Current Issue | PLOS Computational Biology

Hsp70 chaperones, together with J‑domain protein (JDP) co-chaperones, play a central role in maintaining protein homeostasis within cells. Using structural data and all-atom simulations, we found that when a J-domain binds Hsp70 it gives a “steric push” that changes Hsp70’s conformation. These changes, propagated through coordinated global and local rearrangements, reposition the conserved T199 hydroxyl adjacent to the ATP γ-phosphate, promoting ATP hydrolysis. This explains how J-domain binding powers Hsp70’s chaperone activity. Olewniczak et al. 2026

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

Education

Online tutorial on survival analysis for biomarker discovery

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

PLOS Computational Biology: published March 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014046

Review

Physical models of embryonic epithelial healing

Rafael Franco Almada, Nuno André Miguel Araújo, Pedro Patrício

PLOS Computational Biology: published March 25, 2026 | https://doi.org/10.1371/journal.pcbi.1014078

Research Articles

Assessment of dispersion metrics for estimating single-cell transcriptional variability

Tina Chen, Laurie A. Boyer, Divyansh Agarwal

PLOS Computational Biology: published March 2, 2026 | https://doi.org/10.1371/journal.pcbi.1014030

Combining visual motion and luminance features to enhance the detection of small moving objects in a bioinspired model

Shuai Li, Aike Guo, Yizheng Wang, Liang Li, Gang Wang, Zhihua Wu

PLOS Computational Biology: published March 2, 2026 | https://doi.org/10.1371/journal.pcbi.1014036

Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families

Nikhil Ramesh, S. Banu Ozkan, Eleni Panagiotou

PLOS Computational Biology: published March 4, 2026 | https://doi.org/10.1371/journal.pcbi.1013985

Quantifying the spatiotemporal dynamics of the first two epidemic waves of SARS-CoV-2 infections in the United States

Rafael Lopes, Yu Lan, Melanie H. Chitwood, Fayette Klaassen, Joshua A. Salomon, Nicolas A. Menzies, Joshua L. Warren, Nathan D. Grubaugh, Ted Cohen, Nicole A. Swartwood

PLOS Computational Biology: published March 4, 2026 | https://doi.org/10.1371/journal.pcbi.1013983

Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome

Nicholas Pucci, Amke Marije Kaan, Joanne Ujčič-Voortman, Arnoud P. Verhoeff, Egija Zaura, Daniel R. Mende

PLOS Computational Biology: published March 5, 2026 | https://doi.org/10.1371/journal.pcbi.1013185

Contrastive learning for passive acoustic monitoring: A framework for sound source discovery and cross-site comparison in marine soundscapes

Richard Acs, Ali Ibrahim, Hanqi Zhuang, Laurent M. Chérubin

PLOS Computational Biology: published March 6, 2026 | https://doi.org/10.1371/journal.pcbi.1014005

A reinforcement learning and sequential sampling model constrained by gaze data

William M. Hayes, Melanie J. Touchard

PLOS Computational Biology: published March 6, 2026 | https://doi.org/10.1371/journal.pcbi.1014052

Morphological determinants of glycosylation efficiency in Golgi cisternae

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

PLOS Computational Biology: published March 6, 2026 | https://doi.org/10.1371/journal.pcbi.1013993

Reconstructing the incidence rate and immune fraction of the population via a single snapshot survey: A case study of COVID-19 in Japan

Yuta Okada, Hiroshi Nishiura

PLOS Computational Biology: published March 6, 2026 | https://doi.org/10.1371/journal.pcbi.1013990

An integrative analysis reveals the mechanism of plastic stabilizers inducing breast cancer

Xingfa Huo, Xueqin Duan, Xiaojuan Huang, Linyuan Xue, Lantao Zhao, Yufeng Li, Xiaochun Zhang, Na Zhou

PLOS Computational Biology: published March 6, 2026 | https://doi.org/10.1371/journal.pcbi.1014025

Burst firing creates an attractor in synaptic weight dynamics

Kathleen Jacquerie, Danil Tyulmankov, Pierre Sacré, Guillaume Drion

PLOS Computational Biology: published March 9, 2026 | https://doi.org/10.1371/journal.pcbi.1014001

The integrated information Φ of an integrate and fire network

Miłosz Danilczuk, Marek Pokropski, Piotr Suffczynski

PLOS Computational Biology: published March 9, 2026 | https://doi.org/10.1371/journal.pcbi.1014085

Computing the effects of excitatory-inhibitory balance on neuronal input-output properties

Alex D. Reyes

PLOS Computational Biology: published March 9, 2026 | https://doi.org/10.1371/journal.pcbi.1013958

How the dynamic interplay of cortico-basal ganglia-thalamic pathways shapes the time course of deliberation and commitment

Zhuojun Yu, Timothy Verstynen, Jonathan E. Rubin

PLOS Computational Biology: published March 9, 2026 | https://doi.org/10.1371/journal.pcbi.1012966

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

Lu Meng, Lijun Zhou

PLOS Computational Biology: published March 10, 2026 | https://doi.org/10.1371/journal.pcbi.1014053

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

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

PLOS Computational Biology: published March 10, 2026 | https://doi.org/10.1371/journal.pcbi.1013897

Coevolution of host resistance and pathogen exploitation in a propagule-mediated infection model

Prerna Singh, Justin Sheen, Chadi M. Saad-Roy, Michael Z. Levy, C. Jessica E. Metcalf

PLOS Computational Biology: published March 10, 2026 | https://doi.org/10.1371/journal.pcbi.1013999

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

Hua Shi, Yihang Lin, Dachen Liu, Quan Zou

PLOS Computational Biology: published March 11, 2026 | https://doi.org/10.1371/journal.pcbi.1013397

Free energy perturbations in enzyme kinetic models reveal cryptic epistasis

Karol Buda, Nobuhiko Tokuriki

PLOS Computational Biology: published March 11, 2026 | https://doi.org/10.1371/journal.pcbi.1013493

Dynamics of the formation of flat clathrin lattices in response to growth factor stimulus

Lingxia Qiao, Marco A. Alfonzo-Méndez, Justin W. Taraska, Padmini Rangamani

PLOS Computational Biology: published March 11, 2026 | https://doi.org/10.1371/journal.pcbi.1014013

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

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

PLOS Computational Biology: published March 11, 2026 | https://doi.org/10.1371/journal.pcbi.1014077

MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation prediction

Mengyuan Zhao, Xinyue Tang, Jiawei Li, Cheng Liang, Jijun Tang, Fei Guo

PLOS Computational Biology: published March 11, 2026 | https://doi.org/10.1371/journal.pcbi.1014054

Social familiarity strengthens neural and vocal responses to conspecific calls in zebra finches

Carlos M. Gomez-Guzman, Daniela Vallentin, Jonathan I. Benichov

PLOS Computational Biology: published March 11, 2026 | https://doi.org/10.1371/journal.pcbi.1014024

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

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

PLOS Computational Biology: published March 12, 2026 | https://doi.org/10.1371/journal.pcbi.1014050

Interpretable integration of unpaired multi-omics for Alzheimer’s diagnosis via cross-modal transformer reconstruction

Kai Liao, Danfeng Du, Jiawei Li, Jian Huang, Xiaodan Fan, Changshui Chen, Shanshan Wu, Bowei Yan, Haibo Li

PLOS Computational Biology: published March 12, 2026 | https://doi.org/10.1371/journal.pcbi.1014074

Algorithmic reconstruction of trophic networks from open-access species lists reveals key organisms in real ecosystems

Miguel Brun-Usan, Roberto Latorre, Ángela D. Buscalioni, Paloma Alcorlo, Jesús Marugán-Lobón

PLOS Computational Biology: published March 12, 2026 | https://doi.org/10.1371/journal.pcbi.1014061

Towards model-based characterization of individual electrically stimulated nerve fibers

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

PLOS Computational Biology: published March 13, 2026 | https://doi.org/10.1371/journal.pcbi.1013342

Optimizing oral contraceptive timing: Daytime intake reduces doses and enhances efficacy

Brenda Lyn Gavina, Taeyong Lee, Olive Cawiding, Sunhwa Choi, Sungwook Choi, Soyoung Kim, Jae Kyoung Kim

PLOS Computational Biology: published March 13, 2026 | https://doi.org/10.1371/journal.pcbi.1014040

Hierarchical abstraction drives human-like 3-D shape processing in deep learning models

Shuhao Fu, Philip J. Kellman, Hongjing Lu

PLOS Computational Biology: published March 13, 2026 | https://doi.org/10.1371/journal.pcbi.1014047

CFGSCDSA: Predicting circRNA-drug sensitivity associations based on collaborative feature learning and graph structure learning

Xue Zhang, Quan Zou, Chunyu Wang, Mengting Niu

PLOS Computational Biology: published March 13, 2026 | https://doi.org/10.1371/journal.pcbi.1014072

Accurate prediction of flux distributions compatible with metabolite concentration effects in genome-scale metabolic networks

Fayaz Soleymani, Zahra Razaghi-Moghadam, Zoran Nikoloski

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1014066

Slow spatial migration can help eradicate cooperative antimicrobial resistance in time-varying environments

Lluís Hernández-Navarro, Kenneth Distefano, Uwe C. Täuber, Mauro Mobilia

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1013997

Benchmarking spike source localization algorithms in high density probes

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

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1014059

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

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

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1013984

Integrated multi-modal data analysis for computational modeling of healthy and location-dependent myocardial infarction conditions in porcine hearts

Ricardo M. Rosales, Ming Wu, Piet Claus, Stefan Janssens, Gonzalo R. Ríos-Muñoz, María Eugenia Fernández-Santos, Pablo Martínez-Legazpi, Javier Bermejo, Aiden Flanagan, Manuel Doblaré, Ana Mincholé, Esther Pueyo

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1013688

Do we need medical imaging-informed musculoskeletal models for simulations in healthy adults? A new workflow based on magnetic resonance imaging highlights the importance of personalized geometry

Ekaterina Stansfield, Willi Koller, Basílio Gonçalves, Hans Kainz

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1014073

Functional bottlenecks can emerge from non-epistatic underlying traits

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

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1014000

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

Yiling Wang, Zhanpeng Shu, Zhixing Cao, Ramon Grima

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1014014

Live and let die: Lysis time variability and resource limitation shape lytic bacteriophage fitness

Aaron Smith, Michael Hunter, Somenath Bakshi, Diana Fusco

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1013340

A benchmark of semi-supervised scRNA-seq integration methods in real-world scenarios

Xiaoyu Shen, Chuan He, Leying Guan

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1014008

Fast hospital discharge rates blur within-hospital ‘transmission footprint’ in bacterial genomes, as showcased with Staphylococcus aureus

Sanni Översti, Mathilde Boumasmoud, Huldyrch F. Günthard, Hugo Sax, Annelies S. Zinkernagel, Roger D. Kouyos, Denise Kühnert

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1013982

TUSCAN: Tumor segmentation and classification analysis in spatial transcriptomics

Chenxuan Zang, Charles C. Guo, Yaohong Wang, Peng Wei, Ziyi Li

PLOS Computational Biology: published March 17, 2026 | https://doi.org/10.1371/journal.pcbi.1014058

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

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

PLOS Computational Biology: published March 17, 2026 | https://doi.org/10.1371/journal.pcbi.1014004

Separating random and deterministic sources of computational noise in explore-exploit decisions

Siyu Wang, Robert C. Wilson

PLOS Computational Biology: published March 17, 2026 | https://doi.org/10.1371/journal.pcbi.1014026

Learning, sleep replay and consolidation of contextual fear memories: A neural network model

Lars Werne, Angus Chadwick, Peggy Seriès

PLOS Computational Biology: published March 17, 2026 | https://doi.org/10.1371/journal.pcbi.1013251

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

Konstantinos Antonopoulos, Olof Nordenstorm, Avlant Nilsson

PLOS Computational Biology: published March 18, 2026 | https://doi.org/10.1371/journal.pcbi.1014100

Direct causality measures unravel complex networks of cardiovascular dynamics and their modifications with postural stress

Chiara Barà, Laura Sparacino, Luca Faes, Michal Javorka

PLOS Computational Biology: published March 18, 2026 | https://doi.org/10.1371/journal.pcbi.1014075

Epistasis mediates the role of negative frequency-dependent selection in bacterial strain structure

Martin Guillemet, Sonja Lehtinen

PLOS Computational Biology: published March 19, 2026 | https://doi.org/10.1371/journal.pcbi.1014083

PHA synthase variant design using a conditional variational autoencoder

Tuula Tenkanen, Anna Ylinen, Paula Jouhten, Merja Penttilä, Sandra Castillo

PLOS Computational Biology: published March 19, 2026 | https://doi.org/10.1371/journal.pcbi.1014087

Mechanism of Hsp70 activation: How J-domain proteins push for ATP hydrolysis

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

PLOS Computational Biology: published March 19, 2026 | https://doi.org/10.1371/journal.pcbi.1014094

Bayesian inference of RNA velocity incorporating timepoints, lineage bifurcations, and count data

Yichen Gu, Yuxuan Song, David Blaauw, Joshua D. Welch

PLOS Computational Biology: published March 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014060

Thrombin activity confinement and dense granule release drive the dynamics of arterial thrombus

Efim S. Bershadsky, Dmitry Y. Nechipurenko

PLOS Computational Biology: published March 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014062

Deciphering the cardiac neuron landscape in heart failure patients

Shuping Zhuang, Xiuqi Yang, Nan Zhang, JiangQi Liu, Kaidong Liu, Huiming Han, Songmei Zhai, Mingyue Liu, Haihai Liang, Yunyan Gu, Yanjie Lu

PLOS Computational Biology: published March 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014082

Contextual inference through flexible integration of environmental features and behavioural outcomes

Jessica Passlack, Andrew F. MacAskill

PLOS Computational Biology: published March 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014093

Prior-guided factorization for reliable imputation of scRNA-seq data

You Wu, Li Xu, Ye Win Aung, Alex Michel Daoud

PLOS Computational Biology: published March 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014051

Dense and distributed neuropeptide network in the nerve net of Hydra vulgaris

Johanna De La Cruz Rothenfusser, Luis Alfonso Yáñez-Guerra, Felix Teufel, Rafael Yuste

PLOS Computational Biology: published March 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014037

D-LIM: A neural network for interpretable gene–gene interactions

Shuhui Wang, Alexandre Allauzen, Philippe Nghe, Vaitea Opuu

PLOS Computational Biology: published March 23, 2026 | https://doi.org/10.1371/journal.pcbi.1014107

Predicting viral sensitivity to antibodies using genetic sequences and antibody similarities

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

PLOS Computational Biology: published March 23, 2026 | https://doi.org/10.1371/journal.pcbi.1014095

Sensitivity analysis enlightens effects of connectivity in a Neural Mass Model under Control-Target mode

Anaïs Vallet, Stéphane Blanco, Coline Chevallier, Francis Eustache, Jacques Gautrais, Jean-Yves Grandpeix, Jean-Louis Joly, Shailendra Segobin, Pierre Gagnepain

PLOS Computational Biology: published March 23, 2026 | https://doi.org/10.1371/journal.pcbi.1014035

MPCI: A novel metric for quantifying DNA methylation patterns in NGS data

Naghme Nazer, Hoda Mohammadzade, Mahya Mehrmohamadi

PLOS Computational Biology: published March 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014076

A multimodal spatial atlas of transcriptomic, morphological, and electrophysiological cell type densities in the mouse brain

Csaba Verasztó, Yann Roussel, Lida Kanari, Sébastien Piluso, Henry Markram, Daniel Keller

PLOS Computational Biology: published March 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014106

A minimal mathematical model of red blood cell homeostasis in anemia

Herut Dor, Uri Alon

PLOS Computational Biology: published March 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014111

Accounting for sensitivity of latent learning to behavioral statistics with successor representations

Matheus Menezes, Xiangshuai Zeng, Sen Cheng

PLOS Computational Biology: published March 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014131

HiCMamba: Enhancing Hi-C resolution and identifying 3D genome structures with state space modeling

Minghao Yang, Zhi-An Huang, Zhihang Zheng, Yuqiao Liu, Shichen Zhang, Pengfei Zhang, Hui Xiong, Shaojun Tang

PLOS Computational Biology: published March 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014057

Overcoming extrapolation challenges of deep learning by incorporating physics in protein sequence-function modeling

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

PLOS Computational Biology: published March 25, 2026 | https://doi.org/10.1371/journal.pcbi.1013728

Rules railroad: Syntax-inspired diagrams for visualizing and understanding rule-based model specifications

Reesha J. Patel, Michael L. Blinov

PLOS Computational Biology: published March 25, 2026 | https://doi.org/10.1371/journal.pcbi.1014121

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

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

PLOS Computational Biology: published March 26, 2026 | https://doi.org/10.1371/journal.pcbi.1014098

PymiRa: A rapid and accurate classification tool for small non-coding RNAs, including microRNAs

Zachary G. L. Scurlock, Cinzia G. Scarpini, Nicholas Coleman, Matthew J. Murray, Anton J. Enright

PLOS Computational Biology: published March 26, 2026 | https://doi.org/10.1371/journal.pcbi.1014114

Deconvolving cell-type-specific gene expression profiles from bulk RNA-seq samples

Sichen Zhu, Zhengqi Wang, Kevin D. Bunting, Peng Qiu

PLOS Computational Biology: published March 26, 2026 | https://doi.org/10.1371/journal.pcbi.1014101

Bayesian network models to assess antimicrobial resistance patterns of Streptococcus suis isolated from swine production systems in the United States between 2014–2021

Ruwini Rupasinghe, Brittany L. Morgan Bustamante, Rebecca C. Robbins, Maria J. Clavijo, Beatriz Martínez-López

PLOS Computational Biology: published March 26, 2026 | https://doi.org/10.1371/journal.pcbi.1014117

A modular architecture for trial-by-trial learning of redundant muscle activity patterns in novel sensorimotor tasks

Lucas Rebelo Dal’Bello, Denise Jennifer Berger, Daniele Borzelli, Etienne Burdet, Andrea d’Avella

PLOS Computational Biology: published March 27, 2026 | https://doi.org/10.1371/journal.pcbi.1012834

Emergent coexistence and the limits of reductionism in ecological communities

Guim Aguadé-Gorgorió, Sonia Kéfi

PLOS Computational Biology: published March 27, 2026 | https://doi.org/10.1371/journal.pcbi.1014116

An improved dataset for predicting mammal infecting viruses from genetic sequence information

Tyler Reddy, Austin Schneider, Aaron R. Hall, Adam Witmer, Nick Hengartner

PLOS Computational Biology: published March 27, 2026 | https://doi.org/10.1371/journal.pcbi.1014125

Role of fast-spiking interneurons in modulating across-trial variability and within-trial correlations in the striatum

Lihao Guo, Arvind Kumar

PLOS Computational Biology: published March 27, 2026 | https://doi.org/10.1371/journal.pcbi.1014099

ECOD: Classification of domains in AFDB Swiss-Prot structure predictions

R. Dustin Schaeffer, Jing Zhang, Qian Cong, Nick V. Grishin

PLOS Computational Biology: published March 30, 2026 | https://doi.org/10.1371/journal.pcbi.1013431

CAPYBARA: A generalizable framework for predicting serological measurements across human cohorts

Sierra Orsinelli-Rivers, Daniel Beaglehole, Tal Einav

PLOS Computational Biology: published March 30, 2026 | https://doi.org/10.1371/journal.pcbi.1014129

WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology

Pranav Gangwar, Pratik Katte, Manu Bhat, Yatish Turakhia

PLOS Computational Biology: published March 30, 2026 | https://doi.org/10.1371/journal.pcbi.1014124

Kernel-DMD for multiome data integration and control

Iro Pierides, Hannes M. Kramml, Steffen Waldherr, Wolfram Weckwerth

PLOS Computational Biology: published March 31, 2026 | https://doi.org/10.1371/journal.pcbi.1014029

Network-based exploration of 4-(phenylsulfonyl)morpholine molecules for metastatic triple-negative breast cancer suppression

Jung-Chen Su, Chen-Ling Lee, Fan-Wei Yang, Yan-Chih Chen, Te-Lun Mai

PLOS Computational Biology: published March 31, 2026 | https://doi.org/10.1371/journal.pcbi.1014132

Multiscale modeling of the spatial structure of stem cells in neuroblastoma patient-derived tumoroids reveals a critical role for a short-range diffusive process

Thi Nhu Thao Nguyen, Catherine Koering, Elodie Vallin, Sandrine Gonin-Giraud, Laura Broutier, Samuel Bernard, Fabien Crauste, Olivier Gandrillon

PLOS Computational Biology: published March 31, 2026 | https://doi.org/10.1371/journal.pcbi.1014137

BIOPOINT: A particle-based model for probing nuclear mechanics and cell-ECM interactions via experimentally derived parameters

Sandipan Chattaraj, Julius Zimmermann, Francesco Silvio Pasqualini

PLOS Computational Biology: published March 31, 2026 | https://doi.org/10.1371/journal.pcbi.1014113

Metacognitive efficiency in learned value-based choice

Sara Ershadmanesh, Ali Gholamzadeh, Kobe Desender, Peter Dayan

PLOS Computational Biology: published March 31, 2026 | https://doi.org/10.1371/journal.pcbi.1014108

Corrections

Correction: ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii

Lakshmipuram S. Swapna, Grant C. Stevens, Aline Sardinha-Silva, Lucas ZhongMing Hu, Verena Brand, Daniel D. Fusca, Cuihong Wan, Xuejian Xiong, Jon P. Boyle, Michael E. Grigg, Andrew Emili, John Parkinson

PLOS Computational Biology: published March 13, 2026 | https://doi.org/10.1371/journal.pcbi.1014086

Correction: A diel multi-tissue genome-scale metabolic model of Vitis vinifera

Marta Sampaio, Miguel Rocha, Oscar Dias

PLOS Computational Biology: published March 27, 2026 | https://doi.org/10.1371/journal.pcbi.1014135

Correction: Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations

J. Galván Fraile, Franz Scherr, José J. Ramasco, Anton Arkhipov, Wolfgang Maass, Claudio R. Mirasso

PLOS Computational Biology: published March 30, 2026 | https://doi.org/10.1371/journal.pcbi.1014136

Methods

ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries

Moritz Hanke, Theresa Harten, Ronja Foraita

PLOS Computational Biology: published March 6, 2026 | https://doi.org/10.1371/journal.pcbi.1013428

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

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

PLOS Computational Biology: published March 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014084

AEGIS: Individual-based modeling of life history evolution

Martin Bagic, Arian Šajina, William John Bradshaw, Dario Riccardo Valenzano

PLOS Computational Biology: published March 26, 2026 | https://doi.org/10.1371/journal.pcbi.1014109

Extending differential gene expression testing to handle genome aneuploidy in cancer

Katsiaryna Davydzenka, Giulio Caravagna, Guido Sanguinetti

PLOS Computational Biology: published March 27, 2026 | https://doi.org/10.1371/journal.pcbi.1014134

Software

EEG-Pype: An accessible MNE-Python pipeline with graphical user interface for preprocessing and analysis of resting-state electroencephalography data

D. Yorben Lodema, Herman J. van Dellen, Willem de Haan, Margot van Hest, Arjan Hillebrand, Edwin van Dellen

PLOS Computational Biology: published March 2, 2026 | https://doi.org/10.1371/journal.pcbi.1014043

napariTFM: An open-source tool for traction force microscopy and monolayer stress microscopy

Artur Ruppel, Dennis Wörthmüller, Martial Balland, François Fagotto

PLOS Computational Biology: published March 16, 2026 | https://doi.org/10.1371/journal.pcbi.1014045

ARNy plotter: A comprehensive web server for RNA ensemble structural analysis and visualization

Louis Meuret, Julien Rey, Samuela Pasquali

PLOS Computational Biology: published March 31, 2026 | https://doi.org/10.1371/journal.pcbi.1013873

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March 2026

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A Mechanism of Hsp70 Activation: How J-domains Push Hsp70 into an ATP-Hydrolysis Ready State

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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