Current Issue | PLOS Computational Biology

Individuals in a marmoset monkey pair take turns to be vigilant while they are feeding. By modeling the monkeys as coupled oscillators, we investigated how this turn-taking pattern emerges over time. We find that marmosets have remarkable flexibility and control over this turn-taking behavior. The more out-of-sync they are initially, the more effort they put into synchronizing with each other, thus facilitating rapid coordination of vigilance. Phaniraj et al 2024

Image Credit: Rahel K. Brügger and Nikhil Phaniraj

Education

Ten simple rules for teaching an introduction to R

Ava M. Hoffman, Carrie Wright

PLOS Computational Biology: published May 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012018

Perspective

FAIR-USE4OS: Guidelines for creating impactful open-source software

Raphael Sonabend, Hugo Gruson, Leo Wolansky, Agnes Kiragga, Daniel S. Katz

PLOS Computational Biology: published May 9, 2024 | https://doi.org/10.1371/journal.pcbi.1012045

Research Articles

Dissecting Bayes: Using influence measures to test normative use of probability density information derived from a sample

Keiji Ota, Laurence T. Maloney

PLOS Computational Biology: published May 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011999

The quality and complexity of pairwise maximum entropy models for large cortical populations

Valdemar Kargård Olsen, Jonathan R. Whitlock, Yasser Roudi

PLOS Computational Biology: published May 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012074

Re-awakening the brain: Forcing transitions in disorders of consciousness by external in silico perturbation

Paulina Clara Dagnino, Anira Escrichs, Ane López-González, Olivia Gosseries, Jitka Annen, Yonatan Sanz Perl, Morten L. Kringelbach, Steven Laureys, Gustavo Deco

PLOS Computational Biology: published May 3, 2024 | https://doi.org/10.1371/journal.pcbi.1011350

Visual social information use in collective foraging

David Mezey, Dominik Deffner, Ralf H. J. M. Kurvers, Pawel Romanczuk

PLOS Computational Biology: published May 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012087

A mathematical model for the role of dopamine-D2 self-regulation in the production of ultradian rhythms

An Qi Zhang, Martin R. Ralph, Adam R. Stinchcombe

PLOS Computational Biology: published May 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012082

Machine-learning and mechanistic modeling of metastatic breast cancer after neoadjuvant treatment

Sebastien Benzekry, Michalis Mastri, Chiara Nicolò, John M. L. Ebos

PLOS Computational Biology: published May 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012088

A systematic analysis of regression models for protein engineering

Richard Michael, Jacob Kæstel-Hansen, Peter Mørch Groth, Simon Bartels, Jesper Salomon, Pengfei Tian, Nikos S. Hatzakis, Wouter Boomsma

PLOS Computational Biology: published May 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012061

Epidemiological and health economic implications of symptom propagation in respiratory pathogens: A mathematical modelling investigation

Phoebe Asplin, Matt J. Keeling, Rebecca Mancy, Edward M. Hill

PLOS Computational Biology: published May 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012096

On the impact of re-mating and residual fertility on the Sterile Insect Technique efficacy: Case study with the medfly, Ceratitis capitata

Yves Dumont, Clélia F. Oliva

PLOS Computational Biology: published May 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012052

Challenges of COVID-19 Case Forecasting in the US, 2020–2021

Velma K. Lopez, Estee Y. Cramer, Robert Pagano, John M. Drake, Eamon B. O’Dea, Madeline Adee, Turgay Ayer, Jagpreet Chhatwal, Ozden O. Dalgic, Mary A. Ladd, Benjamin P. Linas, Peter P. Mueller, Jade Xiao, Johannes Bracher, Alvaro J. Castro Rivadeneira, Aaron Gerding, Tilmann Gneiting, Yuxin Huang, Dasuni Jayawardena, Abdul H. Kanji, Khoa Le, Anja Mühlemann, Jarad Niemi, Evan L. Ray, Ariane Stark, Yijin Wang, Nutcha Wattanachit, Martha W. Zorn, Sen Pei, Jeffrey Shaman, Teresa K. Yamana, Samuel R. Tarasewicz, Daniel J. Wilson, Sid Baccam, Heidi Gurung, Steve Stage, Brad Suchoski, Lei Gao, Zhiling Gu, Myungjin Kim, Xinyi Li, Guannan Wang, Lily Wang, Yueying Wang, Shan Yu, Lauren Gardner, Sonia Jindal, Maximilian Marshall, Kristen Nixon, Juan Dent, Alison L. Hill, Joshua Kaminsky, Elizabeth C. Lee, Joseph C. Lemaitre, Justin Lessler, Claire P. Smith, Shaun Truelove, Matt Kinsey, Luke C. Mullany, Kaitlin Rainwater-Lovett, Lauren Shin, Katharine Tallaksen, Shelby Wilson, Dean Karlen, Lauren Castro, Geoffrey Fairchild, Isaac Michaud, Dave Osthus, Jiang Bian, Wei Cao, Zhifeng Gao, Juan Lavista Ferres, Chaozhuo Li, Tie-Yan Liu, Xing Xie, Shun Zhang, Shun Zheng, Matteo Chinazzi, Jessica T. Davis, Kunpeng Mu, Ana Pastore y Piontti, Alessandro Vespignani, Xinyue Xiong, Robert Walraven, Jinghui Chen, Quanquan Gu, Lingxiao Wang, Pan Xu, Weitong Zhang, Difan Zou, Graham Casey Gibson, Daniel Sheldon, Ajitesh Srivastava, Aniruddha Adiga, Benjamin Hurt, Gursharn Kaur, Bryan Lewis, Madhav Marathe, Akhil Sai Peddireddy, Przemyslaw Porebski, Srinivasan Venkatramanan, Lijing Wang, Pragati V. Prasad, Jo W. Walker, Alexander E. Webber, Rachel B. Slayton, Matthew Biggerstaff, Nicholas G. Reich, Michael A. Johansson

PLOS Computational Biology: published May 6, 2024 | https://doi.org/10.1371/journal.pcbi.1011200

Differential disruptions in population coding along the dorsal-ventral axis of CA1 in the APP/PS1 mouse model of Aβ pathology

Udaysankar Chockanathan, Krishnan Padmanabhan

PLOS Computational Biology: published May 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012085

Brain2GAN: Feature-disentangled neural encoding and decoding of visual perception in the primate brain

Thirza Dado, Paolo Papale, Antonio Lozano, Lynn Le, Feng Wang, Marcel van Gerven, Pieter Roelfsema, Yağmur Güçlütürk, Umut Güçlü

PLOS Computational Biology: published May 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012058

Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model

István Oszoli, István Zachar

PLOS Computational Biology: published May 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012107

Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot

Luke Trinity, Ulrike Stege, Hosna Jabbari

PLOS Computational Biology: published May 7, 2024 | https://doi.org/10.1371/journal.pcbi.1011787

PESSA: A web tool for pathway enrichment score-based survival analysis in cancer

Hong Yang, Ying Shi, Anqi Lin, Chang Qi, Zaoqu Liu, Quan Cheng, Kai Miao, Jian Zhang, Peng Luo

PLOS Computational Biology: published May 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012024

Scuphr: A probabilistic framework for cell lineage tree reconstruction

Hazal Koptagel, Seong-Hwan Jun, Joanna Hård, Jens Lagergren

PLOS Computational Biology: published May 9, 2024 | https://doi.org/10.1371/journal.pcbi.1012094

Machine learning and multi-omics data reveal driver gene-based molecular subtypes in hepatocellular carcinoma for precision treatment

Meng Wang, Xinyue Yan, Yanan Dong, Xiaoqin Li, Bin Gao

PLOS Computational Biology: published May 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012113

The tuning of tuning: How adaptation influences single cell information transfer

Fleur Zeldenrust, Niccolò Calcini, Xuan Yan, Ate Bijlsma, Tansu Celikel

PLOS Computational Biology: published May 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012043

Agent-based modeling of nuclear chromosome ensembles identifies determinants of homolog pairing during meiosis

Ariana Chriss, G. Valentin Börner, Shawn D. Ryan

PLOS Computational Biology: published May 13, 2024 | https://doi.org/10.1371/journal.pcbi.1011416

Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches

Blox Bloxham, Hyunseok Lee, Jeff Gore

PLOS Computational Biology: published May 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012049

Foraging in a non-foraging task: Fitness maximization explains human risk preference dynamics under changing environment

Yasuhiro Mochizuki, Norihiro Harasawa, Mayank Aggarwal, Chong Chen, Haruaki Fukuda

PLOS Computational Biology: published May 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012080

Network representation of multicellular activity in pancreatic islets: Technical considerations for functional connectivity analysis

Marko Šterk, Yaowen Zhang, Viljem Pohorec, Eva Paradiž Leitgeb, Jurij Dolenšek, Richard K. P. Benninger, Andraž Stožer, Vira Kravets, Marko Gosak

PLOS Computational Biology: published May 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012130

Graph topological transformations in space-filling cell aggregates

Tanmoy Sarkar, Matej Krajnc

PLOS Computational Biology: published May 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012089

Data–driven modelling makes quantitative predictions regarding bacteria surface motility

Daniel L. Barton, Yow-Ren Chang, William Ducker, Jure Dobnikar

PLOS Computational Biology: published May 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012063

What can we learn when fitting a simple telegraph model to a complex gene expression model?

Feng Jiao, Jing Li, Ting Liu, Yifeng Zhu, Wenhao Che, Leonidas Bleris, Chen Jia

PLOS Computational Biology: published May 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012118

Learning with filopodia and spines: Complementary strong and weak competition lead to specialized, graded, and protected receptive fields

Albert Albesa-González, Claudia Clopath

PLOS Computational Biology: published May 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012110

Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life

Sean M. Cascarina, Eric D. Ross

PLOS Computational Biology: published May 15, 2024 | https://doi.org/10.1371/journal.pcbi.1011372

Marmosets mutually compensate for differences in rhythms when coordinating vigilance

Nikhil Phaniraj, Rahel K. Brügger, Judith M. Burkart

PLOS Computational Biology: published May 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012104

Structural and practical identifiability of contrast transport models for DCE-MRI

Martina Conte, Ryan T. Woodall, Margarita Gutova, Bihong T. Chen, Mark S. Shiroishi, Christine E. Brown, Jennifer M. Munson, Russell C. Rockne

PLOS Computational Biology: published May 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012106

Inferring fungal growth rates from optical density data

Tara Hameed, Natasha Motsi, Elaine Bignell, Reiko J. Tanaka

PLOS Computational Biology: published May 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012105

Interpretable online network dictionary learning for inferring long-range chromatin interactions

Vishal Rana, Jianhao Peng, Chao Pan, Hanbaek Lyu, Albert Cheng, Minji Kim, Olgica Milenkovic

PLOS Computational Biology: published May 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012095

Liebig’s law of the minimum in the TGF-β/SMAD pathway

Yuchao Li, Difan Deng, Chris Tina Höfer, Jihye Kim, Won Do Heo, Quanbin Xu, Xuedong Liu, Zhike Zi

PLOS Computational Biology: published May 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012072

Nuclear export is a limiting factor in eukaryotic mRNA metabolism

Jason M. Müller, Katharina Moos, Till Baar, Kerstin C. Maier, Kristina Zumer, Achim Tresch

PLOS Computational Biology: published May 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012059

Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model

Alexander Massey, Corentin Boennec, Claudia Ximena Restrepo-Ortiz, Christophe Blanchet, Samuel Alizon, Mircea T. Sofonea

PLOS Computational Biology: published May 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012124

Learning Micro-C from Hi-C with diffusion models

Tong Liu, Hao Zhu, Zheng Wang

PLOS Computational Biology: published May 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012136

Competition between physical search and a weak-to-strong transition rate-limits kinesin binding times

Trini Nguyen, Babu Reddy Janakaloti Narayanareddy, Steven P. Gross, Christopher E. Miles

PLOS Computational Biology: published May 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012158

Where’s Whaledo: A software toolkit for array localization of animal vocalizations

Eric R. Snyder, Alba Solsona-Berga, Simone Baumann-Pickering, Kait E. Frasier, Sean M. Wiggins, John A. Hildebrand

PLOS Computational Biology: published May 20, 2024 | https://doi.org/10.1371/journal.pcbi.1011456

A computational analysis of the role of integrins and Rho-GTPases in the emergence and disruption of apical-basal polarization in renal epithelial cells

Maria J. Hagelaars, Milica Nikolic, Maud Vermeulen, Sylvia Dekker, Carlijn V. C. Bouten, Sandra Loerakker

PLOS Computational Biology: published May 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012140

Diverse task-driven modeling of macaque V4 reveals functional specialization towards semantic tasks

Santiago A. Cadena, Konstantin F. Willeke, Kelli Restivo, George Denfield, Fabian H. Sinz, Matthias Bethge, Andreas S. Tolias, Alexander S. Ecker

PLOS Computational Biology: published May 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012056

Modeling oxygen transport in the brain: An efficient coarse-grid approach to capture perivascular gradients in the parenchyma

David Pastor-Alonso, Maxime Berg, Franck Boyer, Natalie Fomin-Thunemann, Michel Quintard, Yohan Davit, Sylvie Lorthois

PLOS Computational Biology: published May 23, 2024 | https://doi.org/10.1371/journal.pcbi.1011973

Learning with sparse reward in a gap junction network inspired by the insect mushroom body

Tianqi Wei, Qinghai Guo, Barbara Webb

PLOS Computational Biology: published May 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012086

Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7

Akseli Niemelä, Artturi Koivuniemi

PLOS Computational Biology: published May 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012137

The impact of health inequity on spatial variation of COVID-19 transmission in England

Thomas Rawson, Wes Hinsley, Raphael Sonabend, Elizaveta Semenova, Anne Cori, Neil M Ferguson

PLOS Computational Biology: published May 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012141

Surprise-minimization as a solution to the structural credit assignment problem

Franz Wurm, Benjamin Ernst, Marco Steinhauser

PLOS Computational Biology: published May 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012175

Estimating mutation rates under heterogeneous stress responses

Lucy Lansch-Justen, Meriem El Karoui, Helen K. Alexander

PLOS Computational Biology: published May 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012146

Dorsal and median raphe neuronal firing dynamics characterized by nonlinear measures

Claudia Pascovich, Diego Serantes, Alejo Rodriguez, Diego Mateos, Joaquín González, Diego Gallo, Mayda Rivas, Andrea Devera, Patricia Lagos, Nicolás Rubido, Pablo Torterolo

PLOS Computational Biology: published May 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012111

Adaptive modeling and inference of higher-order coordination in neuronal assemblies: A dynamic greedy estimation approach

Shoutik Mukherjee, Behtash Babadi

PLOS Computational Biology: published May 28, 2024 | https://doi.org/10.1371/journal.pcbi.1011605

Modelling midline shift and ventricle collapse in cerebral oedema following acute ischaemic stroke

Xi Chen, Tamás I. Józsa, Danilo Cardim, Chiara Robba, Marek Czosnyka, Stephen J. Payne

PLOS Computational Biology: published May 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012145

Mathematical modeling of the evolution of resistance and aggressiveness of high-grade serous ovarian cancer from patient CA-125 time series

Kanyarat Jitmana, Jason I. Griffiths, Sian Fereday, Anna DeFazio, David Bowtell, for Australian Ovarian Cancer Study, Frederick R. Adler

PLOS Computational Biology: published May 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012073

Clustering and visualization of single-cell RNA-seq data using path metrics

Andriana Manousidaki, Anna Little, Yuying Xie

PLOS Computational Biology: published May 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012014

Leveraging conformal prediction to annotate enzyme function space with limited false positives

Kerr Ding, Jiaqi Luo, Yunan Luo

PLOS Computational Biology: published May 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012135

The evolution of environmentally mediated social interactions and posthumous spite under isolation by distance

Charles Mullon, Jorge Peña, Laurent Lehmann

PLOS Computational Biology: published May 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012071

Temporal dynamics of short-term neural adaptation across human visual cortex

Amber Marijn Brands, Sasha Devore, Orrin Devinsky, Werner Doyle, Adeen Flinker, Daniel Friedman, Patricia Dugan, Jonathan Winawer, Iris Isabelle Anna Groen

PLOS Computational Biology: published May 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012161

Modeling spatial evolution of multi-drug resistance under drug environmental gradients

Tomas Ferreira Amaro Freire, Zhijian Hu, Kevin B. Wood, Erida Gjini

PLOS Computational Biology: published May 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012098

Astrocytes as a mechanism for contextually-guided network dynamics and function

Lulu Gong, Fabio Pasqualetti, Thomas Papouin, ShiNung Ching

PLOS Computational Biology: published May 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012186

Disentangling the effects of metabolic cost and accuracy on movement speed

Garrick W. Bruening, Robert J. Courter, Shruthi Sukumar, Megan K. O’Brien, Alaa A. Ahmed

PLOS Computational Biology: published May 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012169

How well do models of visual cortex generalize to out of distribution samples?

Yifei Ren, Pouya Bashivan

PLOS Computational Biology: published May 31, 2024 | https://doi.org/10.1371/journal.pcbi.1011145

Evaluating targeted COVID-19 vaccination strategies with agent-based modeling

Thomas J. Hladish, Alexander N. Pillai, Carl A. B. Pearson, Kok Ben Toh, Andrea C. Tamayo, Arlin Stoltzfus, Ira M. Longini

PLOS Computational Biology: published May 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012128

Methods

Removing direct photocurrent artifacts in optogenetic connectivity mapping data via constrained matrix factorization

Benjamin Antin, Masato Sadahiro, Marta Gajowa, Marcus A. Triplett, Hillel Adesnik, Liam Paninski

PLOS Computational Biology: published May 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012053

Topological state-space estimation of functional human brain networks

Moo K. Chung, Shih-Gu Huang, Ian C. Carroll, Vince D. Calhoun, H. Hill Goldsmith

PLOS Computational Biology: published May 13, 2024 | https://doi.org/10.1371/journal.pcbi.1011869

Artificial neural networks for model identification and parameter estimation in computational cognitive models

Milena Rmus, Ti-Fen Pan, Liyu Xia, Anne G. E. Collins

PLOS Computational Biology: published May 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012119

A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens

Sanjeevani Choudhery, Michael A. DeJesus, Aarthi Srinivasan, Jeremy Rock, Dirk Schnappinger, Thomas R. Ioerger

PLOS Computational Biology: published May 20, 2024 | https://doi.org/10.1371/journal.pcbi.1011408

Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from whole genome sequencing data

Zachary S. L. Foster, Andrew S. Tupper, Caroline M. Press, Niklaus J. Grünwald

PLOS Computational Biology: published May 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012139

A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships

Alexander Kroll, Sahasra Ranjan, Martin J. Lercher

PLOS Computational Biology: published May 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012100

Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance

Evan D. Gorman, Manuel E. Lladser

PLOS Computational Biology: published May 20, 2024 | https://doi.org/10.1371/journal.pcbi.1011543

Transferable deep generative modeling of intrinsically disordered protein conformations

Giacomo Janson, Michael Feig

PLOS Computational Biology: published May 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012144

An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity

Andre J. Faure, Ben Lehner, Verónica Miró Pina, Claudia Serrano Colome, Donate Weghorn

PLOS Computational Biology: published May 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012132

Estimating receptive fields of simple and complex cells in early visual cortex: A convolutional neural network model with parameterized rectification

Philippe Nguyen, Jinani Sooriyaarachchi, Qianyu Huang, Curtis L. Baker Jr.

PLOS Computational Biology: published May 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012127

MGDrivE 3: A decoupled vector-human framework for epidemiological simulation of mosquito genetic control tools and their surveillance

Agastya Mondal, Héctor M. Sánchez C., John M. Marshall

PLOS Computational Biology: published May 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012133

Pairtools: From sequencing data to chromosome contacts

Open2C, Nezar Abdennur, Geoffrey Fudenberg, Ilya M. Flyamer, Aleksandra A. Galitsyna, Anton Goloborodko, Maxim Imakaev, Sergey V. Venev

PLOS Computational Biology: published May 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012164

May 2024

Cover

Marmoset monkeys coordinate vigilance while feeding.

Education

Perspective

Research Articles

Methods

Software