Current Issue | PLOS Computational Biology

We introduce EFMouse, an open-source toolbox to model the intracranial electric fields produced by current stimulation and generate predictions that can be tested with mice in-vivo recordings. The image shows the electric field generated by a transcranial direct current stimulation (tDCS) montage targeting the left visual cortex, with four skin anodes surrounding a craniotomy, and one cathode in the back. EFMouse can model cranial recording windows, placement of stimulation electrodes anywhere in or on the animal body, and introduces novel ways to report field predictions, including measures of focality, direction homogeneity and quantification based on Allen Mouse Brain Atlas regions. Sanchez-Romero et al. 2025

Image Credit: Ruben Sanchez-Romero and Bart Krekelberg

Education Articles

Ten simple rules for training by researchers for researchers in a rapidly evolving workforce

Meirian Lovelace-Tozer, John Brown, Robert Clemens, Kathryn Greenhill, Fathima Haseen, Danny Kingsley, Ellen A. Lyrtzis, Katherine Mills, Giorgia Mori, Kathryn M. Steel, Liz Stokes, Kathryn Unsworth, Adeline L. H. Wong, Amany Gouda-Vossos

PLOS Computational Biology: published September 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013408

Ten practical tips and tricks to improve the effectiveness of biological network alignment

Giuseppe Agapito, Mario Cannataro, Pietro Cinaglia, Marianna Milano

PLOS Computational Biology: published September 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013386

Catalyzing computational biology research at an academic institute through an interest network

Jaroslav Zak, Ian Newman, Daniel J. Montiel Garcia, Daniele Parisi, Janet Joy, Steven R. Head, Jean-Christophe Ducom, Padmaja Natarajan, Haissi Cui, Sabah Ul-Hasan

PLOS Computational Biology: published September 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013453

Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings

Ronald Galiwango, Christopher J. Whalen, Grace Kebirungi, Mugume T. Atwine, Rodgers Kimera, Alfred Ssekagiri, Timothy W. Kimbowa, Edward Lukyamuzi, Mike Nsubuga, eLwazi ODSP, Lloyd Ssentongo, Henry Mutegeki, John M. Fonner, Frank Wuerthwein, Ari Berman, Laura B. Okalebo, Meghan McCarthy, Victor S. Kramer, Mariam Quinones, Phillip Cruz, Darrell Hurt, Maria Y. Giovanni, Nicola Mulder, Michael Tartakovsky, Jonathan Kayondo, Daudi Jjingo

PLOS Computational Biology: published September 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013481

Ten quick tips for protecting health data using de-identification and perturbation of structured datasets

Tshikala Eddie Lulamba, Themba Mutemaringa, Nicki Tiffin

PLOS Computational Biology: published September 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013507

How to write a scientific paper in fifteen steps

John M. Drake, Barbara A. Han

PLOS Computational Biology: published September 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013505

Research Articles

Gene regulatory network structure informs the distribution of perturbation effects

Matthew Aguirre, Jeffrey P. Spence, Guy Sella, Jonathan K. Pritchard

PLOS Computational Biology: published September 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013387

Changing cognitive chimera states in human brain networks with age: Variations in cognitive integration and segregation

Andrew Patton, Jörn Davidsen

PLOS Computational Biology: published September 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013093

Using stochastic cellular automata to model and define sufficient conditions for the survival of Enterococcus faecalis biofilms with the pCF10 plasmid under erythromycin treatment

Madison Shoraka, Herby Jean-Baptiste, Bettina Buttaro, Gillian Queisser

PLOS Computational Biology: published September 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013425

Mutualism provides a basis for biodiversity in eco-evolutionary community assembly

Gui Araujo, Miguel Lurgi

PLOS Computational Biology: published September 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013402

Optimal algorithms for controlling infectious diseases in real time using noisy infection data

Sandor Beregi, Kris V. Parag

PLOS Computational Biology: published September 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013426

Deep learning approach for automatic assessment of schizophrenia and bipolar disorder in patients using R-R intervals

Kamil Książek, Wilhelm Masarczyk, Przemysław Głomb, Michał Romaszewski, Krisztián Buza, Przemysław Sekuła, Michał Cholewa, Katarzyna Kołodziej, Piotr Gorczyca, Magdalena Piegza

PLOS Computational Biology: published September 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012983

Molecular dynamics study of differential effects of serotonin-2A-receptor (5-HT_2AR) modulators

Jordy Peeters, Dimitri De Bundel, Kenno Vanommeslaeghe

PLOS Computational Biology: published September 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013000

Drug-induced liver injury prediction based on graph convolutional networks and toxicogenomics

Tong Xiao, Ying Liu, Kaimiao Hu, Kaimin Guo, Mengying Zhang, TingTing Wang, Weihua Lei, Wenjia Wang, Shuiping Zhou, Yunhui Hu, Ran Su

PLOS Computational Biology: published September 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013423

The detection of algebraic auditory structures emerges with self-supervised learning

Pierre Orhan, Yves Boubenec, Jean-Rémi King

PLOS Computational Biology: published September 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013271

Potentials and limitations in the application of Convolutional Neural Networks for mosquito species identification using wing images

Kristopher Nolte, Jan Baumbach, Christian Lins, Jens Johann Georg Lohmann, Philip Kollmannsberger, Felix Gregor Sauer, Renke Lühken

PLOS Computational Biology: published September 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013435

Action subsampling supports policy compression in large action spaces

Shuze Liu, Samuel Joseph Gershman

PLOS Computational Biology: published September 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013444

A history-dependent approach for accurate initial condition estimation in epidemic models

Dongju Lim, Kyeong Tae Ko, Hyukpyo Hong, Hyojung Lee, Boseung Choi, Won Chang, Sunhwa Choi, Jae Kyoung Kim

PLOS Computational Biology: published September 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013438

Understanding thromboembolus transport patterns in the brain for stroke in the presence of carotid artery stenosis

Ricardo Roopnarinesingh, Neel D. Jani, Michelle Leppert, Debanjan Mukherjee

PLOS Computational Biology: published September 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013269

Blood flow in the human cerebral cortex: Large-scale pial vascularization and 1D simulation

Eduardo G. Zilves, Lucas O. Müller, Gonzalo D. M. Talou, Vladimir Hachinski, J. David Spence, Pablo J. Blanco

PLOS Computational Biology: published September 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013459

Transcription reshapes RNA hairpin folding pathways revealed by all-atom molecular dynamics simulations

Peng Tao, Yunda Si, Jie Xia, Yi Xiao

PLOS Computational Biology: published September 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013472

An efficient and flexible framework for inferring global sensitivity of agent-based model parameters

Daniel R. Bergman, Trachette Jackson, Harsh Vardhan Jain, Kerri-Ann Norton

PLOS Computational Biology: published September 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013427

Microtubule-based nucleation results in a large sensitivity to cell geometry of the plant cortical array

Marco Saltini, Eva E. Deinum

PLOS Computational Biology: published September 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013282

serojump: A Bayesian tool for inferring infection timing and antibody kinetics from longitudinal serological data

David Hodgson, James Hay, Sheikh Jarju, Dawda Jobe, Rhys Wenlock, Thushan I. de Silva, Adam J. Kucharski

PLOS Computational Biology: published September 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013467

A generalized theoretical framework to investigate multicomponent actin dynamics

Mintu Nandi, Shashank Shekhar, Sandeep Choubey

PLOS Computational Biology: published September 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013434

The G-OBIM tongue model: An accurate open-source biomechanical model of a male human tongue

Maxime Calka, Pierre Badin, Mohammad Ali Nazari, Michel Rochette, Pascal Perrier, Yohan Payan

PLOS Computational Biology: published September 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013378

Shrinking to bird size with dinosaur-level cancer defences: Evolution of cancer suppression over macroevolutionary time

E. Yagmur Erten, Marc Tollis, Hanna Kokko

PLOS Computational Biology: published September 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013432

Ant visual route navigation: How the fine details of behaviour promote successful route performance and convergence

Amany Azevedo Amin, Andrew Philippides, Paul Graham

PLOS Computational Biology: published September 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012798

Personalizing chemotherapy drug selection using a novel transcriptomic chemogram

Kristi Lin-Rahardja, Jessica Scarborough, Jacob G. Scott

PLOS Computational Biology: published September 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013417

Cortical networks with multiple interneuron types generate oscillatory patterns during predictive coding

Kwangjun Lee, Cyriel M. A. Pennartz, Jorge F. Mejias

PLOS Computational Biology: published September 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013469

Epithelial competition determines gene therapy potential to suppress Fanconi Anemia oral cancer risk

Hunter L. Colegrove, Raymond J. Monnat Jr., Alison F. Feder

PLOS Computational Biology: published September 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012915

In silico biophysics and rheology of blood and red blood cells in Gaucher Disease

Zhaojie Chai, Guansheng Li, Papa Alioune Ndour, Philippe Connes, Pierre A. Buffet, Melanie Franco, George Em Karniadakis

PLOS Computational Biology: published September 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012705

A curriculum learning approach to training antibody language models

Sarah M. Burbach, Bryan Briney

PLOS Computational Biology: published September 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013473

HyperACP: A cutting-edge hybrid framework for anticancer peptide classification via scalable feature extraction and adaptive neighbor-based synthesis

Bangyi Zhang, Yun Zuo, Jun Wan, Jiayue Liu, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng

PLOS Computational Biology: published September 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013489

Human visual grouping based on within- and cross-area temporal correlations

Yen-Ju Chen, Zitang Sun, Shin’ya Nishida

PLOS Computational Biology: published September 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013001

Mathematical modeling and simulation of tumor-induced angiogenesis in retinal hemangioblastoma

Franco Pradelli, Giovanni Minervini, Pradeep Venkatesh, Shorya Azad, Hector Gomez, Silvio C. E. Tosatto

PLOS Computational Biology: published September 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012799

Simulation insights on the compound action potential in multifascicular nerves

Joseph James Tharayil, Ciro Zinno, Filippo Agnesi, Bryn Lloyd, Silvia Farcito, Antonino Cassara, Niels Kuster, Michael Reimann, Silvestro Micera, Esra Neufeld

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013452

Prior expectations guide multisensory integration during face-to-face communication

Giulia Mazzi, Ambra Ferrari, Maria Laura Mencaroni, Chiara Valzolgher, Mirko Tommasini, Francesco Pavani, Stefania Benetti

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013468

A physiologically inspired hybrid CPG/Reflex controller for cycling simulations that generalizes to walking

Giacomo Severini, David Muñoz

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013494

Sparse multitask group Lasso for genome-wide association studies

Asma Nouira, Chloé-Agathe Azencott

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1012734

Variation in the geometry of concept manifolds across human visual cortex

Ghislain St-Yves, Kendrick Kay, Thomas Naselaris

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013416

Paying attention to attention: High attention sites as indicators of protein family and function in language models

Gowri Nayar, Alp Tartici, Russ B. Altman

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013424

Adaptive algorithms for shaping behavior

William L. Tong, Venkatesh N. Murthy, Gautam Reddy

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013454

Competition and cooperation of assembly sequences in recurrent neural networks

Tristan Manfred Stöber, Andrew B. Lehr, Arash Nikzad, Mohammad Ganjtabesh, Marianne Fyhn, Arvind Kumar

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013403

Task-relevant representational spaces in human memory traces

Rebekka Heinen, Elias M. B. Rau, Nora A. Herweg, Nikolai Axmacher

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013476

Default mode network connectivity predicts individual differences in long-term forgetting: Evidence for storage degradation, not retrieval failure

Yinan Xu, Chantel S. Prat, Florian Sense, Hedderik van Rijn, Andrea Stocco

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013485

A nonlinear relationship between prediction errors and learning rates in human reinforcement-learning

Boluwatife Ikwunne, Jolie Parham, Erdem Pulcu

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013445

THLANet: A deep learning framework for predicting TCR-pHLA binding in immunotherapy applications

Xu Long, Qiang Yang, Weihe Dong, Xiaokun Li, Kuanquan Wang, Suyu Dong, Gongning Luo, Xianyu Zhang, Tiansong Yang, Xin Gao, Guohua Wang

PLOS Computational Biology: published September 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013050

Effects of segmentation errors on downstream-analysis in highly-multiplexed tissue imaging

Matthias Bruhns, Jan T. Schleicher, Maximilian Wirth, Marcello Zago, Sepideh Babaei, Manfred Claassen

PLOS Computational Biology: published September 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013350

Clonal heterogeneity and antigenic stimulation shape persistence of the latent reservoir of HIV

Marco Garcia Noceda, Gargi Kher, Shikhar Uttam, John P. Barton

PLOS Computational Biology: published September 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013433

The size-weight illusion and beyond: A new model of perceived weight

Veronica Pisu, Erich W. Graf, Wendy J. Adams

PLOS Computational Biology: published September 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013496

Fast and exact stochastic simulations of epidemics on static and temporal networks

Samuel Cure, Florian G. Pflug, Simone Pigolotti

PLOS Computational Biology: published September 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013490

Personalized pulse wave propagation modeling to improve vasopressor dosing management in patients with severe traumatic brain injury

Kamil Wolos, Leszek Pstras, Urszula Bialonczyk, Malgorzata Debowska, Wojciech Dabrowski, Dorota Siwicka-Gieroba, Jan Poleszczuk

PLOS Computational Biology: published September 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013501

Effects of tDCS of the DLPFC on brain networks: A hybrid brain modeling study

Yanqing Dong, Jing Wei, Songjun Peng, Xinran Wu, Yaru Xu, Jianfeng Feng, Jie Zhang, Viktor Jirsa, Jie Xiang

PLOS Computational Biology: published September 16, 2025 | https://doi.org/10.1371/journal.pcbi.1013486

Dynamical mean-field theory for a highly heterogeneous neural population with graded persistent activity of the entorhinal cortex

Futa Tomita, Jun-nosuke Teramae

PLOS Computational Biology: published September 16, 2025 | https://doi.org/10.1371/journal.pcbi.1013484

Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations

Jiancheng Zhang, Xiangting Li, Xiaolu Guo, Zhaoyi You, Lucas Böttcher, Alex Mogilner, Alexander Hoffmann, Tom Chou, Mingtao Xia

PLOS Computational Biology: published September 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013462

Ligands binding diffusively to protein target act as inhibitors of protein-protein interactions

William Jeffries, Bryan M. Delfing, Xavier E. Laracuente, Xingyu Luo, Audrey Olson, Kenneth W. Foreman, Kyung Hyeon Lee, Greg Petruncio, Vito De Benedictis, Mikell Paige, Kylene Kehn-Hall, Christopher Lockhart, Dmitri K. Klimov

PLOS Computational Biology: published September 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013495

Opportunities for machine learning to predict cross-neutralization in FMDV serotype O

Dennis N. Makau, Jonathan Arzt, Kimberly VanderWaal

PLOS Computational Biology: published September 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013491

Estimating the effectiveness of non-pharmaceutical interventions against COVID-19 transmission in the Netherlands

Jantien A. Backer, Don Klinkenberg, Fuminari Miura, Jacco Wallinga

PLOS Computational Biology: published September 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013502

Optimizing crop varietal mixtures for viral disease management: A case study on cassava virus epidemics

Israël Tankam Chedjou, Ruairí Donnelly, Christopher A. Gilligan

PLOS Computational Biology: published September 18, 2025 | https://doi.org/10.1371/journal.pcbi.1012842

Brainwide hemodynamics predict EEG neural rhythms across sleep and wakefulness in humans

Leandro P. L. Jacob, Sydney M. Bailes, Stephanie D. Williams, Carsen Stringer, Laura D. Lewis

PLOS Computational Biology: published September 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013497

Mouse-Specific Single cell cytokine activity prediction and Estimation (MouSSE)

Azka Javaid, H. Robert Frost

PLOS Computational Biology: published September 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013475

Inheritable cell-states shape drug-persister correlations and population dynamics in cancer cells

Anton Iyer, Adrian Alva, Adrián E. Granada, Shaon Chakrabarti

PLOS Computational Biology: published September 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013446

Modeling neuron-astrocyte interactions in neural networks using distributed simulation

Han-Jia Jiang, Jugoslava Aćimović, Tiina Manninen, Iiro Ahokainen, Jonas Stapmanns, Mikko Lehtimäki, Markus Diesmann, Sacha J. van Albada, Hans Ekkehard Plesser, Marja-Leena Linne

PLOS Computational Biology: published September 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013503

VarPPUD: Pinpointing diagnostic variants from sets of prioritized, strong candidate variants

Rui Yin, Alba Gutiérrez-Sacristán, Undiagnosed Diseases Network, Shilpa Nadimpalli Kobren, Paul Avillach

PLOS Computational Biology: published September 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013414

Modelling the relative contribution of infection, routine vaccination and supplementary immunisation activities to measles seroconversion in Kenyan Children

Caroline Mburu, John Ojal, Rose Selim, Rose Ombati, Donald Akech, Boniface Karia, James Tuju, Antipa Sigilai, Gaby Smits, Pieter van Gageldonk, Fiona van der Klis, Eunice Kagucia, Anthony Scott, Ifedayo Adetifa, Stefan Flasche

PLOS Computational Biology: published September 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013531

Utargetome: A targetome prediction tool for modified U1-snRNAs to identify distal-target positions with improved selectivity

Paolo Pigini, Federico Manuel Giorgi, Keng Boon Wee

PLOS Computational Biology: published September 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013534

Optimizing therapeutic outcomes with Mechanotherapy and Ultrasound Sonopermeation in solid tumors

Marina Koutsi, Triantafyllos Stylianopoulos, Fotios Mpekris

PLOS Computational Biology: published September 23, 2025 | https://doi.org/10.1371/journal.pcbi.1012676

Category-specific perceptual learning of robust object recognition modelled using deep neural networks

Hojin Jang, Frank Tong

PLOS Computational Biology: published September 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013529

Identifying COVID-19 peaks using early warning signals

Joshua Looker, Kat S. Rock, Louise Dyson

PLOS Computational Biology: published September 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013524

Mechanistic within-host mathematical model of inhalational anthrax

Bevelynn Whaler, Grant Lythe, Joseph J. Gillard, Thomas R. Laws, Jonathan Carruthers, Thomas Finnie, Carmen Molina-París, Martín López-García

PLOS Computational Biology: published September 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013439

Elucidating reaction dynamics in a model of human brain energy metabolism

Dimitrios G. Patsatzis, Efstathios-Al. Tingas, Subram Mani Sarathy, Dimitris A. Goussis, Renaud Blaise Jolivet

PLOS Computational Biology: published September 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013504

How peak knee loads are affected by changing the mass of lower-limb body segments during walking

Delaney E. Miller, Ashley E. Brown, Nicholas A. Bianco, Rucha Bhise, Scott L. Delp, Steven H. Collins

PLOS Computational Biology: published September 24, 2025 | https://doi.org/10.1371/journal.pcbi.1012833

A comparative computational analysis of IFN-alpha pharmacokinetics and its induced cellular response in mice and humans

Priyata Kalra, Bastian Kister, Rebekka Fendt, Mario Köster, Julia Pulverer, Sven Sahle, Lars Kuepfer, Ursula Kummer

PLOS Computational Biology: published September 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013509

Mathematical modeling of dopamine rhythms and timing of dopamine reuptake inhibitors

Tianyong Yao, Ruby Kim

PLOS Computational Biology: published September 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013508

Exploration of potential novel drug targets for rheumatoid arthritis by plasma proteome screening

Zhiqiang Ma, Ran Chen, Zibo Feng

PLOS Computational Biology: published September 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013333

Dual process impairments in reinforcement learning and working memory systems underlie learning deficits in physiological anxiety

Jennifer D. Senta, Sonia J. Bishop, Anne G.E. Collins

PLOS Computational Biology: published September 26, 2025 | https://doi.org/10.1371/journal.pcbi.1012872

MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions

Nicola F. Müller, Remco R. Bouckaert, Chieh-Hsi Wu, Trevor Bedford

PLOS Computational Biology: published September 26, 2025 | https://doi.org/10.1371/journal.pcbi.1013421

An explainable covariate compartmental model for predicting the spatio-temporal patterns of dengue in Sri Lanka

Yichao Liu, Peter Fransson, Julian Heidecke, Prasad Liyanage, Jonas Wallin, Joacim Rocklöv

PLOS Computational Biology: published September 26, 2025 | https://doi.org/10.1371/journal.pcbi.1013540

Generalizing population RT-qPCR cycle threshold values-informed estimation of epidemiological dynamics: Impact of surveillance practices and pathogen variability

Yun Lin, James A. Hay, Yu Meng, Benjamin J. Cowling, Bingyi Yang

PLOS Computational Biology: published September 29, 2025 | https://doi.org/10.1371/journal.pcbi.1013527

Coupling plankton and cholera dynamics: Insights into outbreak prediction and practical disease management

Biplab Maity, Swarnendu Banerjee, Abhishek Senapati, Jon Pitchford, Joydev Chattopadhyay

PLOS Computational Biology: published September 29, 2025 | https://doi.org/10.1371/journal.pcbi.1013523

Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization

Théotime Grohens, Sam Meyer, Guillaume Beslon

PLOS Computational Biology: published September 29, 2025 | https://doi.org/10.1371/journal.pcbi.1013482

Early visual signatures and benefits of intra-saccadic motion streaks

Richard Schweitzer, Thomas Seel, Jörg Raisch, Martin Rolfs

PLOS Computational Biology: published September 29, 2025 | https://doi.org/10.1371/journal.pcbi.1013544

A computational framework for the investigation of phosphoinositide regulation

Hilaire Yam Fung Cheung, Chukiat Tantiwong, Dipali Kale, Jonathan M. Gibbins, Steve P. Watson, Johan W. M. Heemskerk, Albert Sickmann, Robert Ahrends, Joanne L. Dunster

PLOS Computational Biology: published September 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013477

Optimization of echinococcosis control measures based on system dynamics

Jinrui Ma, Xingyu Liu, Zengwen He, Haohao Zhang, Yonghui Ma, Ziqiu Fan, Xuehui Zhao, Ji Zhi, Qing Cao, Huiwen Xue, Huitian Gou

PLOS Computational Biology: published September 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013186

Corrections

Correction: Design of field trials for the evaluation of transmissible vaccines in animal populations

The PLOS Computational Biology Staff

PLOS Computational Biology: published September 26, 2025 | https://doi.org/10.1371/journal.pcbi.1013530

Correction: Success-efficient/failure-safe strategy for hierarchical reinforcement motor learning

The PLOS Computational Biology Staff

PLOS Computational Biology: published September 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013537

Methods

Transcriptome-wide root causal inference

Eric V. Strobl, Eric R. Gamazon

PLOS Computational Biology: published September 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013461

Generating correlated data for omics simulation

Jianing Yang, Gregory R. Grant, Thomas G. Brooks

PLOS Computational Biology: published September 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013392

A causal framework for the drivers of animal social network structure

Ben Kawam, Julia Ostner, Richard McElreath, Oliver Schülke, Daniel Redhead

PLOS Computational Biology: published September 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013370

kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies

Anastasia Lucas, Daniel E. Schäffer, Jayamanna Wickramasinghe, Noam Auslander

PLOS Computational Biology: published September 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013470

MRDtarget: A heuristic Gaussian approach for optimizing targeted capture regions to enhance Minimal Residual Disease detection

Xuwen Wang, Yanfang Guan, Wei Gao, Xin Lai, Wuqiang Cao, Xiaoyan Zhu, Xiaoling Zeng, Yuqian Liu, Shenjie Wang, Ruoyu Liu, Xin Yi, Shuanying Yang, Jiayin Wang

PLOS Computational Biology: published September 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013443

Harmony-based data integration for distributed single-cell multi-omics data

Ruizhi Yuan, Ziqi Rong, Haoran Hu, Tianhao Liu, Shiyue Tao, Wei Chen, Lu Tang

PLOS Computational Biology: published September 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013526

A graph neural network-based spatial multi-omics data integration method for deciphering spatial domains

Congqiang Gao, Chenghui Yang, Lihua Zhang

PLOS Computational Biology: published September 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013546

Software

OmnibusX: A unified platform for accessible multi-omics analysis

Linh Truong, Thao Truong, Huy Nguyen

PLOS Computational Biology: published September 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013480

paramix: An R package for parameter discretisation in compartmental models, with application to calculating years of life lost

Lucy Goodfellow, Carl A. B. Pearson, Simon R. Procter

PLOS Computational Biology: published September 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013420

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September 2025

Cover

Stimulation-induced electric field modeling in the mouse brain using EFMouse