Ten simple rules for establishing a mentorship programme

Anne M. Treasure, Siobhan Mackenzie Hall, Igor Lesko, Derek Moore, Malvika Sharan, Menno van Zaanen, Yo Yehudi, Anelda van der Walt

PLOS Computational Biology: published May 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010015

Ten simple rules for navigating the reference letter seeking process

Courtney Peña, Latishya J. Steele, Debra S. Karhson, Judith T. Ned, Crystal M. Botham, Miranda B. Stratton

PLOS Computational Biology: published May 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010102

A topological data analytic approach for discovering biophysical signatures in protein dynamics

Wai Shing Tang, Gabriel Monteiro da Silva, Henry Kirveslahti, Erin Skeens, Bibo Feng, Timothy Sudijono, Kevin K. Yang, Sayan Mukherjee, Brenda Rubenstein, Lorin Crawford

PLOS Computational Biology: published May 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010045

Protein degradation sets the fraction of active ribosomes at vanishing growth

Ludovico Calabrese, Jacopo Grilli, Matteo Osella, Christopher P. Kempes, Marco Cosentino Lagomarsino, Luca Ciandrini

PLOS Computational Biology: published May 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010059

Observing others give & take: A computational account of bystanders’ feelings and actions

Bastien Blain, Joseph Marks, Philipp Czech, Tali Sharot

PLOS Computational Biology: published May 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010010

Analyzing nested experimental designs—A user-friendly resampling method to determine experimental significance

Rishikesh U. Kulkarni, Catherine L. Wang, Carolyn R. Bertozzi

PLOS Computational Biology: published May 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010061

Unsupervised learning for robust working memory

Jintao Gu, Sukbin Lim

PLOS Computational Biology: published May 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009083

Controlling astrocyte-mediated synaptic pruning signals for schizophrenia drug repurposing with deep graph networks

Alessio Gravina, Jennifer L. Wilson, Davide Bacciu, Kevin J. Grimes, Corrado Priami

PLOS Computational Biology: published May 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009531

Conflict and competition between model-based and model-free control

Yuqing Lei, Alec Solway

PLOS Computational Biology: published May 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010047

Spatial dynamics of feedback and feedforward regulation in cell lineages

Peter Uhl, John Lowengrub, Natalia Komarova, Dominik Wodarz

PLOS Computational Biology: published May 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010039

Gene regulation by a protein translation factor at the single-cell level

Roswitha Dolcemascolo, Lucas Goiriz, Roser Montagud-Martínez, Guillermo Rodrigo

PLOS Computational Biology: published May 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010087

A generalized Flory-Stockmayer kinetic theory of connectivity percolation and rigidity percolation of cytoskeletal networks

Carlos Bueno, James Liman, Nicholas P. Schafer, Margaret S. Cheung, Peter G. Wolynes

PLOS Computational Biology: published May 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010105

Modelling the acclimation capacity of coral reefs to a warming ocean

Nomenjanahary Alexia Raharinirina, Esteban Acevedo-Trejos, Agostino Merico

PLOS Computational Biology: published May 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010099

Influence of confinement on the spreading of bacterial populations

Daniel B. Amchin, Jenna A. Ott, Tapomoy Bhattacharjee, Sujit S. Datta

PLOS Computational Biology: published May 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010063

A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota

Alice J. Sommer, Annette Peters, Martina Rommel, Josef Cyrys, Harald Grallert, Dirk Haller, Christian L. Müller, Marie-Abèle C. Bind

PLOS Computational Biology: published May 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010044

Noradrenergic deficits contribute to apathy in Parkinson’s disease through the precision of expected outcomes

Frank H. Hezemans, Noham Wolpe, Claire O’Callaghan, Rong Ye, Catarina Rua, P. Simon Jones, Alexander G. Murley, Negin Holland, Ralf Regenthal, Kamen A. Tsvetanov, Roger A. Barker, Caroline H. Williams-Gray, Trevor W. Robbins, Luca Passamonti, James B. Rowe

PLOS Computational Biology: published May 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010079

Multiscale modeling of presynaptic dynamics from molecular to mesoscale

Jonathan W. Garcia, Thomas M. Bartol, Terrence J. Sejnowski

PLOS Computational Biology: published May 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010068

Role of non-specific interactions in the phase-separation and maturation of macromolecules

Rakesh Krishnan, Srivastav Ranganathan, Samir K. Maji, Ranjith Padinhateeri

PLOS Computational Biology: published May 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010067

Superinfection exclusion: A viral strategy with short-term benefits and long-term drawbacks

Michael Hunter, Diana Fusco

PLOS Computational Biology: published May 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010125

Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap)

Reyhaneh Abbasi, Peter Balazs, Maria Adelaide Marconi, Doris Nicolakis, Sarah M. Zala, Dustin J. Penn

PLOS Computational Biology: published May 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010049

Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding

Helder Veras Ribeiro-Filho, Gabriel Ernesto Jara, Fernanda Aparecida Heleno Batista, Gabriel Ravanhani Schleder, Celisa Caldana Costa Tonoli, Adriana Santos Soprano, Samuel Leite Guimarães, Antonio Carlos Borges, Alexandre Cassago, Marcio Chaim Bajgelman, Rafael Elias Marques, Daniela Barretto Barbosa Trivella, Kleber Gomes Franchini, Ana Carolina Migliorini Figueira, Celso Eduardo Benedetti, Paulo Sergio Lopes-de-Oliveira

PLOS Computational Biology: published May 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010121

Integrated computational and in vivo models reveal Key Insights into macrophage behavior during bone healing

Etienne Baratchart, Chen Hao Lo, Conor C. Lynch, David Basanta

PLOS Computational Biology: published May 13, 2022 | https://doi.org/10.1371/journal.pcbi.1009839

Feature blindness: A challenge for understanding and modelling visual object recognition

Gaurav Malhotra, Marin Dujmović, Jeffrey S. Bowers

PLOS Computational Biology: published May 13, 2022 | https://doi.org/10.1371/journal.pcbi.1009572

CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation

Maarten J. M. F. Reijnders, Robert M. Waterhouse

PLOS Computational Biology: published May 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010075

Characterization and clustering of kinase isoform expression in metastatic melanoma

David O. Holland, Valer Gotea, Kevin Fedkenheuer, Sushil K. Jaiswal, Catherine Baugher, Hua Tan, Michael Fedkenheuer, Laura Elnitski

PLOS Computational Biology: published May 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010065

Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data

Brandon M. Invergo

PLOS Computational Biology: published May 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010110

Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning

Boqiao Lai, Sheng Qian, Hanwei Zhang, Siwei Zhang, Alena Kozlova, Jubao Duan, Jinbo Xu, Xin He

PLOS Computational Biology: published May 16, 2022 | https://doi.org/10.1371/journal.pcbi.1010011

Predicting knee adduction moment response to gait retraining with minimal clinical data

Nataliya Rokhmanova, Katherine J. Kuchenbecker, Peter B. Shull, Reed Ferber, Eni Halilaj

PLOS Computational Biology: published May 16, 2022 | https://doi.org/10.1371/journal.pcbi.1009500

Appropriate relaxation of non-pharmaceutical interventions minimizes the risk of a resurgence in SARS-CoV-2 infections in spite of the Delta variant

Wadim Koslow, Martin J. Kühn, Sebastian Binder, Margrit Klitz, Daniel Abele, Achim Basermann, Michael Meyer-Hermann

PLOS Computational Biology: published May 16, 2022 | https://doi.org/10.1371/journal.pcbi.1010054

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Andonis Gerardos, Nicola Dietler, Anne-Florence Bitbol

PLOS Computational Biology: published May 16, 2022 | https://doi.org/10.1371/journal.pcbi.1010147

Evolution of tunnels in α/β-hydrolase fold proteins—What can we learn from studying epoxide hydrolases?

Maria Bzówka, Karolina Mitusińska, Agata Raczyńska, Tomasz Skalski, Aleksandra Samol, Weronika Bagrowska, Tomasz Magdziarz, Artur Góra

PLOS Computational Biology: published May 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010119

Negative feedback may suppress variation to improve collective foraging performance

Andreagiovanni Reina, James A. R. Marshall

PLOS Computational Biology: published May 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010090

Anomalous diffusion and asymmetric tempering memory in neutrophil chemotaxis

Peter Dieterich, Otto Lindemann, Mats Leif Moskopp, Sebastien Tauzin, Anna Huttenlocher, Rainer Klages, Aleksei Chechkin, Albrecht Schwab

PLOS Computational Biology: published May 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010089

Phase-locking patterns underlying effective communication in exact firing rate models of neural networks

David Reyner-Parra, Gemma Huguet

PLOS Computational Biology: published May 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009342

CBEA: Competitive balances for taxonomic enrichment analysis

Quang P. Nguyen, Anne G. Hoen, H. Robert Frost

PLOS Computational Biology: published May 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010091

Networks of necessity: Simulating COVID-19 mitigation strategies for disabled people and their caregivers

Thomas E. Valles, Hannah Shoenhard, Joseph Zinski, Sarah Trick, Mason A. Porter, Michael R. Lindstrom

PLOS Computational Biology: published May 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010042

Spatially resolved in silico modeling of NKG2D signaling kinetics suggests a key role of NKG2D and Vav1 Co-clustering in generating natural killer cell activation

Rajdeep Kaur Grewal, Jayajit Das

PLOS Computational Biology: published May 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010114

Enhancing long-term forecasting: Learning from COVID-19 models

Hazhir Rahmandad, Ran Xu, Navid Ghaffarzadegan

PLOS Computational Biology: published May 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010100

CystiHuman: A model of human neurocysticercosis

Gabrielle Bonnet, Francesco Pizzitutti, Eloy A. Gonzales-Gustavson, Sarah Gabriël, William K. Pan, Hector H. Garcia, Javier A. Bustos, Percy Vilchez, Seth E. O’Neal, for the Cysticercosis Working Group in Peru

PLOS Computational Biology: published May 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010118

LncRNAs of Saccharomyces cerevisiae bypass the cell cycle arrest imposed by ethanol stress

Lucas Cardoso Lázari, Ivan Rodrigo Wolf, Amanda Piveta Schnepper, Guilherme Targino Valente

PLOS Computational Biology: published May 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010081

Scalable and flexible inference framework for stochastic dynamic single-cell models

Sebastian Persson, Niek Welkenhuysen, Sviatlana Shashkova, Samuel Wiqvist, Patrick Reith, Gregor W. Schmidt, Umberto Picchini, Marija Cvijovic

PLOS Computational Biology: published May 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010082

A computational model of stereoscopic prey capture in praying mantises

James O’Keeffe, Sin Hui Yap, Ichasus Llamas-Cornejo, Vivek Nityananda, Jenny C. A. Read

PLOS Computational Biology: published May 19, 2022 | https://doi.org/10.1371/journal.pcbi.1009666

Linear viscoelastic properties of the vertex model for epithelial tissues

Sijie Tong, Navreeta K. Singh, Rastko Sknepnek, Andrej Košmrlj

PLOS Computational Biology: published May 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010135

Measuring the unknown: An estimator and simulation study for assessing case reporting during epidemics

Christopher I. Jarvis, Amy Gimma, Flavio Finger, Tim P. Morris, Jennifer A. Thompson, Olivier le Polain de Waroux, W. John Edmunds, Sebastian Funk, Thibaut Jombart

PLOS Computational Biology: published May 23, 2022 | https://doi.org/10.1371/journal.pcbi.1008800

A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications

Nicole Pearcy, Marco Garavaglia, Thomas Millat, James P. Gilbert, Yoseb Song, Hassan Hartman, Craig Woods, Claudio Tomi-Andrino, Rajesh Reddy Bommareddy, Byung-Kwan Cho, David A. Fell, Mark Poolman, John R. King, Klaus Winzer, Jamie Twycross, Nigel P. Minton

PLOS Computational Biology: published May 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010106

Anatomy of the first six months of COVID-19 vaccination campaign in Italy

Nicolò Gozzi, Matteo Chinazzi, Jessica T. Davis, Kunpeng Mu, Ana Pastore y Piontti, Marco Ajelli, Nicola Perra, Alessandro Vespignani

PLOS Computational Biology: published May 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010146

The catalytic mechanism of the mitochondrial methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2)

Li Na Zhao, Philipp Kaldis

PLOS Computational Biology: published May 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010140

Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers

Luis Fernando Montaño-Gutierrez, Nahuel Manzanaro Moreno, Iseabail L. Farquhar, Yu Huo, Lucia Bandiera, Peter S. Swain

PLOS Computational Biology: published May 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010138

Sequence dependence of transient Hoogsteen base pairing in DNA

Alberto Pérez de Alba Ortíz, Jocelyne Vreede, Bernd Ensing

PLOS Computational Biology: published May 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010113

Performance-gated deliberation: A context-adapted strategy in which urgency is opportunity cost

Maximilian Puelma Touzel, Paul Cisek, Guillaume Lajoie

PLOS Computational Biology: published May 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010080

Investigating the structural changes due to adenosine methylation of the Kaposi’s sarcoma-associated herpes virus ORF50 transcript

Konstantin Röder, Amy M. Barker, Adrian Whitehouse, Samuela Pasquali

PLOS Computational Biology: published May 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010150

Discovering sparse control strategies in neural activity

Edward D. Lee, Xiaowen Chen, Bryan C. Daniels

PLOS Computational Biology: published May 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010072

Assessing the impact of lateral flow testing strategies on within-school SARS-CoV-2 transmission and absences: A modelling study

Trystan Leng, Edward M. Hill, Robin N. Thompson, Michael J. Tildesley, Matt J. Keeling, Louise Dyson

PLOS Computational Biology: published May 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010158

Designing optimal allocations for cancer screening using queuing network models

Justin Dean, Evan Goldberg, Franziska Michor

PLOS Computational Biology: published May 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010179

A phenomenological computational model of the evoked action potential fitted to human cochlear implant responses

Ángel Ramos-de-Miguel, José M. Escobar, David Greiner, Domingo Benítez, Eduardo Rodríguez, Albert Oliver, Marcos Hernández, Ángel Ramos-Macías

PLOS Computational Biology: published May 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010134

Uncertainty–guided learning with scaled prediction errors in the basal ganglia

Moritz Möller, Sanjay Manohar, Rafal Bogacz

PLOS Computational Biology: published May 27, 2022 | https://doi.org/10.1371/journal.pcbi.1009816

Genome-wide cross-cancer analysis illustrates the critical role of bimodal miRNA in patient survival and drug responses to PI3K inhibitors

Laura Moody, Guanying Bianca Xu, Yuan-Xiang Pan, Hong Chen

PLOS Computational Biology: published May 31, 2022 | https://doi.org/10.1371/journal.pcbi.1010109

BOSO: A novel feature selection algorithm for linear regression with high-dimensional data

Luis V. Valcárcel, Edurne San José-Enériz, Xabier Cendoya, Ángel Rubio, Xabier Agirre, Felipe Prósper, Francisco J. Planes

PLOS Computational Biology: published May 31, 2022 | https://doi.org/10.1371/journal.pcbi.1010180

Mutational analysis of SARS-CoV-2 variants of concern reveals key tradeoffs between receptor affinity and antibody escape

Emily K. Makowski, John S. Schardt, Matthew D. Smith, Peter M. Tessier

PLOS Computational Biology: published May 31, 2022 | https://doi.org/10.1371/journal.pcbi.1010160

Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow

Omer Acar, She Zhang, Ivet Bahar, Anne-Ruxandra Carvunis

PLOS Computational Biology: published May 31, 2022 | https://doi.org/10.1371/journal.pcbi.1010181

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar

Erik Garrison, Zev N. Kronenberg, Eric T. Dawson, Brent S. Pedersen, Pjotr Prins

PLOS Computational Biology: published May 31, 2022 | https://doi.org/10.1371/journal.pcbi.1009123

Correction: Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries

Benjamin Moore, Patricia Carvajal-López, Paballo Abel Chauke, Marco Cristancho, Victoria Dominguez Del Angel, Selene L. Fernandez-Valverde, Amel Ghouila, Piraveen Gopalasingam, Fatma Zahra Guerfali, Alice Matimba, Sarah L. Morgan, Guilherme Oliveira, Verena Ras, Alejandro Reyes, Javier De Las Rivas, Nicola Mulder

PLOS Computational Biology: published May 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010197

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Correction: Linking statistical shape models and simulated function in the healthy adult human heart

Cristobal Rodero, Marina Strocchi, Maciej Marciniak, Stefano Longobardi, John Whitaker, Mark D. O’Neill, Karli Gillette, Christoph Augustin, Gernot Plank, Edward J. Vigmond, Pablo Lamata, Steven A. Niederer

PLOS Computational Biology: published May 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010196

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1. Linking statistical shape models and simulated function in the healthy adult human heart