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Table of Contents

February 2025

Cover

Celebrating 10 Years of Leadership with Dr. Jason Papin
Issue Image

PLOS thanks Jason for his leadership, warmth, and dedication to Open Science.

Image Credit: PLOS

Education

Ten quick tips to build a Model Life Cycle

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

PLOS Computational Biology: published February 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012731

Perspective

Ten simple rules for fostering creativity in research labs

Matthias C. Rillig

PLOS Computational Biology: published February 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012788

Research Articles

Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data

Grace C. McKenzie-Smith, Scott W. Wolf, Julien F. Ayroles, Joshua W. Shaevitz

PLOS Computational Biology: published February 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012753

Simulation-based validation of a method to detect changes in SARS-CoV-2 reinfection risk

Belinda Lombard, Harry Moultrie, Juliet R.C. Pulliam, Cari van Schalkwyk

PLOS Computational Biology: published February 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012792

Design of field trials for the evaluation of transmissible vaccines in animal populations

Justin K. Sheen, Lee Kennedy-Shaffer, Michael Z. Levy, Charlotte Jessica E. Metcalf

PLOS Computational Biology: published February 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012779

Repeated games with partner choice

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

PLOS Computational Biology: published February 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012810

Contributions of action potentials to scalp EEG: Theory and biophysical simulations

Niklas Brake, Anmar Khadra

PLOS Computational Biology: published February 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012794

Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2

Paulina N. Smaruj, Fahad Kamulegeya, David R. Kelley, Geoffrey Fudenberg

PLOS Computational Biology: published February 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012824

Multi-strain phage induced clearance of bacterial infections

Jacopo Marchi, Chau Nguyen Ngoc Minh, Laurent Debarbieux, Joshua S Weitz

PLOS Computational Biology: published February 4, 2025 | https://doi.org/10.1371/journal.pcbi.1012793

Structural prediction of chimeric immunogen candidates to elicit targeted antibodies against betacoronaviruses

Jamel Simpson, Peter M. Kasson

PLOS Computational Biology: published February 5, 2025 | https://doi.org/10.1371/journal.pcbi.1012812

Identification of recurrent dynamics in distributed neural populations

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

PLOS Computational Biology: published February 6, 2025 | https://doi.org/10.1371/journal.pcbi.1012816

A SuperLearner-based pipeline for the development of DNA methylation-derived predictors of phenotypic traits

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

PLOS Computational Biology: published February 6, 2025 | https://doi.org/10.1371/journal.pcbi.1012768

Challenging a paradigm: Staggered versus single-pulse mass dog vaccination strategy for rabies elimination

Brinkley Raynor Bellotti, Elvis W. Díaz, Micaela De la Puente-León, Maria T. Rieders, Sergio E. Recuenco, Michael Z. Levy, Ricardo Castillo-Neyra

PLOS Computational Biology: published February 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012780

Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA

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

PLOS Computational Biology: published February 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012747

Mapping the learning curves of deep learning networks

Yanru Jiang, Rick Dale

PLOS Computational Biology: published February 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012286

Computational mechanism underlying switching of motor actions

Shan Zhong, Nader Pouratian, Vassilios Christopoulos

PLOS Computational Biology: published February 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012811

Decoding biomolecular condensate dynamics: an energy landscape approach

Subhadip Biswas, Davit A Potoyan

PLOS Computational Biology: published February 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012826

A model of Notch signalling control of angiogenesis: Evidence of a role for Notch ligand heterodimerization

Daipeng Chen, Xinxin Liu, Haijiang Wang, Roeland M.H. Merks, David A. Baker

PLOS Computational Biology: published February 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012825

Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities

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

PLOS Computational Biology: published February 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012789

Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses

Ines S. C. Baptista, Suchintak Dash, Amir M. Arsh, Vinodh Kandavalli, Carlo Maria Scandolo, Barry C. Sanders, Andre S. Ribeiro

PLOS Computational Biology: published February 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012817

Reliability-enhanced data cleaning in biomedical machine learning using inductive conformal prediction

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

PLOS Computational Biology: published February 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012803

Detection of latent brain states from spontaneous neural activity in the amygdala

Alexa Aucoin, Kevin K. Lin, Katalin M. Gothard

PLOS Computational Biology: published February 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012247

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

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

PLOS Computational Biology: published February 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012773

Hexagons all the way down: grid cells as a conformal isometric map of space

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

PLOS Computational Biology: published February 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012804

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

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

PLOS Computational Biology: published February 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012778

Integrating multiscale mathematical modeling and multidimensional data reveals the effects of epigenetic instability on acquired drug resistance in cancer

Shun Wang, Jinzhi Lei, Xiufen Zou, Suoqin Jin

PLOS Computational Biology: published February 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012815

An in silico framework for the rational design of vaginal probiotic therapy

Christina Y. Lee, Sina Bonakdar, Kelly B. Arnold

PLOS Computational Biology: published February 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012064

Estimating Mycobacterium tuberculosis transmission in a South African clinic: Spatiotemporal model based on person movements

Nicolas Banholzer, Keren Middelkoop, Juane Leukes, Ernest Weingartner, Remo Schmutz, Kathrin Zürcher, Matthias Egger, Robin Wood, Lukas Fenner

PLOS Computational Biology: published February 18, 2025 | https://doi.org/10.1371/journal.pcbi.1012823

Nowcasting reported covid-19 hospitalizations using de-identified, aggregated medical insurance claims data

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

PLOS Computational Biology: published February 18, 2025 | https://doi.org/10.1371/journal.pcbi.1012717

ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization

Laura M. Gunsalus, Michael J. Keiser, Katherine S. Pollard

PLOS Computational Biology: published February 18, 2025 | https://doi.org/10.1371/journal.pcbi.1012841

Optimal control prevents itself from eradicating stochastic disease epidemics

Rachel Russell, Nik J Cunniffe

PLOS Computational Biology: published February 18, 2025 | https://doi.org/10.1371/journal.pcbi.1012781

Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment

Mai Chan Lau, Jennifer Borowsky, Juha P. Väyrynen, Koichiro Haruki, Melissa Zhao, Andressa Dias Costa, Simeng Gu, Annacarolina da Silva, Tomotaka Ugai, Kota Arima, Minh N. Nguyen, Yasutoshi Takashima, Joe Yeong, David Tai, Tsuyoshi Hamada, Jochen K. Lennerz, Charles S. Fuchs, Catherine J. Wu, Jeffrey A. Meyerhardt, Shuji Ogino, Jonathan A. Nowak

PLOS Computational Biology: published February 18, 2025 | https://doi.org/10.1371/journal.pcbi.1012707

Compression-enabled interpretability of voxelwise encoding models

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

PLOS Computational Biology: published February 19, 2025 | https://doi.org/10.1371/journal.pcbi.1012822

Bayesian classification of OXPHOS deficient skeletal myofibres

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

PLOS Computational Biology: published February 19, 2025 | https://doi.org/10.1371/journal.pcbi.1012770

Quantifying infectious disease epidemic risks: A practical approach for seasonal pathogens

Alexander R Kaye, Giorgio Guzzetta, Michael J Tildesley, Robin N Thompson

PLOS Computational Biology: published February 19, 2025 | https://doi.org/10.1371/journal.pcbi.1012364

Resilience of mobility network to dynamic population response across COVID-19 interventions: Evidences from Chile

Pasquale Casaburi, Lorenzo Dall’Amico, Nicolò Gozzi, Kyriaki Kalimeri, Anna Sapienza, Rossano Schifanella, T. Di Matteo, Leo Ferres, Mattia Mazzoli

PLOS Computational Biology: published February 20, 2025 | https://doi.org/10.1371/journal.pcbi.1012802

An application of nowcasting methods: Cases of norovirus during the winter 2023/2024 in England

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

PLOS Computational Biology: published February 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012849

Information transmission in a cell monolayer: A numerical study

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

PLOS Computational Biology: published February 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012846

An agent-based model to simulate the transmission dynamics of bloodborne pathogens within hospitals

Paul Henriot, Mohamed El-Kassas, Wagida Anwar, Samia A. Girgis, Maha El Gaafary, Kévin Jean, Laura Temime

PLOS Computational Biology: published February 24, 2025 | https://doi.org/10.1371/journal.pcbi.1012850

Noradrenergic and Dopaminergic modulation of meta-cognition and meta-control

Sara Ershadmanesh, Sahar Rajabi, Reza Rostami, Rani Moran, Peter Dayan

PLOS Computational Biology: published February 26, 2025 | https://doi.org/10.1371/journal.pcbi.1012675

Impact of increased diagnosis of early HIV infection and immediate antiretroviral treatment initiation on HIV transmission among men who have sex with men in the Netherlands

Alexandra Teslya, Janneke Cornelia Maria Heijne, Maarten Franciscus Schim van der Loeff, Ard van Sighem, Jacob Aiden Roberts, Maartje Dijkstra, Godelieve J de Bree, Axel Jeremias Schmidt, Kai J Jonas, Mirjam E Kretzschmar, Ganna Rozhnova

PLOS Computational Biology: published February 27, 2025 | https://doi.org/10.1371/journal.pcbi.1012055

Methods

RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies

Nathanaël Hozé, Margarita Pons-Salort, C. Jessica E. Metcalf, Michael White, Henrik Salje, Simon Cauchemez

PLOS Computational Biology: published February 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012777

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

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

PLOS Computational Biology: published February 11, 2025 | https://doi.org/10.1371/journal.pcbi.1012745

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

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

PLOS Computational Biology: published February 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012782

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

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, Riu Yamashita

PLOS Computational Biology: published February 18, 2025 | https://doi.org/10.1371/journal.pcbi.1012854

Software

NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction

Jan-Simon Baasner, Andreas Rempel, Dakota Howard, Boas Pucker

PLOS Computational Biology: published February 18, 2025 | https://doi.org/10.1371/journal.pcbi.1012732