December 2023

This cartoon illustrates the different ‘paths’ available to a reproducing bacteria based on the substrate environment.

Image Credit: Avik Mukherjee

Education Articles

Ten simple rules for managing laboratory information

Casey-Tyler Berezin, Luis U. Aguilera, Sonja Billerbeck, Philip E. Bourne, Douglas Densmore, Paul Freemont, Thomas E. Gorochowski, Sarah I. Hernandez, Nathan J. Hillson, Connor R. King, Michael Köpke, Shuyi Ma, Katie M. Miller, Tae Seok Moon, Jason H. Moore, Brian Munsky, Chris J. Myers, Dequina A. Nicholas, Samuel J. Peccoud, Wen Zhou, Jean Peccoud

PLOS Computational Biology: published December 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011652

Ten simple rules for humane data science

Hassan Masum, Philip E. Bourne

PLOS Computational Biology: published December 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011698

Ten quick tips for fuzzy logic modeling of biomedical systems

Davide Chicco, Simone Spolaor, Marco S. Nobile

PLOS Computational Biology: published December 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011700

Ten simple rules for writing a PLOS Computational Biology quick tips article

Patricia M. Palagi, Russell Schwartz, Scott Markel, B. F. Francis Ouellette

PLOS Computational Biology: published December 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011689

Know-how of holding a Bioinformatics competition: Structure, model, overview, and perspectives

Elvira C. A. Horácio, Lucas M. de Carvalho, Gustavo G. Pereira, Mayla C. Abrahim, Mônica P. Coelho, Deivid A. De Jesus, Glen J. Y. García, Raquel C. de Melo-Minardi, Sheila T. Nagamatsu

PLOS Computational Biology: published December 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011679

Perspectives

From policy to practice: Lessons learned from an open science funding initiative

Sonya B. Dumanis, Kristen Ratan, Souad McIntosh, Hetal V. Shah, Matt Lewis, Timothy H. Vines, Randy Schekman, Ekemini A. Riley

PLOS Computational Biology: published December 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011626

Ten simple rules for starting FAIR discussions in your community

Frédérique Belliard, Angelica Maria Maineri, Esther Plomp, Andrés Felipe Ramos Padilla, Junzi Sun, Maryam Zare Jeddi

PLOS Computational Biology: published December 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011668

Research Articles

Prokaryotic virus host prediction with graph contrastive augmentaion

Zhi-Hua Du, Jun-Peng Zhong, Yun Liu, Jian-Qiang Li

PLOS Computational Biology: published December 1, 2023 | https://doi.org/10.1371/journal.pcbi.1011671

Spatial exclusion leads to “tug-of-war” ecological dynamics between competing species within microchannels

Jeremy Rothschild, Tianyi Ma, Joshua N. Milstein, Anton Zilman

PLOS Computational Biology: published December 1, 2023 | https://doi.org/10.1371/journal.pcbi.1010868

Learning massive interpretable gene regulatory networks of the human brain by merging Bayesian networks

Niko Bernaola, Mario Michiels, Pedro Larrañaga, Concha Bielza

PLOS Computational Biology: published December 1, 2023 | https://doi.org/10.1371/journal.pcbi.1011443

Sparsity in an artificial neural network predicts beauty: Towards a model of processing-based aesthetics

Nicolas M. Dibot, Sonia Tieo, Tamra C. Mendelson, William Puech, Julien P. Renoult

PLOS Computational Biology: published December 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011703

Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations

Xin Y. Dong, Renjie Liu, Dillon T. Seroski, Gregory A. Hudalla, Carol K. Hall

PLOS Computational Biology: published December 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011685

A cell-and-plasma numerical model reveals hemodynamic stress and flow adaptation in zebrafish microvessels after morphological alteration

Swe Soe Maung Ye, Li-Kun Phng

PLOS Computational Biology: published December 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011665

Effective cell membrane tension protects red blood cells against malaria invasion

Haleh Alimohamadi, Padmini Rangamani

PLOS Computational Biology: published December 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011694

RMDGCN: Prediction of RNA methylation and disease associations based on graph convolutional network with attention mechanism

Lian Liu, Yumeng Zhou, Xiujuan Lei

PLOS Computational Biology: published December 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011677

Modelling the impact of JNJ-1802, a first-in-class dengue inhibitor blocking the NS3-NS4B interaction, on in-vitro DENV-2 dynamics

Clare P. McCormack, Olivia Goethals, Nele Goeyvaerts, Xavier D. Woot de Trixhe, Peggy Geluykens, Doortje Borrenberghs, Neil M. Ferguson, Oliver Ackaert, Ilaria Dorigatti

PLOS Computational Biology: published December 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011662

Major depressive disorder and bistability in an HPA-CNS toggle switch

Ben Ron Mizrachi, Avichai Tendler, Omer Karin, Tomer Milo, Dafna Haran, Avi Mayo, Uri Alon

PLOS Computational Biology: published December 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011645

multi-GPA-Tree: Statistical approach for pleiotropy informed and functional annotation tree guided prioritization of GWAS results

Aastha Khatiwada, Ayse Selen Yilmaz, Bethany J. Wolf, Maciej Pietrzak, Dongjun Chung

PLOS Computational Biology: published December 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011686

Motoneuron-driven computational muscle modelling with motor unit resolution and subject-specific musculoskeletal anatomy

Arnault H. Caillet, Andrew T. M. Phillips, Dario Farina, Luca Modenese

PLOS Computational Biology: published December 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011606

Dissolution of spiral wave’s core using cardiac optogenetics

Sayedeh Hussaini, Sarah L. Lädke, Johannes Schröder-Schetelig, Vishalini Venkatesan, Raúl A. Quiñonez Uribe, Claudia Richter, Rupamanjari Majumder, Stefan Luther

PLOS Computational Biology: published December 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011660

Learning context shapes bimanual control strategy and generalization of novel dynamics

Jonathan Orschiedt, David W. Franklin

PLOS Computational Biology: published December 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011189

The neurocognitive role of working memory load when Pavlovian motivational control affects instrumental learning

Heesun Park, Hoyoung Doh, Eunhwi Lee, Harhim Park, Woo-Young Ahn

PLOS Computational Biology: published December 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011692

How well do rudimentary plasticity rules predict adult visual object learning?

Michael J. Lee, James J. DiCarlo

PLOS Computational Biology: published December 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011713

Generalized Michaelis–Menten rate law with time-varying molecular concentrations

Roktaek Lim, Thomas L. P. Martin, Junghun Chae, Woo Joong Kim, Cheol-Min Ghim, Pan-Jun Kim

PLOS Computational Biology: published December 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011711

From dawn till dusk: Time-adaptive bayesian optimization for neurostimulation

John E. Fleming, Ines Pont Sanchis, Oscar Lemmens, Angus Denison-Smith, Timothy O. West, Timothy Denison, Hayriye Cagnan

PLOS Computational Biology: published December 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011674

Machine learning identification of Pseudomonas aeruginosa strains from colony image data

Jennifer B. Rattray, Ryan J. Lowhorn, Ryan Walden, Pedro Márquez-Zacarías, Evgeniya Molotkova, Gabriel Perron, Claudia Solis-Lemus, Daniel Pimentel Alarcon, Sam P. Brown

PLOS Computational Biology: published December 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011699

Sequence representation as an early step in the evolution of language

Anna Jon-And, Markus Jonsson, Johan Lind, Stefano Ghirlanda, Magnus Enquist

PLOS Computational Biology: published December 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011702

Time-resolved dynamic computational modeling of human EEG recordings reveals gradients of generative mechanisms for the MMN response

Arnaud Poublan-Couzardot, Françoise Lecaignard, Enrico Fucci, Richard J. Davidson, Jérémie Mattout, Antoine Lutz, Oussama Abdoun

PLOS Computational Biology: published December 13, 2023 | https://doi.org/10.1371/journal.pcbi.1010557

A combined computational and experimental investigation of the filtration function of splenic macrophages in sickle cell disease

Guansheng Li, Yuhao Qiang, He Li, Xuejin Li, Pierre A. Buffet, Ming Dao, George Em Karniadakis

PLOS Computational Biology: published December 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011223

Unravelling cancer subtype-specific driver genes in single-cell transcriptomics data with CSDGI

Meng Huang, Jiangtao Ma, Guangqi An, Xiucai Ye

PLOS Computational Biology: published December 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011450

Identification of dynamical changes of rabies transmission under quarantine: Community-based measures towards rabies elimination

Kristyna Rysava, Michael J. Tildesley

PLOS Computational Biology: published December 15, 2023 | https://doi.org/10.1371/journal.pcbi.1011187

Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture

Archit Singh, Shaon Chakrabarti

PLOS Computational Biology: published December 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011725

Emergent spatial goals in an integrative model of the insect central complex

Roman Goulard, Stanley Heinze, Barbara Webb

PLOS Computational Biology: published December 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011480

Mechanistic insight into the functional role of human sinoatrial node conduction pathways and pacemaker compartments heterogeneity: A computer model analysis

Jichao Zhao, Roshan Sharma, Anuradha Kalyanasundaram, James Kennelly, Jieyun Bai, Ning Li, Alexander Panfilov, Vadim V. Fedorov

PLOS Computational Biology: published December 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011708

4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction

Zihao Wang, Songhao Luo, Zhenquan Zhang, Tianshou Zhou, Jiajun Zhang

PLOS Computational Biology: published December 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011722

Statistical prediction of microbial metabolic traits from genomes

Zeqian Li, Ahmed Selim, Seppe Kuehn

PLOS Computational Biology: published December 19, 2023 | https://doi.org/10.1371/journal.pcbi.1011705

A kinetic model of iron trafficking in growing Saccharomyces cerevisiae cells; applying mathematical methods to minimize the problem of sparse data and generate viable autoregulatory mechanisms

Shantanu Thorat, Jay R. Walton, Paul A. Lindahl

PLOS Computational Biology: published December 19, 2023 | https://doi.org/10.1371/journal.pcbi.1011701

Method to determine whether sleep phenotypes are driven by endogenous circadian rhythms or environmental light by combining longitudinal data and personalised mathematical models

Anne C. Skeldon, Thalia Rodriguez Garcia, Sean F. Cleator, Ciro della Monica, Kiran K. G. Ravindran, Victoria L. Revell, Derk-Jan Dijk

PLOS Computational Biology: published December 22, 2023 | https://doi.org/10.1371/journal.pcbi.1011743

A computational model of Pseudomonas syringae metabolism unveils a role for branched-chain amino acids in Arabidopsis leaf colonization

Philip J. Tubergen, Greg Medlock, Anni Moore, Xiaomu Zhang, Jason A. Papin, Cristian H. Danna

PLOS Computational Biology: published December 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011651

Recurrence risk stratification of hepatocellular carcinomas based on immune gene expression and features extracted from pathological images

Tao Ding, Xiao Li, Jiu Mo, Gregory Alexander, Jialu Li

PLOS Computational Biology: published December 29, 2023 | https://doi.org/10.1371/journal.pcbi.1011716

Methods

SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network

Xing Zhang, Hongmei Yin, Fei Ling, Jian Zhan, Yaoqi Zhou

PLOS Computational Biology: published December 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011330

Software

resevol: An R package for spatially explicit models of pesticide resistance given evolving pest genomes

A. Bradley Duthie, Rosie Mangan, C. Rose McKeon, Matthew C. Tinsley, Luc F. Bussière

PLOS Computational Biology: published December 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011691

PyRates—A code-generation tool for modeling dynamical systems in biology and beyond

Richard Gast, Thomas R. Knösche, Ann Kennedy

PLOS Computational Biology: published December 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011761

Cover

Education Articles

Perspectives

Research Articles

Methods

Software