September 2023

Multi-decade efforts have yielded voltage gating voltage (∆V1/2) data on almost 500 single mutants of the big potassium (BK) channel. The left panel shows all residues of the BK channel where at least one mutation has been characterized experimentally. While representing enormous efforts, these data alone remain too scarce for deriving quantitative models for predicting the mutational effects using data-driven machine learning approaches. By incorporating physical features derived from molecular modeling and simulations, we show that a random forest model trained using 80% of the experimental shift in gating voltage is able to predict unseen experimental data with 0.79 correlation. The model is also able to capture a central role of hydrophobic gating in BK channels as well as new experimental results on several novel mutations. Nordquist et al 2023

Image Credit: Erik Nordquist, enordquist@umass.edu

Education Articles

Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy

Joshua Atienza, Anjalee Benedict, Lincoln D. Stein, Kashif Pirzada, Cheryl White, Shraddha Pai

PLOS Computational Biology: published September 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011285

Ten simple rules for interpreting and evaluating a meta-analysis

Rebecca B. Carlson, Jennifer R. Martin, Robert D. Beckett

PLOS Computational Biology: published September 28, 2023 | https://doi.org/10.1371/journal.pcbi.1011461

Ten quick tips for building FAIR workflows

Casper de Visser, Lennart F. Johansson, Purva Kulkarni, Hailiang Mei, Pieter Neerincx, K. Joeri van der Velde, Péter Horvatovich, Alain J. van Gool, Morris A. Swertz, Peter A. C. ‘t Hoen, Anna Niehues

PLOS Computational Biology: published September 28, 2023 | https://doi.org/10.1371/journal.pcbi.1011369

Research Articles

Bayesian inference for spatio-temporal stochastic transmission of plant disease in the presence of roguing: A case study to characterise the dispersal of Flavescence dorée

Hola K. Adrakey, Gavin J. Gibson, Sandrine Eveillard, Sylvie Malembic-Maher, Frederic Fabre

PLOS Computational Biology: published September 1, 2023 | https://doi.org/10.1371/journal.pcbi.1011399

Dynamical modelling of viral infection and cooperative immune protection in COVID-19 patients

Zhengqing Zhou, Dianjie Li, Ziheng Zhao, Shuyu Shi, Jianghua Wu, Jianwei Li, Jingpeng Zhang, Ke Gui, Yu Zhang, Qi Ouyang, Heng Mei, Yu Hu, Fangting Li

PLOS Computational Biology: published September 1, 2023 | https://doi.org/10.1371/journal.pcbi.1011383

Evaluating the impact of test-trace-isolate for COVID-19 management and alternative strategies

Kun Zhang, Zhichu Xia, Shudong Huang, Gui-Quan Sun, Jiancheng Lv, Marco Ajelli, Keisuke Ejima, Quan-Hui Liu

PLOS Computational Biology: published September 1, 2023 | https://doi.org/10.1371/journal.pcbi.1011423

Self-loops in evolutionary graph theory: Friends or foes?

Nikhil Sharma, Sedigheh Yagoobi, Arne Traulsen

PLOS Computational Biology: published September 1, 2023 | https://doi.org/10.1371/journal.pcbi.1011387

A multi-layer mean-field model of the cerebellum embedding microstructure and population-specific dynamics

Roberta Maria Lorenzi, Alice Geminiani, Yann Zerlaut, Marialaura De Grazia, Alain Destexhe, Claudia A. M. Gandini Wheeler-Kingshott, Fulvia Palesi, Claudia Casellato, Egidio D’Angelo

PLOS Computational Biology: published September 1, 2023 | https://doi.org/10.1371/journal.pcbi.1011434

RSim: A reference-based normalization method via rank similarity

Bo Yuan, Shulei Wang

PLOS Computational Biology: published September 1, 2023 | https://doi.org/10.1371/journal.pcbi.1011447

Age-differentiated incentives for adaptive behavior during epidemics produce oscillatory and chaotic dynamics

Ronan F. Arthur, May Levin, Alexandre Labrogere, Marcus W. Feldman

PLOS Computational Biology: published September 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011217

The inhibitory control of traveling waves in cortical networks

Grishma Palkar, Jian-young Wu, Bard Ermentrout

PLOS Computational Biology: published September 5, 2023 | https://doi.org/10.1371/journal.pcbi.1010697

Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks

Georgi K. Kanev, Yaran Zhang, Albert J. Kooistra, Andreas Bender, Rob Leurs, David Bailey, Thomas Würdinger, Chris de Graaf, Iwan J. P. de Esch, Bart A. Westerman

PLOS Computational Biology: published September 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011301

iCVS—Inferring Cardio-Vascular hidden States from physiological signals available at the bedside

Neta Ravid Tannenbaum, Omer Gottesman, Azadeh Assadi, Mjaye Mazwi, Uri Shalit, Danny Eytan

PLOS Computational Biology: published September 5, 2023 | https://doi.org/10.1371/journal.pcbi.1010835

What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases

Francis Banville, Dominique Gravel, Timothée Poisot

PLOS Computational Biology: published September 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011458

An automated interface for sedimentation velocity analysis in SEDFIT

Peter Schuck, Samuel C. To, Huaying Zhao

PLOS Computational Biology: published September 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011454

Controlling brain dynamics: Landscape and transition path for working memory

Leijun Ye, Jianfeng Feng, Chunhe Li

PLOS Computational Biology: published September 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011446

Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches

Zheng Jiang, Yue-Yue Shen, Rong Liu

PLOS Computational Biology: published September 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011428

Predictive modeling of antibiotic eradication therapy success for new-onset Pseudomonas aeruginosa pulmonary infections in children with cystic fibrosis

Lucía Graña-Miraglia, Nadia Morales-Lizcano, Pauline W. Wang, David M. Hwang, Yvonne C. W. Yau, Valerie J. Waters, David S. Guttman

PLOS Computational Biology: published September 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011424

Modelling African horse sickness emergence and transmission in the South African control area using a deterministic metapopulation approach

Joanna N. de Klerk, Erin E. Gorsich, John D. Grewar, Benjamin D. Atkins, Warren S. D. Tennant, Karien Labuschagne, Michael J. Tildesley

PLOS Computational Biology: published September 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011448

Spike-timing dependent plasticity partially compensates for neural delays in a multi-layered network of motion-sensitive neurons

Charlie M. Sexton, Anthony N. Burkitt, Hinze Hogendoorn

PLOS Computational Biology: published September 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011457

Computational modeling of multiscale collateral blood supply in a whole-brain-scale arterial network

Tomohiro Otani, Nozomi Nishimura, Hiroshi Yamashita, Satoshi Ii, Shigeki Yamada, Yoshiyuki Watanabe, Marie Oshima, Shigeo Wada

PLOS Computational Biology: published September 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011452

A whole-task brain model of associative recognition that accounts for human behavior and neuroimaging data

Jelmer P. Borst, Sean Aubin, Terrence C. Stewart

PLOS Computational Biology: published September 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011427

Error-independent effect of sensory uncertainty on motor learning when both feedforward and feedback control processes are engaged

Christopher L. Hewitson, David M. Kaplan, Matthew J. Crossley

PLOS Computational Biology: published September 8, 2023 | https://doi.org/10.1371/journal.pcbi.1010526

Emergence of belief-like representations through reinforcement learning

Jay A. Hennig, Sandra A. Romero Pinto, Takahiro Yamaguchi, Scott W. Linderman, Naoshige Uchida, Samuel J. Gershman

PLOS Computational Biology: published September 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011067

iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease

Ziheng Duan, Yi Dai, Ahyeon Hwang, Cheyu Lee, Kaichi Xie, Chutong Xiao, Min Xu, Matthew J. Girgenti, Jing Zhang

PLOS Computational Biology: published September 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011444

Mate selection: A useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding

Billy Tchounke, Leopoldo Sanchez, Joseph Martin Bell, David Cros

PLOS Computational Biology: published September 11, 2023 | https://doi.org/10.1371/journal.pcbi.1010290

Pathfinder: Protein folding pathway prediction based on conformational sampling

Zhaohong Huang, Xinyue Cui, Yuhao Xia, Kailong Zhao, Guijun Zhang

PLOS Computational Biology: published September 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011438

OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates

Shuming Liu, Cong Wang, Andrew P. Latham, Xinqiang Ding, Bin Zhang

PLOS Computational Biology: published September 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011442

Testing predictive coding theories of autism spectrum disorder using models of active inference

Tom Arthur, Sam Vine, Gavin Buckingham, Mark Brosnan, Mark Wilson, David Harris

PLOS Computational Biology: published September 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011473

Simulation-based Reconstructed Diffusion unveils the effect of aging on protein diffusion in Escherichia coli

Luca Mantovanelli, Dmitrii S. Linnik, Michiel Punter, Hildeberto Jardón Kojakhmetov, Wojciech M. Śmigiel, Bert Poolman

PLOS Computational Biology: published September 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011093

Classification of T lymphocyte motility behaviors using a machine learning approach

Yves Carpentier Solorio, Florent Lemaître, Bassam Jabbour, Olivier Tastet, Nathalie Arbour, Elie Bou Assi

PLOS Computational Biology: published September 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011449

Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England

James D. Munday, Sam Abbott, Sophie Meakin, Sebastian Funk

PLOS Computational Biology: published September 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011453

Beyond ℓ₁ sparse coding in V1

Ilias Rentzeperis, Luca Calatroni, Laurent U. Perrinet, Dario Prandi

PLOS Computational Biology: published September 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011459

Uncovering specific mechanisms across cell types in dynamical models

Adrian L. Hauber, Marcus Rosenblatt, Jens Timmer

PLOS Computational Biology: published September 13, 2023 | https://doi.org/10.1371/journal.pcbi.1010867

Mixtures of strategies underlie rodent behavior during reversal learning

Nhat Minh Le, Murat Yildirim, Yizhi Wang, Hiroki Sugihara, Mehrdad Jazayeri, Mriganka Sur

PLOS Computational Biology: published September 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011430

Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data

Simon Boutry, Raphaël Helaers, Tom Lenaerts, Miikka Vikkula

PLOS Computational Biology: published September 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011488

Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels

Erik Nordquist, Guohui Zhang, Shrishti Barethiya, Nathan Ji, Kelli M. White, Lu Han, Zhiguang Jia, Jingyi Shi, Jianmin Cui, Jianhan Chen

PLOS Computational Biology: published September 15, 2023 | https://doi.org/10.1371/journal.pcbi.1011460

Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model

Elias Vera-Siguenza, Cristina Escribano-Gonzalez, Irene Serrano-Gonzalo, Kattri-Liis Eskla, Fabian Spill, Daniel Tennant

PLOS Computational Biology: published September 15, 2023 | https://doi.org/10.1371/journal.pcbi.1011374

Human-environment feedback and the consistency of proenvironmental behavior

Claire Ecotière, Sylvain Billiard, Jean-Baptiste André, Pierre Collet, Régis Ferrière, Sylvie Méléard

PLOS Computational Biology: published September 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011429

Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

Serena Aneli, Piero Fariselli, Elena Chierto, Carla Bini, Carlo Robino, Giovanni Birolo

PLOS Computational Biology: published September 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011474

Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study

Zengmiao Wang, Peiyi Wu, Lin Wang, Bingying Li, Yonghong Liu, Yuxi Ge, Ruixue Wang, Ligui Wang, Hua Tan, Chieh-Hsi Wu, Marko Laine, Henrik Salje, Hongbin Song

PLOS Computational Biology: published September 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011492

Nowcasting the 2022 mpox outbreak in England

Christopher E. Overton, Sam Abbott, Rachel Christie, Fergus Cumming, Julie Day, Owen Jones, Rob Paton, Charlie Turner, Thomas Ward

PLOS Computational Biology: published September 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011463

Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony

Seirana Hashemi, Zahra Razaghi-Moghadam, Zoran Nikoloski

PLOS Computational Biology: published September 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011489

Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression

Bayarbaatar Amgalan, Chi-Ping Day, Teresa M. Przytycka

PLOS Computational Biology: published September 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011472

The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber

Emanuel Cunha, Miguel Silva, Inês Chaves, Huseyin Demirci, Davide Rafael Lagoa, Diogo Lima, Miguel Rocha, Isabel Rocha, Oscar Dias

PLOS Computational Biology: published September 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011499

Mechanistic multiscale modelling of energy metabolism in human astrocytes reveals the impact of morphology changes in Alzheimer’s Disease

Sofia Farina, Valérie Voorsluijs, Sonja Fixemer, David S. Bouvier, Susanne Claus, Mark H. Ellisman, Stéphane P. A. Bordas, Alexander Skupin

PLOS Computational Biology: published September 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011464

CIRCUST: A novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans

Yolanda Larriba, Ivy C. Mason, Richa Saxena, Frank A. J. L. Scheer, Cristina Rueda

PLOS Computational Biology: published September 28, 2023 | https://doi.org/10.1371/journal.pcbi.1011510

Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions

Jaron C. Thompson, Victor M. Zavala, Ophelia S. Venturelli

PLOS Computational Biology: published September 29, 2023 | https://doi.org/10.1371/journal.pcbi.1011436

Transcription factor competition facilitates self-sustained oscillations in single gene genetic circuits

Jasper Landman, Sjoerd M. Verduyn Lunel, Willem K. Kegel

PLOS Computational Biology: published September 29, 2023 | https://doi.org/10.1371/journal.pcbi.1011525

Profile-Wise Analysis: A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models

Matthew J. Simpson, Oliver J. Maclaren

PLOS Computational Biology: published September 29, 2023 | https://doi.org/10.1371/journal.pcbi.1011515

Software

Trackplot: A flexible toolkit for combinatorial analysis of genomic data

Yiming Zhang, Ran Zhou, Lunxu Liu, Lu Chen, Yuan Wang

PLOS Computational Biology: published September 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011477

Cover

Incorporating physics helps overcome data scarcity in predicting mutational effects on BK channel voltage gating

Education Articles

Research Articles

Related Articles

Software