September 2022

Today, there is great interest in diets proposing new macronutrient compositions and fasting schedules. Unfortunately, there is little consensus regarding the impact these new diets have on our metabolism. We lack an approach for integrating partial insights derived from different clinical studies with different measured variables - in different situations and on different populations – into a useful and interconnected big picture. Herein, we present such an integrating tool: a multi-organ and multi-timescale ODE model of human metabolism. This tool predicts both mean human metabolism responses to meals and fasting schedules, and is capable of making person-specific predictions. Silfvergren et al

Image Credit: Christian Simonsson, Linköping University, Sweden.

Editorial

Ten simple rules for getting and giving credit for data

Elisha M. Wood-Charlson, Zachary Crockett, Chris Erdmann, Adam P. Arkin, Carly B. Robinson

PLOS Computational Biology: published September 29, 2022 | https://doi.org/10.1371/journal.pcbi.1010476

Education Articles

Ten simple rules for teaching yourself R

Jake Lawlor, Francis Banville, Norma-Rocio Forero-Muñoz, Katherine Hébert, Juan Andrés Martínez-Lanfranco, Pierre Rogy, A. Andrew M. MacDonald

PLOS Computational Biology: published September 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010372

A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research

Ludmilla Figueiredo, Cédric Scherer, Juliano Sarmento Cabral

PLOS Computational Biology: published September 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010356

Research Articles

Estimation of heterogeneous instantaneous reproduction numbers with application to characterize SARS-CoV-2 transmission in Massachusetts counties

Zhenwei Zhou, Eric D. Kolaczyk, Robin N. Thompson, Laura F. White

PLOS Computational Biology: published September 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010434

High-order functional redundancy in ageing explained via alterations in the connectome in a whole-brain model

Marilyn Gatica, Fernando E. Rosas, Pedro A. M. Mediano, Ibai Diez, Stephan P. Swinnen, Patricio Orio, Rodrigo Cofré, Jesus M. Cortes

PLOS Computational Biology: published September 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010431

Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells

Kapil Newar, Amith Zafal Abdulla, Hossein Salari, Eric Fanchon, Daniel Jost

PLOS Computational Biology: published September 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010450

Optimal anti-amyloid-beta therapy for Alzheimer’s disease via a personalized mathematical model

Wenrui Hao, Suzanne Lenhart, Jeffrey R. Petrella

PLOS Computational Biology: published September 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010481

Optimizing global COVID-19 vaccine allocation: An agent-based computational model of 148 countries

Qingfeng Li, Yajing Huang

PLOS Computational Biology: published September 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010463

A computational framework for modelling infectious disease policy based on age and household structure with applications to the COVID-19 pandemic

Joe Hilton, Heather Riley, Lorenzo Pellis, Rabia Aziza, Samuel P. C. Brand, Ivy K. Kombe, John Ojal, Andrea Parisi, Matt J. Keeling, D. James Nokes, Robert Manson-Sawko, Thomas House

PLOS Computational Biology: published September 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010390

What lies underneath: Precise classification of brain states using time-dependent topological structure of dynamics

Fernando Soler-Toscano, Javier A. Galadí, Anira Escrichs, Yonatan Sanz Perl, Ane López-González, Jacobo D. Sitt, Jitka Annen, Olivia Gosseries, Aurore Thibaut, Rajanikant Panda, Francisco J. Esteban, Steven Laureys, Morten L. Kringelbach, José A. Langa, Gustavo Deco

PLOS Computational Biology: published September 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010412

Role of the reaction-structure coupling in temperature compensation of the KaiABC circadian rhythm

Masaki Sasai

PLOS Computational Biology: published September 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010494

Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model

Polina Suter, Eva Dazert, Jack Kuipers, Charlotte K. Y. Ng, Tuyana Boldanova, Michael N. Hall, Markus H. Heim, Niko Beerenwinkel

PLOS Computational Biology: published September 6, 2022 | https://doi.org/10.1371/journal.pcbi.1009767

Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks

Takaki Yamamoto, Katie Cockburn, Valentina Greco, Kyogo Kawaguchi

PLOS Computational Biology: published September 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010477

MouseNet: A biologically constrained convolutional neural network model for the mouse visual cortex

Jianghong Shi, Bryan Tripp, Eric Shea-Brown, Stefan Mihalas, Michael A. Buice

PLOS Computational Biology: published September 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010427

EpiBeds: Data informed modelling of the COVID-19 hospital burden in England

Christopher E. Overton, Lorenzo Pellis, Helena B. Stage, Francesca Scarabel, Joshua Burton, Christophe Fraser, Ian Hall, Thomas A. House, Chris Jewell, Anel Nurtay, Filippo Pagani, Katrina A. Lythgoe

PLOS Computational Biology: published September 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010406

A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data

Ran Su, Haitang Yang, Leyi Wei, Siqi Chen, Quan Zou

PLOS Computational Biology: published September 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010402

Identifying enhancer properties associated with genetic risk for complex traits using regulome-wide association studies

Alex M. Casella, Carlo Colantuoni, Seth A. Ament

PLOS Computational Biology: published September 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010430

Copper binding leads to increased dynamics in the regulatory N-terminal domain of full-length human copper transporter ATP7B

Fredrik Orädd, Jonas Hyld Steffen, Pontus Gourdon, Magnus Andersson

PLOS Computational Biology: published September 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010074

Comparing and linking machine learning and semi-mechanistic models for the predictability of endemic measles dynamics

Max S. Y. Lau, Alex Becker, Wyatt Madden, Lance A. Waller, C. Jessica E. Metcalf, Bryan T. Grenfell

PLOS Computational Biology: published September 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010251

Connectivity concepts in neuronal network modeling

Johanna Senk, Birgit Kriener, Mikael Djurfeldt, Nicole Voges, Han-Jia Jiang, Lisa Schüttler, Gabriele Gramelsberger, Markus Diesmann, Hans E. Plesser, Sacha J. van Albada

PLOS Computational Biology: published September 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010086

Constructing functional models from biophysically-detailed neurons

Peter Duggins, Chris Eliasmith

PLOS Computational Biology: published September 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010461

Stability criteria for the consumption and exchange of essential resources

Theo Gibbs, Yifan Zhang, Zachary R. Miller, James P. O’Dwyer

PLOS Computational Biology: published September 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010521

Investigating differential abundance methods in microbiome data: A benchmark study

Marco Cappellato, Giacomo Baruzzo, Barbara Di Camillo

PLOS Computational Biology: published September 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010467

Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation

Nirvana Nursimulu, Alan M. Moses, John Parkinson

PLOS Computational Biology: published September 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010452

Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins

Lei Yu, Rafael Brüschweiler

PLOS Computational Biology: published September 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010036

ceRNAR: An R package for identification and analysis of ceRNA-miRNA triplets

Yi-Wen Hsiao, Lin Wang, Tzu-Pin Lu

PLOS Computational Biology: published September 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010497

Species abundance correlations carry limited information about microbial network interactions

Susanne Pinto, Elisa Benincà, Egbert H. van Nes, Marten Scheffer, Johannes A. Bogaards

PLOS Computational Biology: published September 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010491

Ambiguity drives higher-order Pavlovian learning

Tomislav D. Zbozinek, Omar D. Perez, Toby Wise, Michael Fanselow, Dean Mobbs

PLOS Computational Biology: published September 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010410

Patterns of asymmetry and energy cost generated from predictive simulations of hemiparetic gait

Russell T. Johnson, Nicholas A. Bianco, James M. Finley

PLOS Computational Biology: published September 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010466

The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life

Zhen Peng, Jeff Linderoth, David A. Baum

PLOS Computational Biology: published September 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010498

Utility of constraints reflecting system stability on analyses for biological models

Yoshiaki Kariya, Masashi Honma, Keita Tokuda, Akihiko Konagaya, Hiroshi Suzuki

PLOS Computational Biology: published September 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010441

A transcriptional cycling model recapitulates chromatin-dependent features of noisy inducible transcription

M. Elise Bullock, Nataly Moreno-Martinez, Kathryn Miller-Jensen

PLOS Computational Biology: published September 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010152

RNA velocity unraveled

Gennady Gorin, Meichen Fang, Tara Chari, Lior Pachter

PLOS Computational Biology: published September 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010492

PrMFTP: Multi-functional therapeutic peptides prediction based on multi-head self-attention mechanism and class weight optimization

Wenhui Yan, Wending Tang, Lihua Wang, Yannan Bin, Junfeng Xia

PLOS Computational Biology: published September 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010511

Thalamic regulation of frontal interactions in human cognitive flexibility

Ali Hummos, Bin A. Wang, Sabrina Drammis, Michael M. Halassa, Burkhard Pleger

PLOS Computational Biology: published September 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010500

Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level

David Laloum, Marc Robinson-Rechavi

PLOS Computational Biology: published September 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010399

A quantitative modelling approach for DNA repair on a population scale

Leo Zeitler, Cyril Denby Wilkes, Arach Goldar, Julie Soutourina

PLOS Computational Biology: published September 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010488

CINS: Cell Interaction Network inference from Single cell expression data

Ye Yuan, Carlos Cosme Jr., Taylor Sterling Adams, Jonas Schupp, Koji Sakamoto, Nikos Xylourgidis, Matthew Ruffalo, Jiachen Li, Naftali Kaminski, Ziv Bar-Joseph

PLOS Computational Biology: published September 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010468

TAMC: A deep-learning approach to predict motif-centric transcriptional factor binding activity based on ATAC-seq profile

Tianqi Yang, Ricardo Henao

PLOS Computational Biology: published September 12, 2022 | https://doi.org/10.1371/journal.pcbi.1009921

Digital twin predicting diet response before and after long-term fasting

Oscar Silfvergren, Christian Simonsson, Mattias Ekstedt, Peter Lundberg, Peter Gennemark, Gunnar Cedersund

PLOS Computational Biology: published September 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010469

An integrative systems biology approach to overcome venetoclax resistance in acute myeloid leukemia

Michelle Przedborski, David Sharon, Severine Cathelin, Steven Chan, Mohammad Kohandel

PLOS Computational Biology: published September 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010439

In the Body’s Eye: The computational anatomy of interoceptive inference

Micah Allen, Andrew Levy, Thomas Parr, Karl J. Friston

PLOS Computational Biology: published September 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010490

Excitatory and inhibitory effects of HCN channel modulation on excitability of layer V pyramidal cells

Tuomo Mäki-Marttunen, Verónica Mäki-Marttunen

PLOS Computational Biology: published September 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010506

Testing microbiome associations with survival times at both the community and individual taxon levels

Yingtian Hu, Yunxiao Li, Glen A. Satten, Yi-Juan Hu

PLOS Computational Biology: published September 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010509

Distinguishing shadows from surface boundaries using local achromatic cues

Christopher DiMattina, Josiah J. Burnham, Betul N. Guner, Haley B. Yerxa

PLOS Computational Biology: published September 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010473

A normative model of peripersonal space encoding as performing impact prediction

Zdenek Straka, Jean-Paul Noel, Matej Hoffmann

PLOS Computational Biology: published September 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010464

Extracting individual characteristics from population data reveals a negative social effect during honeybee defence

Tatjana Petrov, Matej Hajnal, Julia Klein, David Šafránek, Morgane Nouvian

PLOS Computational Biology: published September 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010305

Mathematical modeling to understand the role of bivalent thrombin-fibrin binding during polymerization

Michael A. Kelley, Karin Leiderman

PLOS Computational Biology: published September 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010414

Demonstration of three-dimensional contact point determination and contour reconstruction during active whisking behavior of an awake rat

Lucie A. Huet, Hannah M. Emnett, Mitra J. Z. Hartmann

PLOS Computational Biology: published September 15, 2022 | https://doi.org/10.1371/journal.pcbi.1007763

Radical triads, not pairs, may explain effects of hypomagnetic fields on neurogenesis

Jess Ramsay, Daniel R. Kattnig

PLOS Computational Biology: published September 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010519

The osteogenetic activities of mesenchymal stem cells in response to Mg²⁺ ions and inflammatory cytokines: a numerical approach using fuzzy logic controllers

Jalil Nourisa, Berit Zeller-Plumhoff, Regine Willumeit-Römer

PLOS Computational Biology: published September 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010482

Graph-based algorithms for Laplace transformed coalescence time distributions

Gertjan Bisschop

PLOS Computational Biology: published September 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010532

Optimal control methods for nonlinear parameter estimation in biophysical neuron models

Nirag Kadakia

PLOS Computational Biology: published September 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010479

Robust inference of population size histories from genomic sequencing data

Gautam Upadhya, Matthias Steinrücken

PLOS Computational Biology: published September 16, 2022 | https://doi.org/10.1371/journal.pcbi.1010419

Emergence of qualitative states in synthetic circuits driven by ultrasensitive growth feedback

Juan Ramon Melendez-Alvarez, Xiao-Jun Tian

PLOS Computational Biology: published September 16, 2022 | https://doi.org/10.1371/journal.pcbi.1010518

Fast and accurate Ab Initio Protein structure prediction using deep learning potentials

Robin Pearce, Yang Li, Gilbert S. Omenn, Yang Zhang

PLOS Computational Biology: published September 16, 2022 | https://doi.org/10.1371/journal.pcbi.1010539

Is cell segregation like oil and water: Asymptotic versus transitory regime

Florian Franke, Sebastian Aland, Hans-Joachim Böhme, Anja Voss-Böhme, Steffen Lange

PLOS Computational Biology: published September 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010460

On the incongruence of genotype-phenotype and fitness landscapes

Malvika Srivastava, Joshua L. Payne

PLOS Computational Biology: published September 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010524

Omitting age-dependent mosquito mortality in malaria models underestimates the effectiveness of insecticide-treated nets

Melissa A. Iacovidou, Priscille Barreaux, Simon E. F. Spencer, Matthew B. Thomas, Erin E. Gorsich, Kat S. Rock

PLOS Computational Biology: published September 19, 2022 | https://doi.org/10.1371/journal.pcbi.1009540

Synaptic balancing: A biologically plausible local learning rule that provably increases neural network noise robustness without sacrificing task performance

Christopher H. Stock, Sarah E. Harvey, Samuel A. Ocko, Surya Ganguli

PLOS Computational Biology: published September 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010418

Comparing human and model-based forecasts of COVID-19 in Germany and Poland

Nikos I. Bosse, Sam Abbott, Johannes Bracher, Habakuk Hain, Billy J. Quilty, Mark Jit, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Edwin van Leeuwen, Anne Cori, Sebastian Funk

PLOS Computational Biology: published September 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010405

A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation

Yuncong Geng, Christopher Herrick Bohrer, Nicolás Yehya, Hunter Hendrix, Lior Shachaf, Jian Liu, Jie Xiao, Elijah Roberts

PLOS Computational Biology: published September 19, 2022 | https://doi.org/10.1371/journal.pcbi.1009788

Bayesian estimation of community size and overlap from random subsamples

Erik K. Johnson, Daniel B. Larremore

PLOS Computational Biology: published September 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010451

AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses

Eric Waltari, Saba Nafees, Krista M. McCutcheon, Joan Wong, John E. Pak

PLOS Computational Biology: published September 20, 2022 | https://doi.org/10.1371/journal.pcbi.1010052

An in-silico analysis of experimental designs to study ventricular function: A focus on the right ventricle

Mitchel J. Colebank, Naomi C. Chesler

PLOS Computational Biology: published September 20, 2022 | https://doi.org/10.1371/journal.pcbi.1010017

GenOtoScope: Towards automating ACMG classification of variants associated with congenital hearing loss

Damianos P. Melidis, Christian Landgraf, Gunnar Schmidt, Anja Schöner-Heinisch, Sandra von Hardenberg, Anke Lesinski-Schiedat, Wolfgang Nejdl, Bernd Auber

PLOS Computational Biology: published September 21, 2022 | https://doi.org/10.1371/journal.pcbi.1009785

Strange attractor of a narwhal (Monodon monoceros)

Evgeny A. Podolskiy, Mads Peter Heide-Jørgensen

PLOS Computational Biology: published September 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010432

Identification of key somatic oncogenic mutation based on a confounder-free causal inference model

Yijun Liu, Ji Sun, Huiyan Sun, Yi Chang

PLOS Computational Biology: published September 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010529

An expert judgment model to predict early stages of the COVID-19 pandemic in the United States

Thomas McAndrew, Nicholas G. Reich

PLOS Computational Biology: published September 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010485

Computational models reveal how chloride dynamics determine the optimal distribution of inhibitory synapses to minimise dendritic excitability

Christopher Brian Currin, Joseph Valentino Raimondo

PLOS Computational Biology: published September 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010534

MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes

Lin Zhang, Likai Chen, Xiaoqian (Annie) Yu, Claire Duvallet, Siavash Isazadeh, Chengzhen Dai, Shinkyu Park, Katya Frois-Moniz, Fabio Duarte, Carlo Ratti, Eric J. Alm, Fangqiong Ling

PLOS Computational Biology: published September 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010472

Systems-level identification of key transcription factors in immune cell specification

Cong Liu, Kyla Omilusik, Clara Toma, Nadia S. Kurd, John T. Chang, Ananda W. Goldrath, Wei Wang

PLOS Computational Biology: published September 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010116

Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants

Eric Wang, Arup K. Chakraborty

PLOS Computational Biology: published September 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010563

General object-based features account for letter perception

Daniel Janini, Chris Hamblin, Arturo Deza, Talia Konkle

PLOS Computational Biology: published September 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010522

A Deep Survival EWAS approach estimating risk profile based on pre-diagnostic DNA methylation: An application to breast cancer time to diagnosis

Michela Carlotta Massi, Lorenzo Dominoni, Francesca Ieva, Giovanni Fiorito

PLOS Computational Biology: published September 26, 2022 | https://doi.org/10.1371/journal.pcbi.1009959

Cross-GWAS coherence test at the gene and pathway level

Daniel Krefl, Sven Bergmann

PLOS Computational Biology: published September 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010517

Using Fluorescence Recovery After Photobleaching data to uncover filament dynamics

J. C. Dallon, Cécile Leduc, Christopher P. Grant, Emily J. Evans, Sandrine Etienne-Manneville, Stéphanie Portet

PLOS Computational Biology: published September 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010573

Towards mouse genetic-specific RNA-sequencing read mapping

Nastassia Gobet, Maxime Jan, Paul Franken, Ioannis Xenarios

PLOS Computational Biology: published September 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010552

Interactions between attributions and beliefs at trial-by-trial level: Evidence from a novel computer game task

Elena Zamfir, Peter Dayan

PLOS Computational Biology: published September 26, 2022 | https://doi.org/10.1371/journal.pcbi.1009920

Optimizing laboratory-based surveillance networks for monitoring multi-genotype or multi-serotype infections

Qu Cheng, Philip A. Collender, Alexandra K. Heaney, Aidan McLoughlin, Yang Yang, Yuzi Zhang, Jennifer R. Head, Rohini Dasan, Song Liang, Qiang Lv, Yaqiong Liu, Changhong Yang, Howard H. Chang, Lance A. Waller, Jon Zelner, Joseph A. Lewnard, Justin V. Remais

PLOS Computational Biology: published September 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010575

Pruning deep neural networks generates a sparse, bio-inspired nonlinear controller for insect flight

Olivia Zahn, Jorge Bustamante Jr., Callin Switzer, Thomas L. Daniel, J. Nathan Kutz

PLOS Computational Biology: published September 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010512

Correcting motion induced fluorescence artifacts in two-channel neural imaging

Matthew S. Creamer, Kevin S. Chen, Andrew M. Leifer, Jonathan W. Pillow

PLOS Computational Biology: published September 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010421

Towards reliable quantification of cell state velocities

Valérie Marot-Lassauzaie, Brigitte Joanne Bouman, Fearghal Declan Donaghy, Yasmin Demerdash, Marieke Alida Gertruda Essers, Laleh Haghverdi

PLOS Computational Biology: published September 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010031

Generalism drives abundance: A computational causal discovery approach

Chuliang Song, Benno I. Simmons, Marie-Josée Fortin, Andrew Gonzalez

PLOS Computational Biology: published September 29, 2022 | https://doi.org/10.1371/journal.pcbi.1010302

Interaction between games give rise to the evolution of moral norms of cooperation

Mohammad Salahshour

PLOS Computational Biology: published September 29, 2022 | https://doi.org/10.1371/journal.pcbi.1010429

Modeling enculturated bias in entrainment to rhythmic patterns

Thomas Kaplan, Jonathan Cannon, Lorenzo Jamone, Marcus Pearce

PLOS Computational Biology: published September 29, 2022 | https://doi.org/10.1371/journal.pcbi.1010579

Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection

Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John S. Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Šulc

PLOS Computational Biology: published September 29, 2022 | https://doi.org/10.1371/journal.pcbi.1010561

Estimation of the firing behaviour of a complete motoneuron pool by combining electromyography signal decomposition and realistic motoneuron modelling

Arnault H. Caillet, Andrew T. M. Phillips, Dario Farina, Luca Modenese

PLOS Computational Biology: published September 29, 2022 | https://doi.org/10.1371/journal.pcbi.1010556

Correction

Correction: MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments

Hamid Alinejad-Rokny, Rassa Ghavami Modegh, Hamid R. Rabiee, Ehsan Ramezani Sarbandi, Narges Rezaie, Kin Tung Tam, Alistair R. R. Forrest

PLOS Computational Biology: published September 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010515