Current Issue | PLOS Computational Biology

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Visualising topological features in red pulp cells of a healthy mouse spleen with PWDS

We introduce Persistence Weighted Death Simplices (PWDS), a visualisation of the topological features detected by persistent homology in 2D imaging data. Each triangle marks the approximate location of a loop in the cell distribution, with colour indicating whether the loop is formed by proximal (red) or distal (blue) cells, and intensity reflecting its prominence. This visualisation highlights the multiscale structure of cell arrangements and provides an interpretable link between topological features and biological tissue organisation. Torras-Pérez et al. 2025

Image Credit: Maria Torras-Pérez et al.

Education Articles

Ten quick tips for developing a reproducible Shiny application

Julien Brun, Greg Janée, Renata G. Curty

PLOS Computational Biology: published October 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013551

Impact of the COVID-19 pandemic on computational biology early career researchers: A global retrospective study

Pradeep Eranti, Megha Hegde, Syed Muktadir Al Sium, R. Gonzalo Parra, Alastair M. Kilpatrick, Sayane Shome, Farzana Rahman

PLOS Computational Biology: published October 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013554

From ideal to practical: Heterogeneity of student-generated variant lists highlights hidden reproducibility gaps

Rumeysa Aslıhan Ertürk, Abdullah Asım Emül, Büşra Nur Darendeli-Kiraz, Fatma Zehra Sarı, Mehmet Arif Ergün, Mehmet Baysan

PLOS Computational Biology: published October 16, 2025 | https://doi.org/10.1371/journal.pcbi.1013552

Ten simple rules for optimal and careful use of generative AI in science

Mohamed Helmy, Lingling Jin, Amr Alhossary, Tamer Mansour, Diogo Pellagrina, Kumar Selvarajoo

PLOS Computational Biology: published October 28, 2025 | https://doi.org/10.1371/journal.pcbi.1013588

Nine quick tips for trustworthy machine learning in the biomedical sciences

Luca Oneto, Davide Chicco

PLOS Computational Biology: published October 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013624

Research Articles

Improving policy design and epidemic response using integrated models of economic choice and disease dynamics with behavioral feedback

Hongru Du, Matthew V. Zahn, Sara L. Loo, Tijs W. Alleman, Shaun Truelove, Bryan Patenaude, Lauren M. Gardner, Nicholas Papageorge, Alison L. Hill

PLOS Computational Biology: published October 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013549

The quarantine hospital strategy as a way to reduce both community and nosocomial transmission in the context of a COVID-like epidemic

Théo Pinettes, Quentin J Leclerc, Kévin Jean, Laura Temime

PLOS Computational Biology: published October 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013548

A Bayesian model of distance perception from ocular convergence

Peter Scarfe, Paul B. Hibbard

PLOS Computational Biology: published October 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013506

Three types of remapping with linear decoders: A population-geometric perspective

Guillermo Martín-Sánchez, Christian K. Machens, William F. Podlaski

PLOS Computational Biology: published October 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013545

Modelling plant disease spread and containment: Simulation and approximate Bayesian Computation for Xylella fastidiosa in Puglia, Italy

Daniel Chapman, Flavia Occhibove, James M. Bullock, Pieter S. A. Beck, Juan A. Navas-Cortes, Steven M. White

PLOS Computational Biology: published October 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013539

A multi-layer encoder prediction model for individual sample specific gene combination effect (MLEC-iGeneCombo)

Yun Shen, Kunjie Fan, Birkan Gökbağ, Nuo Sun, Chen Yang, Lijun Cheng, Lang Li

PLOS Computational Biology: published October 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013547

RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation

Sobhan Shukueian Tabrizi, Sina Barazandeh, Helyasadat Hashemi Aghdam, A. Ercument Cicek

PLOS Computational Biology: published October 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013541

A mixture of attention experts-embedded flow-based generative model to create synthetic cells in single-cell RNA-Seq datasets

Sultan Sevgi Turgut Ögme, Nizamettin Aydin, Zeyneb Kurt

PLOS Computational Biology: published October 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013525

Host responses and viral traits interact to shape the impacts of climate warming on highly pathogenic avian influenza in migratory waterfowl

Claire S. Teitelbaum, Michael L. Casazza, Cory T. Overton, Elliott L. Matchett, Diann J. Prosser

PLOS Computational Biology: published October 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013451

Understanding the high-order network plasticity mechanisms of ultrasound neuromodulation

Marilyn Gatica, Cyril Atkinson-Clement, Carlos Coronel-Oliveros, Mohammad Alkhawashki, Pedro A. M. Mediano, Enzo Tagliazucchi, Fernando E. Rosas, Marcus Kaiser, Giovanni Petri

PLOS Computational Biology: published October 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013514

AI-driven discovery of novel extracellular matrix biomarkers in pelvic organ prolapse

Yanlin Mi, Ben Cahill, Venkata V. B. Yallapragada, Reut Rotem, Barry A. O’Reilly, Sabin Tabirca

PLOS Computational Biology: published October 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013483

Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches

Javiera Cortés-Ríos, Maria Rodriguez-Fernandez, Peter Karl Sorger, Fabian Fröhlich

PLOS Computational Biology: published October 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012890

A digital DNA system favours the superiority of unidirectional inheritance over ‘Lamarckian’ inheritance

Aswathi Shiju, Samantha D. M. Arras, Allen G. Rodrigo, Anthony M. Poole

PLOS Computational Biology: published October 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012677

OCIAD2 as a novel prognostic and therapeutic biomarker for pancreatic cancer: A study based on transcriptomic signature and bioinformatics analysis

Zhongyuan Cui, Xia Lei, Yani Gou, Zhixian Wu, Xiaojun Huang

PLOS Computational Biology: published October 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013566

The mechanism of dynamic steady states in lamellipodia

June Hyung Kim, Taeyoon Kim

PLOS Computational Biology: published October 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013572

Mouse and human striatal projection neurons compared - somatodendritic arbor, spines and in silico analyses

Alexander Kozlov, Lidia Blazquez-Llorca, Ruth Benavides-Piccione, Asta Kastanauskaite, Ana I. Rojo, Alberto Muñoz, Antonio Cuadrado, Javier DeFelipe, Sten Grillner

PLOS Computational Biology: published October 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013569

Superspreading and the evolution of virulence

Xander O’Neill, Andy White, Graham R. Northrup, Chadi M. Saad-Roy, P. Signe White, Mike Boots

PLOS Computational Biology: published October 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013517

Spatial distribution of cytoskeleton-mediated feedback controls cell polarization: A computational study

Parijat Banerjee, Jonathan A. Kuhn, Dhiman Sankar Pal, Yu Deng, Tatsat Banerjee, Peter N. Devreotes, Pablo A. Iglesias

PLOS Computational Biology: published October 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013036

Importance of localized dilatation and distensibility in identifying determinants of thoracic aortic aneurysm with neural operators

David S. Li, Somdatta Goswami, Qianying Cao, Vivek Oommen, Roland Assi, Jay D. Humphrey, George E. Karniadakis

PLOS Computational Biology: published October 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013550

Diverse and flexible behavioral strategies arise in recurrent neural networks trained on multisensory decision making

Thomas S. Wierda, Shirin Dora, Cyriel M. A. Pennartz, Jorge F. Mejias

PLOS Computational Biology: published October 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013559

Assessing parameter identifiability of a hemodynamics PDE model using spectral surrogates and dimension reduction

Mitchel J. Colebank

PLOS Computational Biology: published October 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013553

Environmental motion presented ahead of self-motion modulates heading direction estimation

Liana Nafisa Saftari, Jongmin Moon, Oh-Sang Kwon

PLOS Computational Biology: published October 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013571

Differential equation modeling of cell population dynamics in skeletal muscle regeneration from single-cell transcriptomic data

Renad Al-Ghazawi, Hassan Lezzeik, Xiaojian Shao, Theodore J. Perkins

PLOS Computational Biology: published October 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013575

Learning spatial hearing via innate mechanisms

Yang Chu, Wayne Luk, Dan F. M. Goodman

PLOS Computational Biology: published October 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013543

Enhancing antibody-antigen interaction prediction with atomic flexibility

Sara Joubbi, Alessio Micheli, Paolo Milazzo, Giorgio Ciano, Stéphane M. Gagné, Pietro Liò, Duccio Medini, Giuseppe Maccari

PLOS Computational Biology: published October 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013576

Social imitation dynamics of vaccination driven by vaccine effectiveness and beliefs

Feng Fu, Ran Zhuo, Xingru Chen

PLOS Computational Biology: published October 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013586

Understanding the mechanism of facilitation in hoverfly TSDNs

Anindya Ghosh, Sarah Nicholas, Karin Nordström, Thomas Nowotny, James Knight

PLOS Computational Biology: published October 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012986

Multivariate resilience indicators to anticipate vector-borne disease outbreaks: A West Nile virus case-study

Clara Delecroix, Quirine ten Bosch, Egbert H. Van Nes, Ingrid A. van de Leemput

PLOS Computational Biology: published October 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012703

A compact model of Escherichia coli core and biosynthetic metabolism

Marco Corrao, Hai He, Wolfram Liebermeister, Elad Noor, Arren Bar-Even

PLOS Computational Biology: published October 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013564

Social inequalities in vaccine coverage and their effects on epidemic spreading

Adriana Manna, Márton Karsai, Nicola Perra

PLOS Computational Biology: published October 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013585

InteracTor: Feature engineering and explainable AI for profiling protein structure-interaction-function relationships

Jose Cleydson F. Silva, Layla Schuster, Nick Sexson, Melissa Erdem, Ryan Hulke, Matias Kirst, Marcio F. R. Resende, Raquel Dias

PLOS Computational Biology: published October 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013038

Exact conditions for evolutionary stability in indirect reciprocity under noise

Nikoleta E. Glynatsi, Christian Hilbe, Yohsuke Murase

PLOS Computational Biology: published October 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013584

Model-based inference of cell cycle dynamics captures alterations of the DNA replication programme

Adolfo Alsina, Marco Fumasoni, Pablo Sartori

PLOS Computational Biology: published October 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013570

Deep learning detection of dynamic exocytosis events in fluorescence TIRF microscopy

Hugo Lachuer, Emmanuel Moebel, Anne-Sophie Macé, Arthur Masson, Kristine Schauer, Charles Kervrann

PLOS Computational Biology: published October 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013556

Transmission thresholds for the spread of infections in healthcare facilities

Damon J. A. Toth, Karim Khader, Christopher Mitchell, Matthew H. Samore

PLOS Computational Biology: published October 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013577

CASynergy: A causal attention model for interpretable prediction of cancer drug synergy

Haitao Li, Long Zheng, Lei Li, Yiwei Chen, Junjie Li, Chunhou Zheng, Yansen Su

PLOS Computational Biology: published October 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013567

ArcDFI: Attention regularization guided by CYP450 interactions for predicting drug-food interactions

Mogan Gim, Jaewoo Kang, Donghyeon Park, Minji Jeon

PLOS Computational Biology: published October 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013055

Drug-disease networks and drug repurposing

Austin Polanco, Mark E. J. Newman

PLOS Computational Biology: published October 16, 2025 | https://doi.org/10.1371/journal.pcbi.1013595

Memorization bias impacts modeling of alternative conformational states of solute carrier membrane proteins with methods from deep learning

G.V.T. Swapna, Namita Dube, Monica J. Roth, Gaetano T. Montelione

PLOS Computational Biology: published October 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013590

Multiscale networks in Alzheimer’s disease identify brain hypometabolism as central across biological scales

Elena Lara-Simon, Juan Domingo Gispert, Jordi Garcia-Ojalvo, Pablo Villoslada, for the Alzheimer’s Disease Neuroimaging Initiative

PLOS Computational Biology: published October 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013583

Stabilized marker gene identification and functional annotation from single-cell transcriptomic data

Sandesh Acharya, Pathum Kossinna, Qingrun Zhang, Jiami Guo

PLOS Computational Biology: published October 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013574

Statistical regularities in natural scenes that support figure-ground segregation by neural populations

Clara T. Friedman, Minqi Wang, Thomas Yerxa, Bryce A. Arseneau, Xin Huang, Emily A. Cooper

PLOS Computational Biology: published October 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013573

Homeostatic bidirectional plasticity in upbound and downbound micromodules in a model of the olivocerebellar loop

Elías M. Fernández Santoro, Lennart P.L. Landsmeer, Said Hamdioui, Christos Strydis, Chris I. De Zeeuw, Aleksandra Badura, Mario Negrello

PLOS Computational Biology: published October 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013609

The structural effects of indel polymorphisms outside the binding site on RNA-protein interactions are shaped by selection

Carlos Owusu-Ansah, Elan Shatoff, Ralf Bundschuh

PLOS Computational Biology: published October 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013604

Multi-cellular network model predicts alterations in glomerular endothelial structure in diabetic kidney disease

Krutika Patidar, Ashlee N. Ford Versypt

PLOS Computational Biology: published October 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013598

Predicting residue ionization of OmpF channel using Constant pH Molecular Dynamics as benchmark

Ernesto Tavares-Neto, Marcel Aguilella-Arzo, Vicente M. Aguilella

PLOS Computational Biology: published October 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013628

Simultaneously determining regional heterogeneity and connection directionality from neural activity and symmetric connection

Jiawen Chang, Zhuda Yang, Changsong Zhou

PLOS Computational Biology: published October 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013612

Elastic analysis bridges structure and dynamics of an AAA+ molecular motor

Victor Hugo Mello, Jiri Wald, Thomas C Marlovits, Pablo Sartori

PLOS Computational Biology: published October 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013596

Similarity-based transfer learning with deep learning networks for accurate CRISPR-Cas9 off-target prediction

Jeremy Charlier, Zeinab Sherkatghanad, Vladimir Makarenkov

PLOS Computational Biology: published October 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013606

Synchrony, oscillations, and phase relationships in collective neuronal activity: A highly comparative overview of methods

Fabiano Baroni, Ben D. Fulcher

PLOS Computational Biology: published October 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013597

Manifold transform by recurrent cortical circuit enhances robust encoding of familiar stimuli

Weifan Wang, Xueyan Niu, Liyuan Liang, Tai-Sing Lee

PLOS Computational Biology: published October 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013587

BMDD: A probabilistic framework for accurate imputation of zero-inflated microbiome sequencing data

Huijuan Zhou, Jun Chen, Xianyang Zhang

PLOS Computational Biology: published October 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013124

Improved gene regulatory network inference from single cell data with dropout augmentation

Hao Zhu, Donna K. Slonim

PLOS Computational Biology: published October 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013603

A semi-automated algorithm for image analysis of respiratory organoids

Anna Demchenko, Maxim Balyasin, Elena Kondratyeva, Tatiana Kyian, Alyona Sorokina, Marina Loguinova, Svetlana Smirnikhina

PLOS Computational Biology: published October 27, 2025 | https://doi.org/10.1371/journal.pcbi.1013589

Unpacking the V1 map: Differential covariation of preferred spatial frequency and cortical magnification across spatial dimensions

Marc M. Himmelberg, Yuna Kwak, Marisa Carrasco, Jonathan Winawer

PLOS Computational Biology: published October 27, 2025 | https://doi.org/10.1371/journal.pcbi.1013599

Multi-feature fusion network with marginal focal dice loss for multi-label therapeutic peptide prediction

Yijun Mao, Yurong Weng, Jian Weng, Ming Li, Wanrong Gu, Rui Pang, Xudong Lin, Yunyan Xiong, Deyu Tang

PLOS Computational Biology: published October 27, 2025 | https://doi.org/10.1371/journal.pcbi.1013622

Optimization-based framework with flux balance analysis (FBA) and metabolic pathway analysis (MPA) for identifying metabolic objective functions

Ching-Mei Wen, Eleftherios Papoutsakis, Marianthi Ierapetritou

PLOS Computational Biology: published October 27, 2025 | https://doi.org/10.1371/journal.pcbi.1013635

Noradrenaline and acetylcholine shape functional connectivity organization of NREM substages: An empirical and simulation study

Fernando Lehue, Carlos Coronel-Oliveros, Vicente Medel, Thomas Liebe, Jörn Kaufmann, Sebastián Orellana, Diego Becerra, Enzo Tagliazucchi, Patricio Orio

PLOS Computational Biology: published October 28, 2025 | https://doi.org/10.1371/journal.pcbi.1012852

Inference of weak-form partial differential equations describing migration and proliferation mechanisms in wound healing experiments on cancer cells

Siddhartha Srivastava, Patrick C. Kinnunen, Zhenlin Wang, Kenneth K.Y. Ho, Brock A. Humphries, Siyi Chen, Jennifer J. Linderman, Gary D. Luker, Kathryn E. Luker, Krishna Garikipati

PLOS Computational Biology: published October 28, 2025 | https://doi.org/10.1371/journal.pcbi.1013607

Adaptive proximity to criticality underlies amplification of ultra-slow fluctuations during free recall

Dovi Yellin, Noam Siegel, Rafael Malach, Oren Shriki

PLOS Computational Biology: published October 28, 2025 | https://doi.org/10.1371/journal.pcbi.1013528

Seeing what you hear: Compression of rat visual perceptual space by task-irrelevant sounds

Mattia Zanzi, Francesco G. Rinaldi, Silene Fornasaro, Eugenio Piasini, Davide Zoccolan

PLOS Computational Biology: published October 29, 2025 | https://doi.org/10.1371/journal.pcbi.1013608

The relationship between anxious traits and learning about changes in stochasticity and volatility

Brónagh McCoy, Rebecca P. Lawson

PLOS Computational Biology: published October 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013646

HMFGraph: Novel Bayesian approach for recovering biological networks

Aapo E. Korhonen, Olli Sarala, Tuomas Hautamäki, Markku Kuismin, Mikko J. Sillanpää

PLOS Computational Biology: published October 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013614

Ligand discrimination in immune cells: Signal processing insights into immune dysfunction in ER+ breast cancer

Adina Matache, Joao Rodrigues Lima-Junior, Maxim Kuznetsov, Konstancja Urbaniak, Sergio Branciamore, Andrei S. Rodin, Peter P. Lee, Russell C. Rockne

PLOS Computational Biology: published October 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013615

Block sparse Bayes-based fuzzy system for RNA N6-methyladenosine sites prediction

Leyao Wang, Mengyuan Zhao, Hao Xie, Yuqing Qian, Wenhuan Lu, Yijie Ding, Fei Guo

PLOS Computational Biology: published October 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013621

Corrections

Correction: Low-dimensional controllability of brain networks

Remy Ben Messaoud, Vincent Le Du, Camile Bousfiha, Marie-Constance Corsi, Juliana Gonzalez-Astudillo, Brigitte Charlotte Kaufmann, Tristan Venot, Baptiste Couvy-Duchesne, Raffaella Migliaccio, Charlotte Rosso, Paolo Bartolomeo, Mario Chavez, Fabrizio De Vico Fallani

PLOS Computational Biology: published October 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013601

Low-dimensional controllability of brain networks

Correction: 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 October 27, 2025 | https://doi.org/10.1371/journal.pcbi.1013613

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

Correction: The role of oscillations in grid cells’ toroidal topology

Giovanni di Sarra, Siddharth Jha, Yasser Roudi

PLOS Computational Biology: published October 29, 2025 | https://doi.org/10.1371/journal.pcbi.1013623

The role of oscillations in grid cells’ toroidal topology

Correction: Synthetic method of analogues for emerging infectious disease forecasting

The PLOS Computational Biology Staff

PLOS Computational Biology: published October 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013627

Synthetic method of analogues for emerging infectious disease forecasting

Formal Comments

Response to comment on "Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA"

Eliezyer Fermino de Oliveira, Lucas Sjulson

PLOS Computational Biology: published October 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013557

Generalized contrastive PCA is equivalent to generalized eigendecomposition

Joshua P. Woller, David Menrath, Alireza Gharabaghi

PLOS Computational Biology: published October 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013555

Response to comment on "Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA"

October 2025

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Visualising topological features in red pulp cells of a healthy mouse spleen with PWDS

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