Ten simple rules for quick and dirty scientific programming

Gabriel Balaban, Ivar Grytten, Knut Dagestad Rand, Lonneke Scheffer, Geir Kjetil Sandve

PLOS Computational Biology: published March 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008549

Ten simple rules for hitting a home run with your elevator pitch

Whitney Rachel Morgan, Erik Scott Wright

PLOS Computational Biology: published March 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008756

Collaborating with our community to increase code sharing

Lauren Cadwallader, Jason A. Papin, Feilim Mac Gabhann, Rebecca Kirk

PLOS Computational Biology: published March 30, 2021 | https://doi.org/10.1371/journal.pcbi.1008867

Ten quick tips for staying safe online

Danielle Smalls, Greg Wilson

PLOS Computational Biology: published March 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008563

Hands-on training about overfitting

Janez Demšar, Blaž Zupan

PLOS Computational Biology: published March 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008671

Application of a bioinformatics training delivery method for reaching dispersed and distant trainees

Christina R. Hall, Philippa C. Griffin, Andrew J. Lonie, Jeffrey H. Christiansen

PLOS Computational Biology: published March 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008715

Principles for data analysis workflows

Sara Stoudt, Váleri N. Vásquez, Ciera C. Martinez

PLOS Computational Biology: published March 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008770

Signal-to-signal neural networks for improved spike estimation from calcium imaging data

Jilt Sebastian, Mriganka Sur, Hema A. Murthy, Mathew Magimai-Doss

PLOS Computational Biology: published March 1, 2021 | https://doi.org/10.1371/journal.pcbi.1007921

Learning receptive field properties of complex cells in V1

Yanbo Lian, Ali Almasi, David B. Grayden, Tatiana Kameneva, Anthony N. Burkitt, Hamish Meffin

PLOS Computational Biology: published March 2, 2021 | https://doi.org/10.1371/journal.pcbi.1007957

Linear-nonlinear cascades capture synaptic dynamics

Julian Rossbroich, Daniel Trotter, John Beninger, Katalin Tóth, Richard Naud

PLOS Computational Biology: published March 15, 2021 | https://doi.org/10.1371/journal.pcbi.1008013

Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds

Brian Coventry, David Baker

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008061

Repulsive expansion dynamics in colony growth and gene expression

Yangxiaolu Cao, John Neu, Andrew E. Blanchard, Ting Lu, Lingchong You

PLOS Computational Biology: published March 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008168

Reciprocal interaction between I_K1 and I_f in biological pacemakers: A simulation study

Yacong Li, Kuanquan Wang, Qince Li, Jules C. Hancox, Henggui Zhang

PLOS Computational Biology: published March 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008177

Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases

Janani Durairaj, Elena Melillo, Harro J. Bouwmeester, Jules Beekwilder, Dick de Ridder, Aalt D. J. van Dijk

PLOS Computational Biology: published March 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008197

Combinatorial mathematical modelling approaches to interrogate rear retraction dynamics in 3D cell migration

Joseph H. R. Hetmanski, Matthew C. Jones, Fatima Chunara, Jean-Marc Schwartz, Patrick T. Caswell

PLOS Computational Biology: published March 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008213

BARcode DEmixing through Non-negative Spatial Regression (BarDensr)

Shuonan Chen, Jackson Loper, Xiaoyin Chen, Alex Vaughan, Anthony M. Zador, Liam Paninski

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008256

A prediction tool for plaque progression based on patient-specific multi-physical modeling

Jichao Pan, Yan Cai, Liang Wang, Akiko Maehara, Gary S. Mintz, Dalin Tang, Zhiyong Li

PLOS Computational Biology: published March 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008344

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Integrating across neuroimaging modalities boosts prediction accuracy of cognitive ability

Javier Rasero, Amy Isabella Sentis, Fang-Cheng Yeh, Timothy Verstynen

PLOS Computational Biology: published March 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008347

DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation

Ilya Belevich, Eija Jokitalo

PLOS Computational Biology: published March 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008374

Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples

Xiaoqiang Sun, Ji Zhang, Qing Nie

PLOS Computational Biology: published March 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008379

Positive allosteric modulators of lecithin: Cholesterol acyltransferase adjust the orientation of the membrane-binding domain and alter its spatial free energy profile

Akseli Niemelä, Artturi Koivuniemi

PLOS Computational Biology: published March 15, 2021 | https://doi.org/10.1371/journal.pcbi.1008426

PIEZO1 and the mechanism of the long circulatory longevity of human red blood cells

Simon Rogers, Virgilio L. Lew

PLOS Computational Biology: published March 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008496

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CRISPRbuilder-TB: “CRISPR-builder for tuberculosis”. Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA

Christophe Guyeux, Christophe Sola, Camille Noûs, Guislaine Refrégier

PLOS Computational Biology: published March 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008500

Modeling the circadian regulation of the immune system: Sexually dimorphic effects of shift work

Stéphanie M. C. Abo, Anita T. Layton

PLOS Computational Biology: published March 31, 2021 | https://doi.org/10.1371/journal.pcbi.1008514

Modelling the impact of clot fragmentation on the microcirculation after thrombectomy

Wahbi K. El-Bouri, Andrew MacGowan, Tamás I. Józsa, Matthew J. Gounis, Stephen J. Payne

PLOS Computational Biology: published March 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008515

Perturbations both trigger and delay seizures due to generic properties of slow-fast relaxation oscillators

Alberto Pérez-Cervera, Jaroslav Hlinka

PLOS Computational Biology: published March 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008521

Can subjective pain be inferred from objective physiological data? Evidence from patients with sickle cell disease

Mark J. Panaggio, Daniel M. Abrams, Fan Yang, Tanvi Banerjee, Nirmish R. Shah

PLOS Computational Biology: published March 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008542

A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development

Zixuan Cang, Yangyang Wang, Qixuan Wang, Ken W. Y. Cho, William Holmes, Qing Nie

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008571

The very early evolution of protein translocation across membranes

AJ Harris, Aaron David Goldman

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008623

Testing, tracing and isolation in compartmental models

Simone Sturniolo, William Waites, Tim Colbourn, David Manheim, Jasmina Panovska-Griffiths

PLOS Computational Biology: published March 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008633

Health inequities in influenza transmission and surveillance

Casey M. Zipfel, Vittoria Colizza, Shweta Bansal

PLOS Computational Biology: published March 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008642

Rational inattention and tonic dopamine

John G. Mikhael, Lucy Lai, Samuel J. Gershman

PLOS Computational Biology: published March 24, 2021 | https://doi.org/10.1371/journal.pcbi.1008659

Modelling of malaria risk, rates, and trends: A spatiotemporal approach for identifying and targeting sub-national areas of high and low burden

Jailos Lubinda, Yaxin Bi, Busiku Hamainza, Ubydul Haque, Adrian J. Moore

PLOS Computational Biology: published March 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008669

Thermodynamic and sequential characteristics of phase separation and droplet formation for an intrinsically disordered region/protein ensemble

Wen-Ting Chu, Jin Wang

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008672

Connectivity, reproduction number, and mobility interact to determine communities’ epidemiological superspreader potential in a metapopulation network

Brandon Lieberthal, Allison M. Gardner

PLOS Computational Biology: published March 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008674

Assessing the feasibility and effectiveness of household-pooled universal testing to control COVID-19 epidemics

Pieter J. K. Libin, Lander Willem, Timothy Verstraeten, Andrea Torneri, Joris Vanderlocht, Niel Hens

PLOS Computational Biology: published March 9, 2021 | https://doi.org/10.1371/journal.pcbi.1008688

Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies

David J. Wooten, Jorge Gómez Tejeda Zañudo, David Murrugarra, Austin M. Perry, Anna Dongari-Bagtzoglou, Reinhard Laubenbacher, Clarissa J. Nobile, Réka Albert

PLOS Computational Biology: published March 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008690

A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli

Alexandre Oliveira, Joana Rodrigues, Eugénio Campos Ferreira, Lígia Rodrigues, Oscar Dias

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008704

Up-down biphasic volume response of human red blood cells to PIEZO1 activation during capillary transits

Simon Rogers, Virgilio L. Lew

PLOS Computational Biology: published March 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008706

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Force variability is mostly not motor noise: Theoretical implications for motor control

Akira Nagamori, Christopher M. Laine, Gerald E. Loeb, Francisco J. Valero-Cuevas

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008707

Biological impact of mutually exclusive exon switching

Su Datt Lam, M. Madan Babu, Jonathan Lees, Christine A. Orengo

PLOS Computational Biology: published March 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008708

Using deep neural networks to evaluate object vision tasks in rats

Kasper Vinken, Hans Op de Beeck

PLOS Computational Biology: published March 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008714

Mechanical coupling in the nitrogenase complex

Qi Huang, Monika Tokmina-Lukaszewska, Lewis E. Johnson, Hayden Kallas, Bojana Ginovska, John W. Peters, Lance C. Seefeldt, Brian Bothner, Simone Raugei

PLOS Computational Biology: published March 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008719

Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance

Vincent Brault, Bastien Mallein, Jean-François Rupprecht

PLOS Computational Biology: published March 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008726

Inferring phenomenological models of first passage processes

Catalina Rivera, David Hofmann, Ilya Nemenman

PLOS Computational Biology: published March 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008740

Graph of graphs analysis for multiplexed data with application to imaging mass cytometry

Ya-Wei Eileen Lin, Tal Shnitzer, Ronen Talmon, Franz Villarroel-Espindola, Shruti Desai, Kurt Schalper, Yuval Kluger

PLOS Computational Biology: published March 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008741

Optimal prediction with resource constraints using the information bottleneck

Vedant Sachdeva, Thierry Mora, Aleksandra M. Walczak, Stephanie E. Palmer

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008743

Vocalization with semi-occluded airways is favorable for optimizing sound production

Ingo R. Titze, Anil Palaparthi, Karin Cox, Amanda Stark, Lynn Maxfield, Brian Manternach

PLOS Computational Biology: published March 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008744

Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements

Kseniia Cheloshkina, Maria Poptsova

PLOS Computational Biology: published March 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008749

Parameters and determinants of responses to selection in antibody libraries

Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire

PLOS Computational Biology: published March 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008751

Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action

Peter Czuppon, Florence Débarre, Antonio Gonçalves, Olivier Tenaillon, Alan S. Perelson, Jérémie Guedj, François Blanquart

PLOS Computational Biology: published March 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008752

Using neural networks to mine text and predict metabolic traits for thousands of microbes

Timothy J. Hackmann, Bo Zhang

PLOS Computational Biology: published March 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008757

Optimal timing of one-shot interventions for epidemic control

Francesco Di Lauro, István Z. Kiss, Joel C. Miller

PLOS Computational Biology: published March 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008763

COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data

Song He, Xinyu Song, Xiaoxi Yang, Jijun Yu, Yuqi Wen, Lianlian Wu, Bowei Yan, Jiannan Feng, Xiaochen Bo

PLOS Computational Biology: published March 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008769

Aggregation of Aβ_40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations

Min Wu, Lyudmyla Dorosh, Gerold Schmitt-Ulms, Holger Wille, Maria Stepanova

PLOS Computational Biology: published March 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008771

Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance

Anton J. M. Larsson, Christoph Ziegenhain, Michael Hagemann-Jensen, Björn Reinius, Tina Jacob, Tim Dalessandri, Gert-Jan Hendriks, Maria Kasper, Rickard Sandberg

PLOS Computational Biology: published March 9, 2021 | https://doi.org/10.1371/journal.pcbi.1008772

Assessing criticality in pre-seizure single-neuron activity of human epileptic cortex

Annika Hagemann, Jens Wilting, Bita Samimizad, Florian Mormann, Viola Priesemann

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008773

Complementary phase responses via functional differentiation of dual negative feedback loops

Koichiro Uriu, Hajime Tei

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008774

Reconstructing feedback representations in the ventral visual pathway with a generative adversarial autoencoder

Haider Al-Tahan, Yalda Mohsenzadeh

PLOS Computational Biology: published March 24, 2021 | https://doi.org/10.1371/journal.pcbi.1008775

Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic

Quentin Richard, Samuel Alizon, Marc Choisy, Mircea T. Sofonea, Ramsès Djidjou-Demasse

PLOS Computational Biology: published March 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008776

Assessing the contribution of tumor mutational phenotypes to cancer progression risk

Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz

PLOS Computational Biology: published March 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008777

Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells

Jared Brown, Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Michael P. Schwartz, Amy Van Aartsen, John Steill, Scott Swanson, Ron Stewart, James A. Thomson, Christina Kendziorski

PLOS Computational Biology: published March 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008778

Tuned inhibition in perceptual decision-making circuits can explain seemingly suboptimal confidence behavior

Brian Maniscalco, Brian Odegaard, Piercesare Grimaldi, Seong Hah Cho, Michele A. Basso, Hakwan Lau, Megan A. K. Peters

PLOS Computational Biology: published March 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008779

Public Baseline and shared response structures support the theory of antibody repertoire functional commonality

Matthew I. J. Raybould, Claire Marks, Aleksandr Kovaltsuk, Alan P. Lewis, Jiye Shi, Charlotte M. Deane

PLOS Computational Biology: published March 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008781

SARS-CoV-2 viral dynamics in non-human primates

Antonio Gonçalves, Pauline Maisonnasse, Flora Donati, Mélanie Albert, Sylvie Behillil, Vanessa Contreras, Thibaut Naninck, Romain Marlin, Caroline Solas, Andres Pizzorno, Julien Lemaitre, Nidhal Kahlaoui, Olivier Terrier, Raphael Ho Tsong Fang, Vincent Enouf, Nathalie Dereuddre-Bosquet, Angela Brisebarre, Franck Touret, Catherine Chapon, Bruno Hoen, Bruno Lina, Manuel Rosa Calatrava, Xavier de Lamballerie, France Mentré, Roger Le Grand, Sylvie van der Werf, Jérémie Guedj

PLOS Computational Biology: published March 17, 2021 | https://doi.org/10.1371/journal.pcbi.1008785

Physiologically based pharmacokinetic/pharmacodynamic model for the prediction of morphine brain disposition and analgesia in adults and children

Laurens F. M. Verscheijden, Carlijn H. C. Litjens, Jan B. Koenderink, Ron H. J. Mathijssen, Marcel M. Verbeek, Saskia N. de Wildt, Frans G. M. Russel

PLOS Computational Biology: published March 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008786

Neural modelling of the encoding of fast frequency modulation

Alejandro Tabas, Katharina von Kriegstein

PLOS Computational Biology: published March 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008787

Detection of gene cis-regulatory element perturbations in single-cell transcriptomes

Grace Hui Ting Yeo, Oscar Juez, Qing Chen, Budhaditya Banerjee, Lendy Chu, Max W. Shen, May Sabry, Ive Logister, Richard I. Sherwood, David K. Gifford

PLOS Computational Biology: published March 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008789

Excitatory-inhibitory tone shapes decision strategies in a hierarchical neural network model of multi-attribute choice

Warren Woodrich Pettine, Kenway Louie, John D. Murray, Xiao-Jing Wang

PLOS Computational Biology: published March 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008791

CODON—Software to manual curation of prokaryotic genomes

Bruno Merlin, Jorianne Thyeska Castro Alves, Pablo Henrique Caracciolo Gomes de Sá, Mônica Silva de Oliveira, Larissa Maranhão Dias, Gislenne da Silva Moia, Victória Cardoso dos Santos, Adonney Allan de Oliveira Veras

PLOS Computational Biology: published March 31, 2021 | https://doi.org/10.1371/journal.pcbi.1008797

DCMD: Distance-based classification using mixture distributions on microbiome data

Konstantin Shestopaloff, Mei Dong, Fan Gao, Wei Xu

PLOS Computational Biology: published March 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008799

JSOM: Jointly-evolving self-organizing maps for alignment of biological datasets and identification of related clusters

Hong Seo Lim, Peng Qiu

PLOS Computational Biology: published March 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008804

Gene variants of coagulation related proteins that interact with SARS-CoV-2

David Holcomb, Aikaterini Alexaki, Nancy Hernandez, Ryan Hunt, Kyle Laurie, Jacob Kames, Nobuko Hamasaki-Katagiri, Anton A. Komar, Michael DiCuccio, Chava Kimchi-Sarfaty

PLOS Computational Biology: published March 17, 2021 | https://doi.org/10.1371/journal.pcbi.1008805

A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes’ interactions points to Neutrophil extracellular traps as mediators of thrombosis in COVID-19

Jun Ding, David Earl Hostallero, Mohamed Reda El Khili, Gregory Joseph Fonseca, Simon Milette, Nuzha Noorah, Myriam Guay-Belzile, Jonathan Spicer, Noriko Daneshtalab, Martin Sirois, Karine Tremblay, Amin Emad, Simon Rousseau

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008810

Bridging the gap: Using reservoir ecology and human serosurveys to estimate Lassa virus spillover in West Africa

Andrew J. Basinski, Elisabeth Fichet-Calvet, Anna R. Sjodin, Tanner J. Varrelman, Christopher H. Remien, Nathan C. Layman, Brian H. Bird, David J. Wolking, Corina Monagin, Bruno M. Ghersi, Peter A. Barry, Michael A. Jarvis, Paul E. Gessler, Scott L. Nuismer

PLOS Computational Biology: published March 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008811

Estimating incidence of infection from diverse data sources: Zika virus in Puerto Rico, 2016

Talia M. Quandelacy, Jessica M. Healy, Bradford Greening, Dania M. Rodriguez, Koo-Whang Chung, Matthew J. Kuehnert, Brad J. Biggerstaff, Emilio Dirlikov, Luis Mier-y-Teran-Romero, Tyler M. Sharp, Stephen Waterman, Michael A. Johansson

PLOS Computational Biology: published March 30, 2021 | https://doi.org/10.1371/journal.pcbi.1008812

The biophysical basis underlying the maintenance of early phase long-term potentiation

Moritz F. P. Becker, Christian Tetzlaff

PLOS Computational Biology: published March 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008813

Predicting recognition between T cell receptors and epitopes with TCRGP

Emmi Jokinen, Jani Huuhtanen, Satu Mustjoki, Markus Heinonen, Harri Lähdesmäki

PLOS Computational Biology: published March 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008814

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper

Phillip Andrew Richmond, Alice Mary Kaye, Godfrain Jacques Kounkou, Tamar Vered Av-Shalom, Wyeth W. Wasserman

PLOS Computational Biology: published March 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008815

Predicting microbial growth dynamics in response to nutrient availability

Olga A. Nev, Richard J. Lindsay, Alys Jepson, Lisa Butt, Robert E. Beardmore, Ivana Gudelj

PLOS Computational Biology: published March 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008817

Prediction of amphipathic helix—membrane interactions with Rosetta

Alican Gulsevin, Jens Meiler

PLOS Computational Biology: published March 17, 2021 | https://doi.org/10.1371/journal.pcbi.1008818

Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer

Héctor Climente-González, Christine Lonjou, Fabienne Lesueur, GENESIS study group, Dominique Stoppa-Lyonnet, Nadine Andrieu, Chloé-Agathe Azencott

PLOS Computational Biology: published March 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008819

Discovery of novel dual adenosine A₁/A_2A receptor antagonists using deep learning, pharmacophore modeling and molecular docking

Mukuo Wang, Shujing Hou, Yu Wei, Dongmei Li, Jianping Lin

PLOS Computational Biology: published March 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008821

The evolutionary origin of the universal distribution of mutation fitness effect

Ayuna Barlukova, Igor M. Rouzine

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008822

Addition of new neurons and the emergence of a local neural circuit for precise timing

Yevhen Tupikov, Dezhe Z. Jin

PLOS Computational Biology: published March 17, 2021 | https://doi.org/10.1371/journal.pcbi.1008824

A computational study of co-inhibitory immune complex assembly at the interface between T cells and antigen presenting cells

Zhaoqian Su, Kalyani Dhusia, Yinghao Wu

PLOS Computational Biology: published March 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008825

Analysis of spiking synchrony in visual cortex reveals distinct types of top-down modulation signals for spatial and object-based attention

Nobuhiko Wagatsuma, Brian Hu, Rüdiger von der Heydt, Ernst Niebur

PLOS Computational Biology: published March 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008829

Accuracy in the prediction of disease epidemics when ensembling simple but highly correlated models

Denis A. Shah, Erick D. De Wolf, Pierce A. Paul, Laurence V. Madden

PLOS Computational Biology: published March 15, 2021 | https://doi.org/10.1371/journal.pcbi.1008831

Collective predator evasion: Putting the criticality hypothesis to the test

Pascal P. Klamser, Pawel Romanczuk

PLOS Computational Biology: published March 15, 2021 | https://doi.org/10.1371/journal.pcbi.1008832

PDKit: A data science toolkit for the digital assessment of Parkinson’s Disease

Cosmin Stamate, Joan Saez Pons, David Weston, George Roussos

PLOS Computational Biology: published March 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008833

A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C

Ji Hyun Bak, Min Hyeok Kim, Lei Liu, Changbong Hyeon

PLOS Computational Biology: published March 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008834

Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model

Gregory L. Watson, Di Xiong, Lu Zhang, Joseph A. Zoller, John Shamshoian, Phillip Sundin, Teresa Bufford, Anne W. Rimoin, Marc A. Suchard, Christina M. Ramirez

PLOS Computational Biology: published March 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008837

Elements and evolutionary determinants of genomic divergence between paired primary and metastatic tumors

Ruping Sun, Athanasios N. Nikolakopoulos

PLOS Computational Biology: published March 17, 2021 | https://doi.org/10.1371/journal.pcbi.1008838

Viscoelastic properties of wheat gluten in a molecular dynamics study

Łukasz Mioduszewski, Marek Cieplak

PLOS Computational Biology: published March 24, 2021 | https://doi.org/10.1371/journal.pcbi.1008840

Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling

Yekaterina S. Pavlova, David Paez-Espino, Andrew Yu. Morozov, Ilya S. Belalov

PLOS Computational Biology: published March 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008841

Full-length ribosome density prediction by a multi-input and multi-output model

Tingzhong Tian, Shuya Li, Peng Lang, Dan Zhao, Jianyang Zeng

PLOS Computational Biology: published March 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008842

An elasticity-curvature illusion decouples cutaneous and proprioceptive cues in active exploration of soft objects

Chang Xu, Yuxiang Wang, Gregory J. Gerling

PLOS Computational Biology: published March 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008848

Novel anti-malarial drug strategies to prevent artemisinin partner drug resistance: A model-based analysis

Amber Kunkel, Michael White, Patrice Piola

PLOS Computational Biology: published March 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008850

Personalized computational model quantifies heterogeneity in postprandial responses to oral glucose challenge

Balázs Erdős, Bart van Sloun, Michiel E. Adriaens, Shauna D. O’Donovan, Dominique Langin, Arne Astrup, Ellen E. Blaak, Ilja C. W. Arts, Natal A. W. van Riel

PLOS Computational Biology: published March 31, 2021 | https://doi.org/10.1371/journal.pcbi.1008852

How does Sec63 affect the conformation of Sec61 in yeast?

Pratiti Bhadra, Lalitha Yadhanapudi, Karin Römisch, Volkhard Helms

PLOS Computational Biology: published March 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008855

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Correction: Up-down biphasic volume response of human red blood cells to PIEZO1 activation during capillary transits

The PLOS Computational Biology Staff

PLOS Computational Biology: published March 31, 2021 | https://doi.org/10.1371/journal.pcbi.1008862

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