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Microbial mutation  
PLOS Computational Biology  
Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1

Tyler Cassidy, Kathryn E. Stephenson, Dan H. Barouch, Alan S. Perelson

Research Article | published 29 Mar 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011518

Views: 1116Citations: 1Saves: 5 • Shares: 4

Mutational signature dynamics indicate SARS-CoV-2’s evolutionary capacity is driven by host antiviral molecules

Kieran D. Lamb, Martha M. Luka, Megan Saathoff, Richard J. Orton, My V. T. Phan, Matthew Cotten, Ke Yuan, David L. Robertson

Research Article | published 25 Jan 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011795

Views: 2451Citations: 9Saves: 23 • Shares: 46

PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning

Anand Ramachandran, Steven S. Lumetta, Deming Chen

Research Article | published 19 Jan 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011790

Views: 1212Citations: 3Saves: 7 • Shares: 1

A spatial vaccination strategy to reduce the risk of vaccine-resistant variants

Xiyun Zhang, Gabriela Lobinska, Michal Feldman, Eddie Dekel, Martin A. Nowak, Yitzhak Pilpel, Yonatan Pauzner, Baruch Barzel, Ady Pauzner

Research Article | published 10 Aug 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010391

Views: 2276Citations: 10Saves: 13 • Shares: 5

Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence

Fateme Pourhasanzade, Swami Iyer, Jesslyn Tjendra, Lotta Landor, Selina Våge

Research Article | published 08 Jun 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010228

Views: 1501Citations: 4Saves: 11 • Shares: 13

Mutational analysis of SARS-CoV-2 variants of concern reveals key tradeoffs between receptor affinity and antibody escape

Emily K. Makowski, John S. Schardt, Matthew D. Smith, Peter M. Tessier

Research Article | published 31 May 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010160

Views: 2139Citations: 19Saves: 16 • Shares: 21

Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2

Anna Foix, Daniel López, Francisco Díez-Fuertes, Michael J. McConnell, Antonio J. Martín-Galiano

Research Article | published 10 Feb 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009726

Views: 3544Citations: 13Saves: 26 • Shares: 19

A proposed workflow for proactive virus surveillance and prediction of variants for vaccine design

Jordan J. Baker, Christopher J. P. Mathy, Julia Schaletzky

Perspective | published 16 Dec 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009624

Views: 1968Citations: 2Saves: 24 • Shares: 1

Why are viral genomes so fragile? The bottleneck hypothesis

Nono S. C. Merleau, Sophie Pénisson, Philip J. Gerrish, Santiago F. Elena, Matteo Smerlak

Research Article | published 08 Jul 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009128

Views: 2890Citations: 8Saves: 0 • Shares: 0

How does feedback from phage infections influence the evolution of phase variation in Campylobacter?

Simran K. Sandhu, Christopher D. Bayliss, Andrew Yu. Morozov

Research Article | published 14 Jun 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009067

Views: 2059Citations: 4Saves: 22 • Shares: 3

Insights on cross-species transmission of SARS-CoV-2 from structural modeling

João P. G. L. M. Rodrigues, Susana Barrera-Vilarmau, João M. C. Teixeira, Marija Sorokina, Elizabeth Seckel, Panagiotis L. Kastritis, Michael Levitt

Research Article | published 03 Dec 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008449

Views: 8358Citations: 58Saves: 148 • Shares: 61

Modeling the efficiency of filovirus entry into cells in vitro: Effects of SNP mutations in the receptor molecule

Kwang Su Kim, Tatsunari Kondoh, Yusuke Asai, Ayato Takada, Shingo Iwami

Research Article | published 28 Sep 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007612

Views: 1982Citations: 1Saves: 3 • Shares: 1

Phenotypic delay in the evolution of bacterial antibiotic resistance: Mechanistic models and their implications

Martín Carballo-Pacheco, Michael D. Nicholson, Elin E. Lilja, Rosalind J. Allen, Bartlomiej Waclaw

Research Article | published 29 May 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007930

Views: 3832Citations: 11Saves: 47 • Shares: 1

Resist or perish: Fate of a microbial population subjected to a periodic presence of antimicrobial

Loïc Marrec, Anne-Florence Bitbol

Research Article | published 10 Apr 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007798

Views: 3332Citations: 52Saves: 56 • Shares: 5

Early prediction of antigenic transitions for influenza A/H3N2

Lauren A. Castro, Trevor Bedford, Lauren Ancel Meyers

Research Article | published 18 Feb 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007683

Views: 6902Citations: 18Saves: 44 • Shares: 6

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