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1
Continuous multi-parameter heart rate variability analysis heralds onset of sepsis in adults
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Continuous multi-parameter heart rate variability analysis heralds onset of sepsis in adults

PloS one, 2009-08, Vol.4 (8), p.e6642-e6642 [Peer Reviewed Journal]

COPYRIGHT 2009 Public Library of Science ;2009 Ahmad et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (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. ;Ahmad et al. 2009 ;ISSN: 1932-6203 ;EISSN: 1932-6203 ;DOI: 10.1371/journal.pone.0006642 ;PMID: 19680545

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2
Reverse annealing for nonnegative/binary matrix factorization
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Reverse annealing for nonnegative/binary matrix factorization

PloS one, 2021-01, Vol.16 (1), p.e0244026-e0244026 [Peer Reviewed Journal]

COPYRIGHT 2021 Public Library of Science ;COPYRIGHT 2021 Public Library of Science ;2021 Golden, O’Malley. 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. ;2021 Golden, O’Malley 2021 Golden, O’Malley ;ISSN: 1932-6203 ;EISSN: 1932-6203 ;DOI: 10.1371/journal.pone.0244026 ;PMID: 33406162

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3
Preschoolers' precision of the approximate number system predicts later school mathematics performance
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Preschoolers' precision of the approximate number system predicts later school mathematics performance

PloS one, 2011-09, Vol.6 (9), p.e23749-e23749 [Peer Reviewed Journal]

COPYRIGHT 2011 Public Library of Science ;COPYRIGHT 2011 Public Library of Science ;2011 Mazzocco et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://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. ;Mazzocco et al. 2011 ;ISSN: 1932-6203 ;EISSN: 1932-6203 ;DOI: 10.1371/journal.pone.0023749 ;PMID: 21935362

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4
Direct solution of the Chemical Master Equation using quantized tensor trains
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Direct solution of the Chemical Master Equation using quantized tensor trains

PLoS computational biology, 2014-03, Vol.10 (3), p.e1003359-e1003359 [Peer Reviewed Journal]

COPYRIGHT 2014 Public Library of Science ;COPYRIGHT 2014 Public Library of Science ;2014 Kazeev et al 2014 Kazeev et al ;2014 Kazeev 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: Kazeev V, Khammash M, Nip M, Schwab C (2014) Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains. PLoS Comput Biol 10(3): e1003359. doi:10.1371/journal.pcbi.1003359 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1003359 ;PMID: 24626049

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5
Cutoff Finder: a comprehensive and straightforward Web application enabling rapid biomarker cutoff optimization
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Cutoff Finder: a comprehensive and straightforward Web application enabling rapid biomarker cutoff optimization

PloS one, 2012-12, Vol.7 (12), p.e51862-e51862 [Peer Reviewed Journal]

COPYRIGHT 2012 Public Library of Science ;COPYRIGHT 2012 Public Library of Science ;2012 Budczies et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://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. ;2012 Budczies et al 2012 Budczies et al ;ISSN: 1932-6203 ;EISSN: 1932-6203 ;DOI: 10.1371/journal.pone.0051862 ;PMID: 23251644

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6
Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares
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Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares

PLoS computational biology, 2019-05, Vol.15 (5), p.e1006976-e1006976 [Peer Reviewed Journal]

COPYRIGHT 2019 Public Library of Science ;COPYRIGHT 2019 Public Library of Science ;2019 Hao 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 Hao et al 2019 Hao et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1006976 ;PMID: 31059559

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7
Chaste: an open source C++ library for computational physiology and biology
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Chaste: an open source C++ library for computational physiology and biology

PLoS computational biology, 2013-03, Vol.9 (3), p.e1002970-e1002970 [Peer Reviewed Journal]

COPYRIGHT 2013 Public Library of Science ;COPYRIGHT 2013 Public Library of Science ;Distributed under a Creative Commons Attribution 4.0 International License ;2013 Mirams et al 2013 Mirams et al ;2013 Mirams 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: Mirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, et al. (2013) Chaste: An Open Source C++ Library for Computational Physiology and Biology. PLoS Comput Biol 9(3): e1002970. doi:10.1371/journal.pcbi.1002970 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1002970 ;PMID: 23516352

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8
Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction
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Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction

PLoS computational biology, 2016-02, Vol.12 (2), p.e1004760-e1004760 [Peer Reviewed Journal]

COPYRIGHT 2016 Public Library of Science ;COPYRIGHT 2016 Public Library of Science ;2016 Liu et al 2016 Liu et al ;2016 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: Liu Y, Wu M, Miao C, Zhao P, Li X-L (2016) Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction. PLoS Comput Biol 12(2): e1004760. doi:10.1371/journal.pcbi.1004760 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1004760 ;PMID: 26872142

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9
Prediction of drug-target interactions and drug repositioning via network-based inference
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Prediction of drug-target interactions and drug repositioning via network-based inference

PLoS computational biology, 2012-05, Vol.8 (5), p.e1002503 [Peer Reviewed Journal]

COPYRIGHT 2012 Public Library of Science ;COPYRIGHT 2012 Public Library of Science ;2012 Cheng 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: Cheng F, Liu C, Jiang J, Lu W, Li W, et al. (2012) Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference. PLoS Comput Biol 8(5): e1002503. doi:10.1371/journal.pcbi.1002503 ;Cheng et al. 2012 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1002503 ;PMID: 22589709

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10
Intrinsically-generated fluctuating activity in excitatory-inhibitory networks
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Intrinsically-generated fluctuating activity in excitatory-inhibitory networks

PLoS computational biology, 2017-04, Vol.13 (4), p.e1005498-e1005498 [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: Mastrogiuseppe F, Ostojic S (2017) Intrinsically-generated fluctuating activity in excitatory-inhibitory networks. PLoS Comput Biol 13(4): e1005498. https://doi.org/10.1371/journal.pcbi.1005498 ;Distributed under a Creative Commons Attribution 4.0 International License ;2017 Mastrogiuseppe, Ostojic 2017 Mastrogiuseppe, Ostojic ;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: Mastrogiuseppe F, Ostojic S (2017) Intrinsically-generated fluctuating activity in excitatory-inhibitory networks. PLoS Comput Biol 13(4): e1005498. https://doi.org/10.1371/journal.pcbi.1005498 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005498 ;PMID: 28437436

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11
Microbial co-occurrence relationships in the human microbiome
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Microbial co-occurrence relationships in the human microbiome

PLoS computational biology, 2012-07, Vol.8 (7), p.e1002606-e1002606 [Peer Reviewed Journal]

COPYRIGHT 2012 Public Library of Science ;COPYRIGHT 2012 Public Library of Science ;2012 Faust 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: Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, et al. (2012) Microbial Co-occurrence Relationships in the Human Microbiome. PLoS Comput Biol 8(7): e1002606. doi:10.1371/journal.pcbi.1002606 ;Faust et al. 2012 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1002606 ;PMID: 22807668

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12
Ten years of pathway analysis: current approaches and outstanding challenges
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Ten years of pathway analysis: current approaches and outstanding challenges

PLoS computational biology, 2012-02, Vol.8 (2), p.e1002375-e1002375 [Peer Reviewed Journal]

COPYRIGHT 2012 Public Library of Science ;COPYRIGHT 2012 Public Library of Science ;2012 Khatri 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: Khatri P, Sirota M, Butte AJ (2012) Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. PLoS Comput Biol 8(2): e1002375. doi:10.1371/journal.pcbi.1002375 ;Khatri et al. 2012 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1002375 ;PMID: 22383865

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13
Post-Turing tissue pattern formation: Advent of mechanochemistry
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Post-Turing tissue pattern formation: Advent of mechanochemistry

PLoS computational biology, 2018-07, Vol.14 (7), p.e1006259-e1006259 [Peer Reviewed Journal]

COPYRIGHT 2018 Public Library of Science ;COPYRIGHT 2018 Public Library of Science ;2018 Brinkmann 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. ;2018 Brinkmann et al 2018 Brinkmann et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1006259 ;PMID: 29969460

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14
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
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Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

PLoS computational biology, 2018-01, Vol.14 (1), p.e1005929-e1005929 [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: Cang Z, Mu L, Wei G-W (2018) Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening. PLoS Comput Biol 14(1): e1005929. https://doi.org/10.1371/journal.pcbi.1005929 ;2018 Cang et al 2018 Cang 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: Cang Z, Mu L, Wei G-W (2018) Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening. PLoS Comput Biol 14(1): e1005929. https://doi.org/10.1371/journal.pcbi.1005929 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005929 ;PMID: 29309403

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15
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
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Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

PLoS computational biology, 2015-08, Vol.11 (8), p.e1004321-e1004321 [Peer Reviewed Journal]

COPYRIGHT 2015 Public Library of Science ;COPYRIGHT 2015 Public Library of Science ;2015 King et al 2015 King 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: King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO (2015) Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput Biol 11(8): e1004321. doi:10.1371/journal.pcbi.1004321 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1004321 ;PMID: 26313928

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16
The geography of happiness: connecting twitter sentiment and expression, demographics, and objective characteristics of place
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The geography of happiness: connecting twitter sentiment and expression, demographics, and objective characteristics of place

PloS one, 2013-05, Vol.8 (5), p.e64417-e64417 [Peer Reviewed Journal]

COPYRIGHT 2013 Public Library of Science ;2013 Mitchell et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://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. ;2013 Mitchell et al 2013 Mitchell et al ;ISSN: 1932-6203 ;EISSN: 1932-6203 ;DOI: 10.1371/journal.pone.0064417 ;PMID: 23734200

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17
FIMTrack: An open source tracking and locomotion analysis software for small animals
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FIMTrack: An open source tracking and locomotion analysis software for small animals

PLoS computational biology, 2017-05, Vol.13 (5), p.e1005530-e1005530 [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: Risse B, Berh D, Otto N, Klämbt C, Jiang X (2017) FIMTrack: An open source tracking and locomotion analysis software for small animals. PLoS Comput Biol 13(5): e1005530. https://doi.org/10.1371/journal.pcbi.1005530 ;2017 Risse et al 2017 Risse 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: Risse B, Berh D, Otto N, Klämbt C, Jiang X (2017) FIMTrack: An open source tracking and locomotion analysis software for small animals. PLoS Comput Biol 13(5): e1005530. https://doi.org/10.1371/journal.pcbi.1005530 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005530 ;PMID: 28493862

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18
DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning
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DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning

PLoS computational biology, 2020-04, Vol.16 (4), p.e1007673-e1007673 [Peer Reviewed Journal]

COPYRIGHT 2020 Public Library of Science ;COPYRIGHT 2020 Public Library of Science ;2020 Lugagne 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 Lugagne et al 2020 Lugagne et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1007673 ;PMID: 32282792

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19
Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains
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Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains

PLoS computational biology, 2016-11, Vol.12 (11), p.e1005189-e1005189 [Peer Reviewed Journal]

COPYRIGHT 2016 Public Library of Science ;COPYRIGHT 2016 Public Library of Science ;2016 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: Onken A, Liu JK, Karunasekara PPCR, Delis I, Gollisch T, Panzeri S (2016) Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains. PLoS Comput Biol 12(11): e1005189. doi:10.1371/journal.pcbi.1005189 ;2016 Onken et al 2016 Onken et al ;2016 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: Onken A, Liu JK, Karunasekara PPCR, Delis I, Gollisch T, Panzeri S (2016) Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains. PLoS Comput Biol 12(11): e1005189. doi:10.1371/journal.pcbi.1005189 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005189 ;PMID: 27814363

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20
A comparison of computational models for eukaryotic cell shape and motility
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A comparison of computational models for eukaryotic cell shape and motility

PLoS computational biology, 2012-12, Vol.8 (12), p.e1002793-e1002793 [Peer Reviewed Journal]

COPYRIGHT 2012 Public Library of Science ;COPYRIGHT 2012 Public Library of Science ;2012 Holmes, Edelstein-Keshet. 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: Holmes WR, Edelstein-Keshet L (2012) A Comparison of Computational Models for Eukaryotic Cell Shape and Motility. PLoS Comput Biol 8(12): e1002793. doi:10.1371/journal.pcbi.1002793 ;2012 Holmes, Edelstein-Keshet 2012 Holmes, Edelstein-Keshet ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1002793 ;PMID: 23300403

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