Ten simple rules for supporting historically underrepresented students in science

Suchinta Arif, Melanie Duc Bo Massey, Natalie Klinard, Julie Charbonneau, Loay Jabre, Ana Barbosa Martins, Danielle Gaitor, Rhiannon Kirton, Catalina Albury, Karma Nanglu

PLOS Computational Biology: published September 16, 2021 | https://doi.org/10.1371/journal.pcbi.1009313

Ten simple rules to make your computing more environmentally sustainable

Loïc Lannelongue, Jason Grealey, Alex Bateman, Michael Inouye

PLOS Computational Biology: published September 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009324

Ten simple rules for choosing a PhD supervisor

Loay Jabre, Catherine Bannon, J. Scott P. McCain, Yana Eglit

PLOS Computational Biology: published September 30, 2021 | https://doi.org/10.1371/journal.pcbi.1009330

Ten simple rules for avoiding predatory publishing scams

Michelle Leonard, Suzanne Stapleton, Perry Collins, Terry Kit Selfe, Tara Cataldo

PLOS Computational Biology: published September 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009377

Ten simple rules for being a faculty advocate of first-year graduate students

Kevin A. Janes

PLOS Computational Biology: published September 30, 2021 | https://doi.org/10.1371/journal.pcbi.1009379

Local field potentials in a pre-motor region predict learned vocal sequences

Daril E. Brown II, Jairo I. Chavez, Derek H. Nguyen, Adam Kadwory, Bradley Voytek, Ezequiel M. Arneodo, Timothy Q. Gentner, Vikash Gilja

PLOS Computational Biology: published September 23, 2021 | https://doi.org/10.1371/journal.pcbi.1008100

Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C

Susana Posada-Céspedes, Gert Van Zyl, Hesam Montazeri, Jack Kuipers, Soo-Yon Rhee, Roger Kouyos, Huldrych F. Günthard, Niko Beerenwinkel

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008363

On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo

Charles-Elie Rabier, Vincent Berry, Marnus Stoltz, João D. Santos, Wensheng Wang, Jean-Christophe Glaszmann, Fabio Pardi, Celine Scornavacca

PLOS Computational Biology: published September 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008380

Dynamic modelling of the PI3K/MTOR signalling network uncovers biphasic dependence of mTORC1 activity on the mTORC2 subunit SIN1

Milad Ghomlaghi, Guang Yang, Sung-Young Shin, David E. James, Lan K. Nguyen

PLOS Computational Biology: published September 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008513

Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation

Jiayin Hong, Julius Palme, Bo Hua, Michael Springer

PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1008691

Basis profile curve identification to understand electrical stimulation effects in human brain networks

Kai J. Miller, Klaus-Robert Müller, Dora Hermes

PLOS Computational Biology: published September 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008710

Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations

Andreas Haahr Larsen, Lilya Tata, Laura H. John, Mark S. P. Sansom

PLOS Computational Biology: published September 23, 2021 | https://doi.org/10.1371/journal.pcbi.1008807

Latching dynamics as a basis for short-term recall

Kwang Il Ryom, Vezha Boboeva, Oleksandra Soldatkina, Alessandro Treves

PLOS Computational Biology: published September 15, 2021 | https://doi.org/10.1371/journal.pcbi.1008809

The N-terminal domain of RfaH plays an active role in protein fold-switching

Pablo Galaz-Davison, Ernesto A. Román, César A. Ramírez-Sarmiento

PLOS Computational Biology: published September 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008882

Personalized brain stimulation for effective neurointervention across participants

Nienke E. R. van Bueren, Thomas L. Reed, Vu Nguyen, James G. Sheffield, Sanne H. G. van der Ven, Michael A. Osborne, Evelyn H. Kroesbergen, Roi Cohen Kadosh

PLOS Computational Biology: published September 9, 2021 | https://doi.org/10.1371/journal.pcbi.1008886

Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities

Gil J. B. Henriques, Simon van Vliet, Michael Doebeli

PLOS Computational Biology: published September 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008896

A statistical model for describing and simulating microbial community profiles

Siyuan Ma, Boyu Ren, Himel Mallick, Yo Sup Moon, Emma Schwager, Sagun Maharjan, Timothy L. Tickle, Yiren Lu, Rachel N. Carmody, Eric A. Franzosa, Lucas Janson, Curtis Huttenhower

PLOS Computational Biology: published September 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008913

Learning brain dynamics for decoding and predicting individual differences

Joyneel Misra, Srinivas Govinda Surampudi, Manasij Venkatesh, Chirag Limbachia, Joseph Jaja, Luiz Pessoa

PLOS Computational Biology: published September 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008943

Chromosomal neighbourhoods allow identification of organ specific changes in gene expression

Rishi Das Roy, Outi Hallikas, Mona M. Christensen, Elodie Renvoisé, Jukka Jernvall

PLOS Computational Biology: published September 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008947

An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

Thomas K. F. Wong, Teng Li, Louis Ranjard, Steven H. Wu, Jeet Sukumaran, Allen G. Rodrigo

PLOS Computational Biology: published September 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008949

Insights into the dynamic trajectories of protein filament division revealed by numerical investigation into the mathematical model of pure fragmentation

Magali Tournus, Miguel Escobedo, Wei-Feng Xue, Marie Doumic

PLOS Computational Biology: published September 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008964

Memes: A motif analysis environment in R using tools from the MEME Suite

Spencer L. Nystrom, Daniel J. McKay

PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1008991

No increased circular inference in adults with high levels of autistic traits or autism

Nikitas Angeletos Chrysaitis, Renaud Jardri, Sophie Denève, Peggy Seriès

PLOS Computational Biology: published September 24, 2021 | https://doi.org/10.1371/journal.pcbi.1009006

A model of naturalistic decision making in preference tests

John Ksander, Donald B. Katz, Paul Miller

PLOS Computational Biology: published September 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009012

XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers

Jack B. Maguire, Daniele Grattarola, Vikram Khipple Mulligan, Eugene Klyshko, Hans Melo

PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009037

Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis

Cecilia Wieder, Clément Frainay, Nathalie Poupin, Pablo Rodríguez-Mier, Florence Vinson, Juliette Cooke, Rachel PJ Lai, Jacob G. Bundy, Fabien Jourdan, Timothy Ebbels

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009105

Differences in olfactory bulb mitral cell spiking with ortho- and retronasal stimulation revealed by data-driven models

Michelle F. Craft, Andrea K. Barreiro, Shree Hari Gautam, Woodrow L. Shew, Cheng Ly

PLOS Computational Biology: published September 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009169

Ergodicity-breaking reveals time optimal decision making in humans

David Meder, Finn Rabe, Tobias Morville, Kristoffer H. Madsen, Magnus T. Koudahl, Ray J. Dolan, Hartwig R. Siebner, Oliver J. Hulme

PLOS Computational Biology: published September 9, 2021 | https://doi.org/10.1371/journal.pcbi.1009217

Adaptation supports short-term memory in a visual change detection task

Brian Hu, Marina E. Garrett, Peter A. Groblewski, Douglas R. Ollerenshaw, Jiaqi Shang, Kate Roll, Sahar Manavi, Christof Koch, Shawn R. Olsen, Stefan Mihalas

PLOS Computational Biology: published September 17, 2021 | https://doi.org/10.1371/journal.pcbi.1009246

Optima TB: A tool to help optimally allocate tuberculosis spending

Lara Goscé, Gerard J. Abou Jaoude, David J. Kedziora, Clemens Benedikt, Azfar Hussain, Sarah Jarvis, Alena Skrahina, Dzmitry Klimuk, Henadz Hurevich, Feng Zhao, Nicole Fraser-Hurt, Nejma Cheikh, Marelize Gorgens, David J. Wilson, Romesh Abeysuriya, Rowan Martin-Hughes, Sherrie L. Kelly, Anna Roberts, Robyn M. Stuart, Tom Palmer, Jasmina Panovska-Griffiths, Cliff C. Kerr, David P. Wilson, Hassan Haghparast-Bidgoli, Jolene Skordis, Ibrahim Abubakar

PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009255

Stochastic model of lignocellulosic material saccharification

Eric Behle, Adélaïde Raguin

PLOS Computational Biology: published September 13, 2021 | https://doi.org/10.1371/journal.pcbi.1009262

Eliminating accidental deviations to minimize generalization error and maximize replicability: Applications in connectomics and genomics

Eric W. Bridgeford, Shangsi Wang, Zeyi Wang, Ting Xu, Cameron Craddock, Jayanta Dey, Gregory Kiar, William Gray-Roncal, Carlo Colantuoni, Christopher Douville, Stephanie Noble, Carey E. Priebe, Brian Caffo, Michael Milham, Xi-Nian Zuo, Consortium for Reliability and Reproducibility, Joshua T. Vogelstein

PLOS Computational Biology: published September 16, 2021 | https://doi.org/10.1371/journal.pcbi.1009279

ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves

Eric D. Musselman, Jake E. Cariello, Warren M. Grill, Nicole A. Pelot

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009285

Relaxing restrictions at the pace of vaccination increases freedom and guards against further COVID-19 waves

Simon Bauer, Sebastian Contreras, Jonas Dehning, Matthias Linden, Emil Iftekhar, Sebastian B. Mohr, Alvaro Olivera-Nappa, Viola Priesemann

PLOS Computational Biology: published September 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009288

Probing T-cell response by sequence-based probabilistic modeling

Barbara Bravi, Vinod P. Balachandran, Benjamin D. Greenbaum, Aleksandra M. Walczak, Thierry Mora, Rémi Monasson, Simona Cocco

PLOS Computational Biology: published September 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009297

MicrobeTrace: Retooling molecular epidemiology for rapid public health response

Ellsworth M. Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, Sergey Knyazev, Roxana Cintron, William M. Switzer

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009300

PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial

Michael Pickles, Anne Cori, William J. M. Probert, Rafael Sauter, Robert Hinch, Sarah Fidler, Helen Ayles, Peter Bock, Deborah Donnell, Ethan Wilson, Estelle Piwowar-Manning, Sian Floyd, Richard J. Hayes, Christophe Fraser, HPTN 071 (PopART) Study Team

PLOS Computational Biology: published September 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009301

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge

Zhaoping Xiong, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Hualiang Jiang, Mingyue Zheng, Aik Choon Tan, Xindi Guo, The Multi-Targeting Drug DREAM Challenge Community, Kristen K. Dang, Alex Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger, Ross Cagan

PLOS Computational Biology: published September 14, 2021 | https://doi.org/10.1371/journal.pcbi.1009302

Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level

Suraj Kannan, Michael Farid, Brian L. Lin, Matthew Miyamoto, Chulan Kwon

PLOS Computational Biology: published September 17, 2021 | https://doi.org/10.1371/journal.pcbi.1009305

Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome

Ilario De Toma, Cesar Sierra, Mara Dierssen

PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009317

Mathematical model of a personalized neoantigen cancer vaccine and the human immune system

Marisabel Rodriguez Messan, Osman N. Yogurtcu, Joseph R. McGill, Ujwani Nukala, Zuben E. Sauna, Hong Yang

PLOS Computational Biology: published September 24, 2021 | https://doi.org/10.1371/journal.pcbi.1009318

A Bayesian model based computational analysis of the relationship between bisulfite accessible single-stranded DNA in chromatin and somatic hypermutation of immunoglobulin genes

Guojun Yu, Yingru Wu, Zhi Duan, Catherine Tang, Haipeng Xing, Matthew D. Scharff, Thomas MacCarthy

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009323

Hierarchy and control of ageing-related methylation networks

Gergely Palla, Péter Pollner, Judit Börcsök, András Major, Béla Molnár, István Csabai

PLOS Computational Biology: published September 17, 2021 | https://doi.org/10.1371/journal.pcbi.1009327

Networks of Causal Linkage Between Eigenmodes Characterize Behavioral Dynamics of Caenorhabditis elegans

Erik Saberski, Antonia K. Bock, Rachel Goodridge, Vitul Agarwal, Tom Lorimer, Scott A. Rifkin, George Sugihara

PLOS Computational Biology: published September 10, 2021 | https://doi.org/10.1371/journal.pcbi.1009329

Computational modeling of blood component transport related to coronary artery thrombosis in Kawasaki disease

Noelia Grande Gutiérrez, Mark Alber, Andrew M. Kahn, Jane C. Burns, Mathew Mathew, Brian W. McCrindle, Alison L. Marsden

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009331

Inter-trial effects in priming of pop-out: Comparison of computational updating models

Fredrik Allenmark, Ahu Gokce, Thomas Geyer, Artyom Zinchenko, Hermann J. Müller, Zhuanghua Shi

PLOS Computational Biology: published September 3, 2021 | https://doi.org/10.1371/journal.pcbi.1009332

A hydro-osmotic coarsening theory of biological cavity formation

Mathieu Le Verge-Serandour, Hervé Turlier

PLOS Computational Biology: published September 3, 2021 | https://doi.org/10.1371/journal.pcbi.1009333

An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City

Sheng Zhang, Joan Ponce, Zhen Zhang, Guang Lin, George Karniadakis

PLOS Computational Biology: published September 8, 2021 | https://doi.org/10.1371/journal.pcbi.1009334

Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment

Sepideh Mazrouee, Susan J. Little, Joel O. Wertheim

PLOS Computational Biology: published September 22, 2021 | https://doi.org/10.1371/journal.pcbi.1009336

BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data

Chenhao Li, Tamar V. Av-Shalom, Jun Wei Gerald Tan, Junmei Samantha Kwah, Kern Rei Chng, Niranjan Nagarajan

PLOS Computational Biology: published September 8, 2021 | https://doi.org/10.1371/journal.pcbi.1009343

The color phi phenomenon: Not so special, after all?

Lars Keuninckx, Axel Cleeremans

PLOS Computational Biology: published September 3, 2021 | https://doi.org/10.1371/journal.pcbi.1009344

Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network

Zhengqiao Zhao, Stephen Woloszynek, Felix Agbavor, Joshua Chang Mell, Bahrad A. Sokhansanj, Gail L. Rosen

PLOS Computational Biology: published September 22, 2021 | https://doi.org/10.1371/journal.pcbi.1009345

The importance of non-pharmaceutical interventions during the COVID-19 vaccine rollout

Nicolò Gozzi, Paolo Bajardi, Nicola Perra

PLOS Computational Biology: published September 10, 2021 | https://doi.org/10.1371/journal.pcbi.1009346

Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves

Kris V. Parag

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009347

Evaluating the effectiveness of ensemble voting in improving the accuracy of consensus signals produced by various DTWA algorithms from step-current signals generated during nanopore sequencing

Michael Smith, Rachel Chan, Maaz Khurram, Paul M. K. Gordon

PLOS Computational Biology: published September 10, 2021 | https://doi.org/10.1371/journal.pcbi.1009350

Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections

Thomas Beneteau, Christian Selinger, Mircea T. Sofonea, Samuel Alizon

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009352

STDP and the distribution of preferred phases in the whisker system

Nimrod Sherf, Maoz Shamir

PLOS Computational Biology: published September 17, 2021 | https://doi.org/10.1371/journal.pcbi.1009353

Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model

Federica Gugole, Luc E. Coffeng, Wouter Edeling, Benjamin Sanderse, Sake J. de Vlas, Daan Crommelin

PLOS Computational Biology: published September 17, 2021 | https://doi.org/10.1371/journal.pcbi.1009355

Multiscale model of defective interfering particle replication for influenza A virus infection in animal cell culture

Daniel Rüdiger, Lars Pelz, Marc D. Hein, Sascha Y. Kupke, Udo Reichl

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009357

Envelope reconstruction of speech and music highlights stronger tracking of speech at low frequencies

Nathaniel J. Zuk, Jeremy W. Murphy, Richard B. Reilly, Edmund C. Lalor

PLOS Computational Biology: published September 17, 2021 | https://doi.org/10.1371/journal.pcbi.1009358

Hemodynamics-driven mathematical model of first and second heart sound generation

Mehrdad Shahmohammadi, Hongxing Luo, Philip Westphal, Richard N. Cornelussen, Frits W. Prinzen, Tammo Delhaas

PLOS Computational Biology: published September 22, 2021 | https://doi.org/10.1371/journal.pcbi.1009361

The critical balance between dopamine D2 receptor and RGS for the sensitive detection of a transient decay in dopamine signal

Hidetoshi Urakubo, Sho Yagishita, Haruo Kasai, Yoshiyuki Kubota, Shin Ishii

PLOS Computational Biology: published September 30, 2021 | https://doi.org/10.1371/journal.pcbi.1009364

Ascension of Chlamydia is moderated by uterine peristalsis and the neutrophil response to infection

Torrington Callan, Stephen Woodcock, Wilhelmina May Huston

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009365

Slow manifolds within network dynamics encode working memory efficiently and robustly

Elham Ghazizadeh, ShiNung Ching

PLOS Computational Biology: published September 15, 2021 | https://doi.org/10.1371/journal.pcbi.1009366

Modelling to explore the potential impact of asymptomatic human infections on transmission and dynamics of African sleeping sickness

Maryam Aliee, Matt J. Keeling, Kat S. Rock

PLOS Computational Biology: published September 13, 2021 | https://doi.org/10.1371/journal.pcbi.1009367

Differential contribution to gene expression prediction of histone modifications at enhancers or promoters

Mar González-Ramírez, Cecilia Ballaré, Francesca Mugianesi, Malte Beringer, Alexandra Santanach, Enrique Blanco, Luciano Di Croce

PLOS Computational Biology: published September 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009368

Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders

Jaie Woodard, Wei Zheng, Yang Zhang

PLOS Computational Biology: published September 16, 2021 | https://doi.org/10.1371/journal.pcbi.1009370

Inactivation mode of sodium channels defines the different maximal firing rates of conventional versus atypical midbrain dopamine neurons

Christopher J. Knowlton, Tabea Ines Ziouziou, Niklas Hammer, Jochen Roeper, Carmen C. Canavier

PLOS Computational Biology: published September 17, 2021 | https://doi.org/10.1371/journal.pcbi.1009371

FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution

Gabriel A. Vignolle, Denise Schaffer, Leopold Zehetner, Robert L. Mach, Astrid R. Mach-Aigner, Christian Derntl

PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009372

Genetic dissection of complex traits using hierarchical biological knowledge

Hidenori Tanaka, Jason F. Kreisberg, Trey Ideker

PLOS Computational Biology: published September 17, 2021 | https://doi.org/10.1371/journal.pcbi.1009373

Using test positivity and reported case rates to estimate state-level COVID-19 prevalence and seroprevalence in the United States

Weihsueh A. Chiu, Martial L. Ndeffo-Mbah

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009374

Reconstructing contact network structure and cross-immunity patterns from multiple infection histories

Christian Selinger, Samuel Alizon

PLOS Computational Biology: published September 15, 2021 | https://doi.org/10.1371/journal.pcbi.1009375

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

Ramzan Umarov, Yu Li, Takahiro Arakawa, Satoshi Takizawa, Xin Gao, Erik Arner

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009376

Conventional measures of intrinsic excitability are poor estimators of neuronal activity under realistic synaptic inputs

Adrienn Szabó, Katalin Schlett, Attila Szücs

PLOS Computational Biology: published September 16, 2021 | https://doi.org/10.1371/journal.pcbi.1009378

Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants

Rui Yin, Johnathan D. Guest, Ghazaleh Taherzadeh, Ragul Gowthaman, Ipsa Mittra, Jane Quackenbush, Brian G. Pierce

PLOS Computational Biology: published September 7, 2021 | https://doi.org/10.1371/journal.pcbi.1009380

Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia

James J. Winkle, Bhargav R. Karamched, Matthew R. Bennett, William Ott, Krešimir Josić

PLOS Computational Biology: published September 22, 2021 | https://doi.org/10.1371/journal.pcbi.1009381

Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes

Samantha N. Piekos, Sadhana Gaddam, Pranav Bhardwaj, Prashanth Radhakrishnan, Ramanathan V. Guha, Anthony E. Oro

PLOS Computational Biology: published September 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009382

A unified mechanism for innate and learned visual landmark guidance in the insect central complex

Roman Goulard, Cornelia Buehlmann, Jeremy E. Niven, Paul Graham, Barbara Webb

PLOS Computational Biology: published September 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009383

Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

Abhisek Dwivedy, Richard Mariadasse, Mohammed Ahmad, Sayan Chakraborty, Deepsikha Kar, Satish Tiwari, Sankar Bhattacharyya, Sudipta Sonar, Shailendra Mani, Prafullakumar Tailor, Tanmay Majumdar, Jeyaraman Jeyakanthan, Bichitra Kumar Biswal

PLOS Computational Biology: published September 13, 2021 | https://doi.org/10.1371/journal.pcbi.1009384

FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks

Andrea Tangherloni, Marco S. Nobile, Paolo Cazzaniga, Giulia Capitoli, Simone Spolaor, Leonardo Rundo, Giancarlo Mauri, Daniela Besozzi

PLOS Computational Biology: published September 9, 2021 | https://doi.org/10.1371/journal.pcbi.1009410

ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer

Juan L. Trincado, Marina Reixachs-Solé, Judith Pérez-Granado, Tim Fugmann, Ferran Sanz, Jun Yokota, Eduardo Eyras

PLOS Computational Biology: published September 16, 2021 | https://doi.org/10.1371/journal.pcbi.1009411

Hybrid computational modeling demonstrates the utility of simulating complex cellular networks in type 1 diabetes

Zhenzhen Shi, Yang Li, Majid Jaberi-Douraki

PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009413

Rats spontaneously perceive global motion direction of drifting plaids

Giulio Matteucci, Benedetta Zattera, Rosilari Bellacosa Marotti, Davide Zoccolan

PLOS Computational Biology: published September 14, 2021 | https://doi.org/10.1371/journal.pcbi.1009415

Integration, coincidence detection and resonance in networks of spiking neurons expressing Gamma oscillations and asynchronous states

Eduarda Susin, Alain Destexhe

PLOS Computational Biology: published September 16, 2021 | https://doi.org/10.1371/journal.pcbi.1009416

Phenotypic-dependent variability and the emergence of tolerance in bacterial populations

José Camacho Mateu, Matteo Sireci, Miguel A. Muñoz

PLOS Computational Biology: published September 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009417

Drug-induced resistance evolution necessitates less aggressive treatment

Teemu Kuosmanen, Johannes Cairns, Robert Noble, Niko Beerenwinkel, Tommi Mononen, Ville Mustonen

PLOS Computational Biology: published September 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009418

Heterodimer-heterotetramer formation mediates enhanced sensor activity in a biophysical model for BMP signaling

Md. Shahriar Karim, Aasakiran Madamanchi, James A. Dutko, Mary C. Mullins, David M. Umulis

PLOS Computational Biology: published September 30, 2021 | https://doi.org/10.1371/journal.pcbi.1009422

Acetylcholine-gated current translates wake neuronal firing rate information into a spike timing-based code in Non-REM sleep, stabilizing neural network dynamics during memory consolidation

Quinton M. Skilling, Bolaji Eniwaye, Brittany C. Clawson, James Shaver, Nicolette Ognjanovski, Sara J. Aton, Michal Zochowski

PLOS Computational Biology: published September 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009424

Machine learning approach for automatic recognition of tomato-pollinating bees based on their buzzing-sounds

Alison Pereira Ribeiro, Nádia Felix Felipe da Silva, Fernanda Neiva Mesquita, Priscila de Cássia Souza Araújo, Thierson Couto Rosa, José Neiva Mesquita-Neto

PLOS Computational Biology: published September 16, 2021 | https://doi.org/10.1371/journal.pcbi.1009426

High-integrity human intervention in ecosystems: Tracking self-organization modes

Yuval R. Zelnik, Yair Mau, Moshe Shachak, Ehud Meron

PLOS Computational Biology: published September 29, 2021 | https://doi.org/10.1371/journal.pcbi.1009427

A model of head direction and landmark coding in complex environments

Yijia Yan, Neil Burgess, Andrej Bicanski

PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009434

Levels of SARS-CoV-2 population exposure are considerably higher than suggested by seroprevalence surveys

Siyu Chen, Jennifer A. Flegg, Lisa J. White, Ricardo Aguas

PLOS Computational Biology: published September 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009436

Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders

Matthew R. Whiteway, Dan Biderman, Yoni Friedman, Mario Dipoppa, E. Kelly Buchanan, Anqi Wu, John Zhou, Niccolò Bonacchi, Nathaniel J. Miska, Jean-Paul Noel, Erica Rodriguez, Michael Schartner, Karolina Socha, Anne E. Urai, C. Daniel Salzman, The International Brain Laboratory, John P. Cunningham, Liam Paninski

PLOS Computational Biology: published September 22, 2021 | https://doi.org/10.1371/journal.pcbi.1009439

GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs

Manuel Tognon, Vincenzo Bonnici, Erik Garrison, Rosalba Giugno, Luca Pinello

PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009444

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PLOS Computational Biology: published September 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009446

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PLOS Computational Biology: published September 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009447

dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design

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PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009448

Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species

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PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009450

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PLOS Computational Biology: published September 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009456

Correction: Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention

The PLOS Computational Biology Staff

PLOS Computational Biology: published September 1, 2021 | https://doi.org/10.1371/journal.pcbi.1009359

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PLOS Computational Biology: published September 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009362

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