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1 |
Material Type: Article
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Propagating annotations of molecular networks using in silico fragmentationPLoS computational biology, 2018-04, Vol.14 (4), p.e1006089-e1006089 [Peer Reviewed Journal]COPYRIGHT 2018 Public Library of Science ;COPYRIGHT 2018 Public Library of Science ;2018 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: fragmentation. PLoS Comput Biol 14(4): e1006089. https://doi.org/10.1371/journal.pcbi.1006089 ;2018 da Silva et al 2018 da Silva et al ;Wageningen University & Research ;2018 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: fragmentation. PLoS Comput Biol 14(4): e1006089. https://doi.org/10.1371/journal.pcbi.1006089 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1006089 ;PMID: 29668671Full text available |
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Material Type: Article
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BEAST 2: a software platform for Bayesian evolutionary analysisPLoS computational biology, 2014-04, Vol.10 (4), p.e1003537 [Peer Reviewed Journal]COPYRIGHT 2014 Public Library of Science ;COPYRIGHT 2014 Public Library of Science ;2014 Bouckaert et al 2014 Bouckaert et al ;2014 Bouckaert et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, et al. (2014) BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Comput Biol 10(4): e1003537. doi:10.1371/journal.pcbi.1003537 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1003537 ;PMID: 24722319Full text available |
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Material Type: Article
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Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C dataPLoS computational biology, 2020-09, Vol.16 (9), p.e1008173-e1008173 [Peer Reviewed Journal]COPYRIGHT 2020 Public Library of Science ;COPYRIGHT 2020 Public Library of Science ;2020 Kim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;2020 Kim et al 2020 Kim et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1008173 ;PMID: 32946435Full text available |
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Material Type: Article
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Metacoder: An R package for visualization and manipulation of community taxonomic diversity dataPLoS computational biology, 2017-02, Vol.13 (2), p.e1005404-e1005404 [Peer Reviewed Journal]COPYRIGHT 2017 Public Library of Science ;COPYRIGHT 2017 Public Library of Science ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Foster ZSL, Sharpton TJ, Grünwald NJ (2017) Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput Biol 13(2): e1005404. doi:10.1371/journal.pcbi.1005404 ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Foster ZSL, Sharpton TJ, Grünwald NJ (2017) Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput Biol 13(2): e1005404. doi:10.1371/journal.pcbi.1005404 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005404 ;PMID: 28222096Full text available |
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Material Type: Article
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Reactome graph database: Efficient access to complex pathway dataPLoS computational biology, 2018-01, Vol.14 (1), p.e1005968-e1005968 [Peer Reviewed Journal]COPYRIGHT 2018 Public Library of Science ;COPYRIGHT 2018 Public Library of Science ;2018 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, et al. (2018) Reactome graph database: Efficient access to complex pathway data. PLoS Comput Biol 14(1): e1005968. https://doi.org/10.1371/journal.pcbi.1005968 ;2018 Fabregat et al 2018 Fabregat et al ;2018 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, et al. (2018) Reactome graph database: Efficient access to complex pathway data. PLoS Comput Biol 14(1): e1005968. https://doi.org/10.1371/journal.pcbi.1005968 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005968 ;PMID: 29377902Full text available |
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Material Type: Article
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A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivarPLoS computational biology, 2022-05, Vol.18 (5), p.e1009123-e1009123 [Peer Reviewed Journal]COPYRIGHT 2022 Public Library of Science ;2022 Garrison et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;2022 Garrison et al 2022 Garrison et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1009123 ;PMID: 35639788Full text available |
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Material Type: Article
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Scalable Parameter Estimation for Genome-Scale Biochemical Reaction NetworksPLoS computational biology, 2017-01, Vol.13 (1), p.e1005331-e1005331 [Peer Reviewed Journal]COPYRIGHT 2017 Public Library of Science ;COPYRIGHT 2017 Public Library of Science ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Fröhlich F, Kaltenbacher B, Theis FJ, Hasenauer J (2017) Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PLoS Comput Biol 13(1): e1005331. doi:10.1371/journal.pcbi.1005331 ;2017 Fröhlich et al 2017 Fröhlich et al ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Fröhlich F, Kaltenbacher B, Theis FJ, Hasenauer J (2017) Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PLoS Comput Biol 13(1): e1005331. doi:10.1371/journal.pcbi.1005331 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005331 ;PMID: 28114351Full text available |
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Material Type: Article
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Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuitsPLoS computational biology, 2020-11, Vol.16 (11), p.e1008386-e1008386 [Peer Reviewed Journal]COPYRIGHT 2020 Public Library of Science ;COPYRIGHT 2020 Public Library of Science ;2020 Dai et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;info:eu-repo/semantics/openAccess ;2020 Dai et al 2020 Dai et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1008386 ;PMID: 33253147Full text available |
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Material Type: Article
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A comprehensive benchmark of kernel methods to extract protein-protein interactions from literaturePLoS computational biology, 2010-07, Vol.6 (7), p.e1000837 [Peer Reviewed Journal]COPYRIGHT 2010 Public Library of Science ;COPYRIGHT 2010 Public Library of Science ;Tikk et al. 2010 ;2010 Tikk et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Tikk D, Thomas P, Palaga P, Hakenberg J, Leser U (2010) A Comprehensive Benchmark of Kernel Methods to Extract Protein-Protein Interactions from Literature. PLoS Comput Biol 6(7): e1000837. doi:10.1371/journal.pcbi.1000837 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1000837 ;PMID: 20617200Full text available |
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Material Type: Article
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CNEr: A toolkit for exploring extreme noncoding conservationPLoS computational biology, 2019-08, Vol.15 (8), p.e1006940-e1006940 [Peer Reviewed Journal]COPYRIGHT 2019 Public Library of Science ;COPYRIGHT 2019 Public Library of Science ;2019 Tan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;2019 Tan et al 2019 Tan et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1006940 ;PMID: 31449516Full text available |
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Material Type: Article
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Towards a category theory approach to analogy: Analyzing re-representation and acquisition of numerical knowledgePLoS computational biology, 2017-08, Vol.13 (8), p.e1005683-e1005683 [Peer Reviewed Journal]COPYRIGHT 2017 Public Library of Science ;COPYRIGHT 2017 Public Library of Science ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Navarrete JA, Dartnell P (2017) Towards a category theory approach to analogy: Analyzing re-representation and acquisition of numerical knowledge. PLoS Comput Biol 13(8): e1005683. https://doi.org/10.1371/journal.pcbi.1005683 ;2017 Navarrete, Dartnell 2017 Navarrete, Dartnell ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Navarrete JA, Dartnell P (2017) Towards a category theory approach to analogy: Analyzing re-representation and acquisition of numerical knowledge. PLoS Comput Biol 13(8): e1005683. https://doi.org/10.1371/journal.pcbi.1005683 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005683 ;PMID: 28841643Full text available |
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Material Type: Article
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The layer-oriented approach to declarative languages for biological modelingPLoS computational biology, 2012-05, Vol.8 (5), p.e1002521-e1002521 [Peer Reviewed Journal]COPYRIGHT 2012 Public Library of Science ;COPYRIGHT 2012 Public Library of Science ;2012 Raikov, De Schutter. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Raikov I, De Schutter E (2012) The Layer-Oriented Approach to Declarative Languages for Biological Modeling. PLoS Comput Biol 8(5): e1002521. doi:10.1371/journal.pcbi.1002521 ;Raikov, De Schutter. 2012 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1002521 ;PMID: 22615554Full text available |
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Material Type: Article
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Making informed choices about microarray data analysisPLoS computational biology, 2010-05, Vol.6 (5), p.e1000786-e1000786 [Peer Reviewed Journal]COPYRIGHT 2010 Public Library of Science ;COPYRIGHT 2010 Public Library of Science ;Mark Reimers. 2010 ;2010 Mark Reimers. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Reimers M (2010) Making Informed Choices about Microarray Data Analysis. PLoS Comput Biol 6(5): e1000786. doi:10.1371/journal.pcbi.1000786 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1000786 ;PMID: 20523743Full text available |
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Material Type: Article
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The dynamic brain: from spiking neurons to neural masses and cortical fieldsPLoS computational biology, 2008-08, Vol.4 (8), p.e1000092-e1000092 [Peer Reviewed Journal]COPYRIGHT 2008 Public Library of Science ;Deco et al. 2008 ;2008 Deco et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Deco G, Jirsa VK, Robinson PA, Breakspear M, Friston K (2008) The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields. PLoS Comput Biol 4(8): e1000092. doi:10.1371/journal.pcbi.1000092 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1000092 ;PMID: 18769680Full text available |
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Material Type: Article
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The FACTS model of speech motor control: Fusing state estimation and task-based controlPLoS computational biology, 2019-09, Vol.15 (9), p.e1007321-e1007321 [Peer Reviewed Journal]COPYRIGHT 2019 Public Library of Science ;COPYRIGHT 2019 Public Library of Science ;2019 Parrell et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;2019 Parrell et al 2019 Parrell et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1007321 ;PMID: 31479444Full text available |
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Material Type: Article
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Machine learning and its applications to biologyPLoS computational biology, 2007-06, Vol.3 (6), p.e116-e116 [Peer Reviewed Journal]COPYRIGHT 2007 Public Library of Science ;2007 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Citation: Tarca AL, Carey VJ, Chen X-w, Romero R, Dr?ghici S (2007) Machine Learning and Its Applications to Biology. PLoS Comput Biol 3(6): e116. doi:10.1371/journal.pcbi.0030116 ;This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. 2007 ;2007 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Citation: Tarca AL, Carey VJ, Chen X-w, Romero R, Dr?ghici S (2007) Machine Learning and Its Applications to Biology. PLoS Comput Biol 3(6): e116. doi:10.1371/journal.pcbi.0030116 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.0030116 ;PMID: 17604446Full text available |
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Material Type: Article
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Nonnegative matrix factorization: an analytical and interpretive tool in computational biologyPLoS computational biology, 2008-07, Vol.4 (7), p.e1000029-e1000029 [Peer Reviewed Journal]COPYRIGHT 2008 Public Library of Science ;Karthik Devarajan. 2008 ;2008 Karthik Devarajan. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Devarajan K (2008) Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology. PLoS Comput Biol 4(7): e1000029. doi:10.1371/journal.pcbi.1000029 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1000029 ;PMID: 18654623Full text available |
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Material Type: Article
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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysisPLoS computational biology, 2019-04, Vol.15 (4), p.e1006650-e1006650 [Peer Reviewed Journal]COPYRIGHT 2019 Public Library of Science ;COPYRIGHT 2019 Public Library of Science ;2019 Bouckaert et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;2019 Bouckaert et al 2019 Bouckaert et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1006650 ;PMID: 30958812Full text available |
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Material Type: Article
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Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegansPLoS computational biology, 2015-04, Vol.11 (4), p.e1004194-e1004194 [Peer Reviewed Journal]COPYRIGHT 2015 Public Library of Science ;COPYRIGHT 2015 Public Library of Science ;2015 Zhan et al 2015 Zhan et al ;2015 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: . PLoS Comput Biol 11(4): e1004194. doi:10.1371/journal.pcbi.1004194 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1004194 ;PMID: 25910032Full text available |
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Material Type: Article
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Software for computing and annotating genomic rangesPLoS computational biology, 2013-08, Vol.9 (8), p.e1003118-e1003118 [Peer Reviewed Journal]COPYRIGHT 2013 Public Library of Science ;COPYRIGHT 2013 Public Library of Science ;2013 Lawrence et al 2013 Lawrence et al ;2013 Lawrence et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi:10.1371/journal.pcbi.1003118 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1003118 ;PMID: 23950696Full text available |