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1	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
2	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
3	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
4	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
5	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
6	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
7	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
8	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
9	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
10	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
11	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
12	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
13	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
14	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
15	Material Type: Article	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 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
16	Material Type: Article	A deep convolutional neural network for classification of red blood cells in sickle cell anemia PLoS computational biology, 2017-10, Vol.13 (10), p.e1005746-e1005746 [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: Xu M, Papageorgiou DP, Abidi SZ, Dao M, Zhao H, Karniadakis GE (2017) A deep convolutional neural network for classification of red blood cells in sickle cell anemia. PLoS Comput Biol13(10): e1005746. https://doi.org/10.1371/journal.pcbi.1005746 ;2017 Xu et al 2017 Xu 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: Xu M, Papageorgiou DP, Abidi SZ, Dao M, Zhao H, Karniadakis GE (2017) A deep convolutional neural network for classification of red blood cells in sickle cell anemia. PLoS Comput Biol13(10): e1005746. https://doi.org/10.1371/journal.pcbi.1005746 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005746 ;PMID: 29049291 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
17	Material Type: Article	COBRAme: A computational framework for genome-scale models of metabolism and gene expression PLoS computational biology, 2018-07, Vol.14 (7), p.e1006302-e1006302 [Peer Reviewed Journal] COPYRIGHT 2018 Public Library of Science ;COPYRIGHT 2018 Public Library of Science ;2018 Lloyd 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 Lloyd et al 2018 Lloyd et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1006302 ;PMID: 29975681 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
18	Material Type: Article	Slow manifolds within network dynamics encode working memory efficiently and robustly PLoS computational biology, 2021-09, Vol.17 (9), p.e1009366-e1009366 [Peer Reviewed Journal] COPYRIGHT 2021 Public Library of Science ;2021 Ghazizadeh, Ching. 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 Ghazizadeh, Ching 2021 Ghazizadeh, Ching ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1009366 ;PMID: 34525089 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
19	Material Type: Article	Modeling latently infected cell activation: viral and latent reservoir persistence, and viral blips in HIV-infected patients on potent therapy PLoS computational biology, 2009-10, Vol.5 (10), p.e1000533-e1000533 [Peer Reviewed Journal] COPYRIGHT 2009 Public Library of Science ;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. 2009 ;2009 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: Rong L, Perelson AS (2009) Modeling Latently Infected Cell Activation: Viral and Latent Reservoir Persistence, and Viral Blips in HIV-infected Patients on Potent Therapy. PLoS Comput Biol 5(10): e1000533. doi:10.1371/journal.pcbi.1000533 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1000533 ;PMID: 19834532 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by
20	Material Type: Article	Human mobility and the spatial transmission of influenza in the United States PLoS computational biology, 2017-02, Vol.13 (2), p.e1005382-e1005382 [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: Charu V, Zeger S, Gog J, Bjørnstad ON, Kissler S, Simonsen L, et al. (2017) Human mobility and the spatial transmission of influenza in the United States. PLoS Comput Biol 13(2): e1005382. doi:10.1371/journal.pcbi.1005382 ;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: Charu V, Zeger S, Gog J, Bjørnstad ON, Kissler S, Simonsen L, et al. (2017) Human mobility and the spatial transmission of influenza in the United States. PLoS Comput Biol 13(2): e1005382. doi:10.1371/journal.pcbi.1005382 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005382 ;PMID: 28187123 Full text available View Online Details Recommendations Reviews Times Cited External Links Citations Cited by