaël Varoquaux and Hans Peter Langtangen},
title = {{Publishing scientific software matters}},
journal = {Journal of Computational Science},
}
@article{Check_Hayden_2015,
doi = {10.1038/520276a},
url = {http://dx.doi.org/10.1038/520276a},
year = {2015},
month = {apr},
publisher = {Nature Publishing Group},
volume = {520},
number = {7547},
pages = {276--277},
author = {Erika Check Hayden},
title = {{Rule rewrite aims to clean up scientific software}},
journal = {Nature},
}
@article{Check_Hayden_2013,
doi = {10.1038/501472a},
url = {http://dx.doi.org/10.1038/501472a},
year = {2013},
month = {sep},
publisher = {Nature Publishing Group},
volume = {501},
number = {7468},
pages = {472--472},
author = {Erika Check Hayden},
title = {{Mozilla plan seeks to debug scientific code}},
journal = {Nature},
}
@article{Ince_2012,
doi = {10.1038/nature10836},
url = {http://dx.doi.org/10.1038/nature10836},
year = {2012},
month = {feb},
publisher = {Nature Publishing Group},
volume = {482},
number = {7386},
pages = {485--488},
author = {Darrel C. Ince and Leslie Hatton and John Graham-Cumming},
title = {{The case for open computer programs}},
journal = {Nature},
}
@article{Freeman_2015,
doi = {10.1016/j.conb.2015.04.002},
url = {http://dx.doi.org/10.1016/j.conb.2015.04.002},
year = {2015},
month = {jun},
publisher = {Elsevier {BV}},
volume = {32},
pages = {156--163},
author = {Jeremy Freeman},
title = {{Open source tools for large-scale neuroscience}},
journal = {Current Opinion in Neurobiology},
}
@article{Murphy2014,
archiveprefix = {arXiv},
arxivid = {1412.6402},
journal = {ArXiv},
author = {Murphy, Rebecca R. and Jackson, Sophie E. and Klenerman, David},
eprint = {1412.6402},
keywords = {smFRET,software},
mendeley-tags = {smFRET,software},
month = {dec},
title = {{pyFRET: A Python Library for Single Molecule Fluorescence Data Analysis}},
url = {http://arxiv.org/abs/1412.6402},
year = {2014},
note = {\href{http://arxiv.org/abs/1412.6402}{arXiv:1412.6402}},
}
@article{Vihinen_2015,
doi = {10.1038/521261a},
url = {http://dx.doi.org/10.1038/521261a},
year = {2015},
month = {may},
publisher = {Nature Publishing Group},
volume = {521},
number = {7552},
pages = {261--261},
author = {Mauno Vihinen},
title = {{No more hidden solutions in bioinformatics}},
journal = {Nature},
}
@article{Blischak_2016,
doi = {10.1371/journal.pcbi.1004668},
url = {http://dx.doi.org/10.1371/journal.pcbi.1004668},
year = {2016},
month = {jan},
publisher = {Public Library of Science ({PLoS})},
volume = {12},
number = {1},
pages = {e1004668},
author = {John D. Blischak and Emily R. Davenport and Greg Wilson},
editor = {Francis Ouellette},
title = {{A Quick Introduction to Version Control with Git and {GitHub}}},
journal = {{PLOS} Computational Biology},
}
@article{Robb_2013,
doi = {10.1016/j.jmb.2012.12.015},
url = {http://dx.doi.org/10.1016/j.jmb.2012.12.015},
year = {2013},
month = {mar},
publisher = {Elsevier {BV}},
volume = {425},
number = {5},
pages = {875--885},
author = {Nicole C. Robb and Thorben Cordes and Ling Chin Hwang and Kristofer Gryte and Diego Duchi and Timothy D. Craggs and Yusdi Santoso and Shimon Weiss and Richard H. Ebright and Achillefs N. Kapanidis},
title = {{The Transcription Bubble of the {RNA} Polymerase{\textendash}Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics: Implications for Transcription Start-Site Selection}},
journal = {Journal of Molecular Biology},
}
@misc{lmfit,
author = {Matt Newville and Andrew Nelson and Till Stensitzki and Antonino Ingargiola and Dan Allan and Michał and Yoav Ram and MerlinSmiles and Li Li and Glenn and Christoph Deil and Gustavo Pasquevich and Stuermer and Tim Spillane and stonebig and Per A. Brodtkorb and Nicholas Earl and Anthony Almarza and Ben Gamari and Kostis Anagnostopoulos},
title = {{lmfit-py: release 0.9.3}},
month = {apr},
year = {2016},
doi = {10.5281/zenodo.49428},
url = {http://dx.doi.org/10.5281/zenodo.49428},
note = {\href{http://dx.doi.org/10.5281/zenodo.49428}{doi:10.5281/zenodo.49428}},
}
@misc{seaborn,
author = {Michael Waskom and Olga Botvinnik and drewokane and Paul Hobson and Yaroslav Halchenko and Saulius Lukauskas and Jordi Warmenhoven and John B. Cole and Stephan Hoyer and Jake Vanderplas and gkunter and Santi Villalba and Eric Quintero and Marcel Martin and Alistair Miles and Kyle Meyer and Tom Augspurger and Tal Yarkoni and Pete Bachant and Constantine Evans and Clark Fitzgerald and Tamas Nagy and Erik Ziegler and Tobias Megies and Daniel Wehner and Samuel St-Jean and Luis Pedro Coelho and Gregory Hitz and Antony Lee and Luc Rocher},
title = {{seaborn: v0.7.0}},
month = {jan},
year = {2016},
doi = {10.5281/zenodo.45133},
url = {http://dx.doi.org/10.5281/zenodo.45133},
note = {\href{http://dx.doi.org/10.5281/zenodo.45133}{doi:10.5281/zenodo.45133}},
}
@misc{matplotlib,
author = {Michael Droettboom and John Hunter and Thomas A Caswell and Eric Firing and Jens Hedegaard Nielsen and Phil Elson and Benjamin Root and Darren Dale and Jae-Joon Lee and Jouni K. Seppänen and Damon McDougall and Andrew Straw and Ryan May and Nelle Varoquaux and Tony S Yu and Eric Ma and Charlie Moad and Steven Silvester and Christoph Gohlke and Peter Würtz and Thomas Hisch and Federico Ariza and Cimarron and Ian Thomas and James Evans and Paul Ivanov and Jeff Whitaker and Paul Hobson and mdehoon and Matt Giuca},
title = {{matplotlib: matplotlib v1.5.1}},
month = {jan},
year = {2016},
doi = {10.5281/zenodo.44579},
url = {http://dx.doi.org/10.5281/zenodo.44579},
note = {\href{http://dx.doi.org/10.5281/zenodo.44579}{doi:10.5281/zenodo.44579}},
}
@article{Tsukanov_2013,
doi = {10.1021/jp4059214},
url = {http://dx.doi.org/10.1021/jp4059214},
year = {2013},
month = {oct},
publisher = {American Chemical Society ({ACS})},
volume = {117},
number = {40},
pages = {11932--11942},
author = {Roman Tsukanov and Toma E. Tomov and Rula Masoud and Hagai Drory and Noa Plavner and Miran Liber and Eyal Nir},
title = {{Detailed Study of {DNA} Hairpin Dynamics Using Single-Molecule Fluorescence Assisted by {DNA} Origami}},
journal = {The Journal of Physical Chemistry B},
}
@article{Soergel_2015,
doi = {10.12688/f1000research.5930.2},
url = {http://dx.doi.org/10.12688/f1000research.5930.2},
year = {2015},
month = {jul},
publisher = {F1000 Research Ltd.},
author = {David A. W. Soergel},
title = {{Rampant software errors may undermine scientific results}},
journal = {F1000Research},
note = {\href{http://dx.doi.org/10.12688/f1000research.5930.2}{doi:10.12688/f1000research.5930.2}},
}
@article{Roy_2008,
doi = {10.1038/nmeth.1208},
url = {http://dx.doi.org/10.1038/nmeth.1208},
year = {2008},
month = {jun},
publisher = {Nature Publishing Group},
volume = {5},
number = {6},
pages = {507--516},
author = {Rahul Roy and Sungchul Hohng and Taekjip Ha},
title = {{A practical guide to single-molecule {FRET}}},
journal = {Nature Methods},
}
@article{Selvin_2000,
doi = {10.1038/78948},
url = {http://dx.doi.org/10.1038/78948},
year = {2000},
month = {sep},
publisher = {Nature Publishing Group},
volume = {7},
number = {9},
pages = {730--734},
author = {Paul R. Selvin},
title = {{The renaissance of fluorescence resonance energy transfer}},
journal = {Nat. Struct Biol.},
}
@article{Greenfeld_2012,
doi = {10.1371/journal.pone.0030024},
url = {http://dx.doi.org/10.1371/journal.pone.0030024},
year = {2012},
month = {feb},
publisher = {Public Library of Science ({PLoS})},
volume = {7},
number = {2},
pages = {e30024},
author = {Max Greenfeld and Dmitri S. Pavlichin and Hideo Mabuchi and Daniel Herschlag},
editor = {Daniel J. Muller},
title = {{Single Molecule Analysis Research Tool ({SMART}): An Integrated Approach for Analyzing Single Molecule Data}},
journal = {{PLoS} {ONE}},
}
@article{K_nig_2013,
doi = {10.1371/journal.pone.0084157},
url = {http://dx.doi.org/10.1371/journal.pone.0084157},
year = {2013},
month = {dec},
publisher = {Public Library of Science ({PLoS})},
volume = {8},
number = {12},
pages = {e84157},
author = {Sebastian L. B. König and M{\'{e}}lodie Hadzic and Erica Fiorini and Richard Börner and Danny Kowerko and Wolf U. Blanckenhorn and Roland K. O. Sigel},
editor = {Lukasz Kurgan},
title = {{{BOBA} {FRET}: Bootstrap-Based Analysis of Single-Molecule {FRET} Data}},
journal = {{PLoS} {ONE}},
}
@inproceedings{Ingargiola_2016,
doi = {10.1117/12.2212085},
url = {http://dx.doi.org/10.1117/12.2212085},
year = {2016},
publisher = {{SPIE}},
volume = {971405},
author = {Antonino Ingargiola and Ted Laurence and Robert Boutelle and Shimon Weiss and Xavier Michalet},
title = {{Photon-{HDF}5: open data format and computational tools for timestamp-based single-molecule experiments}},
booktitle = {Single Molecule Spectroscopy and Superresolution Imaging {IX}},
note = {\href{http://dx.doi.org/10.1117/12.2212085}{doi:10.1117/12.2212085}},
}
@article{Bronson_2009,
doi = {10.1016/j.bpj.2009.09.031},
url = {http://dx.doi.org/10.1016/j.bpj.2009.09.031},
year = {2009},
month = {dec},
publisher = {Elsevier {BV}},
volume = {97},
number = {12},
pages = {3196--3205},
author = {Jonathan E. Bronson and Jingyi Fei and Jake M. Hofman and Ruben L. Gonzalez and Chris H. Wiggins},
title = {{Learning Rates and States from Biophysical Time Series: A Bayesian Approach to Model Selection and Single-Molecule {FRET} Data}},
journal = {Biophysical Journal},
}
@article{Schuler_2008,
doi = {10.1016/j.sbi.2007.12.003},
url = {http://dx.doi.org/10.1016/j.sbi.2007.12.003},
year = {2008},
month = {feb},
publisher = {Elsevier {BV}},
volume = {18},
number = {1},
pages = {16--26},
author = {Benjamin Schuler and William A Eaton},
title = {{Protein folding studied by single-molecule {FRET}}},
journal = {Current Opinion in Structural Biology},
}
@incollection{Sisamakis_2010,
doi = {10.1016/s0076-6879(10)75018-7},
url = {http://dx.doi.org/10.1016/S0076-6879(10)75018-7},
year = {2010},
publisher = {Elsevier {BV}},
volume = {475},
pages = {455--514},
author = {Evangelos Sisamakis and Alessandro Valeri and Stanislav Kalinin and Paul J. Rothwell and Claus A.M. Seidel},
title = {{Accurate Single-Molecule {FRET} Studies Using Multiparameter Fluorescence Detection}},
booktitle = {Methods in Enzymology},
}
@article{Haran_2012,
doi = {10.1016/j.sbi.2011.10.005},
url = {http://dx.doi.org/10.1016/j.sbi.2011.10.005},
year = {2012},
month = {feb},
publisher = {Elsevier {BV}},
volume = {22},
number = {1},
pages = {14--20},
author = {Gilad Haran},
title = {{How when and why proteins collapse: the relation to folding}},
journal = {Current Opinion in Structural Biology},
}
@article{Merali_2010,
doi = {10.1038/467775a},
url = {http://dx.doi.org/10.1038/467775a},
year = {2010},
month = {oct},
publisher = {Nature Publishing Group},
volume = {467},
number = {7317},
pages = {775--777},
author = {Zeeya Merali},
title = {{Computational science: ...Error}},
journal = {Nature},
}
@article{Deniz_1999,
doi = {10.1073/pnas.96.7.3670},
url = {http://dx.doi.org/10.1073/pnas.96.7.3670},
year = {1999},
month = {mar},
publisher = {Proceedings of the National Academy of Sciences},
volume = {96},
number = {7},
pages = {3670--3675},
author = {A. A. Deniz and M. Dahan and J. R. Grunwell and T. Ha and A. E. Faulhaber and D. S. Chemla and S. Weiss and P. G. Schultz},
title = {{Single-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Forster distance dependence and subpopulations}},
journal = {Proceedings of the National Academy of Sciences},
}
@article{McKinney_2006,
doi = {10.1529/biophysj.106.082487},
url = {http://dx.doi.org/10.1529/biophysj.106.082487},
year = {2006},
month = {sep},
publisher = {Elsevier {BV}},
volume = {91},
number = {5},
pages = {1941--1951},
author = {Sean A. McKinney and Chirlmin Joo and Taekjip Ha},
title = {{Analysis of Single-Molecule {FRET} Trajectories Using Hidden Markov Modeling}},
journal = {Biophysical Journal},
}
@article{van_de_Meent_2014,
doi = {10.1016/j.bpj.2013.12.055},
url = {http://dx.doi.org/10.1016/j.bpj.2013.12.055},
year = {2014},
month = {mar},
publisher = {Elsevier {BV}},
volume = {106},
number = {6},
pages = {1327--1337},
author = {Jan-Willem van~de~Meent and Jonathan~E. Bronson and Chris~H. Wiggins and Ruben~L. Gonzalez},
title = {{Empirical Bayes Methods Enable Advanced Population-Level Analyses of Single-Molecule {FRET} Experiments}},
journal = {Biophysical Journal},
}
@article{Eglen_2016,
doi = {10.1101/045104},
url = {http://dx.doi.org/10.1101/045104},
year = {2016},
month = {mar},
publisher = {Cold Spring Harbor Laboratory Press},
journal = {{bioRxiv}},
author = {Stephen Eglen and Ben Marwick and Yaroslav Halchenko and Michael Hanke and Shoaib Sufi and Padraig Gleeson and R. Angus Silver and Andrew Davison and Linda Lanyon and Mathew Abrams and Thomas Wachtler and David J Willshaw and Christophe Pouzat and Jean-Baptiste Poline},
title = {{Towards standard practices for sharing computer code and programs in neuroscience}},
note = {\href{http://dx.doi.org/10.1101/045104}{doi:10.1101/045104}},
}
@article{Edman_1996,
doi = {10.1073/pnas.93.13.6710},
url = {http://dx.doi.org/10.1073/pnas.93.13.6710},
year = {1996},
month = {jun},
publisher = {Proceedings of the National Academy of Sciences},
volume = {93},
number = {13},
pages = {6710--6715},
author = {L. Edman and U. Mets and R. Rigler},
title = {{Conformational transitions monitored for single molecules in solution.}},
journal = {Proceedings of the National Academy of Sciences},
}
@article{Kapanidis_2004,
doi = {10.1073/pnas.0401690101},
url = {http://dx.doi.org/10.1073/pnas.0401690101},
year = {2004},
month = {jun},
publisher = {Proceedings of the National Academy of Sciences},
volume = {101},
number = {24},
pages = {8936--8941},
author = {A. N. Kapanidis and N. K. Lee and T. A. Laurence and S. Doose and E. Margeat and S. Weiss},
title = {{Fluorescence-aided molecule sorting: Analysis of structure and interactions by alternating-laser excitation of single molecules}},
journal = {Proceedings of the National Academy of Sciences},
}
