Current Issue | PLOS Computational Biology

Studying the propagation of brain oscillations across the cortex is challenging with non-invasive methods. To overcome this, we developed a novel approach that integrates brain imaging techniques with computational modeling. We simulated traveling waves of neural activity in the primary visual cortex and predicted their signatures in magnetoencephalography and electroencephalography recordings. By using carefully designed visual stimuli that evoke traveling waves in visual areas, we provided a proof-of-concept demonstrating the model's validity. Grabot et al. 2025

Image Credit: Eddy Malrat

Education Articles

Logic-based modeling of biological networks with Netflux

Alexander P. Clark, Mukti Chowkwale, Alexander Paap, Stephen Dang, Jeffrey J. Saucerman

PLOS Computational Biology: published April 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012864

Ten simple rules for getting started with knowledge mobilization

Rime Diany, Laura K. Fitzgibbon-Collins, Sarah A. Gagliano Taliun

PLOS Computational Biology: published April 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012888

Ten quick tips to get you started with Bayesian statistics

Olivier Gimenez, Andy Royle, Marc Kéry, Chloé R. Nater

PLOS Computational Biology: published April 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012898

Combining flipped-classroom and spaced-repetition learning in a master-level bioinformatics course

Gabriele Pozzati, Samuel Coulbourn Flores

PLOS Computational Biology: published April 15, 2025 | https://doi.org/10.1371/journal.pcbi.1012863

Eleven quick tips to unlock the power of in vivo data science

Troy J. Kieran, Taronna R. Maines, Jessica A. Belser

PLOS Computational Biology: published April 17, 2025 | https://doi.org/10.1371/journal.pcbi.1012947

Learning and teaching biological data science in the Bioconductor community

Jenny Drnevich, Frederick J. Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C. Culhane, Sean Davis, Maria A. Doyle, Ludwig Geistlinger, Andrew R. Ghazi, Susan Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin Rue-Albrecht, David J. H. Shih, Laurent Gatto, Charlotte Soneson

PLOS Computational Biology: published April 22, 2025 | https://doi.org/10.1371/journal.pcbi.1012925

Perspective

Why the growth of arboviral diseases necessitates a new generation of global risk maps and future projections

Oliver J. Brady, Leonardo S. Bastos, Jamie M. Caldwell, Simon Cauchemez, Hannah E. Clapham, Illaria Dorigatti, Katy A. M. Gaythorpe, Wenbiao Hu, Laith Hussain-Alkhateeb, Michael A. Johansson, Ahyoung Lim, Velma K. Lopez, Richard James Maude, Jane P. Messina, Erin A. Mordecai, Andrew Townsend Peterson, Isabel Rodriquez-Barraquer, Ingrid B. Rabe, Diana P. Rojas, Sadie J. Ryan, Henrik Salje, Jan C. Semenza, Quan Minh Tran

PLOS Computational Biology: published April 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012771

Research Articles

Host centric drug repurposing for viral diseases

Suzana de Siqueira Santos, Haixuan Yang, Aldo Galeano, Alberto Paccanaro

PLOS Computational Biology: published April 2, 2025 | https://doi.org/10.1371/journal.pcbi.1012876

CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution

Khanh N. Dinh, Ignacio Vázquez-García, Andrew Chan, Rhea Malhotra, Adam Weiner, Andrew W. McPherson, Simon Tavaré

PLOS Computational Biology: published April 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012902

Predicting and comparing transcription start sites in single cell populations

Shiwei Fu, Wei Vivian Li

PLOS Computational Biology: published April 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012878

Integrating multiple spatial transcriptomics data using community-enhanced graph contrastive learning

Wenqian Tu, Lihua Zhang

PLOS Computational Biology: published April 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012948

Spatial structure facilitates evolutionary rescue by drug resistance

Cecilia Fruet, Ella Linxia Müller, Claude Loverdo, Anne-Florence Bitbol

PLOS Computational Biology: published April 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012861

SpaMask: Dual masking graph autoencoder with contrastive learning for spatial transcriptomics

Wenwen Min, Donghai Fang, Jinyu Chen, Shihua Zhang

PLOS Computational Biology: published April 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012881

TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics

Chengze Shen, Eleanor Wedell, Mihai Pop, Tandy Warnow

PLOS Computational Biology: published April 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012593

Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion

Chenyang Gu, Shoji Takada, Giovanni B. Brandani, Tsuyoshi Terakawa

PLOS Computational Biology: published April 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012493

Seizure and redox rescue in a model of glucose transport deficiency

Jay S. Coggan, Polina Shichkova, Henry Markram, Daniel Keller

PLOS Computational Biology: published April 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012959

scTrans: Sparse attention powers fast and accurate cell type annotation in single-cell RNA-seq data

Zhiyi Zou, Ying Liu, Yuting Bai, Jiawei Luo, Zhaolei Zhang

PLOS Computational Biology: published April 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012904

Quantifying the impact of contact tracing interview prioritisation strategies on disease transmission: A modelling study

Logan Wu, Christopher M Baker, Nicholas Tierney, Kylie Carville, Jodie McVernon, Nick Golding, James M McCaw, Freya M Shearer

PLOS Computational Biology: published April 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012906

Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images

Vincent Hickl, Abid Khan, René M. Rossi, Bruno F. B. Silva, Katharina Maniura-Weber

PLOS Computational Biology: published April 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012874

The multiscale self-similarity of the weighted human brain connectome

Laia Barjuan, Muhua Zheng, M Ángeles Serrano

PLOS Computational Biology: published April 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012848

Neural energy coding patterns of dopaminergic neural microcircuit and its impairment in major depressive disorder: A computational study

Yuanxi Li, Bing Zhang, Jinqi Liu, Rubin Wang

PLOS Computational Biology: published April 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012961

Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory

Atsushi Matsuda, Mohammad R K Mofrad

PLOS Computational Biology: published April 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012909

Flux-sum coupling analysis of metabolic network models

Mihriban Seyis, Zahra Razaghi-Moghadam, Zoran Nikoloski

PLOS Computational Biology: published April 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012972

A burst-dependent thalamocortical substrate for perceptual awareness

Christopher J. Whyte, Eli J. Müller, Jaan Aru, Matthew Larkum, Yohan John, Brandon R. Munn, James M. Shine

PLOS Computational Biology: published April 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012951

Analysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats

Sara Javadzadeh, Aaron Adamson, Jonghun Park, Se-Young Jo, Yuan-Chun Ding, Mehrdad Bakhtiari, Vikas Bansal, Susan L. Neuhausen, Vineet Bafna

PLOS Computational Biology: published April 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012885

Nanometer scale difference in myofilament lattice structure of muscle alters muscle function in a spatially explicit model

Travis Carver Tune, Simon Sponberg

PLOS Computational Biology: published April 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012862

Cell size and selection for stress-induced cell fusion in unicellular eukaryotes

Xiaoyuan Liu, Jonathan W. Pitchford, George W. A. Constable

PLOS Computational Biology: published April 8, 2025 | https://doi.org/10.1371/journal.pcbi.1012418

The impact of climate change on ecology of tick associated with tick-borne diseases

Heejin Choi, Chang Hyeong Lee

PLOS Computational Biology: published April 8, 2025 | https://doi.org/10.1371/journal.pcbi.1012903

Federated epidemic surveillance

Ruiqi Lyu, Roni Rosenfeld, Bryan Wilder

PLOS Computational Biology: published April 8, 2025 | https://doi.org/10.1371/journal.pcbi.1012907

DelaySSA: stochastic simulation of biochemical systems and gene regulatory networks with or without time delays

Ziyan Jin, Xinyi Zhou, Zhaoyuan Fang

PLOS Computational Biology: published April 8, 2025 | https://doi.org/10.1371/journal.pcbi.1012919

Chromatin structures from integrated AI and polymer physics model

Eric R. Schultz, Soren Kyhl, Rebecca Willett, Juan J. de Pablo

PLOS Computational Biology: published April 9, 2025 | https://doi.org/10.1371/journal.pcbi.1012912

Multiple patterns of persistent inward currents with multiple types of repetitive firings in medullary serotonergic neurons of mice: An experimental and modeling study

Yi Cheng, Xingyu Wang, Qiang Zhang, Renkai Ge, Mei Zhou, Yue Dai

PLOS Computational Biology: published April 9, 2025 | https://doi.org/10.1371/journal.pcbi.1012918

Mathematical modeling unveils the timeline of CAR-T cell therapy and macrophage-mediated cytokine release syndrome

Daniela S Santurio, Luciana R C Barros, Ingmar Glauche, Artur c Fassoni

PLOS Computational Biology: published April 9, 2025 | https://doi.org/10.1371/journal.pcbi.1012908

Transcriptomic landscape around wound bed defines regenerative versus non-regenerative outcomes in mouse digit amputation

Archana Prabahar, Connie S. Chamberlain, Ray Vanderby, William L. Murphy, William Dangelo, Kulkarni Mangesh, Bryan Brown, Barsanjit Mazumder, Stephen Badylak, Peng Jiang

PLOS Computational Biology: published April 9, 2025 | https://doi.org/10.1371/journal.pcbi.1012997

Comprehensive characterization of respiratory genes based on a computational framework in pan-cancer to develop stratified treatment strategies

Caiyu Zhang, Chenyu Liu, Zhuoru Wang, Di Wang, Wenli Chen, Jian Li, Qianyi Lu, Jiajun Zhou, Yetong Chang, Peng Wang, Yue Gao, Junwei Wang, Hui Zhi, Shangwei Ning

PLOS Computational Biology: published April 9, 2025 | https://doi.org/10.1371/journal.pcbi.1012963

Flow mechanisms of the air-blood barrier

James B. Grotberg, Francesco Romanò, John C. Grotberg

PLOS Computational Biology: published April 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012917

A comprehensive investigation of intracortical and corticothalamic models of the alpha rhythm

Sorenza P. Bastiaens, Davide Momi, John D. Griffiths

PLOS Computational Biology: published April 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012926

Biases in neural population codes with a few active neurons

Sander W. Keemink, Mark C.W. van Rossum

PLOS Computational Biology: published April 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012969

Virtual epilepsy patient cohort: Generation and evaluation

Borana Dollomaja, Huifang E. Wang, Maxime Guye, Julia Makhalova, Fabrice Bartolomei, Viktor K. Jirsa

PLOS Computational Biology: published April 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012911

Dynamic brain connectivity predicts emotional arousal during naturalistic movie-watching

Jin Ke, Hayoung Song, Zihan Bai, Monica D. Rosenberg, Yuan Chang Leong

PLOS Computational Biology: published April 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012994

How does date-rounding affect phylodynamic inference for public health?

Leo A. Featherstone, Danielle J. Ingle, Wytamma Wirth, Sebastian Duchene

PLOS Computational Biology: published April 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012900

IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes

Caesar Tawfeeq, Jiyao Wang, Umesh Khaniya, Thomas Madej, James Song, Ravinder Abrol, Philippe Youkharibache

PLOS Computational Biology: published April 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012813

A teaching proposal for a short course on biomedical data science

Davide Chicco, Vasco Coelho

PLOS Computational Biology: published April 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012946

On the validity of electric brain signal predictions based on population firing rates

Torbjørn V. Ness, Tom Tetzlaff, Gaute T. Einevoll, David Dahmen

PLOS Computational Biology: published April 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012303

Limitations and optimizations of cellular lineages tracking

Nava Leibovich, Sidhartha Goyal

PLOS Computational Biology: published April 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012880

A generalized higher-order correlation analysis framework for multi-omics network inference

Weixuan Liu, Katherine A. Pratte, Peter J. Castaldi, Craig Hersh, Russell P. Bowler, Farnoush Banaei-Kashani, Katerina J. Kechris

PLOS Computational Biology: published April 14, 2025 | https://doi.org/10.1371/journal.pcbi.1011842

Revealing non-trivial information structures in aneural biological tissues via functional connectivity

Douglas Blackiston, Hannah Dromiack, Caitlin Grasso, Thomas F Varley, Douglas G Moore, Krishna Kannan Srinivasan, Olaf Sporns, Joshua Bongard, Michael Levin, Sara I Walker

PLOS Computational Biology: published April 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012149

Estimating R_e and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2

Emma B Hodcroft, Martin S Wohlfender, Richard A Neher, Julien Riou, Christian L Althaus

PLOS Computational Biology: published April 15, 2025 | https://doi.org/10.1371/journal.pcbi.1012960

Modelling the spatiotemporal dynamics of senescent cells in wound healing, chronic wounds, and fibrosis

Sharmilla Chandrasegaran, James P. Sluka, Daryl Shanley

PLOS Computational Biology: published April 15, 2025 | https://doi.org/10.1371/journal.pcbi.1012298

Quantifying expression and metabolic activity of genes regulated by pregnane X receptor in primary human hepatocyte spheroids

Lukáš Lochman, Ellen Tanaka Kahiya, Bechara Saade, Tomáš Smutný, Jurjen Duintjer Tebbens, Petr Pávek, Veronika Bernhauerová

PLOS Computational Biology: published April 15, 2025 | https://doi.org/10.1371/journal.pcbi.1012886

Perceptual learning improves discrimination but does not reduce distortions in appearance

Sarit F.A. Szpiro, Charlie S. Burlingham, Eero P. Simoncelli, Marisa Carrasco

PLOS Computational Biology: published April 15, 2025 | https://doi.org/10.1371/journal.pcbi.1012980

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

Fillipe Georgiou, Camille Buhl, J. E. F. Green, Bishnu Lamichhane, Ngamta Thamwattana

PLOS Computational Biology: published April 15, 2025 | https://doi.org/10.1371/journal.pcbi.1011469

Lipidome visualisation, comparison, and analysis in a vector space

Timur Olzhabaev, Lukas Müller, Daniel Krause, Dominik Schwudke, Andrew Ernest Torda

PLOS Computational Biology: published April 15, 2025 | https://doi.org/10.1371/journal.pcbi.1012892

How distinct sources of nuisance variability in natural images and scenes limit human stereopsis

David N. White, Johannes Burge

PLOS Computational Biology: published April 15, 2025 | https://doi.org/10.1371/journal.pcbi.1012945

Viral escape-inspired framework for structure-guided dual bait protein biosensor design

Yee Chuen Teoh, Mohammed Sakib Noor, Sina Aghakhani, Jack Girton, Guiping Hu, Ratul Chowdhury

PLOS Computational Biology: published April 15, 2025 | https://doi.org/10.1371/journal.pcbi.1012964

Fitting dynamic measles models to subnational case notification data from Ethiopia: Methodological challenges and key considerations

Alyssa N. Sbarra, Emily Haeuser, Samuel Kidane, Andargie Abate, Ayele M. Abebe, Muktar Ahmed, Tsegaye Alemayehu, Erkihun Amsalu, Aleksandr Y. Aravkin, Akeza A. Asgedom, Nebiyou Bayleyegn, Mulat Dagnew, Biniyam Demisse, Werku Etafa, Getahun Fetensa, Teferi G. Gebremeskel, Habtamu Geremew, Abraham T. Gizaw, Gamechu A. Hunde, Hadush N. Meles, Sibhat Migbar, Jason Q. Nguyen, Eshetu Nigussie, Rebecca E. Ramshaw, Sam Rolfe, Biniyam Sahiledengle, Noga Shalev, Yonatan Solomon, Latera Tesfaye, Gesila E. Yesera, Mark Jit, Jonathan F. Mosser

PLOS Computational Biology: published April 16, 2025 | https://doi.org/10.1371/journal.pcbi.1012922

Contributions of mechanical loading and hormonal changes to eccentric hypertrophy during volume overload: A Bayesian analysis using logic-based network models

Johane H. Bracamonte, Lionel Watkins, Betty Pat, Louis J. Dell’Italia, Jeffrey J. Saucerman, Jeffrey W. Holmes

PLOS Computational Biology: published April 16, 2025 | https://doi.org/10.1371/journal.pcbi.1012390

A Boolean network model of hypoxia, mechanosensing and TGF-β signaling captures the role of phenotypic plasticity and mutations in tumor metastasis

Grant Greene, Ian Zonfa, Erzsébet Ravasz Regan

PLOS Computational Biology: published April 16, 2025 | https://doi.org/10.1371/journal.pcbi.1012735

Modeling diffusive search by non-adaptive sperm: Empirical and computational insights

Benjamin M. Brisard, Kylie D. Cashwell, Stephanie M. Stewart, Logan M. Harrison, Aidan C. Charles, Chelsea V. Dennis, Ivie R. Henslee, Ethan L. Carrow, Heather A. Belcher, Debajit Bhowmick, Paul W. Vos, Maciej Majka, Martin Bier, David M. Hart, Cameron A. Schmidt

PLOS Computational Biology: published April 17, 2025 | https://doi.org/10.1371/journal.pcbi.1012865

Joint estimation of hand-foot-mouth disease model and prediction in korea using the ensemble kalman filter

Wasim Abbas, Sieun Lee, Sangil Kim

PLOS Computational Biology: published April 17, 2025 | https://doi.org/10.1371/journal.pcbi.1012996

Mycobacterium susceptibility to ivermectin by inhibition of eccD3, an ESX-3 secretion system component.

Ana Laura Granados-Tristán, Mauricio Carrillo-Tripp, Carlos Eduardo Hernández-Luna, Aldo Herrera-Rodulfo, Laura Adiene González-Escalante, Ana Leticia Arriaga-Guerrero, Beatriz Silva-Ramírez, Brenda Leticia Escobedo-Guajardo, Roberto Mercado-Hernández, Mario Bermúdez de León, Katia Peñuelas-Urquides

PLOS Computational Biology: published April 17, 2025 | https://doi.org/10.1371/journal.pcbi.1012936

Traveling waves in the human visual cortex: An MEG-EEG model-based approach

Laetitia Grabot, Garance Merholz, Jonathan Winawer, David J. Heeger, Laura Dugué

PLOS Computational Biology: published April 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013007

Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics

Alexander Morin, Ching Pan Chu, Paul Pavlidis

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012962

Theory of axo-axonic inhibition

Romain Brette

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013047

The NOSTRA model: Coherent estimation of infection sources in the case of possible nosocomial transmission

David J. Pascall, Christopher Jackson, Stephanie Evans, Theodore Gouliouris, Christopher J.R. Illingworth, Stefan G. Piatek, Julie V. Robotham, Oliver Stirrup, Ben Warne, Judith Breuer, Daniela De Angelis

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012949

A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes

Ihab Hashem, Jian Wang, Jan F.M. Van Impe

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012974

The confidence-noise confidence-boost (CNCB) model of confidence rating data

Pascal Mamassian, Vincent de Gardelle

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012451

Transfer learning of multicellular organization via single-cell and spatial transcriptomics

Yecheng Tan, Ai Wang, Zezhou Wang, Wei Lin, Yan Yan, Qing Nie, Jifan Shi

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012991

Temporal resolution of spike coding in feedforward networks with signal convergence and divergence

Zach Mobille, Usama Bin Sikandar, Simon Sponberg, Hannah Choi

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012971

Modelling transmission thresholds and hypoendemic stability for onchocerciasis elimination

Jacob N. Stapley, Jonathan I.D. Hamley, Maria-Gloria Basáñez, Martin Walker

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013026

Statistical signature of subtle behavioral changes in large-scale assays

Alexandre Blanc, François Laurent, Alex Barbier-Chebbah, Hugues Van Assel, Benjamin T. Cocanougher, Benjamin M.W. Jones, Peter Hague, Marta Zlatic, Rayan Chikhi, Christian L. Vestergaard, Tihana Jovanic, Jean-Baptiste Masson, Chloé Barré

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012990

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning

Matheus VF Ferraz, W Camilla S Adan, Tayná E Lima, Adriele JC Santos, Sérgio O de Paula, Rafael Dhalia, Gabriel L Wallau, Rebecca C Wade, Isabelle FT Viana, Roberto D Lins

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012921

Fluid and solute transport by cells and a model of systemic circulation

Yufei Wu, Morgan A. Benson, Sean X. Sun

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012935

Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model

Ian Roberts, Richard G. Everitt, Jere Koskela, Xavier Didelot

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012995

A new paradigm considering multicellular adhesion, repulsion and attraction represent diverse cellular tile patterns

Jose A. Carrillo, Hideki Murakawa, Makoto Sato, Miaoxing Wang

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1011909

A computational account of multiple motives guiding context-dependent prosocial behavior

Claire Lugrin, Jie Hu, Christian C. Ruff

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013032

Meta-Reinforcement Learning reconciles surprise, value, and control in the anterior cingulate cortex

Tim Vriens, Eliana Vassena, Giovanni Pezzulo, Gianluca Baldassarre, Massimo Silvetti

PLOS Computational Biology: published April 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013025

Repetitive training enhances the pattern recognition capability of cultured neural networks

Wen-Wei Shao, Qi Shao, Hai-Huan Xu, Guan-Ji Qiao, Run-Xuan Wang, Zhi-Yun Ma, Wei-Wei Meng, Zhuo-Bin Yang, Yun-Liang Zang, Xiao-Hong Li

PLOS Computational Biology: published April 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013043

Emergence and maintenance of modularity in neural networks with Hebbian and anti-Hebbian inhibitory STDP

Raphaël Bergoin, Alessandro Torcini, Gustavo Deco, Mathias Quoy, Gorka Zamora-López

PLOS Computational Biology: published April 22, 2025 | https://doi.org/10.1371/journal.pcbi.1012973

Mechanism of Arrhythmogenesis Driven by Early After Depolarizations in Cardiac Tissue

Jack Stein, D’Artagnan Greene, Flavio Fenton, Yohannes Shiferaw

PLOS Computational Biology: published April 22, 2025 | https://doi.org/10.1371/journal.pcbi.1012635

TGF-M: Topology-augmented geometric features enhance molecular property prediction

Wei He, Xu Tian, Xue Li, Peifu Han, Shuang Wang, Lin Liu, Tao Song

PLOS Computational Biology: published April 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013004

Cell-type-specific firing patterns in a V1 cortical column model depend on feedforward and feedback-driven states

Giulia Moreni, Rares A. Dorcioman, Cyriel M. A. Pennartz, Jorge F. Mejias

PLOS Computational Biology: published April 23, 2025 | https://doi.org/10.1371/journal.pcbi.1012036

An evolutionary model of rhythmic accelerando in animal vocal signalling

Yannick Jadoul, Taylor A. Hersh, Elias Fernández Domingos, Marco Gamba, Livio Favaro, Andrea Ravignani

PLOS Computational Biology: published April 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013011

Resource competition-driven bistability and stochastic switching amplify gene expression noise

Hanah Goetz, Rong Zhang, Xiao Wang, Xiao-Jun Tian

PLOS Computational Biology: published April 23, 2025 | https://doi.org/10.1371/journal.pcbi.1012931

Complexity reduction by symmetry: Uncovering the minimal regulatory network for logical computation in bacteria

Luis A. Álvarez-García, Wolfram Liebermeister, Ian Leifer, Hernán A. Makse

PLOS Computational Biology: published April 24, 2025 | https://doi.org/10.1371/journal.pcbi.1013005

Efficient discovery of frequently co-occurring mutations in a sequence database with matrix factorization

Michael Robert Kolar, Debasis Mitra, Valerie Kobzarenko

PLOS Computational Biology: published April 24, 2025 | https://doi.org/10.1371/journal.pcbi.1012391

Balancing complexity, performance and plausibility to meta learn plasticity rules in recurrent spiking networks

Basile Confavreux, Everton J. Agnes, Friedemann Zenke, Henning Sprekeler, Tim P. Vogels

PLOS Computational Biology: published April 24, 2025 | https://doi.org/10.1371/journal.pcbi.1012910

Simulating dynamic insecticide selection pressures for resistance management in mosquitoes assuming polygenic resistance

Neil Philip Hobbs, Ian Hastings

PLOS Computational Biology: published April 28, 2025 | https://doi.org/10.1371/journal.pcbi.1012944

scPEDSSC: proximity enhanced deep sparse subspace clustering method for scRNA-seq data

Xiaopeng Wei, Jingli Wu, Gaoshi Li, Jiafei Liu, Xi Wu, Chang He

PLOS Computational Biology: published April 28, 2025 | https://doi.org/10.1371/journal.pcbi.1012924

Dynamic modeling of EEG responses to natural speech reveals earlier processing of predictable words

Jin Dou, Andrew J. Anderson, Aaron S. White, Samuel V. Norman-Haignere, Edmund C. Lalor

PLOS Computational Biology: published April 28, 2025 | https://doi.org/10.1371/journal.pcbi.1013006

Computational modeling of frequency-dependent neocortical response to thalamic neurostimulation in epilepsy

Linda Iris Joseph Tomy, Elif Köksal-Ersöz, Anca Nica, Maxime Yochum, Pascal Benquet, Fabrice Wendling

PLOS Computational Biology: published April 28, 2025 | https://doi.org/10.1371/journal.pcbi.1012943

Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City

Renquan Zhang, Jilei Tai, Qing Yao, Wan Yang, Kai Ruggeri, Jeffrey Shaman, Sen Pei

PLOS Computational Biology: published April 29, 2025 | https://doi.org/10.1371/journal.pcbi.1012979

Structure-based mechanism of RyR channel operation by calcium and magnesium ions

Alexandra Zahradníková, Jana Pavelková, Miroslav Sabo, Sefer Baday, Ivan Zahradník

PLOS Computational Biology: published April 29, 2025 | https://doi.org/10.1371/journal.pcbi.1012950

Heuristic energy-based cyclic peptide design

Qiyao Zhu, Vikram Khipple Mulligan, Dennis Shasha

PLOS Computational Biology: published April 30, 2025 | https://doi.org/10.1371/journal.pcbi.1012290

Foraging animals use dynamic Bayesian updating to model meta-uncertainty in environment representations

James Webb, Paul Steffan, Benjamin Y. Hayden, Daeyeol Lee, Caleb Kemere, Matthew McGinley

PLOS Computational Biology: published April 30, 2025 | https://doi.org/10.1371/journal.pcbi.1012989

Falsifying computational models of endothelial cell network formation through quantitative comparison with in vitro models

Tessa M. Vergroesen, Vincent Vermeulen, Roeland M. H. Merks

PLOS Computational Biology: published April 30, 2025 | https://doi.org/10.1371/journal.pcbi.1012965

Correction

Correction: Mathematical modeling suggests heterogeneous replication of Mycobacterium tuberculosis in rabbits

Vitaly V. Ganusov, Afsal Kolloli, Selvakumar Subbian

PLOS Computational Biology: published April 25, 2025 | https://doi.org/10.1371/journal.pcbi.1013048

Methods

Visualization and quantification of coral reef soundscapes using CoralSoundExplorer software

Lana Minier, Jérémy Rouch, Bamdad Sabbagh, Frédéric Bertucci, Eric Parmentier, David Lecchini, Frédéric Sèbe, Nicolas Mathevon, Rémi Emonet

PLOS Computational Biology: published April 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012050

A spectral framework to map QTLs affecting joint differential networks of gene co-expression

Jiaxin Hu, Jesse N. Weber, Lauren E. Fuess, Natalie C. Steinel, Daniel I. Bolnick, Miaoyan Wang

PLOS Computational Biology: published April 17, 2025 | https://doi.org/10.1371/journal.pcbi.1012953

An expandable synthetic library of human paired antibody sequences

Toma M. Marinov, Perry T. Wasdin, Gwen Jordaan, Alexis K. Janke, Alexandra A. Abu-Shmais, Ivelin S. Georgiev

PLOS Computational Biology: published April 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012932

Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out

Ben Williams, Santiago M. Balvanera, Sarab S. Sethi, Timothy A.C. Lamont, Jamaluddin Jompa, Mochyudho Prasetya, Laura Richardson, Lucille Chapuis, Emma Weschke, Andrew Hoey, Ricardo Beldade, Suzanne C. Mills, Anne Haguenauer, Frederic Zuberer, Stephen D. Simpson, David Curnick, Kate E. Jones

PLOS Computational Biology: published April 28, 2025 | https://doi.org/10.1371/journal.pcbi.1013029

Software

Playbook workflow builder: Interactive construction of bioinformatics workflows

Daniel J.B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Anna I. Byrd, Mano R. Maurya, Sumana Srinivasan, Keyang Yu, Varduhi Petrosyan, Matthew E. Roth, Miroslav Milinkov, Charles Hadley King, Jeet Kiran Vora, Jonathon Keeney, Christopher Nemarich, William Khan, Alexander Lachmann, Nasheath Ahmed, Alexandra Agris, Juncheng Pan, Srinivasan Ramachandran, Eoin Fahy, Emmanuel Esquivel, Aleksandar Mihajlovic, Bosko Jevtic, Vuk Milinovic, Sean Kim, Patrick McNeely, Tianyi Wang, Eric Wenger, Miguel A. Brown, Alexander Sickler, Yuankun Zhu, Sherry L. Jenkins, Philip D. Blood, Deanne M. Taylor, Adam C. Resnick, Raja Mazumder, Aleksandar Milosavljevic, Shankar Subramaniam, Avi Ma’ayan

PLOS Computational Biology: published April 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012901

Editorial Notes

Editorial Note: In silico knockout studies of xenophagic capturing of Salmonella

The PLOS Computational Biology Editors

PLOS Computational Biology: published April 9, 2025 | https://doi.org/10.1371/journal.pcbi.1012998

Editorial Note: Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis

The PLOS Computational Biology Editors

PLOS Computational Biology: published April 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013003

Expression of Concern

Expression of Concern: HiSV: A control-free method for structural variation detection from Hi-C data

The PLOS Computational Biology Editors

PLOS Computational Biology: published April 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013016

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April 2025

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An MEG-EEG model-based approach to study traveling waves

Education Articles

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Correction

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Expression of Concern

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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