Current Issue | PLOS Computational Biology

Computer simulations based on detailed musculoskeletal models reproduce human walking under varied conditions such as incline, load, and speed. By comparing these simulations to experimental gait data, we assess how well they predict real movement and metabolic energy use. The simulations accurately capture overall gait patterns but underestimate metabolic cost—particularly during energetically demanding tasks like uphill walking—due to overly efficient metabolic modeling and overestimated muscle fiber work. Improving these models in the future may help develop more effective assistive devices and therapies for people with movement difficulties. Afschrift et al. 2025

Image Credit: Maarten Afschrift

Education Articles

Ten simple rules for making biomedical data resources accessible

Thomas C. Smits, Lawrence Weru, Nils Gehlenborg, Sehi L’Yi

PLOS Computational Biology: published November 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013657

Ten simple rules for early-career researchers supervising short-term student projects

Rebecca M. Crossley, Philip K. Maini

PLOS Computational Biology: published November 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013690

Ten simple rules for maximizing summer research experiences for students, mentors, and research groups

Miriam B. Goodman

PLOS Computational Biology: published November 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013731

Perspective

Building a continuous benchmarking ecosystem in bioinformatics

Izaskun Mallona, Charlotte Soneson, Ben Carrillo, Almut Lütge, Daniel Incicau, Reto Gerber, Anthony Sonrel, Mark D. Robinson

PLOS Computational Biology: published November 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013658

Research Articles

Branch-specific gene discovery in cell differentiation using multi-omics graph attention

Yihao Yin, Linzhi Zhuang, Yulei Wang, Yazhou Shi, Bengong Zhang

PLOS Computational Biology: published November 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013664

Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture

Tien Comlekoglu, J. Quetzalcóatl Toledo-Marín, Tina Comlekoglu, Douglas W. DeSimone, Shayn M. Peirce, Geoffrey Fox, James A. Glazier

PLOS Computational Biology: published November 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013626

Machine learning augmented diagnostic testing to identify sources of variability in test performance

Christopher Jon Banks, Aeron Sanchez, Vicki Stewart, Kate Bowen, Thomas Doherty, Oliver Tearne, Graham Smith, Rowland R. Kao

PLOS Computational Biology: published November 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013651

Calibration of transmission-dynamic infectious disease models: A scoping review and reporting framework

Emmanuelle A. Dankwa, Léa Cavalli, Ruchita Balasubramanian, Melike Hazal Can, Hening Cui, Katherine M. Jia, Yunfei Li, Sylvia K. Ofori, Nicole A. Swartwood, Carrie G. Wade, Caroline O. Buckee, Jeffrey W. Imai-Eaton, Nicolas A. Menzies

PLOS Computational Biology: published November 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013647

Regional heterogeneity in left atrial stiffness impacts passive deformation in a cohort of patient-specific models

Tiffany M.G. Baptiste, Cristobal Rodero, Charles P. Sillett, Marina Strocchi, Christopher W. Lanyon, Christoph M. Augustin, Angela W. C. Lee, José Alonso Solís-Lemus, Caroline H. Roney, Daniel B. Ennis, Ronak Rajani, Christopher A. Rinaldi, Gernot Plank, Richard D. Wilkinson, Steven E. Williams, Steven A. Niederer

PLOS Computational Biology: published November 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013656

Resource diversity and supply drive colonization resistance

Ethan S. Rappaport, Renato Mirollo, Babak Momeni

PLOS Computational Biology: published November 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013648

TXSelect: A multi-task learning model to identify secretory effectors

Jing Li, Qing Liu, Quan Zou, Chao Zhan

PLOS Computational Biology: published November 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013677

Data-driven identification of biological systems using multi-scale analysis

Ismaila Muhammed, Dimitris M. Manias, Dimitris A. Goussis, Haralampos Hatzikirou

PLOS Computational Biology: published November 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013193

Cortical state contributions to neuronal response variability in the early visual cortex: A system identification approach

Jinani Sooriyaarachchi, Chang’an A. Zhan, Curtis L. Baker Jr

PLOS Computational Biology: published November 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013661

Role of connectivity anisotropies in the dynamics of cultured neuronal networks

Akke Mats Houben, Jordi Garcia-Ojalvo, Jordi Soriano

PLOS Computational Biology: published November 6, 2025 | https://doi.org/10.1371/journal.pcbi.1012727

Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations

Yue Huang, Tianqi Tang, Xiaowu Dai, Fengzhu Sun

PLOS Computational Biology: published November 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013691

Splicing-aware scRNA-Seq resolution reveals execution-ready programs in effector Tregs

Daniil K. Lukyanov, Evgeniy S. Egorov, Valeriia V. Kriukova, Denis Syrko, Victor V. Kotliar, Kristin Ladell, David A. Price, Andre Franke, Dmitry M. Chudakov

PLOS Computational Biology: published November 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013682

A linear pathway for inositol pyrophosphate metabolism revealed by ¹⁸O labeling and model reduction

Jacques Hermes, Geun-Don Kim, Guizhen Liu, Maria Giovanna De Leo, Andreas Mayer, Henning Jessen, Jens Timmer

PLOS Computational Biology: published November 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013680

Optimization of experimental designs for biological rhythm discovery

Turner Silverthorne, Matthew Carlucci, Arturas Petronis, Adam R. Stinchcombe

PLOS Computational Biology: published November 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013662

A Bayesian neural ordinary differential equations framework to study the effects of chemical mixtures on survival

Virgile Baudrot, Nina Cedergreen, Thomas Kleiber, André Gergs, Sandrine Charles

PLOS Computational Biology: published November 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013681

PathoRM: Computational inference of pathogenic RNA methylation sites by incorporating multi-view features

Hui Liu, Jiani Ma, Xianjun Ma, Lin Zhang

PLOS Computational Biology: published November 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013654

Automated C. elegans behavior analysis via deep learning-based detection and tracking

Xiaoke Liu, Jianming Liu, Wenjie Teng, Yuzhong Peng, Boao Li, Xiaoqing Han, Jing Huo

PLOS Computational Biology: published November 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013707

Differential effect of supercoiling on bacterial transcription in topological domains

Boaz Goldberg, Nicolás Yehya, Jie Xiao, Sam Meyer

PLOS Computational Biology: published November 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012764

IPScan: Detecting novel intronic PolyAdenylation events with RNA-seq data

Naima Ahmed Fahmi, Sze Cheng, Jeovani Overstreet, Qianqian Song, Jeongsik Yong, Wei Zhang

PLOS Computational Biology: published November 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013668

Individual trajectories for recovery of neocortical activity in disorders of consciousness

Prejaas K. B. Tewarie, Romesh Abeysuriya, Rajanikant Panda, Pablo Nùñez, Marie M. Vitello, Glenn van der Lande, Olivia Gosseries, Aurore Thibaut, Steven Laureys, Gustavo Deco, Jitka Annen

PLOS Computational Biology: published November 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013659

Zero-shot segmentation using embeddings from a protein language model identifies functional regions in the human proteome

Ami G. Sangster, Cameron Dufault, Haoning Qu, Denise Le, Julie D. Forman-Kay, Alan M. Moses

PLOS Computational Biology: published November 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012929

Improving the accuracy of automated labeling of specimen images datasets via a confidence-based process

Quentin Bateux, Jonathan Koss, Patrick W. Sweeney, Erika Edwards, Nelson Rios, Aaron M. Dollar

PLOS Computational Biology: published November 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013650

SpaMWGDA: Identifying spatial domains of spatial transcriptomes using multi-view weighted fusion graph convolutional network and data augmentation

Lin Yuan, Boyuan Meng, Qingxiang Wang, Chunyu Hu, Cuihong Wang, De-Shuang Huang

PLOS Computational Biology: published November 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013667

ScRDAVis: An R shiny application for single-cell transcriptome data analysis and visualization

Sankarasubramanian Jagadesan, Chittibabu Guda

PLOS Computational Biology: published November 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013721

Library size-stabilized metacells construction enhances co-expression network analysis in single-cell data

Tianjiao Zhang, Haibin Zhu

PLOS Computational Biology: published November 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013697

Incorporating human mobility to enhance epidemic response and estimate real-time reproduction numbers

Mousumi Roy, Hannah E. Clapham, Swapnil Mishra

PLOS Computational Biology: published November 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013642

Stimulus-to-stimulus learning in RNNs with cortical inductive biases

Pantelis Vafidis, Antonio Rangel

PLOS Computational Biology: published November 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013672

The topology of synergy: Linking topological and information-theoretic approaches to higher-order interactions in complex systems

Thomas F. Varley, Pedro A. M. Mediano, Alice Patania, Josh Bongard

PLOS Computational Biology: published November 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013649

OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders

Klemens Flöge, Srisruthi Udayakumar, Johanna Sommer, Marie Piraud, Stefan Kesselheim, Vincent Fortuin, Stephan Günnemann, Karel J. van der Weg, Holger Gohlke, Erinc Merdivan, Alina Bazarova

PLOS Computational Biology: published November 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013679

Different antigenic distance metrics generate similar predictions of influenza vaccine response breadth despite moderate correlation

W. Zane Billings, Yang Ge, Amanda L. Skarlupka, Savannah L. Miller, Hayley Hemme, Murphy John, Natalie E. Dean, Sarah Cobey, Benjamin J. Cowling, Ye Shen, Ted M. Ross, Andreas Handel

PLOS Computational Biology: published November 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013720

Spatial close-kin mark-recapture methods to estimate dispersal parameters and barrier strength for mosquitoes

John M. Marshall, Shuyi Yang, Jared B. Bennett, Igor Filipović, Gordana Rašić

PLOS Computational Biology: published November 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013713

Multi-view fusion based on graph convolutional network with attention mechanism for predicting miRNA related to drugs

Nan Sheng, Yunzhi Liu, Ling Gao, Lei Wang, Lan Huang, Yan Wang

PLOS Computational Biology: published November 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013703

Trial-by-trial learning of successor representations in human behavior

Ari E. Kahn, Dani S. Bassett, Nathaniel D. Daw

PLOS Computational Biology: published November 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013696

Benchmarking the predictive capability of human gait simulations

Maarten Afschrift, Dinant Kistemaker, Maarten Bobbert, Friedl De Groote

PLOS Computational Biology: published November 17, 2025 | https://doi.org/10.1371/journal.pcbi.1012713

In vivo neural activity of electrosensory pyramidal cells: Biophysical characterization and phenomenological modeling

Amin Akhshi, Michael G. Metzen, Maurice J. Chacron, Anmar Khadra

PLOS Computational Biology: published November 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013711

tvsfglasso: Time-varying scale-free graphical lasso for network estimation from time-series data

Markku Kuismin, Mikko J. Sillanpää

PLOS Computational Biology: published November 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013710

An evolutionary approach to predict the orientation of CRISPR arrays

Axel Fehrenbach, Alexander Mitrofanov, Omer S. Alkhnbashi, Rolf Backofen, Franz Baumdicker

PLOS Computational Biology: published November 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013706

Clinical progression parameters associated with SARS-CoV-2, influenza, and respiratory syncytial virus infections in a large US integrated healthcare population

Noah T. Parker, Vennis Hong, Gregg S. Davis, Magdalena Pomichowski, Iris A. Reyes, Fagen Xie, Nicola F. Mueller, Isabel Rodriguez-Barraquer, Sara Y. Tartof, Joseph A. Lewnard

PLOS Computational Biology: published November 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013723

Molecular insights on the mechanism of α₁-antitrypsin condensate formation and maturation

Ignacio Sanchez-Burgos, Andres R. Tejedor, Rosana Collepardo-Guevara, Jorge Bernardino de la Serna, Jorge R. Espinosa

PLOS Computational Biology: published November 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013634

Biphasic effects on human atrial arrhythmogenicity of L-type calcium channel mutations associated with a Brugada/Short QT overlap syndrome - insights from a multiscale simulation study

Yirong Xiang, Jules C. Hancox, Henggui Zhang

PLOS Computational Biology: published November 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013616

Real-time forecasting of data revisions in epidemic surveillance streams

Jingjing Tang, Aaron Rumack, Bryan Wilder, Roni Rosenfeld

PLOS Computational Biology: published November 20, 2025 | https://doi.org/10.1371/journal.pcbi.1013709

How cortico-basal ganglia-thalamic subnetworks can shift decision policies to increase reward rate

Jyotika Bahuguna, Timothy Verstynen, Jonathan E. Rubin

PLOS Computational Biology: published November 20, 2025 | https://doi.org/10.1371/journal.pcbi.1013712

Unlocking plant health survey data: An approach to quantify the sensitivity and specificity of visual inspections

Matt Combes, Nathan Brown, Robin N. Thompson, Alexander Mastin, Peter Crow, Stephen Parnell

PLOS Computational Biology: published November 20, 2025 | https://doi.org/10.1371/journal.pcbi.1012957

CrossLabFit: A novel framework for integrating qualitative and quantitative data across multiple labs for model calibration

Rodolfo Blanco-Rodriguez, Tanya A. Miura, Esteban Hernandez-Vargas

PLOS Computational Biology: published November 20, 2025 | https://doi.org/10.1371/journal.pcbi.1013704

Multi-physics modeling for ion homeostasis in multi-compartment plant cells using an energy function

Guillaume Mestdagh, Alexis De Angeli, Christophe Godin

PLOS Computational Biology: published November 20, 2025 | https://doi.org/10.1371/journal.pcbi.1013474

Nash equilibrium of attack and defense behaviors between predators and prey

Hiroyuki Ichijo, Yuichiro Kawamura, Tomoya Nakamura

PLOS Computational Biology: published November 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013730

Protein drift-diffusion in membranes with non-equilibrium fluctuations arising from gradients in concentration or temperature

Dev Jasuja, Paul J. Atzberger

PLOS Computational Biology: published November 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013678

Universal scale-free representations in human visual cortex

Raj Magesh Gauthaman, Brice Ménard, Michael F. Bonner

PLOS Computational Biology: published November 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013714

Parameterization of cell-free systems with time-series data using KETCHUP

Mengqi Hu, Syed Bilal Jilani, Daniel G. Olson, Costas D. Maranas

PLOS Computational Biology: published November 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013724

Emergence of sparse coding, balance and decorrelation from a biologically-grounded spiking neural network model of learning in the primary visual cortex

Marko A. Ruslim, Martin J. Spencer, Hinze Hogendoorn, Hamish Meffin, Yanbo Lian, Anthony N. Burkitt

PLOS Computational Biology: published November 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013644

Federated learning for COVID-19 mortality prediction in a multicentric sample of 21 hospitals

Roberta Moreira Wichmann, Murilo Afonso Robiati Bigoto, Alexandre Dias Porto Chiavegatto Filho

PLOS Computational Biology: published November 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013695

Prediction of graft loss in living donor liver transplantation during the early postoperative period

Raiki Yoshimura, Naotoshi Nakamura, Takeru Matsuura, Takeo Toshima, Takasuke Fukuhara, Kazuyuki Aihara, Katsuhito Fujiu, Shingo Iwami, Tomoharu Yoshizumi

PLOS Computational Biology: published November 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013734

TransMarker: Unveiling dynamic network biomarkers in cancer progression through cross-state graph alignment and optimal transport

Fatemeh Keikha, Chuanyuan Wang, Zhixia Yang, Zhi-Ping Liu

PLOS Computational Biology: published November 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013743

T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters

August Guang, Casey W Dunn, Vlad Novitsky, Mark Howison, Rami Kantor

PLOS Computational Biology: published November 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013676

Lipid-driven alignment and binding of p7 dimers in early oligomer assembly

Oluwatoyin Campbell, Dina Dahhan, Viviana Monje

PLOS Computational Biology: published November 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013736

Multi-scale modelling of location- and frequency-dependent synaptic plasticity induced by repetitive magnetic stimulation in the dendrites of pyramidal neurons

Nicholas Hananeia, Christian Ebner, Christos Galanis, Hermann Cuntz, Alexander Opitz, Andreas Vlachos, Peter Jedlicka

PLOS Computational Biology: published November 25, 2025 | https://doi.org/10.1371/journal.pcbi.1012295

Linking multiple serological assays to infer dengue virus infections from paired samples using mixture models

Marco Hamins-Puértolas, Darunee Buddhari, Henrik Salje, Angkana T. Huang, Taweewun Hunsawong, Derek A.T. Cummings, Stefan Fernandez, Aaron Farmer, Surachai Kaewhiran, Direk Khampaen, Anon Srikiatkhachorn, Sopon Iamsirithaworn, Adam Waickman, Stephen J. Thomas, Timothy Endy, Alan L. Rothman, Kathryn B. Anderson, Isabel Rodriguez-Barraquer

PLOS Computational Biology: published November 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013708

Candidate correlates of protection in the HVTN505 HIV-1 vaccine efficacy trial identified by positive-unlabeled learning

Shiwei Xu, Aaron Hudson, Holly E. Janes, Georgia D. Tomaras, Margaret E. Ackerman

PLOS Computational Biology: published November 26, 2025 | https://doi.org/10.1371/journal.pcbi.1013705

Multiscale modelling shows how cell-ECM interactions impact ECM fibre alignment and cell detachment

Juan Arellano-Tintó, Daria Stepanova, Helen M. Byrne, Philip K. Maini, Tomás Alarcón

PLOS Computational Biology: published November 26, 2025 | https://doi.org/10.1371/journal.pcbi.1012698

Corrections

Correction: Facilitating the propagation of spiking activity in feedforward networks by including feedback

Hedyeh Rezaei, Ad Aertsen, Arvind Kumar, Alireza Valizadeh

PLOS Computational Biology: published November 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013639

Correction: Perturbing low dimensional activity manifolds in spiking neuronal networks

Emil Wärnberg, Arvind Kumar

PLOS Computational Biology: published November 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013636

Correction: Uncoupling the roles of firing rates and spike bursts in shaping the STN-GPe beta band oscillations

Jyotika Bahuguna, Ajith Sahasranamam, Arvind Kumar

PLOS Computational Biology: published November 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013638

Correction: The specious art of single-cell genomics

The PLOS Computational Biology Staff

PLOS Computational Biology: published November 4, 2025 | https://doi.org/10.1371/journal.pcbi.1013655

Methods

Null models for comparing information decomposition across complex systems

Alberto Liardi, Fernando E. Rosas, Robin L. Carhart-Harris, George Blackburne, Daniel Bor, Pedro A. M. Mediano

PLOS Computational Biology: published November 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013629

APDCA: An accurate and effective method for predicting associations between RBPs and AS-events during epithelial-mesenchymal transition

Yangsong He, Zheng-Jian Bai, Wai-Ki Ching, Quan Zou, Yushan Qiu

PLOS Computational Biology: published November 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013665

HAPP: High-accuracy pipeline for processing deep metabarcoding data

John Sundh, Emma Granqvist, Ela Iwaszkiewicz-Eggebrecht, Lokeshwaran Manoharan, Laura J. A. van Dijk, Robert Goodsell, Nerivania N. Godeiro, Bruno C. Bellini, Johanna Orsholm, Piotr Łukasik, Andreia Miraldo, Tomas Roslin, Ayco J. M. Tack, Anders F. Andersson, Fredrik Ronquist

PLOS Computational Biology: published November 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013558

Inferring pathway activity from single-cell and spatial transcriptomics data with PaaSc

Xiqi Liao, Yuyang Hong, Yan Feng, Henghui Li, Hai Fang, Jiantao Shi

PLOS Computational Biology: published November 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013666

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November 2025

Cover

Evaluating Human Gait Simulations Across Diverse Walking Conditions

Education Articles

Perspective

Research Articles

Corrections

Related Articles

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Methods

Software

This page is brought to you by Brian Golding (Golding@McMaster.CA) and is copied locally here to speed your access. To go to the original page (should you find something interesting or should you wish to follow links) click on

Current Issue of PLoSBiology