Current Issue | PLOS Computational Biology

Microorganisms such as E. coli and algae typically adjust their motility in response to external stimuli. While their behavioral response patterns are readily measurable, the underlying internal reaction dynamics are complex and more challenging to measure directly. Here, we propose a neural network approach that uncovers the governing rules from observable stimulus-response data, enabling the revelation of potential internal signaling structures. Lei et al. 2025

Image Credit: Shicong Lei and Min Tang

Education Articles

Ten simple rules for leading a many-author non-empirical paper

Tracey L. Weissgerber, Natascha Drude, Rima-Maria Rahal, Friederike E. Kohrs

PLOS Computational Biology: published August 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013283

Ten simple rules for being a co-author on a many-author non-empirical paper

Friederike E. Kohrs, Natascha Drude, Anita Bandrowski, Tracey L. Weissgerber

PLOS Computational Biology: published August 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013317

Why and how to set up a Bioinformatics Learning Lab (BILL)

Anna-Sophie Fiston-Lavier, Emira Cherif, Marie-ka Tilak, Arnaud Soulier, Catherine Breton, Anthony Boureux, Remy Costa, Xavier Miahle, Clothilde Chenal, Floris Schatt1, Camelia Sennaoui, Jean-Christophe Avarre, Anne-Sophie Gosselin-Grenet

PLOS Computational Biology: published August 28, 2025 | https://doi.org/10.1371/journal.pcbi.1013236

Perspective

Ten simple rules for research with humans

Madeline K. Coates, Tudor V. Sava, Sarah M. Tashjian

PLOS Computational Biology: published August 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013362

Research Articles

Mathematical modeling suggests 14-3-3 proteins modulate RAF paradoxical activation

Gaurav Mendiratta, Kodye Abbott, Yao-Cheng Li, Jingting Yu, Peter Carlip, Melinda Tong, Jianfeng Huang, Maxim N. Shokhirev, Thomas McFall, Geoffrey M. Wahl, Edward C. Stites

PLOS Computational Biology: published August 1, 2025 | https://doi.org/10.1371/journal.pcbi.1013297

Continual familiarity decoding from recurrent connections in spiking networks

Viktoria Zemliak, Gordon Pipa, Pascal Nieters

PLOS Computational Biology: published August 1, 2025 | https://doi.org/10.1371/journal.pcbi.1013304

SuperEdgeGO: Edge-supervised graph representation learning for enhanced protein function prediction

Shugang Zhang, Yuntong Li, Wenjian Ma, Qing Cai, Jing Qin, Xiangpeng Bi, Huasen Jiang, Xiaoyu Huang, Zhiqiang Wei

PLOS Computational Biology: published August 1, 2025 | https://doi.org/10.1371/journal.pcbi.1013343

Integrating AlphaFold2 models and clinical data to improve the assessment of Short Linear Motifs (SLiMs) and their variants’ pathogenicity

Franco Gino Brunello, Lorenzo Erra, Juan Nicola, Marcelo Adrián Martí

PLOS Computational Biology: published August 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012829

Nonparametric serial interval estimation with uniform mixtures

Oswaldo Gressani, Niel Hens

PLOS Computational Biology: published August 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013338

Emergence of cooperation promoted by higher-order strategy updates

Dini Wang, Peng Yi, Yiguang Hong, Jie Chen, Gang Yan

PLOS Computational Biology: published August 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012891

Socioeconomic determinants of protective behaviors and contact patterns in the post-COVID-19 pandemic era: A cross-sectional study in Italy

Michele Tizzani, Laetitia Gauvin

PLOS Computational Biology: published August 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013262

Mutations in tumor signaling, metastases, and synthetic lethality establish distinct patterns

Bengi Ruken Yavuz, Ugur Sahin, Hyunbum Jang, Ruth Nussinov, Nurcan Tuncbag

PLOS Computational Biology: published August 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013351

Identification of the governing equation of stimulus-response data for run-and-tumble dynamics

Shicong Lei, Yu’an Li, Zheng Ma, Hepeng Zhang, Min Tang

PLOS Computational Biology: published August 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013287

Modelling the potential use of pre-exposure prophylaxis to reduce nosocomial SARS-CoV-2 transmission

Lauren Stewart, Stephanie Evans, Teresa Brevini, Fotios Sampaziotis, Christopher J. R. Illingworth

PLOS Computational Biology: published August 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013361

Excitatory/inhibitory ratio disruption modulates neural synchrony and flow directions in a cortical microcircuit

Nobuhiko Wagatsuma, Sou Nobukawa, Tomoki Kurikawa

PLOS Computational Biology: published August 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013306

Multi-context modeling of driver pathways reveals common and specific mechanisms across 23 cancer types

Wenjia Zhou, Junhua Zhang

PLOS Computational Biology: published August 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013349

Machine learning on multiple epigenetic features reveals H3K27Ac as a driver of gene expression prediction across patients with glioblastoma

Yusuke Suita, Hardy Bright Jr, Yuan Pu, Merih Deniz Toruner, Jordan Idehen, Nikos Tapinos, Ritambhara Singh

PLOS Computational Biology: published August 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012272

Optimal control of multiple myeloma assuming drug resistance and off-target effects

James G. Lefevre, Brodie A. J. Lawson, Pamela M. Burrage, Diane M. Donovan, Kevin Burrage

PLOS Computational Biology: published August 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012225

Barking up the right tree: Immune checkpoint signatures of human and dog cancers

Mikolaj Kocikowski, Marcos Yébenes Mayordomo, Javier Alfaro, Maciej Parys

PLOS Computational Biology: published August 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013270

Visuoinertial and visual feedback in online steering control

Jo-Yu Liu, James R. H. Cooke, Luc J. P. Selen, W. Pieter Medendorp

PLOS Computational Biology: published August 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012659

A hierarchical multiscale model of forward and backward alpha-band traveling waves in the visual system

Jakob C. B. Schwenk, Andrea Alamia

PLOS Computational Biology: published August 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013294

Comparing the effectiveness of ring and block-vaccination strategies on networks

Matteo Scianna, Riccardo Gallotti, Michele Tizzoni, Oriol Artime, Lucila G. Alvarez-Zuzek

PLOS Computational Biology: published August 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013274

Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics

Nandan Haloi, Rebecca J. Howard, Erik Lindahl

PLOS Computational Biology: published August 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013367

A model of anaerobic tissue perfusion during trauma—Lactate trajectory curvature can determine recovery

Austin Baird, Steven A. White, Erika K. Bisgaard, Rachel K. Wentz, Edward M. Sims, David Hananel

PLOS Computational Biology: published August 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012820

Emergence of a complex network structure on a Spatial Prisoner’s Dilemma

Tomoko Sakiyama, Akihiro Takahara

PLOS Computational Biology: published August 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013329

Near-random connections support top-down feature-based attentional modulations in early sensory cortex

Sunyoung Park, John T. Serences

PLOS Computational Biology: published August 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013396

An empirical model of aminoacylation kinetics for E. coli class I and II aminoacyl tRNA synthetases

Eric C. Dykeman

PLOS Computational Biology: published August 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013353

The role of feedforward and feedback inhibition in modulating theta-gamma cross-frequency interactions in neural circuits

Dimitrios Chalkiadakis, Jaime Sánchez-Claros, Víctor J. López-Madrona, Santiago Canals, Claudio R. Mirasso

PLOS Computational Biology: published August 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013363

Risk factors for fluoroquinolone- and macrolide-resistance among swine Campylobacter coli using multi-layered chain graphs

Christine A. Wang, William J. Love, Manuel Jara, Arnoud H. M. van Vliet, Siddhartha Thakur, Cristina Lanzas

PLOS Computational Biology: published August 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012797

Does Zipf’s law of abbreviation shape birdsong?

R. Tucker Gilman, CD Durrant, Lucy Malpas, Rebecca N. Lewis

PLOS Computational Biology: published August 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013228

Mechanistic modeling suggests stroma-targeting antibody-drug conjugates as an alternative to cancer-targeting in cases of heterogeneous target exspression

N. Ezgi Wood, Anıl Cengiz, Ming Gao, Alexander V. Ratushny, Ronny Straube

PLOS Computational Biology: published August 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012839

Constructing the first comorbidity networks in companion dogs in the Dog Aging Project

Antoinette Fang, Lakshin Kumar, Kate E. Creevy, Daniel E.L. Promislow, Jing Ma, the Dog Aging Project Consortium

PLOS Computational Biology: published August 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012728

Temporal evolution of hemodynamics in murine arteriovenous fistula: A micro-CT based CFD study

Lianxia Li, Unimunkh Uriyanghai, Christine Wai, Hong Yuan, Eric W. Livingston, Edward M. Bahnson, Vinay Sudarsanam, Samuel Haddad, Prabir Roy-Chaudhury, Boyce E. Griffith, Gang Xi

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1012985

Stochastic activity in low-rank recurrent neural networks

Francesca Mastrogiuseppe, Joana Carmona, Christian K. Machens

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013371

Mechanistic computational modeling of sFLT1 secretion dynamics

Amy Gill, Karina Kinghorn, Victoria L. Bautch, Feilim Mac Gabhann

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013324

Heterogeneous synaptic homeostasis: A novel mechanism boosting information propagation in the cortex

Farhad Razi, Belén Sancristóbal

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013398

Modelling the effects of adult emergence on the surveillance and age distribution of medically important mosquitoes

Isaac J. Stopard, Ellie Sherrard-Smith, Hilary Ranson, Kobié Hyacinthe Toe, Jackie Cook, Joseph Biggs, Ben Lambert, Thomas S. Churcher

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013035

Predicting organoid morphology through a phase field model: Insights into cell division and lumenal pressure

Sakurako Tanida, Kana Fuji, Linjie Lu, Tristan Guyomar, Byung Ho Lee, Alf Honigmann, Anne Grapin-Botton, Daniel Riveline, Tetsuya Hiraiwa, Makiko Nonomura, Masaki Sano

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1012090

Tactile stimulations reduce or promote the segregation of auditory streams: psychophysics and modeling

Farzaneh Darki, James Rankin, Piotr Słowiński

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1012701

Connecting mass-action models and network models for infectious diseases

Thien-Minh Le, Jukka-Pekka Onnela

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013373

A feedforward mechanism for human-like contour integration

Fenil R. Doshi, Talia Konkle, George A. Alvarez

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013391

3D structure and stability prediction of DNA with multi-way junctions in ionic solutions

Xunxun Wang, Ya-Zhou Shi

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013346

The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon

Jędrzej Kubica, Sevastianos Korsak, Krzysztof H. Banecki, Dvir Schirman, Anurupa Devi Yadavalli, Ariana Brenner Clerkin, David Kouřil, Michał Kadlof, Ben Busby, Dariusz Plewczynski

PLOS Computational Biology: published August 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013358

Assessing variant effect predictors and disease mechanisms in intrinsically disordered proteins

Mohamed Fawzy, Joseph A. Marsh

PLOS Computational Biology: published August 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013400

Human-like monocular depth biases in deep neural networks

Yuki Kubota, Taiki Fukiage

PLOS Computational Biology: published August 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013020

Leaky or polarised immunity: Non-Markovian modelling highlights the impact of immune memory assumptions

Bastien Reyné, Tsukushi Kamiya, Ramsès Djidjou-Demasse, Samuel Alizon, Mircea T. Sofonea

PLOS Computational Biology: published August 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013399

Modelling the effectiveness of Integrated Pest Management strategies for the control of Septoria tritici blotch

Elliot M.R. Vincent, Edward M. Hill, Stephen Parnell

PLOS Computational Biology: published August 20, 2025 | https://doi.org/10.1371/journal.pcbi.1013352

Decoding decision-making behavior from sparse neural spiking activity

Yuhang Zhang, Tao Sun, Boyang Zang, Sen Wan

PLOS Computational Biology: published August 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013335

Improving cell-type composition inference in spatial transcriptomics with SpaDAMA

Lin Huang, Xiaofei Liu, Fangfang Zhu, Wenwen Min

PLOS Computational Biology: published August 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013354

CytoSpatio: Learning cell type spatial relationships using multirange, multitype point process models

Haoran Chen, Yangyuan Zhang, Robert F. Murphy

PLOS Computational Biology: published August 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013409

NextVir: Enabling classification of tumor-causing viruses with genomic foundation models

John Robertson, Shorya Consul, Haris Vikalo

PLOS Computational Biology: published August 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013360

In silico modeling of directed differentiation of induced pluripotent stem cells to definitive endoderm

Amirmahdi Mostofinejad, David A. Romero, Dana Brinson, Thomas K. Waddell, Golnaz Karoubi, Cristina H. Amon

PLOS Computational Biology: published August 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013407

A computational workflow for assessing drug effects on temporal signaling dynamics reveals robustness in stimulus-specific NFκB signaling

Emily R. Bozich, Xiaolu Guo, Jennifer L. Wilson, Alexander Hoffmann

PLOS Computational Biology: published August 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013344

Stochastic model of IP₃-induced Ca²⁺ spiking of HEK293 cells

Caterina Azzoni, Rene Jüttner, Anje Sporbert, Michael Gotthardt, H. Llewelyn Roderick, Martin Falcke

PLOS Computational Biology: published August 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013322

Effects of recombination on multi-drug resistance evolution in Plasmodium falciparum malaria

Kien Trung Tran, Tran Dang Nguyen, Daniel B. Weissman, Eric Zhewen Li, Sachel Mok, Jennifer L. Small-Saunders, Teun Bousema, Robert J. Zupko, Thu Nguyen-Anh Tran, Maciej F. Boni

PLOS Computational Biology: published August 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013401

Age polyethism can emerge from social learning: A game-theoretic investigation

Moein Khajehnejad, Julian García, Bernd Meyer

PLOS Computational Biology: published August 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013415

Intra-vector infection dynamics challenge how to model the extrinsic incubation period for major arboviruses: dengue, Zika, and chikungunya

Léa Loisel, Vincent Raquin, Maxime Ratinier, Pauline Ezanno, Gaël Beaunée

PLOS Computational Biology: published August 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013393

Evaluating COVID-19 vaccination policy in Québec (Canada) using a data-driven dynamic transmission model

Samuel Torres-Florez, Jorge Luis Flores Anato, Jiahuan Helen He, Vicente Garrido Portilla, Yichen Wu, Mathieu Maheu-Giroux, Étienne Racine, Caroline E. Wagner

PLOS Computational Biology: published August 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013207

Leveraging structure-informed machine learning for fast steric zipper propensity prediction across whole proteomes

Samantha Zink, Songrong Qu, Thomas Holton, Eesha Shankar, Paulina Stanley, David S. Eisenberg, Michael R. Sawaya, Jose A. Rodriguez

PLOS Computational Biology: published August 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013395

Integrated pan-cancer analysis of RNA binding protein HuR investigates its biomarker potential in prognosis, immunotherapy, and drug sensitivity

Jian Peng, Jichuan Quan, Xiaoru Wang

PLOS Computational Biology: published August 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013374

Deep neural networks explain spiking activity in auditory cortex

Bilal Ahmed, Joshua D. Downer, Brian J. Malone, Joseph G. Makin

PLOS Computational Biology: published August 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013334

Maynard Smith revisited: A multi-agent reinforcement learning approach to the coevolution of signalling behaviour

Olivia Macmillan-Scott, Mirco Musolesi

PLOS Computational Biology: published August 26, 2025 | https://doi.org/10.1371/journal.pcbi.1013302

Mixotrophy for carbon-conserving waste upcycling

Michael Weldon, Christian Euler

PLOS Computational Biology: published August 26, 2025 | https://doi.org/10.1371/journal.pcbi.1013379

Data-driven analysis of fine-scale badger movement in the UK

Jessica R. Furber, Richard J. Delahay, Ruth Cox, Rosie Woodroffe, Maria O’Hagan, Naratip Santitissadeekorn, Stefan Klus, Giovanni Lo Iacono, Mark A. Chambers, David J. B. Lloyd

PLOS Computational Biology: published August 28, 2025 | https://doi.org/10.1371/journal.pcbi.1013372

Dual-purpose dynamics emerge from a heterogeneous cell population in Drosophila metamorphosis

Daiki Wakita, Satoshi Yamaji, Daiki Umetsu, Takeshi Kano

PLOS Computational Biology: published August 28, 2025 | https://doi.org/10.1371/journal.pcbi.1013331

SimPep and OP-AND: A deep learning framework and curated database for predicting osteogenic peptides

Maryam Ghobakhloo, Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Roya Abbaszadeh, Mohammad Taheri-Ledari, Bahman Zeynali

PLOS Computational Biology: published August 29, 2025 | https://doi.org/10.1371/journal.pcbi.1013422

The R-loop grammar predicts R-loop formation under different topological constraints

Margherita Maria Ferrari, Svetlana Poznanović, Manda Riehl, Jacob Lusk, Stella Hartono, Georgina Gonzalez-Isunza, Frédéric Chédin, Mariel Vázquez, Nataša Jonoska

PLOS Computational Biology: published August 29, 2025 | https://doi.org/10.1371/journal.pcbi.1013376

Mechanistic modeling of cell viability assays with in silico lineage tracing

Arnab Mutsuddy, Jonah R. Huggins, Aurore K. Amrit, Atalanta Manuela Harley-Gasaway, Cemal Erdem, Evan T. Jones, Olivia G. Laurine, Jon C. Calhoun, Marc R. Birtwistle

PLOS Computational Biology: published August 29, 2025 | https://doi.org/10.1371/journal.pcbi.1013156

Corrections

Correction: Aggregating multiple test results to improve medical decision-making

Lucas Böttcher, Maria R. D’Orsogna, Tom Chou

PLOS Computational Biology: published August 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013347

Correction: Modelling African horse sickness emergence and transmission in the South African control area using a deterministic metapopulation approach

Joanna N. de Klerk, Erin E. Gorsich, John D. Grewar, Benjamin D. Atkins, Warren S. D. Tennant, Karien Labuschagne, Michael J. Tildesley

PLOS Computational Biology: published August 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013377

Methods

COEXIST: Coordinated single-cell integration of serial multiplexed tissue images

Robert T. Heussner, Cameron F. Watson, Christopher Z. Eddy, Kunlun Wang, Eric M. Cramer, Allison L. Creason, Gordon B. Mills, Young Hwan Chang

PLOS Computational Biology: published August 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013325

A neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens

Weheliye H. Weheliye, Javier Rodriguez, Luigi Feriani, Avelino Javer, Virginie Uhlmann, André E. X. Brown

PLOS Computational Biology: published August 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013345

IonBench: A benchmark of optimisation strategies for mathematical models of ion channel currents

Matt J. Owen, Gary R. Mirams

PLOS Computational Biology: published August 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013319

PLNMFG: Pseudo-label guided non-negative matrix factorization model with graph constraint for single-cell multi-omics data clustering

Hui Yuan, Mingzhu Liu, Yushan Qiu, Wai-Ki Ching, Quan Zou

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013375

Software

novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection

Vikas Upadhyay, Mohit Anand, Costas D. Maranas

PLOS Computational Biology: published August 6, 2025 | https://doi.org/10.1371/journal.pcbi.1012516

A software ecosystem for brain tractometry processing, analysis, and insight

John Kruper, Adam Richie-Halford, Joanna Qiao, Asa Gilmore, Kelly Chang, Mareike Grotheer, Ethan Roy, Sendy Caffarra, Teresa Gomez, Sam Chou, Matthew Cieslak, Serge Koudoro, Eleftherios Garyfallidis, Theodore D. Satterthwaite, Jason D. Yeatman, Ariel Rokem

PLOS Computational Biology: published August 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013323

G4SNVHunter: An R/Bioconductor Package for Evaluating SNV-Induced Disruption of G-Quadruplex Structures Leveraging the G4Hunter Algorithm

Rongxin Zhang, Wenyong Zhu, Ke Xiao, Jean-Louis Mergny, Xiao Sun

PLOS Computational Biology: published August 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013368

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August 2025

Cover

Neural Network Identification of Run-and-Tumble Dynamics Governing Rules