Ten simple rules for effectively assessing lab environments

Kristen M. Naegle, Jeffrey J. Saucerman, Julie Leonard-Duke, Michael Rariden, Yonathan Tamrat Aberra

PLOS Computational Biology: published June 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013223

F-BIAS: Towards a distributed national core facility for bioimage analysis ^†

Mélodie Ambroset, Anselmet Marie, Benedetti Clément, Meslin Arthur, Maillot Aurélien, Rouvière Christian, Maucort Guillaume, Breuilly Marine, Albert Marvin, Letort Gaëlle, Trullo Antonio, Bäcker Volker, Mutterer Jérôme, Cordelières Fabrice, Pécot Thierry, Phan Minh-Son, Rigaud Stéphane, Feyeux Magali, Paul-Gilloteaux Perrine, Macé Anne-Sophie, Tinevez Jean-Yves

PLOS Computational Biology: published June 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013058

Indirect punishment can outperform direct punishment in promoting cooperation in structured populations

Yujia Wen, Zhixue He, Chen Shen, Jun Tanimoto

PLOS Computational Biology: published June 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013068

Regulation of replication timing in Saccharomyces cerevisiae

Rosie Berners-Lee, Eamonn Gilmore, Francisco Berkemeier, Michael A. Boemo

PLOS Computational Biology: published June 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013066

Features influencing the health and economic impact of preventing COVID-19 in immunocompromised individuals

Siyu Chen, Sudhir Venkatesan, Sofie Arnetorp, Klas Bergenheim, Sabada Dube, Wilhelmine Meeraus, Cátia Ferreira, Sylvia Taylor, Lisa J. White

PLOS Computational Biology: published June 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013072

Tumor microenvironment governs the prognostic landscape of immunotherapy for head and neck squamous cell carcinoma: A computational model-guided analysis

Priyan Bhattacharya, Alban Linnenbach, Andrew P. South, Ubaldo Martinez-Outschoorn, Joseph M. Curry, Jennifer M. Johnson, Larry A. Harshyne, Mỹ G. Mahoney, Adam J. Luginbuhl, Rajanikanth Vadigepalli

PLOS Computational Biology: published June 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013127

The impact of model assumptions in interpreting cell kinetic studies

Ada Wing Chi Yan, Ildar Sadreev, Jonas Mackerodt, Yan Zhang, Derek Macallan, Robert Busch, Becca Asquith

PLOS Computational Biology: published June 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012704

Spatiotemporal dynamics of tumor–CAR T-cell interaction following local administration in solid cancers

Katherine Owens, Aminur Rahman, Ivana Bozic

PLOS Computational Biology: published June 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013117

DeepDeconUQ estimates malignant cell fraction prediction intervals in bulk RNA-seq tissue

Jiawei Huang, Yuxuan Du, Kevin R. Kelly, Jinchi Lv, Yingying Fan, Jiang F. Zhong, Fengzhu Sun

PLOS Computational Biology: published June 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013133

A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell

Caroline I. Larkin, Matthew D. Dunn, Jason E. Shoemaker, William B. Klimstra, James R. Faeder

PLOS Computational Biology: published June 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013082

GABAergic neurons can facilitate the propagation of cortical spreading depolarization: experiments in mouse neocortical slices and a novel neural field computational model

Emre Baspinar, Martina Simonti, Hadi Srour, Mathieu Desroches, Daniele Avitabile, Massimo Mantegazza

PLOS Computational Biology: published June 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013099

Adaptation across the 2D population code explains the spatially distributive nature of motor learning

Jana Masselink, Markus Lappe

PLOS Computational Biology: published June 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013041

Isolating single cycles of neural oscillations in population spiking

Ehsan Sabri, Renata Batista-Brito

PLOS Computational Biology: published June 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013084

Designing diverse and high-performance proteins with a large language model in the loop

Carlos A. Gomez-Uribe, Japheth Gado, Meiirbek Islamov

PLOS Computational Biology: published June 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013119

A mathematical model suggests collectivity and inconstancy enhance the efficiency of neuronal migration in the adult brain

Daiki Wakita, Yuriko Sobu, Naoko Kaneko, Takeshi Kano

PLOS Computational Biology: published June 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013105

Nonequilibrium brain dynamics elicited as the origin of perturbative complexity

Wiep Stikvoort, Eider Pérez-Ordoyo, Iván Mindlin, Anira Escrichs, Jacobo D. Sitt, Morten L. Kringelbach, Gustavo Deco, Yonatan Sanz Perl

PLOS Computational Biology: published June 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013150

Fusing multisensory signals across channels and time

Swathi Anil, Dan F. M. Goodman, Marcus Ghosh

PLOS Computational Biology: published June 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013125

Resource acquisition in diel cycles and the cost of growing quickly

Kevin J. Flynn, Andrew Yu. Morozov

PLOS Computational Biology: published June 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013132

History-dependent switch-like differentiation of keratinocytes in response to skin barrier damage

Elisa Domíguez-Hüttinger, Eliezer Flores-Garza, José Luis Caldú-Primo, Harley Day, Abihail Roque Ramírez, Reiko J. Tanaka

PLOS Computational Biology: published June 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013162

Using virtual patient cohorts to uncover immune response differences in cancer and immunosuppressed COVID-19 patients

Sonia T. Gazeau, Xiaoyan Deng, Elsa Brunet-Ratnasingham, Daniel E. Kaufmann, Catherine Larochelle, Penelope A. Morel, Jane M. Heffernan, Courtney L. Davis, Amber M. Smith, Adrianne L. Jenner, Morgan Craig

PLOS Computational Biology: published June 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013170

Variance in C. elegans gut bacterial load suggests complex host-microbe dynamics

Satya Spandana Boddu, K. Michael Martini, Ilya Nemenman, Nic M. Vega

PLOS Computational Biology: published June 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013110

Computational modeling of ketamine-induced changes in gamma-band oscillations: The contribution of parvalbumin and somatostatin interneurons

Jessie Rademacher, Tineke Grent-'t-Jong, Davide Rivolta, Andreas Sauer, Bertram Scheller, Guillermo Gonzalez-Burgos, Christoph Metzner, Peter J. Uhlhaas

PLOS Computational Biology: published June 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013118

A linear perception-action mapping accounts for response range-dependent biases in heading estimation from optic flow

Qi Sun, Ling-Hao Xu, Alan A. Stocker

PLOS Computational Biology: published June 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013147

Computing generalized cophenetic distances under all L_p norms: A near-linear time algorithmic framework

Paweł Górecki, Alexey Markin, Sriram Vijendran, Oliver Eulenstein

PLOS Computational Biology: published June 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013069

Stochastic gene expression in proliferating cells: Differing noise intensity in single-cell and population perspectives

Zhanhao Zhang, Iryna Zabaikina, Cesar Nieto, Zahra Vahdat, Pavol Bokes, Abhyudai Singh

PLOS Computational Biology: published June 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013014

Energy optimization induces predictive-coding properties in a multi-compartment spiking neural network model

Mingfang Zhang, Raluca Chitic, Sander M. Bohté

PLOS Computational Biology: published June 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013112

Sensorimotor integration enhances temperature stimulus processing

Lindsay S. Anderson, Jamie D. Costabile, Sina Schwinn, Delia Calderon, Martin Haesemeyer

PLOS Computational Biology: published June 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013134

ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data

Hannah Waddel, Katia Koelle, Max S. Y. Lau

PLOS Computational Biology: published June 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012657

Predicting potential recovery of the endangered bromeliad Tillandsia utriculata: An agent-based modeling approach

Alexandra M. Campbell, Anna C. Kula, Rachel S. Jabaily, Brad Oberle, Brian Sidoti, Alex Capaldi, Erin N. Bodine

PLOS Computational Biology: published June 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013157

Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways

William R. Cannon, Ethan King, Katherine A. Huening, Justin A. North

PLOS Computational Biology: published June 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013015

Balanced state of networks of winner-take-all units

Rich Pang

PLOS Computational Biology: published June 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013081

Network architecture of transcriptomic stress responses in zebrafish embryos

Kaylee Beine, Lauric Feugere, Alexander P. Turner, Katharina C. Wollenberg Valero

PLOS Computational Biology: published June 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013164

Semantic influences on object detection: Drift diffusion modeling provides insights regarding mechanism

Jingming Xue, Robert C. Wilson, Mary A. Peterson

PLOS Computational Biology: published June 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012269

Electrodiffusion dynamics in the cardiomyocyte dyad at nano-scale resolution using the Poisson-Nernst-Planck (PNP) equations

Karoline Horgmo Jæ ger, Aslak Tveito

PLOS Computational Biology: published June 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013149

Uncertainty-aware traction force microscopy

Adithan Kandasamy, Yi-Ting Yeh, Ricardo Serrano, Mark Mercola, Juan C. del Alamo

PLOS Computational Biology: published June 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013079

Biomarkers of mRNA vaccine efficacy derived from mechanistic modeling of tumor-immune interactions

Chrysovalantis Voutouri, Lance L. Munn, Triantafyllos Stylianopoulos, Rakesh K. Jain

PLOS Computational Biology: published June 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013163

Sparse deconvolution of cell type medleys in spatial transcriptomics

Nuray Sogunmez Erdogan, Deniz Eroglu

PLOS Computational Biology: published June 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013169

From experimental clues to theoretical modeling: Evolution associated with the membrane-takeover at an early stage of life

Wentao Ma, Chunwu Yu

PLOS Computational Biology: published June 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012763

Unveiling the role of local metabolic constraints on the structure and activity of spiking neural networks

Ismael Jaras, Marcos E. Orchard, Pedro E. Maldonado, Rodrigo C. Vergara

PLOS Computational Biology: published June 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013148

iPAR: A framework for modelling and inferring information about disease spread when the populations at risk are unknown

Stephen Catterall, Thibaud Porphyre, Glenn Marion

PLOS Computational Biology: published June 16, 2025 | https://doi.org/10.1371/journal.pcbi.1012622

RIDDEN: Data-driven inference of receptor activity from transcriptomic data

Szilvia Barsi, Eszter Varga, Daniel Dimitrov, Julio Saez-Rodriguez, László Hunyady, Bence Szalai

PLOS Computational Biology: published June 16, 2025 | https://doi.org/10.1371/journal.pcbi.1013188

Uncovering the impact of randomness in HIV hotspot formation: A mathematical modeling study

Nao Yamamoto, Daniel T. Citron, Samuel M. Mwalili, Duncan K. Gathungu, Diego F. Cuadros, Anna Bershteyn

PLOS Computational Biology: published June 16, 2025 | https://doi.org/10.1371/journal.pcbi.1013178

Parameterization of intraoperative human microelectrode recordings: Linking action potential morphology to brain anatomy

Matthew R. Baker, Bryan T. Klassen, Michael A. Jensen, Gabriela Ojeda Valencia, Hossein Heydari, Nuri F. Ince, Klaus-Robert Müller, Kai J. Miller

PLOS Computational Biology: published June 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013184

Cholinergic modulation of neural networks supports sequential and complementary roles for NREM and REM states in memory consolidation

Michael Satchell, Edith Butel-Fry, Zahraa Noureddine, Alexis Simmons, Nicolette Ognjanovski, Sara J. Aton, Michal R. Zochowski

PLOS Computational Biology: published June 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013097

Proteostasis signatures in human diseases

Christine M. Lim, Michele Vendruscolo

PLOS Computational Biology: published June 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013155

The role of learned song in the evolution and speciation of Eastern and Spotted towhees

Ximena León Du’Mottuchi, Nicole Creanza

PLOS Computational Biology: published June 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013135

Predicting antibody kinetics and duration of protection against SARS-CoV-2 following vaccination from sparse serological data

Julia Deichmann, Noam Barda, Michal Canetti, Yovel Peretz, Yael Weiss-Ottolenghi, Yaniv Lustig, Gili Regev-Yochay, Marc Lipsitch

PLOS Computational Biology: published June 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013192

Embodied decisions as active inference

Matteo Priorelli, Ivilin Peev Stoianov, Giovanni Pezzulo

PLOS Computational Biology: published June 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013180

Predicting neuronal firing from calcium imaging using a control theoretic approach

Nicholas A. Rondoni, Fan Lu, Daniel B. Turner-Evans, Marcella Gomez

PLOS Computational Biology: published June 19, 2025 | https://doi.org/10.1371/journal.pcbi.1012603

MVHGCN: Predicting circRNA-disease associations with multi-view heterogeneous graph convolutional neural networks

Yan Miao, Xuan Tang, Chunyu Wang, Zhenyuan Sun, Guohua Wang, Shan Huang

PLOS Computational Biology: published June 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013225

Computations that sustain neural feature selectivity across processing stages

Ryan J. Rowekamp, Tatyana O. Sharpee

PLOS Computational Biology: published June 20, 2025 | https://doi.org/10.1371/journal.pcbi.1013075

Lateralised memory networks may explain the use of higher-order visual features in navigating insects

Giulio Filippi, James Knight, Andrew Philippides, Paul Graham

PLOS Computational Biology: published June 23, 2025 | https://doi.org/10.1371/journal.pcbi.1012670

Impact of symmetry in local learning rules on predictive neural representations and generalization in spatial navigation

Janis Keck, Caswell Barry, Christian F. Doeller, Jürgen Jost

PLOS Computational Biology: published June 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013056

MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction

Xuexin Yu, Jing Hu, Yuhao Tan, Mingyao Pan, Hongyi Zhang, Bo Li

PLOS Computational Biology: published June 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013090

Synthetic method of analogues for emerging infectious disease forecasting

Alexander C. Murph, G. Casey Gibson, Elizabeth B. Amona, Lauren J. Beesley, Lauren A. Castro, Sara Y. Del Valle, Dave Osthus

PLOS Computational Biology: published June 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013203

Identifiability of phenotypic adaptation from low-cell-count experiments and a stochastic model

Alexander P. Browning, Rebecca M. Crossley, Chiara Villa, Philip K. Maini, Adrianne L. Jenner, Tyler Cassidy, Sara Hamis

PLOS Computational Biology: published June 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013202

A mammalian inferior colliculus model for sound source separation using interaural time differences

Christian Leibold, Sebastian Groß

PLOS Computational Biology: published June 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013243

Evolutionary divergence of induced versus constitutive antiviral gene expression levels between primates and rodents

Lilach Schneor, Dafna Tussia-Cohen, Evgeny Fraimovitch, Sivan Friedman, Tzachi Hagai

PLOS Computational Biology: published June 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013165

The roles of feedback loops in the Caenorhabditis elegans rhythmic forward locomotion

Peng Zhao, Boyang Wang, Yi Rong, Ye Yuan, Jian Liu, Hong Huo, Zhuyong Liu, Zhaoyu Li, Tao Fang

PLOS Computational Biology: published June 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013171

Optimal sampling frequency and site selection for wastewater and environmental surveillance of infectious pathogens: A value of information assessment

Isabella Impalli, Erik Bergland, Chadi M. Saad-Roy, Bryan T. Grenfell, Simon A. Levin, D. G. Joakim Larsson, Ramanan Laxminarayan

PLOS Computational Biology: published June 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013190

Studying gastrulation by invagination: The bending of a cell sheet by mechanical cell properties using 3D deformable cell based simulations

Roland M. Dries, Kim Y. Renders, Jaap A. Kaandorp

PLOS Computational Biology: published June 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013151

On the usage of artificial intelligence in leprosy care: A systematic literature review

Hilson Gomes Vilar de Andrade, Elisson da Silva Rocha, Kayo H. de Carvalho Monteiro, Cleber Matos de Morais, Danielle Christine Moura dos Santos, Dimas Cassimiro Nascimento, Raphael A. Dourado, Theo Lynn, Patricia Takako Endo

PLOS Computational Biology: published June 26, 2025 | https://doi.org/10.1371/journal.pcbi.1012550

AI-first structural identification of pathogenic protein target interfaces

Mihkel Saluri, Michael Landreh, Patrick Bryant

PLOS Computational Biology: published June 26, 2025 | https://doi.org/10.1371/journal.pcbi.1013168

Allosteric modulation of proton binding confers Cl^- activation and glutamate selectivity to vesicular glutamate transporters

Bart Borghans, Daniel Kortzak, Piersilvio Longo, Bettina Kolen, Jan-Philipp Machtens, Christoph Fahlke

PLOS Computational Biology: published June 26, 2025 | https://doi.org/10.1371/journal.pcbi.1013214

Robust pleiotropy-decomposed polygenic scores identify distinct contributions to elevated coronary artery disease polygenic risk

Jiaqi Hu, Yixuan Ye, Chi Zhang, Yunfeng Ruan, Pradeep Natarajan, Hongyu Zhao

PLOS Computational Biology: published June 26, 2025 | https://doi.org/10.1371/journal.pcbi.1013191

Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology

Yuxi Long, Bruce R. Donald

PLOS Computational Biology: published June 27, 2025 | https://doi.org/10.1371/journal.pcbi.1013216

Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold

Samuel Eriksson Lidbrink, Rebecca J. Howard, Nandan Haloi, Erik Lindahl

PLOS Computational Biology: published June 27, 2025 | https://doi.org/10.1371/journal.pcbi.1013187

Investigate channel rectifications and neural dynamics by an electrodiffusive Gauss-Nernst-Planck approach

Zichao Liu, Yinyun Li

PLOS Computational Biology: published June 30, 2025 | https://doi.org/10.1371/journal.pcbi.1012883

Feedback parameters for a closed-loop multiple-input multiple-output model of the upper limb

Ian Syndergaard, Daniel B. Free, Dario Farina, Steven K. Charles

PLOS Computational Biology: published June 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013183

H- and m-channel overexpression promotes seizure-like events by impairing the ability of inhibitory neurons to process correlated inputs

Scott Rich, Taufik A. Valiante, Jérémie Lefebvre

PLOS Computational Biology: published June 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013199

Correction: Including population and environmental dynamic heterogeneities in continuum models of collective behaviour with applications to locust foraging and group structure

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PLOS Computational Biology: published June 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013167

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Correction: cytoNet: Spatiotemporal network analysis of cell communities

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PLOS Computational Biology: published June 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013176

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Correction: Catalyst: Fast and flexible modeling of reaction networks

Torkel E. Loman, Yingbo Ma, Vasily Ilin, Shashi Gowda, Niklas Korsbo, Nikhil Yewale, Chris Rackauckas, Samuel A. Isaacson

PLOS Computational Biology: published June 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013175

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Correction: A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway

Gabriella J. Gerlach, Rachel Carrock, Robyn Stix, Elliott J. Stollar, K. Aurelia Ball

PLOS Computational Biology: published June 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013201

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Multimodal CustOmics: A unified and interpretable multi-task deep learning framework for multimodal integrative data analysis in oncology

Hakim Benkirane, Maria Vakalopoulou, David Planchard, Julien Adam, Ken Olaussen, Stefan Michiels, Paul-Henry Cournède

PLOS Computational Biology: published June 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013012

OrgaCCC: Orthogonal graph autoencoders for constructing cell-cell communication networks on spatial transcriptomics data

Xixuan Feng, Shuqin Zhang, Limin Li

PLOS Computational Biology: published June 27, 2025 | https://doi.org/10.1371/journal.pcbi.1013212

scRepertoire 2: Enhanced and efficient toolkit for single-cell immune profiling

Qile Yang, Ksenia R. Safina, Kieu Diem Quynh Nguyen, Zewen Kelvin Tuong, Nicholas Borcherding

PLOS Computational Biology: published June 27, 2025 | https://doi.org/10.1371/journal.pcbi.1012760