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Table of Contents

April 2024

Cover

PIEZO1 activity inhibits collective keratinocyte migration.
Issue Image

Representative fields of view show the trajectories of individual cells tracked from Control keratinocytes (left) and keratinocytes with enhanced PIEZO1 activity (right) during collective cell migration. Each color-coded trajectory delineates the path of an individual cell. Chen & Holt et al 2024

Image Credit: Jesse R. Holt and Medha M. Pathak

Education

Ten simple rules for leading a successful undergraduate-intensive research lab

KJE Hickman, Geoffrey Zahn

PLOS Computational Biology: published April 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011994

Research Articles

The mechanical influence of densification on epithelial architecture

Christian Cammarota, Nicole S. Dawney, Philip M. Bellomio, Maren Jüng, Alexander G. Fletcher, Tara M. Finegan, Dan T. Bergstralh

PLOS Computational Biology: published April 1, 2024 | https://doi.org/10.1371/journal.pcbi.1012001

Predictive coding networks for temporal prediction

Beren Millidge, Mufeng Tang, Mahyar Osanlouy, Nicol S. Harper, Rafal Bogacz

PLOS Computational Biology: published April 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011183

Comparison of stochastic and deterministic models for gambiense sleeping sickness at different spatial scales: A health area analysis in the DRC

Christopher N. Davis, Ronald E. Crump, Samuel A. Sutherland, Simon E. F. Spencer, Alice Corbella, Shampa Chansy, Junior Lebuki, Erick Mwamba Miaka, Kat S. Rock

PLOS Computational Biology: published April 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011993

Modelling cell shape in 3D structured environments: A quantitative comparison with experiments

Rabea Link, Mona Jaggy, Martin Bastmeyer, Ulrich S. Schwarz

PLOS Computational Biology: published April 4, 2024 | https://doi.org/10.1371/journal.pcbi.1011412

Mesoscale simulations predict the role of synergistic cerebellar plasticity during classical eyeblink conditioning

Alice Geminiani, Claudia Casellato, Henk-Jan Boele, Alessandra Pedrocchi, Chris I. De Zeeuw, Egidio D’Angelo

PLOS Computational Biology: published April 4, 2024 | https://doi.org/10.1371/journal.pcbi.1011277

DBDNMF: A Dual Branch Deep Neural Matrix Factorization method for drug response prediction

Hui Liu, Feng Wang, Jian Yu, Yong Pan, Chaoju Gong, Liang Zhang, Lin Zhang

PLOS Computational Biology: published April 4, 2024 | https://doi.org/10.1371/journal.pcbi.1012012

A probabilistic knowledge graph for target identification

Chang Liu, Kaimin Xiao, Cuinan Yu, Yipin Lei, Kangbo Lyu, Tingzhong Tian, Dan Zhao, Fengfeng Zhou, Haidong Tang, Jianyang Zeng

PLOS Computational Biology: published April 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011945

Partial label learning for automated classification of single-cell transcriptomic profiles

Malek Senoussi, Thierry Artieres, Paul Villoutreix

PLOS Computational Biology: published April 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012006

PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration

Jinghao Chen, Jesse R. Holt, Elizabeth L. Evans, John S. Lowengrub, Medha M. Pathak

PLOS Computational Biology: published April 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011855

DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction

Chaoyue Sun, Ruogu Fang, Marco Salemi, Mattia Prosperi, Brittany Rife Magalis

PLOS Computational Biology: published April 10, 2024 | https://doi.org/10.1371/journal.pcbi.1011351

Mathematical model for the role of multiple pericentromeric repeats on heterochromatin assembly

Puranjan Ghimire, Mo Motamedi, Richard Joh

PLOS Computational Biology: published April 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012027

Perturbation Variability Does Not Influence Implicit Sensorimotor Adaptation

Tianhe Wang, Guy Avraham, Jonathan S. Tsay, Sabrina J. Abram, Richard B. Ivry

PLOS Computational Biology: published April 10, 2024 | https://doi.org/10.1371/journal.pcbi.1011951

Benchmarking multi-ancestry prostate cancer polygenic risk scores in a real-world cohort

Yajas Shah, Scott Kulm, Jones T. Nauseef, Zhengming Chen, Olivier Elemento, Kevin H. Kensler, Ravi N. Sharaf

PLOS Computational Biology: published April 10, 2024 | https://doi.org/10.1371/journal.pcbi.1011990

Modeling single cell trajectory using forward-backward stochastic differential equations

Kevin Zhang, Junhao Zhu, Dehan Kong, Zhaolei Zhang

PLOS Computational Biology: published April 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012015

Dopamine encoding of novelty facilitates efficient uncertainty-driven exploration

Yuhao Wang, Armin Lak, Sanjay G. Manohar, Rafal Bogacz

PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011516

Gradient boosted decision trees reveal nuances of auditory discrimination behavior

Carla S. Griffiths, Jules M. Lebert, Joseph Sollini, Jennifer K. Bizley

PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011985

Spatio-temporal spread of artemisinin resistance in Southeast Asia

Jennifer A. Flegg, Sevvandi Kandanaarachchi, Philippe J. Guerin, Arjen M. Dondorp, Francois H. Nosten, Sabina Dahlström Otienoburu, Nick Golding

PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012017

How robust are estimates of key parameters in standard viral dynamic models?

Carolin Zitzmann, Ruian Ke, Ruy M. Ribeiro, Alan S. Perelson

PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011437

Network-neuron interactions underlying sensory responses of layer 5 pyramidal tract neurons in barrel cortex

Arco Bast, Rieke Fruengel, Christiaan P. J. de Kock, Marcel Oberlaender

PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011468

SubGE-DDI: A new prediction model for drug-drug interaction established through biomedical texts and drug-pairs knowledge subgraph enhancement

Yiyang Shi, Mingxiu He, Junheng Chen, Fangfang Han, Yongming Cai

PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011989

Precise cortical contributions to sensorimotor feedback control during reactive balance

Scott Boebinger, Aiden Payne, Giovanni Martino, Kennedy Kerr, Jasmine Mirdamadi, J. Lucas McKay, Michael Borich, Lena Ting

PLOS Computational Biology: published April 17, 2024 | https://doi.org/10.1371/journal.pcbi.1011562

CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression

Satyaki Roy, Shehzad Z. Sheikh, Terrence S. Furey

PLOS Computational Biology: published April 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012016

Encoding surprise by retinal ganglion cells

Danica Despotović, Corentin Joffrois, Olivier Marre, Matthew Chalk

PLOS Computational Biology: published April 17, 2024 | https://doi.org/10.1371/journal.pcbi.1011965

Mathematical analysis of left ventricular elastance with respect to afterload change during ejection phase

Shiro Kato, Yukiko Himeno, Akira Amano

PLOS Computational Biology: published April 18, 2024 | https://doi.org/10.1371/journal.pcbi.1011974

Ranking of cell clusters in a single-cell RNA-sequencing analysis framework using prior knowledge

Anastasis Oulas, Kyriaki Savva, Nestoras Karathanasis, George M. Spyrou

PLOS Computational Biology: published April 18, 2024 | https://doi.org/10.1371/journal.pcbi.1011550

Non-invasive assessment of stroke volume and cardiovascular parameters based on peripheral pressure waveform

Kamil Wołos, Leszek Pstras, Malgorzata Debowska, Wojciech Dabrowski, Dorota Siwicka-Gieroba, Jan Poleszczuk

PLOS Computational Biology: published April 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012013

What does the mean mean? A simple test for neuroscience

Alejandro Tlaie, Katharine Shapcott, Thijs L. van der Plas, James Rowland, Robert Lees, Joshua Keeling, Adam Packer, Paul Tiesinga, Marieke L. Schölvinck, Martha N. Havenith

PLOS Computational Biology: published April 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012000

Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses

Emma Beniston, Jordan P. Skittrall

PLOS Computational Biology: published April 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012009

Temperature-driven coordination of circadian transcriptional regulation

Bingxian Xu, Dae-Sung Hwangbo, Sumit Saurabh, Clark Rosensweig, Ravi Allada, William L. Kath, Rosemary Braun

PLOS Computational Biology: published April 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012029

Neutral competition explains the clonal composition of neural organoids

Florian G. Pflug, Simon Haendeler, Christopher Esk, Dominik Lindenhofer, Jürgen A. Knoblich, Arndt von Haeseler

PLOS Computational Biology: published April 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012054

Validity conditions of approximations for a target-mediated drug disposition model: A novel first-order approximation and its comparison to other approximations

Jong Hyuk Byun, Hye Seon Jeon, Hwi-yeol Yun, Jae Kyoung Kim

PLOS Computational Biology: published April 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012066

A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution

Patrick Gemmell, Timothy B. Sackton, Scott V. Edwards, Jun S. Liu

PLOS Computational Biology: published April 24, 2024 | https://doi.org/10.1371/journal.pcbi.1011995

Indirect reciprocity with Bayesian reasoning and biases

Bryce Morsky, Joshua B. Plotkin, Erol Akçay

PLOS Computational Biology: published April 25, 2024 | https://doi.org/10.1371/journal.pcbi.1011979

Method for cycle detection in sparse, irregularly sampled, long-term neuro-behavioral timeseries: Basis pursuit denoising with polynomial detrending of long-term, inter-ictal epileptiform activity

Irena Balzekas, Joshua Trzasko, Grace Yu, Thomas J. Richner, Filip Mivalt, Vladimir Sladky, Nicholas M. Gregg, Jamie Van Gompel, Kai Miller, Paul E. Croarkin, Vaclav Kremen, Gregory A. Worrell

PLOS Computational Biology: published April 25, 2024 | https://doi.org/10.1371/journal.pcbi.1011152

A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis

Florian E. C. Blanc, Anne Houdusse, Marco Cecchini

PLOS Computational Biology: published April 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012005

Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation

Marc D. Singleton, Michael B. Eisen

PLOS Computational Biology: published April 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012028

Emergent neural dynamics and geometry for generalization in a transitive inference task

Kenneth Kay, Natalie Biderman, Ramin Khajeh, Manuel Beiran, Christopher J. Cueva, Daphna Shohamy, Greg Jensen, Xue-Xin Wei, Vincent P. Ferrera, LF Abbott

PLOS Computational Biology: published April 25, 2024 | https://doi.org/10.1371/journal.pcbi.1011954

Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment

Tracy J. Kuper, Mohammad Mazharul Islam, Shayn M. Peirce-Cottler, Jason A. Papin, Roseanne M Ford

PLOS Computational Biology: published April 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012031

Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model

Rui Meng, Kristofer E. Bouchard

PLOS Computational Biology: published April 26, 2024 | https://doi.org/10.1371/journal.pcbi.1011975

Human decision making balances reward maximization and policy compression

Lucy Lai, Samuel J. Gershman

PLOS Computational Biology: published April 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012057

Wagers for work: Decomposing the costs of cognitive effort

Sarah L. Master, Clayton E. Curtis, Peter Dayan

PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012060

Informing policy via dynamic models: Cholera in Haiti

Jesse Wheeler, AnnaElaine Rosengart, Zhuoxun Jiang, Kevin Tan, Noah Treutle, Edward L. Ionides

PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012032

A novel hypergraph model for identifying and prioritizing personalized drivers in cancer

Naiqian Zhang, Fubin Ma, Dong Guo, Yuxuan Pang, Chenye Wang, Yusen Zhang, Xiaoqi Zheng, Mingyi Wang

PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012068

Recurrent neural networks that learn multi-step visual routines with reinforcement learning

Sami Mollard, Catherine Wacongne, Sander M. Bohte, Pieter R. Roelfsema

PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012030

Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models

Judith A. Bouman, Anthony Hauser, Simon L. Grimm, Martin Wohlfender, Samir Bhatt, Elizaveta Semenova, Andrew Gelman, Christian L. Althaus, Julien Riou

PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011575

Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error

H. Robert Frost

PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012084

Synergistic epistasis among cancer drivers can rescue early tumors from the accumulation of deleterious passengers

Carla Alejandre, Jorge Calle-Espinosa, Jaime Iranzo

PLOS Computational Biology: published April 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012081

Methods

TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments

Yixiao Zhai, Jiannan Chao, Yizheng Wang, Pinglu Zhang, Furong Tang, Quan Zou

PLOS Computational Biology: published April 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011988

Optimizing strategies for slowing the spread of invasive species

Adam Lampert

PLOS Computational Biology: published April 3, 2024 | https://doi.org/10.1371/journal.pcbi.1011996

StellarPath: Hierarchical-vertical multi-omics classifier synergizes stable markers and interpretable similarity networks for patient profiling

Luca Giudice, Ahmed Mohamed, Tarja Malm

PLOS Computational Biology: published April 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012022

Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates

Adrian Lison, Sam Abbott, Jana Huisman, Tanja Stadler

PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012021

HGCLAMIR: Hypergraph contrastive learning with attention mechanism and integrated multi-view representation for predicting miRNA-disease associations

Dong Ouyang, Yong Liang, Jinfeng Wang, Le Li, Ning Ai, Junning Feng, Shanghui Lu, Shuilin Liao, Xiaoying Liu, Shengli Xie

PLOS Computational Biology: published April 23, 2024 | https://doi.org/10.1371/journal.pcbi.1011927

Combined multiplex panel test results are a poor estimate of disease prevalence without adjustment for test error

Robert Challen, Anastasia Chatzilena, George Qian, Glenda Oben, Rachel Kwiatkowska, Catherine Hyams, Adam Finn, Krasimira Tsaneva-Atanasova, Leon Danon

PLOS Computational Biology: published April 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012062

Learning spatio-temporal patterns with Neural Cellular Automata

Alex D. Richardson, Tibor Antal, Richard A. Blythe, Linus J. Schumacher

PLOS Computational Biology: published April 26, 2024 | https://doi.org/10.1371/journal.pcbi.1011589

Ensemble learning and ground-truth validation of synaptic connectivity inferred from spike trains

Christian Donner, Julian Bartram, Philipp Hornauer, Taehoon Kim, Damian Roqueiro, Andreas Hierlemann, Guillaume Obozinski, Manuel Schröter

PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011964

Software

MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface

Adam Husar, Mariam Ordyan, Guadalupe C. Garcia, Joel G. Yancey, Ali S. Saglam, James R. Faeder, Thomas M. Bartol, Mary B. Kennedy, Terrence J. Sejnowski

PLOS Computational Biology: published April 24, 2024 | https://doi.org/10.1371/journal.pcbi.1011800

UNNT: A novel Utility for comparing Neural Net and Tree-based models

Vineeth Gutta, Satish Ranganathan Ganakammal, Sara Jones, Matthew Beyers, Sunita Chandrasekaran

PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011504