PLOS Computational Biology

2005 - 2026

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Volume 22, issue 3, 2026

From noise to models to numbers: Evaluating negative binomial models and parameter estimations in single-cell RNA-seq pp. 1-37

Yiling Wang, Zhanpeng Shu, Zhixing Cao and Ramon Grima

iSTTC: A robust method for accurate estimation of intrinsic neural timescales from single-unit recordings pp. 1-30

Irina Pochinok, Ileana L Hanganu-Opatz and Mattia Chini

Inverse game theory characterizes frequency-dependent selection driven by karyotypic diversity in triple negative breast cancer pp. 1-18

Thomas Veith, Richard J Beck, Joel S Brown and Noemi Andor

Morphological determinants of glycosylation efficiency in Golgi cisternae pp. 1-18

Christopher K Revell, Martin Lowe, Nicola L Stevenson and Oliver E Jensen

An approximate-copula distribution for statistical modeling pp. 1-21

Sarah S Ji, Benjamin B Chu, Hua Zhou and Kenneth Lange

Sub-national modelling of surveillance sensitivity to inform declaration of disease elimination: A retrospective validation against the elimination of wild poliovirus in Nigeria pp. 1-21

Emily S Nightingale, Ly Pham-Minh, Isah Mohammed Bello, Samuel Okrior, Tesfaye Bedada Erbeto, Marycelin Baba, Adekunle Adeneji, Megan Auzenbergs, W John Edmunds and Kathleen M O’Reilly

Assessing the impact of climate and control interventions on spatio-temporal malaria dynamics using a stochastic metapopulation model pp. 1-21

Alexandros Angelakis, Anton Beloconi, Bryan O Nyawanda, Sammy Khagayi, Simon Kariuki, Stephen Munga, Patrick K Munywoki, Godfrey Bigogo and Penelope Vounatsou

Separating random and deterministic sources of computational noise in explore-exploit decisions pp. 1-21

Siyu Wang and Robert C Wilson

Assessment of dispersion metrics for estimating single-cell transcriptional variability pp. 1-21

Tina Chen, Laurie A Boyer and Divyansh Agarwal

Mechanism of Hsp70 activation: How J-domain proteins push for ATP hydrolysis pp. 1-21

Michał Olewniczak, Marcin Pitek, Jacek Czub, Jaroslaw Marszalek, Łukasz Nierzwicki and Bartlomiej Tomiczek

Contextual inference through flexible integration of environmental features and behavioural outcomes pp. 1-42

Jessica Passlack and Andrew F MacAskill

Bayesian-calibrated global sensitivity analysis for mathematical models using generative AI pp. 1-28

Xuyuan Wang

Fast and accessible morphology-free functional fluorescence imaging analysis pp. 1-22

Alejandro Estrada Berlanga, Gabrielle Y Kang, Amanda Kwok, Thomas Broggini, Jennifer Lawlor, Kishore V Kuchibhotla, David Kleinfeld, Gal Mishne and Adam S Charles

Large-scale paired chain BCR analysis reveals antibody clonal family inference bias and enhances resolution with machine learning pp. 1-22

Hao Wang, Kaixuan Wang, Qihang Xu, Linru Cai, Chuanxiang Huang, Linlin Chen, Yunliang Zang, Xihao Hu and Jian Zhang

Epistasis mediates the role of negative frequency-dependent selection in bacterial strain structure pp. 1-22

Martin Guillemet and Sonja Lehtinen

Predicting viral sensitivity to antibodies using genetic sequences and antibody similarities pp. 1-22

Kai S Shimagaki, Gargi Kher, Rebecca M Lynch and John P Barton

Online tutorial on survival analysis for biomarker discovery pp. 1-11

Jaka Kokošar, Ela Praznik, Martin Špendl, Nancy P Moreno, Alana Newell, Gad Shaulsky and Blaž Zupan

Free energy perturbations in enzyme kinetic models reveal cryptic epistasis pp. 1-16

Karol Buda and Nobuhiko Tokuriki

Approximate Bayesian inference of directed acyclic graphs in biology with flexible priors on edge states pp. 1-24

Evan A Martin, Venkata Patchigolla and Audrey Qiuyan Fu

A reinforcement learning and sequential sampling model constrained by gaze data pp. 1-24

William M Hayes and Melanie J Touchard

ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries pp. 1-19

Moritz Hanke, Theresa Harten and Ronja Foraita

PepLM-GNN: A graph neural network framework leveraging pre-trained language models for peptide-protein binding prediction pp. 1-19

Ke Yan, Meijing Li, Shutao Chen, Tianyi Liu, Jing Hao, Bin Liu and Zhen Li

napariTFM: An open-source tool for traction force microscopy and monolayer stress microscopy pp. 1-15

Artur Ruppel, Dennis Wörthmüller, Martial Balland and François Fagotto

MoCETSE: A mixture-of-convolutional experts and transformer-based model for predicting Gram-negative bacterial secreted effectors pp. 1-23

Hua Shi, Yihang Lin, Dachen Liu and Quan Zou

Overcoming extrapolation challenges of deep learning by incorporating physics in protein sequence-function modeling pp. 1-23

Shrishti Barethiya, Jian Huang, Clarice Stumpf, Xiao Liu, Hui Guan and Jianhan Chen

Multi-ACPNet: A multi-scale sequence-structure feature fusion framework for anticancer peptide identification and functional prediction pp. 1-23

Lu Meng and Lijun Zhou

D-LIM: A neural network for interpretable gene–gene interactions pp. 1-23

Shuhui Wang, Alexandre Allauzen, Philippe Nghe and Vaitea Opuu

Benchmarking spike source localization algorithms in high density probes pp. 1-14

Hao Zhao, Xinhe Zhang, Arnau Marin-Llobet, Xinyi Lin and Jia Liu

Towards model-based characterization of individual electrically stimulated nerve fibers pp. 1-27

Rebecca C Felsheim, David J Sly, Stephen J O’Leary and Mathias Dietz

Multi-omics and network pharmacology identify IGFBP1 as an m6A-Epigenetic target of pueraria in NSCLC therapy pp. 1-29

Rui Li, Dong-Mei Hu, Yong-Li Liu, Wei Zhao, Yu-Xin Zhang and Yi-Qing Qu

Enhancing anticancer peptide discovery: A fusion-centric framework with conditional diffusion for prediction and generation pp. 1-29

Binyu Li, Xin Zhang, Zhihua Huang, Prayag Tiwari, Quan Zou, Yijie Ding and Xiaoyi Guo

Functional bottlenecks can emerge from non-epistatic underlying traits pp. 1-20

Anna Ottavia Schulte, Samar Alqatari, Saverio Rossi and Francesco Zamponi

Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries pp. 1-20

Konstantinos Antonopoulos, Olof Nordenstorm and Avlant Nilsson

Volume 22, issue 2, 2026

A 2D Gabor-wavelet baseline model out-performs a 3D surface model in scene-responsive cortex pp. 1-22

Anna Shafer-Skelton, Timothy F Brady and John T Serences

Degradation graphs reveal hidden proteolytic activity in peptidomes pp. 1-21

Erik Hartman, Johan Malmström and Jonas Wallin

Information theoretic measures of neural and behavioural coupling predict representational drift pp. 1-18

Kristine Heiney, Mónika Józsa, Michael E Rule, Henning Sprekeler, Stefano Nichele and Timothy O’Leary

Cluster dispersal shapes microbial diversity during community assembly pp. 1-18

Loïc Marrec and Sonja Lehtinen

PON-Del predictor for sequence retaining protein deletions pp. 1-18

Haoyang Zhang, Muhammad Kabir and Mauno Vihinen

A theory for self-sustained balanced states in absence of strong external currents pp. 1-38

David Angulo-Garcia and Alessandro Torcini

SpaLSTF: Diffusion-based generative model with BiLSTM and XCA-Transformer for spatial transcriptomics imputation pp. 1-20

Lin Yuan, Yufeng Jiang, Boyuan Meng, Qingxiang Wang, Cuihong Wang and Huang De-Shuang

Start small: A model for tissue-wide planar cell polarity without morphogens pp. 1-29

Abhisha Thayambath and Julio M Belmonte

FKSUDDAPre: A drug–disease association prediction framework based on F-TEST feature selection and AMDKSU resampling with interpretability analysis pp. 1-29

Yun Zuo, Chenyi Zhang, Ge Hua, Qiao Ning, Xiangrong Liu, Xiangxiang Zeng and Zhaohong Deng

Putting BASIL in a BLT: A Bayesian filtering method for estimating the fitness effects of nascent adaptive mutations pp. 1-27

Huan-Yu Kuo and Sergey Kryazhimskiy

Learning genetic perturbation effects with variational causal inference pp. 1-15

Emily Liu, Jiaqi Zhang and Caroline Uhler

Information uncertainty influences learning strategy from sequentially delayed rewards pp. 1-23

Sean R Maulhardt, Alec Solway and Caroline J Charpentier

Introducing gold-standard essential gene datasets for Pseudomonas aeruginosa to enhance Tn-Seq analyses pp. 1-19

Cléophée Van Maele, Ségolène Caboche, Nathan Nicolau-Guillaumet, Anaëlle Muggeo and Thomas Guillard

A framework for evaluating predicted sperm trajectories in crowded microscopy videos pp. 1-19

David Hart, Kylie Cashwell, Anita Bhandari, Jayath Premasinghe and Cameron Schmidt

A comparative study of statistical methods for identifying differentially expressed genes in spatial transcriptomics pp. 1-19

Yishan Wang, Chenxuan Zang, Ziyi Li, Charles C Guo, Dejian Lai and Peng Wei

Efficient Gaussian process-based motor hotspot hunting with concurrent optimization of TMS coil location and orientation pp. 1-17

David Luis Schultheiss, Zsolt Turi, Joschka Boedecker and Andreas Vlachos

Controllable protein design via autoregressive direct coupling analysis conditioned on principal components pp. 1-17

Francesco Caredda, Lisa Gennai, Paolo De Los Rios and Andrea Pagnani

Coevolutionary dynamics of cooperation, risk, and cost in collective risk games pp. 1-13

Lichen Wang, Shijia Hua, Yuyuan Liu, Liang Zhang, Linjie Liu and Attila Szolnoki

CA-CAE: A deep learning-based multi-omics model for pan-cancer subtype classification and prognosis prediction pp. 1-24

Shumei Zhang, Yicheng Lu, Peixian Li, Junxuan Wu, Guohua Wang and Wen Yang

Paraplume: A fast and accurate antibody paratope prediction method provides insights into repertoire-scale binding dynamics pp. 1-25

Gabriel Athènes, Adam Woolfe, Thierry Mora and Aleksandra M Walczak

SHADE: A multilevel Bayesian framework for modeling directional spatial interactions in tissue microenvironments pp. 1-16

Joel Eliason, Michele Peruzzi and Arvind Rao

Volume 22, issue 1, 2026

Persistence diagrams as morphological signatures of cells: A method to measure and compare cells within a population pp. 1-32

Yossi Bokor Bleile, Pooja Yadav, Patrice Koehl and Florian Rehfeldt

Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study pp. 1-20

Tanya T Karagiannis, Ye Chen, Sarah Bald, Albert Tai, Eric R Reed, Sofiya Milman, Stacy L Andersen, Thomas T Perls, Daniel Segrè, Paola Sebastiani and Meghan I Short

Linking brain and behavior states in Zebrafish Larvae locomotion using hidden Markov models pp. 1-27

Mattéo Dommanget-Kott, Jorge Fernandez- de-Cossio-Diaz, Monica Coraggioso, Volker Bormuth, Rémi Monasson, Georges Debrégeas and Simona Cocco

DSCA-HLAII: A dual-stream cross-attention model for predicting peptide–HLA class II interaction and presentation pp. 1-23

Ke Yan, Hongjun Yu, Shutao Chen, Alexey K Shaytan, Bin Liu and Youyu Wang

Powerful large scale inference in high dimensional mediation analysis pp. 1-23

Asmita Roy and Xianyang Zhang

Peak strain dispersion as a nonlinear mediator in HFpEF: Unraveling subtype-specific pathways via SHAP-augmented ensemble modeling pp. 1-15

Mingming Lin, Kai Li, Xiaofan Wang, Juanjuan Sun, Kun Gong, Zhibin Wang and Pin Sun

Exosome-mediated chemotaxis optimizes leader-follower cell migration pp. 1-14

Louis González and Andrew Mugler

Network models for bridging denoising and identifying spatial domains of spatially resolved transcriptomics pp. 1-26

Haiyue Wang, Wensheng Zhang, Zaiyi Liu and Xiaoke Ma

Measuring real-time disease transmissibility with temperature-dependent generation intervals pp. 1-17

Esther Li Wen Choo, Kris V Parag, Jo Yi Chow and Jue Tao Lim

ShapeSpaceExplorer: Analysis of morphological transitions in migrating cells using similarity-based shape space mapping pp. 1-16

Samuel D R Jefferyes, Roswitha Gostner, Laura Cooper, Mohammed M Abdelsamea, Elly Straube, Nasir Rajpoot, David B A Epstein and Anne Straube

Compaction of chromatin domains regulates target search times of proteins pp. 1-25

Shuvadip Dutta, Adarshkrishnan Rajakumar, Ranjith Padinhateeri and Mithun K Mitra

Novel artificial selection method improves function of simulated microbial communities pp. 1-25

Björn Vessman, Pablo Guridi-Fernández, Flor Inés Arias-Sánchez and Sara Mitri

Higher-level spatial prediction in natural vision across mouse visual cortex pp. 1-21

Micha Heilbron and Floris P de Lange

CoFormerSurv: Collaborative transformer for multi-omics survival analysis pp. 1-21

Gang Wen and Limin Li

PlasticEnz: An integrated database and screening tool combining homology and machine learning to identify plastic-degrading enzymes in meta-omics datasets pp. 1-21

Anna Krzynowek, Jasper Snoeks and Karoline Faust

Spatial variation in socio-economic vulnerability to Influenza-like Infection for the US population pp. 1-18

Shrabani S Tripathy, Joseph V Puthussery, Taveen S Kapoor, John R Cirrito and Rajan K Chakrabarty

Hierarchical analysis of RNA secondary structures with pseudoknots based on sections pp. 1-18

Ryota Masuki, Donn Liew and Ee Hou Yong