Current Issue | PLOS Computational Biology

This image illustrates a digital twin heart framework designed for personalized cardiovascular treatment. A patient-specific virtual heart is constructed using mechanistic and statistical models informed by disease-relevant variables. When localized signs of heart disease are detected (highlighted in red), sex-specific digital twins are generated and exposed to thousands of drug simulations. The treatment demonstrating optimal efficacy on the patient’s twin (highlighted in green) is selected for clinical use. This approach enables precision therapy tailored to individual biological and sex-specific factors, representing a convergence of computational modeling and personalized medicine. Bai et al. 2025

Image Credit: Jieyun Bai

Education Articles

LabOps: A flexible self-hosted workflow of open source tools for efficient collaboration within research laboratories

Héctor D. García-Verdugo, Cristian Román-Palacios

PLOS Computational Biology: published July 1, 2025 | https://doi.org/10.1371/journal.pcbi.1013248

Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines

Seth R. Berke, Kanika Kanchan, Mary L. Marazita, Eric Tobin, Ingo Ruczinski

PLOS Computational Biology: published July 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013215

Ten simple rules for faculty members building just and equitable environments in academic science

Veronica Martinez Acosta, Carlita Favero, Barbara Lom, Deanne Buffalari, Amy Jo Stavnezer, Leah Chase

PLOS Computational Biology: published July 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013177

Ten quick tips for navigating intellectual property in FAIR educational resources

Eva Maria Funk, Ulf Toelch, Rebecca Ludwig, Silke Kniffert

PLOS Computational Biology: published July 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013208

Ten simple rules for developing a training program

Leanna B. Blevins, Amy M. Harrigan, Kevin A. Janes, Jason A. Papin

PLOS Computational Biology: published July 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013200

Ten simple rules for success as a trainee-led outreach organization in computational biology education

Jennifer Blanc, Margaret C. Steiner, Lauren E. Blake, Elizabeth Gibbons, Mariadaria K. Ianni-Ravn, Roxroy C. Morgan, Suzanna Parkinson, Christian Porras, Ethan Zhong

PLOS Computational Biology: published July 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013281

Ten simple rules for navigating AI in science

Aidan Crilly, Alice Malivert, Andreas Christ Sølvsten Jørgensen, Claire E. Heaney, Gema I. Vera Gonzalez, Marcus Ghosh, Manolo Fernandez Perez, Mikael M. Mieskolainen, Mohammed Azzouzi, Zhenzhu Li

PLOS Computational Biology: published July 18, 2025 | https://doi.org/10.1371/journal.pcbi.1013259

Perspectives

Ten simple rules for thriving in a post-baccalaureate research program

Michaelle E. DiMaggio-Potter, Angelica Velosa, John C. Brent IV, Osmar Del Rio, Eyerusalem F. Abebaw, Fernando Aguilar-Ortega, Dante Rogers, Patrick E. Rothwell, Angeline J. Dukes

PLOS Computational Biology: published July 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013174

How multi-scale modeling can help examine social determinants of health and resulting disparities

Kyoko Yoshida, Elsje Pienaar, Shalanda A. Bynum, Naomi Chesler, Mitchel J. Colebank, Jessie Heneghan, Nadra Tyus, Jasmine Miller-Kleinhenz, Bruce Y. Lee

PLOS Computational Biology: published July 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013284

Research Articles

Identifying predictors and assessing causal effect on hypertension risk among adults using Double Machine Learning models: Insights from Bangladesh Demographic and Health Survey

Probir Kumar Ghosh, Md. Aminul Islam, Md. Ahshanul Haque, Md. Tariqujjaman, Novel Chandra Das, Mohammad Ali, Md. Rasel Uddin, Md. Golam Dostogir Harun

PLOS Computational Biology: published July 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013211

Nucleus accumbens dopamine release reflects Bayesian inference during instrumental learning

Albert J. Qü, Lung-Hao Tai, Christopher D. Hall, Emilie M. Tu, Maria K. Eckstein, Karyna Mishchanchuk, Wan Chen Lin, Juliana B. Chase, Andrew F. MacAskill, Anne G. E. Collins, Samuel J. Gershman, Linda Wilbrecht

PLOS Computational Biology: published July 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013226

Herbivore community function shapes resilience and bistability of coral reefs

Shayna A. Sura, James O. Lloyd-Smith, Peggy Fong

PLOS Computational Biology: published July 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013221

Cooperative coding of continuous variables in networks with sparsity constraint

Paul Züge, Natalie Schieferstein, Raoul-Martin Memmesheimer

PLOS Computational Biology: published July 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012156

Digital twin for sex-specific identification of class III antiarrhythmic drugs based on in vitro measurements, computer models, and machine learning tools

Jieyun Bai, Weishan Wang, Xiaoshen Zhang, Hua Lu, Henggui Zhang, Alexander V. Panfilov, Jichao Zhao

PLOS Computational Biology: published July 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013154

Understanding disease-associated metabolic changes in human colonic epithelial cells using the iColonEpithelium metabolic reconstruction

Boyu Jiang, Nick Quinn-Bohmann, Christian Diener, Vignesh Bose Nathan, Yu Han-Hallett, Lavanya Reddivari, Sean M. Gibbons, Priyanka Baloni

PLOS Computational Biology: published July 3, 2025 | https://doi.org/10.1371/journal.pcbi.1013253

Comparison of in silico predictions of action potential duration in response to inhibition of I_Kr and I_CaL with new human ex vivo recordings

Yann-Stanislas H. M. Barral, Liudmila Polonchuk, Michael Clerx, David J. Gavaghan, Gary R. Mirams, Ken Wang

PLOS Computational Biology: published July 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012913

Changes in Spo0A~P pulsing frequency control biofilm matrix deactivation

Cristina S. D. Palma, Daniel J. Haller, Jeffrey J. Tabor, Oleg A. Igoshin

PLOS Computational Biology: published July 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013263

Estimating behavioural relaxation induced by COVID-19 vaccines in the first months of their rollout

Yuhan Li, Nicolò Gozzi, Nicola Perra

PLOS Computational Biology: published July 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013266

From imaging to computational domains for physics-driven molecular biology simulations: Hindered diffusion in platelet masses

Catherine House, Ziyi Huang, Kaushik N. Shankar, Sandra J. Young, Meghan E. Roberts, Scott L. Diamond, Maurizio Tomaiuolo, Timothy J. Stalker, Lu Lu, Talid Sinno

PLOS Computational Biology: published July 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012853

Selective inhibition in CA3: A mechanism for stable pattern completion through heterosynaptic plasticity

Gyeongtae Kim, Pilwon Kim

PLOS Computational Biology: published July 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013267

Single-cell mutational burden distributions in birth–death processes

Christo Morison, Dudley Stark, Weini Huang

PLOS Computational Biology: published July 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013241

Infectivity and fatality of influenza in pre- and post-COVID-19 pandemic year

Shuanglin Jing, Hao Wang

PLOS Computational Biology: published July 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013229

Evolution of foraging behaviour induces variable complexity-stability relationships in mutualist-exploiter-predator communities

Lin Wang, Ting Wang, Xiao-Wei Zhang, Xiao-Fen Lin, Jia Li, Jin-Bao Liao, Rui-Wu Wang

PLOS Computational Biology: published July 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013245

Anatomical-electrical coupling of cardiac axes: Definitions and population variability for advancing personalised ECG interpretation

Mohammad Kayyali, Ana Mincholé, Shuang Qian, Alistair Young, Devran Ugurlu, Elliot Fairweather, Steven Niederer, John Whitaker, Martin Bishop, Pablo Lamata

PLOS Computational Biology: published July 10, 2025 | https://doi.org/10.1371/journal.pcbi.1013161

Neural network approaches, including use of topological data analysis, enhance classification of human induced pluripotent stem cell colonies by treatment condition

Alexander Ruys de Perez, Paul E. Anderson, Elena S. Dimitrova, Melissa L. Kemp

PLOS Computational Biology: published July 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012801

Perceptual clustering in auditory streaming

Nathanael Larigaldie, Tim Yates, Ulrik R. Beierholm

PLOS Computational Biology: published July 11, 2025 | https://doi.org/10.1371/journal.pcbi.1013189

Allocating limited surveillance effort for outbreak detection of endemic foot and mouth disease

Ariel Greiner, José L. Herrera-Diestra, Michael Tildesley, Katriona Shea, Matthew Ferrari

PLOS Computational Biology: published July 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012395

Time-series modeling of epidemics in complex populations: Detecting changes in incidence volatility over time

Rachael Aber, Yanming Di, Benjamin D. Dalziel

PLOS Computational Biology: published July 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012882

Multi-scale phylodynamic modelling of rapid punctuated pathogen evolution

Quang Dang Nguyen, Sheryl L. Chang, Carl J. E. Suster, Rebecca J. Rockett, Vitali Sintchenko, Tania C. Sorrell, Mikhail Prokopenko

PLOS Computational Biology: published July 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013295

Statistical analysis supports the size control mechanism of Chlamydia development

Jinsu Kim, Christine Sütterlin, Ming Tan, German Enciso

PLOS Computational Biology: published July 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013227

Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome

Tarun Mahajan, Sergei Maslov

PLOS Computational Biology: published July 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013222

How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors

Rui Wang, Tamar Schlick

PLOS Computational Biology: published July 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013230

Cardiogenic and chronobiological mechanisms in seizure-induced sinus arrhythmias

Pan Li, Sangbo Lee, Kwang-Yeon Choi, Jonathan E. Rubin, Jae Kyoung Kim

PLOS Computational Biology: published July 16, 2025 | https://doi.org/10.1371/journal.pcbi.1013318

Multi-scale computational modeling towards efficacy in radiopharmaceutical therapies while minimizing side effects: Modeling of amino acid infusion

Aryan Golzaryan, Mohammad Souri, Farshad M. Kashkooli, Arman Rahmim, M. Soltani

PLOS Computational Biology: published July 16, 2025 | https://doi.org/10.1371/journal.pcbi.1013247

EUP: Enhanced cross-species prediction of ubiquitination sites via a conditional variational autoencoder network based on ESM2

Junhao Liu, Zeyu Luo, Rui Wang, Xin Li, Yawen Sun, Zongqing Chen, Yu-Juan Zhang

PLOS Computational Biology: published July 16, 2025 | https://doi.org/10.1371/journal.pcbi.1013268

Impact of ligand binding on VEGFR1, VEGFR2, and NRP1 localization in human endothelial cells

Sarvenaz Sarabipour, Karina Kinghorn, Kaitlyn M. Quigley, Anita Kovacs-Kasa, Brian H. Annex, Victoria L. Bautch, Feilim Mac Gabhann

PLOS Computational Biology: published July 16, 2025 | https://doi.org/10.1371/journal.pcbi.1013254

Modular, focused data science education improves biomedical learners’ abilities: A study of the Data and Analytics for Research Training (DART) program

Rose Hartman, Karen Joy Payton, Rose Franzen, Meredith Lee, Elizabeth Drellich, Ali Shokoufandeh, Jeffrey Pennington

PLOS Computational Biology: published July 17, 2025 | https://doi.org/10.1371/journal.pcbi.1013249

Tensor decomposition of multi-dimensional splicing events across multiple tissues to identify splicing-mediated risk genes associated with complex traits

Yan Yan, Rui Chen, Hakmook Kang, Yuting Tan, Anshul Tiwari, Siyuan Ma, Zhexing Wen, Xue Zhong, Bingshan Li

PLOS Computational Biology: published July 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013303

Population-level toggling of T cell immune escape at human leukocyte antigen anchor residues in SARS-CoV-2 Spike proteins, in an ethnically diverse population region

Nobubelo K. Ngandu, Burtram C. Fielding, Peter van Heusden, Kuhle Mcinga, Kriheska Francis, Gordon Harkins

PLOS Computational Biology: published July 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013261

Disentangling signal and noise in neural responses through generative modeling

Kendrick Kay, Jacob S. Prince, Thomas Gebhart, Greta Tuckute, Jingyang Zhou, Thomas Naselaris, Heiko H. Schütt

PLOS Computational Biology: published July 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012092

Modeling full-scale leaf venation networks

Lars Erik J. Skjegstad, Julius B. Kirkegaard

PLOS Computational Biology: published July 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013292

Comparison of FORCE trained spiking and rate neural networks shows spiking networks learn slowly with noisy, cross-trial firing rates

Thomas Robert Newton, Wilten Nicola

PLOS Computational Biology: published July 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013224

A modular model integrating metabolism, growth, and cell cycle predicts that fermentation is required to modulate cell size in yeast populations

Marco Vanoni, Pasquale Palumbo, Federico Papa, Stefano Busti, Laura Gotti, Meike Wortel, Bas Teusink, Ivan Orlandi, Alex Pessina, Cristina Airoldi, Luca Brambilla, Marina Vai, Lilia Alberghina

PLOS Computational Biology: published July 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013296

Analyzing greedy vaccine allocation algorithms for metapopulation disease models

Jeffrey Keithley, Akash Choudhuri, Bijaya Adhikari, Sriram V. Pemmaraju

PLOS Computational Biology: published July 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012539

Using homologous network to identify reassortment risk in H5Nx avian influenza viruses

Ruihao Gong, Zijian Feng, Yanyun Zhang

PLOS Computational Biology: published July 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013301

Waveform distortion for temperature compensation and synchronization in circadian rhythms: An approach based on the renormalization group method

Shingo Gibo, Teiji Kunihiro, Tetsuo Hatsuda, Gen Kurosawa

PLOS Computational Biology: published July 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013246

Correction

Correction: A Well-Defined Readily Releasable Pool with Fixed Capacity for Storing Vesicles at Calyx of Held

Kashif Mahfooz, Mahendra Singh, Robert Renden, John F. Wesseling

PLOS Computational Biology: published July 31, 2025 | https://doi.org/10.1371/journal.pcbi.1013339

Methods

PoweREST: Statistical power estimation for spatial transcriptomics experiments to detect differentially expressed genes between two conditions

Lan Shui, Anirban Maitra, Ying Yuan, Ken Lau, Harsimran Kaur, Liang Li, Ziyi Li, Translational and Basic Science Research in Early Lesions Research Consortia

PLOS Computational Biology: published July 29, 2025 | https://doi.org/10.1371/journal.pcbi.1013293

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

July 2025

Cover

Simulating the Digital Twin Heart for Precision Cardiac Therapy

Education Articles

Perspectives

Research Articles

Correction

Related Articles

Methods

Software

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