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

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

PLOS Computational Biology: published January 2, 2026 | https://doi.org/10.1371/journal.pcbi.1013836

GAN-enhanced machine learning and metabolic modeling identify reprogramming in pancreatic cancer

Tahereh Razmpour, Masoud Tabibian, Arman Roohi, Rajib Saha

PLOS Computational Biology: published January 2, 2026 | https://doi.org/10.1371/journal.pcbi.1013862

Beyond the first glance: How human presence enhances visual entropy and promotes spatial learning

Tracy Sánchez Pacheco, Debora Nolte, Sabine U. König, Gordon Pipa, Peter König

PLOS Computational Biology: published January 5, 2026 | https://doi.org/10.1371/journal.pcbi.1013173

A modelling assessment of the impact of control measures on highly pathogenic avian influenza transmission in poultry in Great Britain

Christopher N. Davis, Edward M. Hill, Chris P. Jewell, Kristyna Rysava, Robin N. Thompson, Michael J. Tildesley

PLOS Computational Biology: published January 5, 2026 | https://doi.org/10.1371/journal.pcbi.1013874

Linking brain and behavior states in Zebrafish Larvae locomotion using hidden Markov models

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

PLOS Computational Biology: published January 5, 2026 | https://doi.org/10.1371/journal.pcbi.1013762

Biologically-constrained spiking neural network for neuromodulation in locomotor recovery after spinal cord injury

Raymond Chia, Chin-Teng Lin

PLOS Computational Biology: published January 6, 2026 | https://doi.org/10.1371/journal.pcbi.1013866

TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations

Devin Burke, Jishnu Raychaudhuri, Edward Chuong, William Taylor, Ryan Layer

PLOS Computational Biology: published January 6, 2026 | https://doi.org/10.1371/journal.pcbi.1013122

CoFormerSurv: Collaborative transformer for multi-omics survival analysis

Gang Wen, Limin Li

PLOS Computational Biology: published January 7, 2026 | https://doi.org/10.1371/journal.pcbi.1013875

The role of ducks in detecting Highly Pathogenic Avian Influenza in small-scale backyard poultry farms

Steven Xingyu Wu, Christopher N. Davis, Mark Arnold, Michael J. Tildesley

PLOS Computational Biology: published January 9, 2026 | https://doi.org/10.1371/journal.pcbi.1013357

Overcoming the widespread flaws in the annotation of vertebrate selenoprotein genes in public databases

Max Ticó, Emerson Sullivan, Roderic Guigó, Marco Mariotti

PLOS Computational Biology: published January 12, 2026 | https://doi.org/10.1371/journal.pcbi.1013885

Characterization of the heterogeneity in SARS-CoV-2 fitness dynamics via graph representation learning

Zengmiao Wang, Ziqin Zhou, Junfu Wang, Lingyue Yang, Zhirui Zhang, Weina Xu, Zeming Liu, Yuxi Ge, Liang Yang, Xiaoli Wang, Peng Yang, Quanyi Wang, Yunlong Cao, Yuanfang Guo, Huaiyu Tian

PLOS Computational Biology: published January 12, 2026 | https://doi.org/10.1371/journal.pcbi.1013582

The role of the spleen in red blood cell loss caused by malaria: A mathematical model

Robert Moss, Saber Dini, Steven Kho, Bridget E. Barber, Pierre A. Buffet, Megha Rajasekhar, David J. Price, Nicholas M. Anstey, Julie A. Simpson

PLOS Computational Biology: published January 12, 2026 | https://doi.org/10.1371/journal.pcbi.1013865

Complex relationship among vessel diameter, shear stress and blood pressure controlling vessel pruning during angiogenesis

Vivek Kumar, Yosuke Hasegawa, Prashant Kumar, Takao Hikita, Mingqian Ding, Yukinori Kametani, Masanori Nakayama

PLOS Computational Biology: published January 12, 2026 | https://doi.org/10.1371/journal.pcbi.1013565

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

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

PLOS Computational Biology: published January 12, 2026 | https://doi.org/10.1371/journal.pcbi.1013883

Exosome-mediated chemotaxis optimizes leader-follower cell migration

Louis González, Andrew Mugler

PLOS Computational Biology: published January 13, 2026 | https://doi.org/10.1371/journal.pcbi.1013894

Network models for bridging denoising and identifying spatial domains of spatially resolved transcriptomics

Haiyue Wang, Wensheng Zhang, Zaiyi Liu, Xiaoke Ma

PLOS Computational Biology: published January 13, 2026 | https://doi.org/10.1371/journal.pcbi.1013867

Novel artificial selection method improves function of simulated microbial communities

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

PLOS Computational Biology: published January 13, 2026 | https://doi.org/10.1371/journal.pcbi.1013863

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

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

PLOS Computational Biology: published January 14, 2026 | https://doi.org/10.1371/journal.pcbi.1013891

Cross-linking mass spectrometry for structure analysis of the intrinsically disordered Tau and phosphorylated Tau protein

Cristian Arsene, Alexander Gates, Anne-Katrin Römmert, André Märtens, Valentina Faustinelli, Luise Luckau, Gavin O’Connor

PLOS Computational Biology: published January 14, 2026 | https://doi.org/10.1371/journal.pcbi.1013868

TCR2HLA: Calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes

Koshlan Mayer-Blackwell, Anastasia Minervina, Mikhail Pogorelyy, Puneet Rawat, Melanie R. Shapiro, Leeana D. Peters, Emily S. Ford, Amanda L. Posgai, Kasi Vegesana, Samuel Minot, David M. Koelle, Victor Greiff, Philip Bradley, Todd M. Brusko, Paul G. Thomas, Andrew Fiore-Gartland

PLOS Computational Biology: published January 16, 2026 | https://doi.org/10.1371/journal.pcbi.1013767

Structural analysis of antigenic variation and adaptive evolution of the H5N1 neuraminidase gene

Muyiwa S. Adegbaju, Oluwabuyikunmi Owo-Odusi, Eden T. Wirtz, Olanrewaju B. Morenikeji, Olusola Ojurongbe, Bolaji N. Thomas

PLOS Computational Biology: published January 16, 2026 | https://doi.org/10.1371/journal.pcbi.1013903

Conditions for replay of neuronal assemblies

Gaspar Cano, Richard Kempter

PLOS Computational Biology: published January 16, 2026 | https://doi.org/10.1371/journal.pcbi.1013844

Evaluating the limitations of Bayesian metabolic control analysis

Janis Shin, James M. Carothers, Herbert M. Sauro

PLOS Computational Biology: published January 16, 2026 | https://doi.org/10.1371/journal.pcbi.1012987

A wavelet-based approach generates quantitative, scale-free and hierarchical descriptions of 3D genome structures and new biological insights

Ryan Pellow, Josep M. Comeron

PLOS Computational Biology: published January 20, 2026 | https://doi.org/10.1371/journal.pcbi.1013887

Therapeutic targeting of oligodendrocytes in an agent-based model of multiple sclerosis

Georgia R. Weatherley, Robyn P. Araujo, Samantha J. Dando, Adrianne L. Jenner

PLOS Computational Biology: published January 20, 2026 | https://doi.org/10.1371/journal.pcbi.1013273

Anatomically aware simulation of patient-specific glioblastoma xenografts

Adam A. Malik, Cecilia Krona, Soumi Kundu, Philip Gerlee, Sven Nelander

PLOS Computational Biology: published January 20, 2026 | https://doi.org/10.1371/journal.pcbi.1013831

MMP release following cartilage injury leads to collagen loss in intact tissue: A computational study

Moustafa Hamada, Atte S. A. Eskelinen, Joonas P. Kosonen, Cristina Florea, Alan J. Grodzinsky, Petri Tanska, Rami K. Korhonen

PLOS Computational Biology: published January 20, 2026 | https://doi.org/10.1371/journal.pcbi.1013209

Linking spatial drug heterogeneity to microbial growth dynamics in theory and experiment

Zhijian Hu, Yuzhen Wu, Tomas Freire, Erida Gjini, Kevin Wood

PLOS Computational Biology: published January 20, 2026 | https://doi.org/10.1371/journal.pcbi.1013896

Compaction of chromatin domains regulates target search times of proteins

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

PLOS Computational Biology: published January 20, 2026 | https://doi.org/10.1371/journal.pcbi.1013843

Higher-level spatial prediction in natural vision across mouse visual cortex

Micha Heilbron, Floris P. de Lange

PLOS Computational Biology: published January 20, 2026 | https://doi.org/10.1371/journal.pcbi.1013136

Learning collective multicellular dynamics with an interacting mean field neural SDE model

Qi Jiang, Longquan Li, Lei Zhang, Lin Wan

PLOS Computational Biology: published January 21, 2026 | https://doi.org/10.1371/journal.pcbi.1013916

Histo-Miner: Deep learning based tissue features extraction pipeline from H&E whole slide images of cutaneous squamous cell carcinoma

Lucas Sancéré, Carina Lorenz, Doris Helbig, Oana-Diana Persa, Sonja Dengler, Alexander Kreuter, Martim Laimer, Roland Lang, Anne Fröhlich, Jennifer Landsberg, Johannes Brägelmann, Katarzyna Bozek

PLOS Computational Biology: published January 21, 2026 | https://doi.org/10.1371/journal.pcbi.1013907

Measuring real-time disease transmissibility with temperature-dependent generation intervals

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

PLOS Computational Biology: published January 21, 2026 | https://doi.org/10.1371/journal.pcbi.1013820

Bayesian data driven modelling of kinetochore dynamics: Space-time organisation of the human metaphase plate

Constandina Koki, Alessio V. Inchingolo, Abdullahi Daniyan, Enyu Li, Andrew D. McAinsh, Nigel J. Burroughs

PLOS Computational Biology: published January 22, 2026 | https://doi.org/10.1371/journal.pcbi.1013884

Homeostasis after injury: How intertwined inference and control underpin post-injury pain and behaviour

Pranav Mahajan, Peter Dayan, Ben Seymour

PLOS Computational Biology: published January 22, 2026 | https://doi.org/10.1371/journal.pcbi.1013538

A predicted structural interactome reveals binding interference from intrinsically disordered regions

Junhui Peng, Li Zhao

PLOS Computational Biology: published January 22, 2026 | https://doi.org/10.1371/journal.pcbi.1013899

Composing egocentric and allocentric maps for flexible navigation

Daniel Shani, Peter Dayan

PLOS Computational Biology: published January 23, 2026 | https://doi.org/10.1371/journal.pcbi.1013905

AugGCL: Multimodal graph learning for spatial transcriptomics analysis with enhanced gene and morphological data

Tengfei Ji, Bo Yang, Meng Wang, Hong Ji, Huazhe Yang, Yizhuo Liu

PLOS Computational Biology: published January 23, 2026 | https://doi.org/10.1371/journal.pcbi.1013912

How do tumor-associated neutrophils regulate the microenvironmental landscape of brain tumors: Delivery of nano-particles through BBB

Haneol Cho, Junho Lee, Sean Lawler, Yangjin Kim

PLOS Computational Biology: published January 23, 2026 | https://doi.org/10.1371/journal.pcbi.1013906

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

Anna Krzynowek, Jasper Snoeks, Karoline Faust

PLOS Computational Biology: published January 26, 2026 | https://doi.org/10.1371/journal.pcbi.1013892

PCR bias impacts microbiome ecological analyses

Dharmik R. Rathod, Justin D. Silverman

PLOS Computational Biology: published January 27, 2026 | https://doi.org/10.1371/journal.pcbi.1013908

Hierarchical analysis of RNA secondary structures with pseudoknots based on sections

Ryota Masuki, Donn Liew, Ee Hou Yong

PLOS Computational Biology: published January 27, 2026 | https://doi.org/10.1371/journal.pcbi.1013904

Forecasting drug resistant HIV protease evolution

Manu Aggarwal, Vipul Periwal

PLOS Computational Biology: published January 27, 2026 | https://doi.org/10.1371/journal.pcbi.1013913

A model for the human fetal ventricular myocyte electrophysiology

Adelisa Avezzú, Stefano Longobardi, Anita Alvarez-Laviada, Francisca Schultz, Julia Gorelik, Catherine Williamson, Steven A. Niederer

PLOS Computational Biology: published January 27, 2026 | https://doi.org/10.1371/journal.pcbi.1013889

Abundant positively-charged proteins underlie JCVI-Syn3A’s expanded nucleoid and ribosome distribution

Gesse Roure, Vishal S. Sivasankar, Roseanna N. Zia

PLOS Computational Biology: published January 27, 2026 | https://doi.org/10.1371/journal.pcbi.1013898

Learning cardiac activation and repolarization times with operator learning

Giovanni Ziarelli, Edoardo Centofanti, Nicola Parolini, Simone Scacchi, Marco Verani, Luca F. Pavarino

PLOS Computational Biology: published January 27, 2026 | https://doi.org/10.1371/journal.pcbi.1013920

Deep learning models to map osteocyte networks from confocal microscopy can successfully distinguish between young and aged bone

Simon D. Vetter, Charles A. Schurman, Tamara Alliston, Gregory Slabaugh, Stefaan W. Verbruggen

PLOS Computational Biology: published January 27, 2026 | https://doi.org/10.1371/journal.pcbi.1013914

Persistence diagrams as morphological signatures of cells: A method to measure and compare cells within a population

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

PLOS Computational Biology: published January 28, 2026 | https://doi.org/10.1371/journal.pcbi.1013890

Spatial variation in socio-economic vulnerability to Influenza-like Infection for the US population

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

PLOS Computational Biology: published January 28, 2026 | https://doi.org/10.1371/journal.pcbi.1013839

SpaConTDS: A multimodal contrastive learning framework for identifying spatial domains by applying tuple disturbing strategy

Ruiwen Xu, Xiaoqing Cheng, Waiki Ching, Siyao Wu, Yuanben Zhang, Yidan Zhang

PLOS Computational Biology: published January 29, 2026 | https://doi.org/10.1371/journal.pcbi.1013893

Capturing individual variation in children’s electroencephalograms during nREM sleep

Verna Heikkinen, Susanne Merz, Riitta Salmelin, Sampsa Vanhatalo, Leena Lauronen, Mia Liljeström, Hanna Renvall

PLOS Computational Biology: published January 30, 2026 | https://doi.org/10.1371/journal.pcbi.1013931

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

Fengzhu Sun, Yue Huang, Tianqi Tang, Xiaowu Dai

PLOS Computational Biology: published January 6, 2026 | https://doi.org/10.1371/journal.pcbi.1013876

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Correction: 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 January 6, 2026 | https://doi.org/10.1371/journal.pcbi.1013877

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Correction: Competition and cooperation: The plasticity of bacterial interactions across environments

Josephine Solowiej-Wedderburn, Jennifer T. Pentz, Ludvig Lizana, Bjoern O. Schroeder, Peter A. Lind, Eric Libby

PLOS Computational Biology: published January 15, 2026 | https://doi.org/10.1371/journal.pcbi.1013809

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Correction: Simulation insights on the compound action potential in multifascicular nerves

The PLOS Computational Biology Staff

PLOS Computational Biology: published January 20, 2026 | https://doi.org/10.1371/journal.pcbi.1013902

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CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning

Yan Liu, Yu Xia, He Yan, Long-Chen Shen, Yiheng Zhu, Ji-Peng Qiang, Guo Wei

PLOS Computational Biology: published January 2, 2026 | https://doi.org/10.1371/journal.pcbi.1013824

Powerful large scale inference in high dimensional mediation analysis

Asmita Roy, Xianyang Zhang

PLOS Computational Biology: published January 14, 2026 | https://doi.org/10.1371/journal.pcbi.1013880

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

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

PLOS Computational Biology: published January 5, 2026 | https://doi.org/10.1371/journal.pcbi.1013864

TEvarSim: A genome simulator for transposable element (TE) variants

Jian Miao, Dawei Li

PLOS Computational Biology: published January 30, 2026 | https://doi.org/10.1371/journal.pcbi.1013933