PLOS Computational Biology

2005 - 2025

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Volume 21, issue 4, 2025

Ten quick tips to get you started with Bayesian statistics pp. 1-13

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

DelaySSA: stochastic simulation of biochemical systems and gene regulatory networks with or without time delays pp. 1-13

Ziyan Jin, Xinyi Zhou and Zhaoyuan Fang

Biases in neural population codes with a few active neurons pp. 1-13

Sander W Keemink and Mark CW van Rossum

On the validity of electric brain signal predictions based on population firing rates pp. 1-29

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

Dynamic brain connectivity predicts emotional arousal during naturalistic movie-watching pp. 1-26

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

Simulating dynamic insecticide selection pressures for resistance management in mosquitoes assuming polygenic resistance pp. 1-37

Neil Philip Hobbs and Ian Hastings

Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model pp. 1-37

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

Limitations and optimizations of cellular lineages tracking pp. 1-18

Nava Leibovich and Sidhartha Goyal

MINT: A toolbox for the analysis of multivariate neural information coding and transmission pp. 1-18

Gabriel Matías Lorenz, Nicola Marie Engel, Marco Celotto, Loren Koçillari, Sebastiano Curreli, Tommaso Fellin and Stefano Panzeri

Falsifying computational models of endothelial cell network formation through quantitative comparison with in vitro models pp. 1-18

Tessa M Vergroesen, Vincent Vermeulen and Roeland M H Merks

Meta-Reinforcement Learning reconciles surprise, value, and control in the anterior cingulate cortex pp. 1-18

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

Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out pp. 1-18

Ben Williams, Santiago M Balvanera, Sarab S Sethi, Timothy AC 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 and Kate E Jones

RMPJ: An ImageJ plugin for morphological information processing in biomedical images pp. 1-10

Yoshitaka Kimori

A computational account of multiple motives guiding context-dependent prosocial behavior pp. 1-34

Claire Lugrin, Jie Hu and Christian C Ruff

scPEDSSC: proximity enhanced deep sparse subspace clustering method for scRNA-seq data pp. 1-15

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

Quantifying the impact of contact tracing interview prioritisation strategies on disease transmission: A modelling study pp. 1-14

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

A teaching proposal for a short course on biomedical data science pp. 1-16

Davide Chicco and Vasco Coelho

The multiscale self-similarity of the weighted human brain connectome pp. 1-20

Laia Barjuan, Muhua Zheng and M Ángeles Serrano

Statistical signature of subtle behavioral changes in large-scale assays pp. 1-28

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

Dynamic modeling of EEG responses to natural speech reveals earlier processing of predictable words pp. 1-28

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

The confidence-noise confidence-boost (CNCB) model of confidence rating data pp. 1-25

Pascal Mamassian and Vincent de Gardelle

Modeling diffusive search by non-adaptive sperm: Empirical and computational insights pp. 1-25

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 and Cameron A Schmidt

Quantifying expression and metabolic activity of genes regulated by pregnane X receptor in primary human hepatocyte spheroids pp. 1-25

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

Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory pp. 1-19

Atsushi Matsuda and Mohammad R K Mofrad

Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2 pp. 1-19

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

A new paradigm considering multicellular adhesion, repulsion and attraction represent diverse cellular tile patterns pp. 1-23

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

A generalized higher-order correlation analysis framework for multi-omics network inference pp. 1-33

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

Heuristic energy-based cyclic peptide design pp. 1-33

Qiyao Zhu, Vikram Khipple Mulligan and Dennis Shasha

Foraging animals use dynamic Bayesian updating to model meta-uncertainty in environment representations pp. 1-41

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

Including population and environmental dynamic heterogeneities in continuum models of collective behaviour with applications to locust foraging and group structure pp. 1-21

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

Federated epidemic surveillance pp. 1-21

Ruiqi Lyu, Roni Rosenfeld and Bryan Wilder

Balancing complexity, performance and plausibility to meta learn plasticity rules in recurrent spiking networks pp. 1-21

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

A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes pp. 1-21

Ihab Hashem, Jian Wang and Jan FM Van Impe

Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City pp. 1-21

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

Joint estimation of hand-foot-mouth disease model and prediction in korea using the ensemble kalman filter pp. 1-21

Wasim Abbas, Sieun Lee and Sangil Kim

How distinct sources of nuisance variability in natural images and scenes limit human stereopsis pp. 1-42

David N White and Johannes Burge

Volume 21, issue 3, 2025

Computational studies reveal structural characterization and novel families of Puccinia striiformis f. sp. tritici effectors pp. 1-26

Raheel Asghar, Nan Wu, Noman Ali, Yulei Wang and Mahinur Akkaya

DySCo: A general framework for dynamic functional connectivity pp. 1-32

Giuseppe de Alteriis, Oliver Sherwood, Alessandro Ciaramella, Robert Leech, Joana Cabral, Federico E Turkheimer and Paul Expert

Gauge fixing for sequence-function relationships pp. 1-24

Anna Posfai, Juannan Zhou, David M McCandlish and Justin B Kinney

Post-processing and weighted combination of infectious disease nowcasts pp. 1-24

André Victor Ribeiro Amaral, Daniel Wolffram, Paula Moraga and Johannes Bracher

Synthetic population generation with public health characteristics for spatial agent-based models pp. 1-22

Emma Von Hoene, Amira Roess, Hamdi Kavak and Taylor Anderson

Efficient numerosity estimation under limited time pp. 1-22

Joseph A Heng, Michael Woodford and Rafael Polania

Suprachiasmatic nucleus-wide estimation of oscillatory temporal dynamics pp. 1-22

Yifan Yao, Scott Pauls, Duncan Foley, Tomoko Yoshikawa, Sato Honma, Ken-Ichi Honma, Ellie McVeigh, Nicolas C Foley and Rae Silver

GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data pp. 1-25

Simonida Zehr, Sebastian Wolf, Thomas Oellerich, Matthias S Leisegang, Ralf P Brandes, Marcel H Schulz and Timothy Warwick

Exploring the transmission of cognitive task information through optimal brain pathways pp. 1-28

Zhengdong Wang, Yifeixue Yang, Ziyi Huang, Wanyun Zhao, Kaiqiang Su, Hengcheng Zhu and Dazhi Yin

Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills pp. 1-28

Russell Dinnage and Marian Kleineberg

Volume 21, issue 2, 2025

ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature pp. 1-33

Luca Musella, Alejandro Afonso Castro, Xin Lai, Max Widmann and Julio Vera

Early detection of disease outbreaks and non-outbreaks using incidence data: A framework using feature-based time series classification and machine learning pp. 1-21

Shan Gao, Amit K Chakraborty, Russell Greiner, Mark A Lewis and Hao Wang

Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities pp. 1-21

Lars Berling, Jonathan Klawitter, Remco Bouckaert, Dong Xie, Alex Gavryushkin and Alexei J Drummond

Bayesian classification of OXPHOS deficient skeletal myofibres pp. 1-22

Jordan Childs, Tiago Bernardino Gomes, Amy E Vincent, Andrew Golightly and Conor Lawless

SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data pp. 1-22

Shunsuke A Sakai, Ryosuke Nomura, Satoi Nagasawa, SungGi Chi, Ayako Suzuki, Yutaka Suzuki, Mitsuho Imai, Yoshiaki Nakamura, Takayuki Yoshino, Shumpei Ishikawa, Katsuya Tsuchihara, Shun-Ichiro Kageyama and Riu Yamashita

Repeated games with partner choice pp. 1-19

Christopher Graser, Takako Fujiwara-Greve, Julián García and Matthijs van Veelen

Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA pp. 1-23

Eliezyer Fermino de Oliveira, Pranjal Garg, Jens Hjerling-Leffler, Renata Batista-Brito and Lucas Sjulson

AWGE-ESPCA: An edge sparse PCA model based on adaptive noise elimination regularization and weighted gene network for Hermetia illucens genomic data analysis pp. 1-23

Rui Miao, Hao-Yang Yu, Bing-Jie Zhong, Hong-Xia Sun and Qiang Xia

A SuperLearner-based pipeline for the development of DNA methylation-derived predictors of phenotypic traits pp. 1-20

Dennis Khodasevich, Nina Holland, Lars van der Laan and Andres Cardenas

Compression-enabled interpretability of voxelwise encoding models pp. 1-20

Fatemeh Kamali, Amir Abolfazl Suratgar, Mohammadbagher Menhaj and Reza Abbasi-Asl

An application of nowcasting methods: Cases of norovirus during the winter 2023/2024 in England pp. 1-20

Jonathon Mellor, Maria L Tang, Emilie Finch, Rachel Christie, Oliver Polhill, Christopher E Overton, Ann Hoban, Amy Douglas, Sarah R Deeny and Thomas Ward

Optimal control prevents itself from eradicating stochastic disease epidemics pp. 1-25

Rachel Russell and Nik J Cunniffe

Ten simple rules for fostering creativity in research labs pp. 1-7

Matthias C Rillig

Ten quick tips to build a Model Life Cycle pp. 1-10

Timothée Poisot, Daniel J Becker, Cole B Brookson, Ellie Graeden, Sadie J Ryan, Gemma Turon and Colin Carlson

Reliability-enhanced data cleaning in biomedical machine learning using inductive conformal prediction pp. 1-27

Xianghao Zhan, Qinmei Xu, Yuanning Zheng, Guangming Lu and Olivier Gevaert

Nowcasting reported covid-19 hospitalizations using de-identified, aggregated medical insurance claims data pp. 1-26

Xueda Shen, Aaron Rumack, Bryan Wilder and Ryan J Tibshirani

Using a multi-strain infectious disease model with physical information neural networks to study the time dependence of SARS-CoV-2 variants of concern pp. 1-26

Wenxuan Li, Xu Chen, Suli Liu, Chiyu Zhang and Guyue Liu

Hexagons all the way down: grid cells as a conformal isometric map of space pp. 1-26

Vemund Sigmundson Schøyen, Kosio Beshkov, Markus Borud Pettersen, Erik Hermansen, Konstantin Holzhausen, Anders Malthe-Sørenssen, Marianne Fyhn and Mikkel Elle Lepperød

Identification of recurrent dynamics in distributed neural populations pp. 1-26

Rodrigo Osuna-Orozco, Edward Castillo, Kameron Decker Harris and Samantha R Santacruz

Information transmission in a cell monolayer: A numerical study pp. 1-24

Paweł Nałęcz-Jawecki, Przemysław Szyc, Frederic Grabowski, Marek Kochańczyk and Tomasz Lipniacki

Volume 21, issue 1, 2025

The calcitron: A simple neuron model that implements many learning rules via the calcium control hypothesis pp. 1-30

Toviah Moldwin, Li Shay Azran and Idan Segev

A robust transfer learning approach for high-dimensional linear regression to support integration of multi-source gene expression data pp. 1-16

Lulu Pan, Qian Gao, Kecheng Wei, Yongfu Yu, Guoyou Qin and Tong Wang

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data pp. 1-28

Evan Gorstein, Rosa Aghdam and Claudia Solís-Lemus

Role and modulation of various spinal pathways for human upper limb control in different gravity conditions pp. 1-20

Alice Bruel, Lina Bacha, Emma Boehly, Constance De Trogoff, Luca Represa, Gregoire Courtine and Auke Ijspeert

Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers pp. 1-20

Kwang Su Kim, Masashi Iwamoto, Kosaku Kitagawa, Hyeongki Park, Sanae Hayashi, Senko Tsukuda, Takeshi Matsui, Masanori Atsukawa, Kentaro Matsuura, Natthaya Chuaypen, Pisit Tangkijvanich, Lena Allweiss, Takara Nishiyama, Naotoshi Nakamura, Yasuhisa Fujita, Eiryo Kawakami, Shinji Nakaoka, Masamichi Muramatsu, Kazuyuki Aihara, Takaji Wakita, Alan S Perelson, Maura Dandri, Koichi Watashi, Shingo Iwami and Yasuhito Tanaka

Data-driven discovery and parameter estimation of mathematical models in biological pattern formation pp. 1-25

Hidekazu Hishinuma, Hisako Takigawa-Imamura and Takashi Miura

Benchmarking uncertainty quantification for protein engineering pp. 1-19

Kevin P Greenman, Ava P Amini and Kevin K Yang

Trajectory inference from single-cell genomics data with a process time model pp. 1-33

Meichen Fang, Gennady Gorin and Lior Pachter

Integration of unpaired single cell omics data by deep transfer graph convolutional network pp. 1-21

Yulong Kan, Yunjing Qi, Zhongxiao Zhang, Xikeng Liang, Weihao Wang and Shuilin Jin

Ten simple rules for good model-sharing practices pp. 1-21

Ismael Kherroubi Garcia, Christopher Erdmann, Sandra Gesing, Michael Barton, Lauren Cadwallader, Geerten Hengeveld, Christine R Kirkpatrick, Kathryn Knight, Carsten Lemmen, Rebecca Ringuette, Qing Zhan, Melissa Harrison, Feilim Mac Gabhann, Natalie Meyers, Cailean Osborne, Charlotte Till, Paul Brenner, Matt Buys, Min Chen, Allen Lee, Jason Papin and Yuhan Rao

Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data pp. 1-21

Xu Shi, Xiao Wang, Lu Jin, Leena Halakivi-Clarke, Robert Clarke, Andrew F Neuwald and Jianhua Xuan

Bayesian active sound localisation: To what extent do humans perform like an ideal-observer? pp. 1-22

Glen McLachlan, Piotr Majdak, Jonas Reijniers, Michael Mihocic and Herbert Peremans

Eight quick tips for biologically and medically informed machine learning pp. 1-13

Luca Oneto and Davide Chicco

Deciphering the interplay between biology and physics with a finite element method-implemented vertex organoid model: A tool for the mechanical analysis of cell behavior on a spherical organoid shell pp. 1-29

Julien Laussu, Deborah Michel, Léa Magne, Stephane Segonds, Steven Marguet, Dimitri Hamel, Muriel Quaranta-Nicaise, Frederick Barreau, Emmanuel Mas, Vincent Velay, Florian Bugarin and Audrey Ferrand

Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense pp. 1-29

Nicole M Moody, Cole M Williams, Sohini Ramachandran and Matthew J Fuxjager

Exploiting the similarity of dissimilarities for biomedical applications and enhanced machine learning pp. 1-12

Mohammad Neamul Kabir, Li Rong Wang and Wilson Wen Bin Goh

Multi-region infectious disease prediction modeling based on spatio-temporal graph neural network and the dynamic model pp. 1-26

Xiaoyi Wang and Zhen Jin

Mechanisms for dysregulation of excitatory-inhibitory balance underlying allodynia in dorsal horn neural subcircuits pp. 1-37

Alexander G Ginsberg, Scott F Lempka, Bo Duan, Victoria Booth and Jennifer Crodelle

Ten simple rules to complete successfully a computational MSc thesis project pp. 1-10

Edoardo Saccenti and Cristina Furlan

Extracting the fingerprints of sequences of random rhythmic auditory stimuli from electrophysiological data pp. 1-18

Fernando A Najman, Antonio Galves, Marcela Svarc and Claudia D Vargas

Optimal control of agent-based models via surrogate modeling pp. 1-27

Luis L Fonseca, Lucas Böttcher, Borna Mehrad and Reinhard C Laubenbacher

Learning predictive signatures of HLA type from T-cell repertoires pp. 1-15

María Ruiz Ortega, Mikhail V Pogorelyy, Anastasia A Minervina, Paul G Thomas, Thierry Mora and Aleksandra M Walczak