October 2023

The mechanism by which thermosensitive ion channels translate temperature increase to gate activation is hidden within a network of temperature-sensitive residue interactions. The different temperature-dependent interaction modes which promote activation dynamics are revealed with replica exchange molecular dynamics and machine learning. Regions of the structure characterized by specific modes are depicted here in various colors. Burns et al 2023

Image Credit: Dan Burns

Research Articles

Mouse visual cortex as a limited resource system that self-learns an ecologically-general representation

Aran Nayebi, Nathan C. L. Kong, Chengxu Zhuang, Justin L. Gardner, Anthony M. Norcia, Daniel L. K. Yamins

PLOS Computational Biology: published October 2, 2023 | https://doi.org/10.1371/journal.pcbi.1011506

XA4C: eXplainable representation learning via Autoencoders revealing Critical genes

Qing Li, Yang Yu, Pathum Kossinna, Theodore Lun, Wenyuan Liao, Qingrun Zhang

PLOS Computational Biology: published October 2, 2023 | https://doi.org/10.1371/journal.pcbi.1011476

Perfusion estimation using synthetic MRI-based measurements and a porous media flow model

Rolf Johan Lorentzen, Geir Nævdal, Ove Sævareid, Erlend Hodneland, Erik Andreas Hanson, Antonella Munthe-Kaas

PLOS Computational Biology: published October 2, 2023 | https://doi.org/10.1371/journal.pcbi.1011127

Patch formation driven by stochastic effects of interaction between viruses and defective interfering particles

Qiantong Liang, Johnny Yang, Wai-Tong Louis Fan, Wing-Cheong Lo

PLOS Computational Biology: published October 2, 2023 | https://doi.org/10.1371/journal.pcbi.1011513

Predicting regional somatic mutation rates using DNA motifs

Cong Liu, Zengmiao Wang, Jun Wang, Chengyu Liu, Mengchi Wang, Vu Ngo, Wei Wang

PLOS Computational Biology: published October 2, 2023 | https://doi.org/10.1371/journal.pcbi.1011536

Particle-based simulations reveal two positive feedback loops allow relocation and stabilization of the polarity site during yeast mating

Kaiyun Guan, Erin R. Curtis, Daniel J. Lew, Timothy C. Elston

PLOS Computational Biology: published October 2, 2023 | https://doi.org/10.1371/journal.pcbi.1011523

Natural variability in bee brain size and symmetry revealed by micro-CT imaging and deep learning

Philipp D. Lösel, Coline Monchanin, Renaud Lebrun, Alejandra Jayme, Jacob J. Relle, Jean-Marc Devaud, Vincent Heuveline, Mathieu Lihoreau

PLOS Computational Biology: published October 2, 2023 | https://doi.org/10.1371/journal.pcbi.1011529

Mechanistic characterization of oscillatory patterns in unperturbed tumor growth dynamics: The interplay between cancer cells and components of tumor microenvironment

Aymara Sancho-Araiz, Zinnia P. Parra-Guillen, Jean Bragard, Sergio Ardanza, Victor Mangas-Sanjuan, Iñaki F. Trocóniz

PLOS Computational Biology: published October 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011507

Adaptive representations of sound for automatic insect recognition

Marius Faiß, Dan Stowell

PLOS Computational Biology: published October 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011541

Metacommunity structure preserves genome diversity in the presence of gene-specific selective sweeps under moderate rates of horizontal gene transfer

Simone Pompei, Edoardo Bella, Joshua S. Weitz, Jacopo Grilli, Marco Cosentino Lagomarsino

PLOS Computational Biology: published October 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011532

Rapid runtime learning by curating small datasets of high-quality items obtained from memory

Joseph Scott German, Guofeng Cui, Chenliang Xu, Robert A. Jacobs

PLOS Computational Biology: published October 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011445

Circadian distribution of epileptiform discharges in epilepsy: Candidate mechanisms of variability

Isabella Marinelli, Jamie J. Walker, Udaya Seneviratne, Wendyl D’Souza, Mark J. Cook, Clare Anderson, Andrew P. Bagshaw, Stafford L. Lightman, Wessel Woldman, John R. Terry

PLOS Computational Biology: published October 5, 2023 | https://doi.org/10.1371/journal.pcbi.1010508

Force-dependent focal adhesion assembly and disassembly: A computational study

Kailas Shankar Honasoge, Zeynep Karagöz, Benjamin T. Goult, Haguy Wolfenson, Vanessa L. S. LaPointe, Aurélie Carlier

PLOS Computational Biology: published October 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011500

Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Tracker

Oliver J. Meacock, William M. Durham

PLOS Computational Biology: published October 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011524

Pan-cancer characterization of ncRNA synergistic competition uncovers potential carcinogenic biomarkers

Junpeng Zhang, Lin Liu, Xuemei Wei, Chunwen Zhao, Sijing Li, Jiuyong Li, Thuc Duy Le

PLOS Computational Biology: published October 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011308

Mechanistic modelling of within-mosquito viral dynamics: Insights into infection and dissemination patterns

Jennifer S. Lord, Michael B. Bonsall

PLOS Computational Biology: published October 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011520

Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors

Leah L. Weber, Chuanyi Zhang, Idoia Ochoa, Mohammed El-Kebir

PLOS Computational Biology: published October 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011544

Modeling functional cell types in spike train data

Daniel N. Zdeblick, Eric T. Shea-Brown, Daniela M. Witten, Michael A. Buice

PLOS Computational Biology: published October 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011509

Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task

Joseph D. Valencia, David A. Hendrix

PLOS Computational Biology: published October 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011526

Reproducibility of biophysical in silico neuron states and spikes from event-based partial histories

Evan Cudone, Amelia M. Lower, Robert A. McDougal

PLOS Computational Biology: published October 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011548

Assessing the performance of methods for cell clustering from single-cell DNA sequencing data

Rituparna Khan, Xian Mallory

PLOS Computational Biology: published October 12, 2023 | https://doi.org/10.1371/journal.pcbi.1010480

Short-term neuronal and synaptic plasticity act in synergy for deviance detection in spiking networks

Felix Benjamin Kern, Zenas C. Chao

PLOS Computational Biology: published October 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011554

Temperature sensitive contact modes allosterically gate TRPV3

Daniel Burns, Vincenzo Venditti, Davit A. Potoyan

PLOS Computational Biology: published October 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011545

Conserved and divergent signals in 5’ splice site sequences across fungi, metazoa and plants

Maximiliano S. Beckel, Bruno Kaufman, Marcelo Yanovsky, Ariel Chernomoretz

PLOS Computational Biology: published October 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011540

Lévy movements and a slowly decaying memory allow efficient collective learning in groups of interacting foragers

Andrea Falcón-Cortés, Denis Boyer, Maximino Aldana, Gabriel Ramos-Fernández

PLOS Computational Biology: published October 16, 2023 | https://doi.org/10.1371/journal.pcbi.1011528

Rational social distancing policy during epidemics with limited healthcare capacity

Simon K. Schnyder, John J. Molina, Ryoichi Yamamoto, Matthew S. Turner

PLOS Computational Biology: published October 16, 2023 | https://doi.org/10.1371/journal.pcbi.1011533

Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies

Yilin Gao, Fengzhu Sun

PLOS Computational Biology: published October 16, 2023 | https://doi.org/10.1371/journal.pcbi.1010608

Pervasive, conserved secondary structure in highly charged protein regions

Catherine G. Triandafillou, Rosalind Wenshan Pan, Aaron R. Dinner, D. Allan Drummond

PLOS Computational Biology: published October 16, 2023 | https://doi.org/10.1371/journal.pcbi.1011565

Establishing brain states in neuroimaging data

Zalina Dezhina, Jonathan Smallwood, Ting Xu, Federico E. Turkheimer, Rosalyn J. Moran, Karl J. Friston, Robert Leech, Erik D. Fagerholm

PLOS Computational Biology: published October 16, 2023 | https://doi.org/10.1371/journal.pcbi.1011571

A 2D model to study how secondary growth affects the self-supporting behaviour of climbing plants

Giacomo Vecchiato, Tom Hattermann, Michele Palladino, Fabio Tedone, Patrick Heuret, Nick P. Rowe, Pierangelo Marcati

PLOS Computational Biology: published October 16, 2023 | https://doi.org/10.1371/journal.pcbi.1011538

Integrated information theory (IIT) 4.0: Formulating the properties of phenomenal existence in physical terms

Larissa Albantakis, Leonardo Barbosa, Graham Findlay, Matteo Grasso, Andrew M. Haun, William Marshall, William G. P. Mayner, Alireza Zaeemzadeh, Melanie Boly, Bjørn E. Juel, Shuntaro Sasai, Keiko Fujii, Isaac David, Jeremiah Hendren, Jonathan P. Lang, Giulio Tononi

PLOS Computational Biology: published October 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011465

Reframing dopamine: A controlled controller at the limbic-motor interface

Kevin Lloyd, Peter Dayan

PLOS Computational Biology: published October 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011569

Combining the dynamic model and deep neural networks to identify the intensity of interventions during COVID-19 pandemic

Mengqi He, Sanyi Tang, Yanni Xiao

PLOS Computational Biology: published October 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011535

Catalyst: Fast and flexible modeling of reaction networks

Torkel E. Loman, Yingbo Ma, Vasily Ilin, Shashi Gowda, Niklas Korsbo, Nikhil Yewale, Chris Rackauckas, Samuel A. Isaacson

PLOS Computational Biology: published October 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011530

Wall shear stress and pressure patterns in aortic stenosis patients with and without aortic dilation captured by high-performance image-based computational fluid dynamics

Hadi Zolfaghari, Mervyn Andiapen, Andreas Baumbach, Anthony Mathur, Rich R. Kerswell

PLOS Computational Biology: published October 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011479

A recurrent neural network model of prefrontal brain activity during a working memory task

Emilia P. Piwek, Mark G. Stokes, Christopher Summerfield

PLOS Computational Biology: published October 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011555

Distilling identifiable and interpretable dynamic models from biological data

Gemma Massonis, Alejandro F. Villaverde, Julio R. Banga

PLOS Computational Biology: published October 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011014

OpenCap: Human movement dynamics from smartphone videos

Scott D. Uhlrich, Antoine Falisse, Łukasz Kidziński, Julie Muccini, Michael Ko, Akshay S. Chaudhari, Jennifer L. Hicks, Scott L. Delp

PLOS Computational Biology: published October 19, 2023 | https://doi.org/10.1371/journal.pcbi.1011462

PARROT: Prediction of enzyme abundances using protein-constrained metabolic models

Mauricio Alexander de Moura Ferreira, Wendel Batista da Silveira, Zoran Nikoloski

PLOS Computational Biology: published October 19, 2023 | https://doi.org/10.1371/journal.pcbi.1011549

Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model

Carole Chevalier, Jérôme Dorignac, Yahaya Ibrahim, Armelle Choquet, Alexandre David, Julie Ripoll, Eric Rivals, Frédéric Geniet, Nils-Ole Walliser, John Palmeri, Andrea Parmeggiani, Jean-Charles Walter

PLOS Computational Biology: published October 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011522

Modelling how plant cell-cycle progression leads to cell size regulation

Daniel Williamson, William Tasker-Brown, James A. H. Murray, Angharad R. Jones, Leah R. Band

PLOS Computational Biology: published October 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011503

Analyzing histone ChIP-seq data with a bin-based probability of being signal

Vivian Hecht, Kevin Dong, Sreshtaa Rajesh, Polina Shpilker, Siddarth Wekhande, Noam Shoresh

PLOS Computational Biology: published October 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011568

Phi fluctuates with surprisal: An empirical pre-study for the synthesis of the free energy principle and integrated information theory

Christoffer Lundbak Olesen, Peter Thestrup Waade, Larissa Albantakis, Christoph Mathys

PLOS Computational Biology: published October 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011346

Corrections

Correction: Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence

Fateme Pourhasanzade, Swami Iyer, Jesslyn Tjendra, Lotta Landor, Selina Våge

PLOS Computational Biology: published October 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011600

Correction: Intrinsic motivation for choice varies with individual risk attitudes and the controllability of the environment

Jérôme Munuera, Marta Ribes Agost, David Bendetowicz, Adrien Kérébel, Valérian Chambon, Brian Lau

PLOS Computational Biology: published October 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011599

Methods

Rapid automated 3-D pose estimation of larval zebrafish using a physical model-trained neural network

Aniket Ravan, Ruopei Feng, Martin Gruebele, Yann R. Chemla

PLOS Computational Biology: published October 23, 2023 | https://doi.org/10.1371/journal.pcbi.1011566

Software

AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals

Jan G. Kosiński, Marek Żywicki

PLOS Computational Biology: published October 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011527

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