July 2021

Artistic representation of how pathogenomics can outline virulence factors and their contribution to overall bacterial pathogenesis. The illustration shows the comparison of repertoires of Ehrlichia spp. candidate type IV effectors, prepared using Circos software (Krzywinski et al., Genome Res 2009), and superimposed on a scanning electron microscopy picture (40 000x magnification) of Ehrlichia ruminantium (yellow) adhering to host endothelial cell (purple). Noroy et al.

Image Credit: Images credit: O. Gros, A. Moumene and C. Noroy/Univ. Antilles; artwork credit: C. Noroy and D. Meyer/Cirad.

Editorials

Ten simple rules to improve academic work–life balance

Michael John Bartlett, Feyza Nur Arslan, Adriana Bankston, Sarvenaz Sarabipour

PLOS Computational Biology: published July 15, 2021 | https://doi.org/10.1371/journal.pcbi.1009124

Ten simple rules for attending your first conference

Elizabeth Leininger, Kelly Shaw, Niema Moshiri, Kelly Neiles, Getiria Onsongo, Anna Ritz

PLOS Computational Biology: published July 15, 2021 | https://doi.org/10.1371/journal.pcbi.1009133

Responses to 10 common criticisms of anti-racism action in STEMM

Maya L. Gosztyla, Lydia Kwong, Naomi A. Murray, Claire E. Williams, Nicholas Behnke, Porsia Curry, Kevin D. Corbett, Karen N. DSouza, Julia Gala de Pablo, Joanina Gicobi, Monica Javidnia, Navina Lotay, Sidney Madison Prescott, James P. Quinn, Zeena M. G. Rivera, Markia A. Smith, Karen T. Y. Tang, Aarya Venkat, Megan A. Yamoah

PLOS Computational Biology: published July 15, 2021 | https://doi.org/10.1371/journal.pcbi.1009141

Research Articles

Modeling the role of gap junctions between excitatory neurons in the developing visual cortex

Jennifer Crodelle, David W. McLaughlin

PLOS Computational Biology: published July 6, 2021 | https://doi.org/10.1371/journal.pcbi.1007915

An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain

Marte J. Sætra, Gaute T. Einevoll, Geir Halnes

PLOS Computational Biology: published July 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008143

Modelling locust foraging: How and why food affects group formation

Fillipe Georgiou, Jerome Buhl, J. E. F. Green, Bishnu Lamichhane, Ngamta Thamwattana

PLOS Computational Biology: published July 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008353

Modeling changes in probabilistic reinforcement learning during adolescence

Liyu Xia, Sarah L. Master, Maria K. Eckstein, Beth Baribault, Ronald E. Dahl, Linda Wilbrecht, Anne Gabrielle Eva Collins

PLOS Computational Biology: published July 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008524

A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement

Samuel A. Ramirez, Michael Pablo, Sean Burk, Daniel J. Lew, Timothy C. Elston

PLOS Computational Biology: published July 15, 2021 | https://doi.org/10.1371/journal.pcbi.1008525

Immune selection suppresses the emergence of drug resistance in malaria parasites but facilitates its spread

Alexander O. B. Whitlock, Jonathan J. Juliano, Nicole Mideo

PLOS Computational Biology: published July 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008577

Evolution to alternative levels of stable diversity leaves areas of niche space unexplored

Ilan N. Rubin, Iaroslav Ispolatov, Michael Doebeli

PLOS Computational Biology: published July 28, 2021 | https://doi.org/10.1371/journal.pcbi.1008650

Selection of stimulus parameters for enhancing slow wave sleep events with a neural-field theory thalamocortical model

Felipe A. Torres, Patricio Orio, María-José Escobar

PLOS Computational Biology: published July 30, 2021 | https://doi.org/10.1371/journal.pcbi.1008758

The super repertoire of type IV effectors in the pangenome of Ehrlichia spp. provides insights into host-specificity and pathogenesis

Christophe Noroy, Damien F. Meyer

PLOS Computational Biology: published July 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008788

Three-dimensional stochastic simulation of chemoattractant-mediated excitability in cells

Debojyoti Biswas, Peter N. Devreotes, Pablo A. Iglesias

PLOS Computational Biology: published July 14, 2021 | https://doi.org/10.1371/journal.pcbi.1008803

Modelling the visual world of a velvet worm

Mikael Ljungholm, Dan-E. Nilsson

PLOS Computational Biology: published July 28, 2021 | https://doi.org/10.1371/journal.pcbi.1008808

Choice of method of place cell classification determines the population of cells identified

Dori M. Grijseels, Kira Shaw, Caswell Barry, Catherine N. Hall

PLOS Computational Biology: published July 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008835

Gene name errors: Lessons not learned

Mandhri Abeysooriya, Megan Soria, Mary Sravya Kasu, Mark Ziemann

PLOS Computational Biology: published July 30, 2021 | https://doi.org/10.1371/journal.pcbi.1008984

Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort

Arghya Datta, Noah R. Flynn, Dustyn A. Barnette, Keith F. Woeltje, Grover P. Miller, S. Joshua Swamidass

PLOS Computational Biology: published July 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009053

Predicting seasonal influenza using supermarket retail records

Ioanna Miliou, Xinyue Xiong, Salvatore Rinzivillo, Qian Zhang, Giulio Rossetti, Fosca Giannotti, Dino Pedreschi, Alessandro Vespignani

PLOS Computational Biology: published July 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009087

Integration of sleep homeostasis and navigation in Drosophila

Andres Flores-Valle, Pedro J. Gonçalves, Johannes D. Seelig

PLOS Computational Biology: published July 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009088

Spatially resolved simulations of the spread of COVID-19 in three European countries

Andrea Parisi, Samuel P. C. Brand, Joe Hilton, Rabia Aziza, Matt J. Keeling, D. James Nokes

PLOS Computational Biology: published July 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009090

Multitask learning over shared subspaces

Nicholas Menghi, Kemal Kacar, Will Penny

PLOS Computational Biology: published July 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009092

Accumulation of continuously time-varying sensory evidence constrains neural and behavioral responses in human collision threat detection

Gustav Markkula, Zeynep Uludağ, Richard McGilchrist Wilkie, Jac Billington

PLOS Computational Biology: published July 15, 2021 | https://doi.org/10.1371/journal.pcbi.1009096

Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era

Kiesha Prem, Kevin van Zandvoort, Petra Klepac, Rosalind M. Eggo, Nicholas G. Davies, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Alex R. Cook, Mark Jit

PLOS Computational Biology: published July 26, 2021 | https://doi.org/10.1371/journal.pcbi.1009098

Elementary integrate-and-fire process underlies pulse amplitudes in Electrodermal activity

Sandya Subramanian, Patrick L. Purdon, Riccardo Barbieri, Emery N. Brown

PLOS Computational Biology: published July 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009099

Insights into substrate recognition and specificity for IgG by Endoglycosidase S2

Asaminew H. Aytenfisu, Daniel Deredge, Erik H. Klontz, Jonathan Du, Eric J. Sundberg, Alexander D. MacKerell Jr

PLOS Computational Biology: published July 26, 2021 | https://doi.org/10.1371/journal.pcbi.1009103

Sperm migration in the genital tract—In silico experiments identify key factors for reproductive success

Jorin Diemer, Jens Hahn, Björn Goldenbogen, Karin Müller, Edda Klipp

PLOS Computational Biology: published July 15, 2021 | https://doi.org/10.1371/journal.pcbi.1009109

Measuring and mitigating PCR bias in microbiota datasets

Justin D. Silverman, Rachael J. Bloom, Sharon Jiang, Heather K. Durand, Eric Dallow, Sayan Mukherjee, Lawrence A. David

PLOS Computational Biology: published July 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009113

From reaction kinetics to dementia: A simple dimer model of Alzheimer’s disease etiology

Michael R. Lindstrom, Manuel B. Chavez, Elijah A. Gross-Sable, Eric Y. Hayden, David B. Teplow

PLOS Computational Biology: published July 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009114

Average beta burst duration profiles provide a signature of dynamical changes between the ON and OFF medication states in Parkinson’s disease

Benoit Duchet, Filippo Ghezzi, Gihan Weerasinghe, Gerd Tinkhauser, Andrea A. Kühn, Peter Brown, Christian Bick, Rafal Bogacz

PLOS Computational Biology: published July 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009116

COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission

Paul Tupper, Caroline Colijn

PLOS Computational Biology: published July 8, 2021 | https://doi.org/10.1371/journal.pcbi.1009120

Optimizing testing for COVID-19 in India

Philip Cherian, Sandeep Krishna, Gautam I. Menon

PLOS Computational Biology: published July 22, 2021 | https://doi.org/10.1371/journal.pcbi.1009126

Why are viral genomes so fragile? The bottleneck hypothesis

Nono S. C. Merleau, Sophie Pénisson, Philip J. Gerrish, Santiago F. Elena, Matteo Smerlak

PLOS Computational Biology: published July 8, 2021 | https://doi.org/10.1371/journal.pcbi.1009128

On the influence of prior information evaluated by fully Bayesian criteria in a personalized whole-brain model of epilepsy spread

Meysam Hashemi, Anirudh N. Vattikonda, Viktor Sip, Sandra Diaz-Pier, Alexander Peyser, Huifang Wang, Maxime Guye, Fabrice Bartolomei, Marmaduke M. Woodman, Viktor K. Jirsa

PLOS Computational Biology: published July 14, 2021 | https://doi.org/10.1371/journal.pcbi.1009129

Robustness of neuronal tuning to binaural sound localization cues against age-related loss of inhibitory synaptic inputs

Go Ashida, Daniel J. Tollin, Jutta Kretzberg

PLOS Computational Biology: published July 9, 2021 | https://doi.org/10.1371/journal.pcbi.1009130

MiDAS—Meaningful Immunogenetic Data at Scale

Maciej Migdal, Dan Fu Ruan, William F. Forrest, Amir Horowitz, Christian Hammer

PLOS Computational Biology: published July 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009131

eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants

Alexis M. Thornton, Lishan Fang, April Lo, Maria McSharry, David Haan, Casey O’Brien, Alice H. Berger, Marios Giannakis, Angela N. Brooks

PLOS Computational Biology: published July 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009132

Internality and the internalisation of failure: Evidence from a novel task

Federico Mancinelli, Jonathan Roiser, Peter Dayan

PLOS Computational Biology: published July 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009134

Leveraging high-throughput screening data, deep neural networks, and conditional generative adversarial networks to advance predictive toxicology

Adrian J. Green, Martin J. Mohlenkamp, Jhuma Das, Meenal Chaudhari, Lisa Truong, Robyn L. Tanguay, David M. Reif

PLOS Computational Biology: published July 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009135

Perturbations in dynamical models of whole-brain activity dissociate between the level and stability of consciousness

Yonatan Sanz Perl, Carla Pallavicini, Ignacio Pérez Ipiña, Athena Demertzi, Vincent Bonhomme, Charlotte Martial, Rajanikant Panda, Jitka Annen, Agustin Ibañez, Morten Kringelbach, Gustavo Deco, Helmut Laufs, Jacobo Sitt, Steven Laureys, Enzo Tagliazucchi

PLOS Computational Biology: published July 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009139

Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities

Liliana Angeles-Martinez, Vassily Hatzimanikatis

PLOS Computational Biology: published July 22, 2021 | https://doi.org/10.1371/journal.pcbi.1009140

Modelling-informed cell-seeded nerve repair construct designs for treating peripheral nerve injuries

Rachel Coy, Maxime Berg, James B. Phillips, Rebecca J. Shipley

PLOS Computational Biology: published July 8, 2021 | https://doi.org/10.1371/journal.pcbi.1009142

PEDF, a pleiotropic WTC-LI biomarker: Machine learning biomarker identification and validation

George Crowley, James Kim, Sophia Kwon, Rachel Lam, David J. Prezant, Mengling Liu, Anna Nolan

PLOS Computational Biology: published July 21, 2021 | https://doi.org/10.1371/journal.pcbi.1009144

OpenABM-Covid19—An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing

Robert Hinch, William J. M. Probert, Anel Nurtay, Michelle Kendall, Chris Wymant, Matthew Hall, Katrina Lythgoe, Ana Bulas Cruz, Lele Zhao, Andrea Stewart, Luca Ferretti, Daniel Montero, James Warren, Nicole Mather, Matthew Abueg, Neo Wu, Olivier Legat, Katie Bentley, Thomas Mead, Kelvin Van-Vuuren, Dylan Feldner-Busztin, Tommaso Ristori, Anthony Finkelstein, David G. Bonsall, Lucie Abeler-Dörner, Christophe Fraser

PLOS Computational Biology: published July 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009146

The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins

Lukasz Jaroszewski, Mallika Iyer, Arghavan Alisoltani, Mayya Sedova, Adam Godzik

PLOS Computational Biology: published July 8, 2021 | https://doi.org/10.1371/journal.pcbi.1009147

POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis

Pol Castellano-Escuder, Raúl González-Domínguez, Francesc Carmona-Pontaque, Cristina Andrés-Lacueva, Alex Sánchez-Pla

PLOS Computational Biology: published July 1, 2021 | https://doi.org/10.1371/journal.pcbi.1009148

Covasim: An agent-based model of COVID-19 dynamics and interventions

Cliff C. Kerr, Robyn M. Stuart, Dina Mistry, Romesh G. Abeysuriya, Katherine Rosenfeld, Gregory R. Hart, Rafael C. Núñez, Jamie A. Cohen, Prashanth Selvaraj, Brittany Hagedorn, Lauren George, Michał Jastrzębski, Amanda S. Izzo, Greer Fowler, Anna Palmer, Dominic Delport, Nick Scott, Sherrie L. Kelly, Caroline S. Bennette, Bradley G. Wagner, Stewart T. Chang, Assaf P. Oron, Edward A. Wenger, Jasmina Panovska-Griffiths, Michael Famulare, Daniel J. Klein

PLOS Computational Biology: published July 26, 2021 | https://doi.org/10.1371/journal.pcbi.1009149

Data integration uncovers the metabolic bases of phenotypic variation in yeast

Marianyela Sabina Petrizzelli, Dominique de Vienne, Thibault Nidelet, Camille Noûs, Christine Dillmann

PLOS Computational Biology: published July 15, 2021 | https://doi.org/10.1371/journal.pcbi.1009157

The influence of the crowding assumptions in biofilm simulations

Liliana Angeles-Martinez, Vassily Hatzimanikatis

PLOS Computational Biology: published July 22, 2021 | https://doi.org/10.1371/journal.pcbi.1009158

Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19

Hamish Gibbs, Emily Nightingale, Yang Liu, James Cheshire, Leon Danon, Liam Smeeth, Carl A. B. Pearson, Chris Grundy, LSHTM CMMID COVID-19 working group, Adam J. Kucharski, Rosalind M. Eggo

PLOS Computational Biology: published July 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009162

SCMFMDA: Predicting microRNA-disease associations based on similarity constrained matrix factorization

Lei Li, Zhen Gao, Yu-Tian Wang, Ming-Wen Zhang, Jian-Cheng Ni, Chun-Hou Zheng, Yansen Su

PLOS Computational Biology: published July 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009165

Risk sensitivity and theory of mind in human coordination

Pedro L. Ferreira, Francisco C. Santos, Sérgio Pequito

PLOS Computational Biology: published July 15, 2021 | https://doi.org/10.1371/journal.pcbi.1009167

Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE

Francesco Trozzi, Feng Wang, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao

PLOS Computational Biology: published July 26, 2021 | https://doi.org/10.1371/journal.pcbi.1009168

Mechanical feedback and robustness of apical constrictions in Drosophila embryo ventral furrow formation

Michael C. Holcomb, Guo-Jie Jason Gao, Mahsa Servati, Dylan Schneider, Presley K. McNeely, Jeffrey H. Thomas, Jerzy Blawzdziewicz

PLOS Computational Biology: published July 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009173

Spatial and temporal invasion dynamics of the 2014–2017 Zika and chikungunya epidemics in Colombia

Kelly Charniga, Zulma M. Cucunubá, Marcela Mercado, Franklyn Prieto, Martha Ospina, Pierre Nouvellet, Christl A. Donnelly

PLOS Computational Biology: published July 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009174

A hybrid of light-field and light-sheet imaging to study myocardial function and intracardiac blood flow during zebrafish development

Zhaoqiang Wang, Yichen Ding, Sandro Satta, Mehrdad Roustaei, Peng Fei, Tzung K. Hsiai

PLOS Computational Biology: published July 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009175

Adaptive control of movement deceleration during saccades

Simon P. Orozco, Scott T. Albert, Reza Shadmehr

PLOS Computational Biology: published July 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009176

COVID-19 modeling and non-pharmaceutical interventions in an outpatient dialysis unit

Hankyu Jang, Philip M. Polgreen, Alberto M. Segre, Sriram V. Pemmaraju

PLOS Computational Biology: published July 8, 2021 | https://doi.org/10.1371/journal.pcbi.1009177

A benchmark dataset for canopy crown detection and delineation in co-registered airborne RGB, LiDAR and hyperspectral imagery from the National Ecological Observation Network

Ben G. Weinstein, Sarah J. Graves, Sergio Marconi, Aditya Singh, Alina Zare, Dylan Stewart, Stephanie A. Bohlman, Ethan P. White

PLOS Computational Biology: published July 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009180

Sample size calculation for phylogenetic case linkage

Shirlee Wohl, John R. Giles, Justin Lessler

PLOS Computational Biology: published July 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009182

COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity

Vladimir Naumov, Evgeny Putin, Stefan Pushkov, Ekaterina Kozlova, Konstantin Romantsov, Alexander Kalashnikov, Fedor Galkin, Nina Tihonova, Anastasia Shneyderman, Egor Galkin, Arsenii Zinkevich, Stephanie M. Cope, Ramanathan Sethuraman, Tudor I. Oprea, Alexander T. Pearson, Savas Tay, Nishant Agrawal, Alexey Dubovenko, Quentin Vanhaelen, Ivan Ozerov, Alex Aliper, Evgeny Izumchenko, Alex Zhavoronkov

PLOS Computational Biology: published July 14, 2021 | https://doi.org/10.1371/journal.pcbi.1009183

Neuron tracing and quantitative analyses of dendritic architecture reveal symmetrical three-way-junctions and phenotypes of git-1 in C. elegans

Omer Yuval, Yael Iosilevskii, Anna Meledin, Benjamin Podbilewicz, Tom Shemesh

PLOS Computational Biology: published July 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009185

Shrinking Bouma’s window: How to model crowding in dense displays

Alban Bornet, Adrien Doerig, Michael H. Herzog, Gregory Francis, Erik Van der Burg

PLOS Computational Biology: published July 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009187

A model explaining mRNA level fluctuations based on activity demands and RNA age

Zhongneng Xu, Shuichi Asakawa

PLOS Computational Biology: published July 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009188

Rational design of complex phenotype via network models

Marcio Gameiro, Tomáš Gedeon, Shane Kepley, Konstantin Mischaikow

PLOS Computational Biology: published July 29, 2021 | https://doi.org/10.1371/journal.pcbi.1009189

Machine learning reveals mesenchymal breast carcinoma cell adaptation in response to matrix stiffness

Vlada S. Rozova, Ayad G. Anwer, Anna E. Guller, Hamidreza Aboulkheyr Es, Zahra Khabir, Anastasiya I. Sokolova, Maxim U. Gavrilov, Ewa M. Goldys, Majid Ebrahimi Warkiani, Jean Paul Thiery, Andrei V. Zvyagin

PLOS Computational Biology: published July 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009193

Prioritizing and characterizing functionally relevant genes across human tissues

Gowthami Somepalli, Sarthak Sahoo, Arashdeep Singh, Sridhar Hannenhalli

PLOS Computational Biology: published July 16, 2021 | https://doi.org/10.1371/journal.pcbi.1009194

Partial information decomposition reveals that synergistic neural integration is greater downstream of recurrent information flow in organotypic cortical cultures

Samantha P. Sherrill, Nicholas M. Timme, John M. Beggs, Ehren L. Newman

PLOS Computational Biology: published July 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009196

Multidimensional analysis of immune responses identified biomarkers of recent Mycobacterium tuberculosis infection

Tessa Lloyd, Pia Steigler, Cheleka A. M. Mpande, Virginie Rozot, Boitumelo Mosito, Constance Schreuder, Timothy D. Reid, Mark Hatherill, Thomas J. Scriba, Francesca Little, Elisa Nemes, the ACS Study Team

PLOS Computational Biology: published July 28, 2021 | https://doi.org/10.1371/journal.pcbi.1009197

Explaining distortions in metacognition with an attractor network model of decision uncertainty

Nadim A. A. Atiya, Quentin J. M. Huys, Raymond J. Dolan, Stephen M. Fleming

PLOS Computational Biology: published July 26, 2021 | https://doi.org/10.1371/journal.pcbi.1009201

ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements

Xi Chen, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan

PLOS Computational Biology: published July 22, 2021 | https://doi.org/10.1371/journal.pcbi.1009203

Mathematical modeling of N-803 treatment in SIV-infected non-human primates

Jonathan W. Cody, Amy L. Ellis-Connell, Shelby L. O’Connor, Elsje Pienaar

PLOS Computational Biology: published July 28, 2021 | https://doi.org/10.1371/journal.pcbi.1009204

Bridging cell-scale simulations and radiologic images to explain short-time intratumoral oxygen fluctuations

Jessica L. Kingsley, James R. Costello, Natarajan Raghunand, Katarzyna A. Rejniak

PLOS Computational Biology: published July 26, 2021 | https://doi.org/10.1371/journal.pcbi.1009206

The effect of natural selection on the propagation of protein expression noise to bacterial growth

Laurens H. J. Krah, Rutger Hermsen

PLOS Computational Biology: published July 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009208

Bayesian back-calculation and nowcasting for line list data during the COVID-19 pandemic

Tenglong Li, Laura F. White

PLOS Computational Biology: published July 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009210

A mechanistic and data-driven reconstruction of the time-varying reproduction number: Application to the COVID-19 epidemic

Bernard Cazelles, Clara Champagne, Benjamin Nguyen-Van-Yen, Catherine Comiskey, Elisabeta Vergu, Benjamin Roche

PLOS Computational Biology: published July 26, 2021 | https://doi.org/10.1371/journal.pcbi.1009211

An association between prediction errors and risk-seeking: Theory and behavioral evidence

Moritz Moeller, Jan Grohn, Sanjay Manohar, Rafal Bogacz

PLOS Computational Biology: published July 16, 2021 | https://doi.org/10.1371/journal.pcbi.1009213

Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes

Davin Lunz, Gregory Batt, Jakob Ruess, J. Frédéric Bonnans

PLOS Computational Biology: published July 28, 2021 | https://doi.org/10.1371/journal.pcbi.1009214

Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure

Toru Niina, Yasuhiro Matsunaga, Shoji Takada

PLOS Computational Biology: published July 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009215

Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors

Shirit Dvorkin, Reut Levi, Yoram Louzoun

PLOS Computational Biology: published July 26, 2021 | https://doi.org/10.1371/journal.pcbi.1009225

Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts

Kaiyi Zhu, Lingyi Cai, Chenqian Cui, Juan R. de los Toyos, Dimitris Anastassiou

PLOS Computational Biology: published July 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009228

Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression

Yuansheng Liu, Jinyan Li

PLOS Computational Biology: published July 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009229

Accurate influenza forecasts using type-specific incidence data for small geographic units

James Turtle, Pete Riley, Michal Ben-Nun, Steven Riley

PLOS Computational Biology: published July 29, 2021 | https://doi.org/10.1371/journal.pcbi.1009230

A Keller-Segel model for C elegans L1 aggregation

Leon Avery, Brian Ingalls, Catherine Dumur, Alexander Artyukhin

PLOS Computational Biology: published July 29, 2021 | https://doi.org/10.1371/journal.pcbi.1009231

Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region

Dheeraj Prakaash, Graham P. Cook, Oreste Acuto, Antreas C. Kalli

PLOS Computational Biology: published July 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009232

Integrating systemic and molecular levels to infer key drivers sustaining metabolic adaptations

Pedro de Atauri, Míriam Tarrado-Castellarnau, Josep Tarragó-Celada, Carles Foguet, Effrosyni Karakitsou, Josep Joan Centelles, Marta Cascante

PLOS Computational Biology: published July 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009234

Theta-gamma coupling emerges from spatially heterogeneous cholinergic neuromodulation

Yihao Yang, Howard Gritton, Martin Sarter, Sara J. Aton, Victoria Booth, Michal Zochowski

PLOS Computational Biology: published July 30, 2021 | https://doi.org/10.1371/journal.pcbi.1009235

Modeling Na_V1.1/SCN1A sodium channel mutations in a microcircuit with realistic ion concentration dynamics suggests differential GABAergic mechanisms leading to hyperexcitability in epilepsy and hemiplegic migraine

Louisiane Lemaire, Mathieu Desroches, Martin Krupa, Lara Pizzamiglio, Paolo Scalmani, Massimo Mantegazza

PLOS Computational Biology: published July 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009239

Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources

Maximilian Hanussek, Felix Bartusch, Jens Krüger

PLOS Computational Biology: published July 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009244

Computational Eurotransplant kidney allocation simulations demonstrate the feasibility and benefit of T-cell epitope matching

Matthias Niemann, Nils Lachmann, Kirsten Geneugelijk, Eric Spierings

PLOS Computational Biology: published July 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009248

Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

Hiroki Koide, Noriyuki Kodera, Shveta Bisht, Shoji Takada, Tsuyoshi Terakawa

PLOS Computational Biology: published July 30, 2021 | https://doi.org/10.1371/journal.pcbi.1009265

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