July 2023

This figure presents a complex map of human chromosome 10, showing DNA interactions in three dimensions and cross-scale folding relationships. Each filled circle represents a specific chromosome region whose radius corresponds to the region’s length. The image center depicts the entire chromosome as one giant 3D community that splits when moving toward the outer rim along the lines indicating the folding pathways. Some regions neatly nest within larger ones, while others obey different patterns. This variation is critical for understanding how our chromosomes fold and function. For example, neatly nested regions often associate with transcriptionally active chromatin. Bernenko et al 2023

Image Credit: Dolores Bernenko, dolores.bernenko@umu.se

Education Articles

Ten quick tips for avoiding pitfalls in multi-omics data integration analyses

Davide Chicco, Fabio Cumbo, Claudio Angione

PLOS Computational Biology: published July 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011224

Ten quick tips for editing Wikidata

Thomas Shafee, Daniel Mietchen, Tiago Lubiana, Dariusz Jemielniak, Andra Waagmeester

PLOS Computational Biology: published July 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011235

Ten quick tips for bioinformatics analyses using an Apache Spark distributed computing environment

Davide Chicco, Umberto Ferraro Petrillo, Giuseppe Cattaneo

PLOS Computational Biology: published July 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011272

Perspectives

Ten simple rules for scientists engaging in science communication

Brittney G. Borowiec

PLOS Computational Biology: published July 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011251

The Canadian Open Neuroscience Platform—An open science framework for the neuroscience community

Rachel J. Harding, Patrick Bermudez, Alexander Bernier, Michael Beauvais, Pierre Bellec, Sean Hill, Agâh Karakuzu, Bartha M. Knoppers, Paul Pavlidis, Jean-Baptiste Poline, Jane Roskams, Nikola Stikov, Jessica Stone, Stephen Strother, CONP Consortium, Alan C. Evans

PLOS Computational Biology: published July 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011230

Research Articles

Biological complexity facilitates tuning of the neuronal parameter space

Marius Schneider, Alexander D. Bird, Albert Gidon, Jochen Triesch, Peter Jedlicka, Hermann Cuntz

PLOS Computational Biology: published July 3, 2023 | https://doi.org/10.1371/journal.pcbi.1011212

Integrative modeling of diverse protein-peptide systems using CABS-dock

Wojciech Puławski, Andrzej Koliński, Michał Koliński

PLOS Computational Biology: published July 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011275

M-current modulation of cortical slow oscillations: Network dynamics and computational modeling

Leonardo Dalla Porta, Almudena Barbero-Castillo, Jose Manuel Sanchez-Sanchez, Maria V. Sanchez-Vives

PLOS Computational Biology: published July 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011246

Unified tumor growth mechanisms from multimodel inference and dataset integration

Samantha P. Beik, Leonard A. Harris, Michael A. Kochen, Julien Sage, Vito Quaranta, Carlos F. Lopez

PLOS Computational Biology: published July 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011215

DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design

Cameron Andress, Kalli Kappel, Marcus Elbert Villena, Miroslava Cuperlovic-Culf, Hongbin Yan, Yifeng Li

PLOS Computational Biology: published July 5, 2023 | https://doi.org/10.1371/journal.pcbi.1010774

Computational model of integrin adhesion elongation under an actin fiber

Samuel Campbell, Michelle C. Mendoza, Aravind Rammohan, Matthew E. McKenzie, Tamara C. Bidone

PLOS Computational Biology: published July 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011237

Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes

Shaoke Lou, Mingjun Yang, Tianxiao Li, Weihao Zhao, Hannah Cevasco, Yucheng T. Yang, Mark Gerstein

PLOS Computational Biology: published July 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011222

Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants

Ahmed Taha, Mauricio Patón, David R. Penas, Julio R. Banga, Jorge Rodríguez

PLOS Computational Biology: published July 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011264

Explainable multi-task learning improves the parallel estimation of polygenic risk scores for many diseases through shared genetic basis

Adrien Badré, Chongle Pan

PLOS Computational Biology: published July 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011211

Multiscale effects of excitatory-inhibitory homeostasis in lesioned cortical networks: A computational study

Francisco Páscoa dos Santos, Jakub Vohryzek, Paul F. M. J. Verschure

PLOS Computational Biology: published July 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011279

LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity

Juan Xie, Hyeongseon Jeon, Gang Xin, Qin Ma, Dongjun Chung

PLOS Computational Biology: published July 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011300

Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation

Brittany Baur, Junha Shin, Jacob Schreiber, Shilu Zhang, Yi Zhang, Mohith Manjunath, Jun S. Song, William Stafford Noble, Sushmita Roy

PLOS Computational Biology: published July 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011286

Sequential mutations in exponentially growing populations

Michael D. Nicholson, David Cheek, Tibor Antal

PLOS Computational Biology: published July 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011289

Image-based flow simulation of platelet aggregates under different shear rates

Yue Hao, Gábor Závodszky, Claudia Tersteeg, Mojtaba Barzegari, Alfons G. Hoekstra

PLOS Computational Biology: published July 10, 2023 | https://doi.org/10.1371/journal.pcbi.1010965

Mapping the semi-nested community structure of 3D chromosome contact networks

Dolores Bernenko, Sang Hoon Lee, Per Stenberg, Ludvig Lizana

PLOS Computational Biology: published July 11, 2023 | https://doi.org/10.1371/journal.pcbi.1011185

Improve the model of disease subtype heterogeneity by leveraging external summary data

Sheng Fu, Mark P. Purdue, Han Zhang, Jing Qin, Lei Song, Sonja I. Berndt, Kai Yu

PLOS Computational Biology: published July 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011236

DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks

Tong Liu, Zheng Wang

PLOS Computational Biology: published July 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011307

The interplay between age structure and cultural transmission

Anne Kandler, Laurel Fogarty, Folgert Karsdorp

PLOS Computational Biology: published July 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011297

Modality independent or modality specific? Common computations underlie confidence judgements in visual and auditory decisions

Rebecca K. West, William J. Harrison, Natasha Matthews, Jason B. Mattingley, David K. Sewell

PLOS Computational Biology: published July 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011245

A multi-scale clutch model for adhesion complex mechanics

Chiara Venturini, Pablo Sáez

PLOS Computational Biology: published July 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011250

RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure

Elena Rivas

PLOS Computational Biology: published July 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011262

Influence of the vessel wall geometry on the wall-induced migration of red blood cells

Ying Zhang, Thomas G. Fai

PLOS Computational Biology: published July 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011241

Development of Accurate Long-lead COVID-19 Forecast

Wan Yang, Jeffrey Shaman

PLOS Computational Biology: published July 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011278

Continuous action with a neurobiologically inspired computational approach reveals the dynamics of selection history

Mukesh Makwana, Fan Zhang, Dietmar Heinke, Joo-Hyun Song

PLOS Computational Biology: published July 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011283

Monte Carlo samplers for efficient network inference

Zeliha Kilic, Max Schweiger, Camille Moyer, Steve Pressé

PLOS Computational Biology: published July 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011256

LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses

Alexei J. Drummond, Kylie Chen, Fábio K. Mendes, Dong Xie

PLOS Computational Biology: published July 18, 2023 | https://doi.org/10.1371/journal.pcbi.1011226

Repeatability and timing of tropical influenza epidemics

Joseph L. Servadio, Pham Quang Thai, Marc Choisy, Maciej F. Boni

PLOS Computational Biology: published July 19, 2023 | https://doi.org/10.1371/journal.pcbi.1011317

Network feature-based phenotyping of leaf venation robustly reconstructs the latent space

Kohei Iwamasa, Koji Noshita

PLOS Computational Biology: published July 20, 2023 | https://doi.org/10.1371/journal.pcbi.1010581

Indirect reciprocity with stochastic and dual reputation updates

Yohsuke Murase, Christian Hilbe

PLOS Computational Biology: published July 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011271

Risk averse reproduction numbers improve resurgence detection

Kris V. Parag, Uri Obolski

PLOS Computational Biology: published July 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011332

Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment

Roger Vargas, Liam Abbott, Daniel Bower, Nicole Frahm, Mike Shaffer, Wen-Han Yu

PLOS Computational Biology: published July 20, 2023 | https://doi.org/10.1371/journal.pcbi.1010770

Neural activity induces strongly coupled electro-chemo-mechanical interactions and fluid flow in astrocyte networks and extracellular space—A computational study

Marte J. Sætra, Ada J. Ellingsrud, Marie E. Rognes

PLOS Computational Biology: published July 21, 2023 | https://doi.org/10.1371/journal.pcbi.1010996

Correction

Correction: Opponent learning with different representations in the cortico-basal ganglia pathways can develop obsession-compulsion cycle

The PLOS Computational Biology Staff

PLOS Computational Biology: published July 24, 2023 | https://doi.org/10.1371/journal.pcbi.1011338

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Cross-Scale Relationships in 3D Chromosomal Organization

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