Current Issue | PLOS Computational Biology

Natural images occupy a small subset of the high-dimensional manifold of possible images, and are therefore characterized by certain statistical properties. The image shown here is a synthetic "dead-leaves" image, which preserves many of the statistical structures common to natural images. Artificial neural networks were trained to recognize surfaces within these images under illumination that vary in space and time, with the result that the trained networks exhibited responses commensurate with human lightness illusions (see Corney and Lotto, e180).

Image Credit: Image by David Corney and R. Beau Lotto (http://www.lottolab.org)

Editorial

Celebrating a body of work

Jason A. Papin, Feilim Mac Gabhann, Virginia E. Pitzer

PLOS Computational Biology: published September 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012441

Education Articles

Ten simple rules for scientific code review

Ariel Rokem

PLOS Computational Biology: published September 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012375

Ten simple rules for training scientists to make better software

Kit Gallagher, Richard Creswell, Ben Lambert, Martin Robinson, Chon Lok Lei, Gary R. Mirams, David J. Gavaghan

PLOS Computational Biology: published September 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012410

Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics

Seema B. Plaisier, Danielle O. Alarid, Joelle A. Denning, Sara E. Brownell, Kenneth H. Buetow, Katelyn M. Cooper, Melissa A. Wilson

PLOS Computational Biology: published September 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012384

Ten simple rules for successfully carrying out funded research projects

Diego A. Forero, Walter H. Curioso, Wei Wang

PLOS Computational Biology: published September 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012431

Ten quick tips for ensuring machine learning model validity

Wilson Wen Bin Goh, Mohammad Neamul Kabir, Sehwan Yoo, Limsoon Wong

PLOS Computational Biology: published September 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012402

Review

Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data

Michiel Stock, Wim Van Criekinge, Dimitri Boeckaerts, Steff Taelman, Maxime Van Haeverbeke, Pieter Dewulf, Bernard De Baets

PLOS Computational Biology: published September 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012426

Research Articles

Learning to integrate parts for whole through correlated neural variability

Zhichao Zhu, Yang Qi, Wenlian Lu, Jianfeng Feng

PLOS Computational Biology: published September 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012401

Maintenance of delay-period activity in working memory task is modulated by local network structure

Dong Yu, Tianyu Li, Qianming Ding, Yong Wu, Ziying Fu, Xuan Zhan, Lijian Yang, Ya Jia

PLOS Computational Biology: published September 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012415

Selective consistency of recurrent neural networks induced by plasticity as a mechanism of unsupervised perceptual learning

Yujin Goto, Keiichi Kitajo

PLOS Computational Biology: published September 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012378

Energy landscapes of peptide-MHC binding

Laura Collesano, Marta Łuksza, Michael Lässig

PLOS Computational Biology: published September 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012380

Applying Super-Resolution and Tomography Concepts to Identify Receptive Field Subunits in the Retina

Steffen Krüppel, Mohammad H. Khani, Helene M. Schreyer, Shashwat Sridhar, Varsha Ramakrishna, Sören J. Zapp, Matthias Mietsch, Dimokratis Karamanlis, Tim Gollisch

PLOS Computational Biology: published September 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012370

Overcoming CRISPR-Cas9 off-target prediction hurdles: A novel approach with ESB rebalancing strategy and CRISPR-MCA model

Yanpeng Yang, Yanyi Zheng, Quan Zou, Jian Li, Hailin Feng

PLOS Computational Biology: published September 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012340

Finding the rhythm: Humans exploit nonlinear intrinsic dynamics of compliant systems in periodic interaction tasks

Annika Schmidt, Marion Forano, Arne Sachtler, Davide Calzolari, Bernhard M. Weber, David W. Franklin, Alin Albu-Schäffer

PLOS Computational Biology: published September 3, 2024 | https://doi.org/10.1371/journal.pcbi.1011478

Moderate confirmation bias enhances decision-making in groups of reinforcement-learning agents

Clémence Bergerot, Wolfram Barfuss, Pawel Romanczuk

PLOS Computational Biology: published September 4, 2024 | https://doi.org/10.1371/journal.pcbi.1012404

Springs vs. motors: Ideal assistance in the lower limbs during walking at different speeds

Israel Luis, Maarten Afschrift, Elena M. Gutierrez-Farewik

PLOS Computational Biology: published September 4, 2024 | https://doi.org/10.1371/journal.pcbi.1011837

HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures

Olav N. L. Aga, Morten Brun, Kazeem A. Dauda, Ramon Diaz-Uriarte, Konstantinos Giannakis, Iain G. Johnston

PLOS Computational Biology: published September 4, 2024 | https://doi.org/10.1371/journal.pcbi.1012393

pyPAGE: A framework for Addressing biases in gene-set enrichment analysis—A case study on Alzheimer’s disease

Artemy Bakulin, Noam B. Teyssier, Martin Kampmann, Matvei Khoroshkin, Hani Goodarzi

PLOS Computational Biology: published September 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012346

Unveiling inter-embryo variability in spindle length over time: Towards quantitative phenotype analysis

Yann Le Cunff, Laurent Chesneau, Sylvain Pastezeur, Xavier Pinson, Nina Soler, Danielle Fairbrass, Benjamin Mercat, Ruddi Rodriguez-Garcia, Zahraa Alayan, Ahmed Abdouni, Gary de Neidhardt, Valentin Costes, Mélodie Anjubault, Hélène Bouvrais, Christophe Héligon, Jacques Pécréaux

PLOS Computational Biology: published September 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012330

Surveillance strategies for the detection of new pathogen variants across epidemiological contexts

Kirstin I. Oliveira Roster, Stephen M. Kissler, Enoma Omoregie, Jade C. Wang, Helly Amin, Steve Di Lonardo, Scott Hughes, Yonatan H. Grad

PLOS Computational Biology: published September 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012416

Information dynamics of in silico EEG Brain Waves: Insights into oscillations and functions

Gustavo Menesse, Joaquín J. Torres

PLOS Computational Biology: published September 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012369

A Physics-Informed Neural Network approach for compartmental epidemiological models

Caterina Millevoi, Damiano Pasetto, Massimiliano Ferronato

PLOS Computational Biology: published September 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012387

MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks

Hao Duan, Qingchen Zhang, Feifei Cui, Quan Zou, Zilong Zhang

PLOS Computational Biology: published September 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012409

Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency

Eslam Abousamra, Marlin Figgins, Trevor Bedford

PLOS Computational Biology: published September 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012443

Cracking the neural code for word recognition in convolutional neural networks

Aakash Agrawal, Stanislas Dehaene

PLOS Computational Biology: published September 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012430

Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases

Joseph Shingleton, David Mustard, Steven Dyke, Hannah Williams, Emma Bennett, Thomas Finnie

PLOS Computational Biology: published September 6, 2024 | https://doi.org/10.1371/journal.pcbi.1010817

Mutant fate in spatially structured populations on graphs: Connecting models to experiments

Alia Abbara, Lisa Pagani, Celia García-Pareja, Anne-Florence Bitbol

PLOS Computational Biology: published September 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012424

A comparison of EEG encoding models using audiovisual stimuli and their unimodal counterparts

Maansi Desai, Alyssa M. Field, Liberty S. Hamilton

PLOS Computational Biology: published September 9, 2024 | https://doi.org/10.1371/journal.pcbi.1012433

Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies

Adrian J. Green, Lisa Truong, Preethi Thunga, Connor Leong, Melody Hancock, Robyn L. Tanguay, David M. Reif

PLOS Computational Biology: published September 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012423

The primacy model and the structure of olfactory space

Hamza Giaffar, Sergey Shuvaev, Dmitry Rinberg, Alexei A. Koulakov

PLOS Computational Biology: published September 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012379

Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model

Ahmadou Sylla, Christine Chevillon, Ramsès Djidjiou-Demasse, Ousmane Seydi, Carlos A. Vargas Campos, Magdalene Dogbe, Kayla M. Fast, Jennifer L. Pechal, Alex Rakestraw, Matthew E. Scott, Michael W. Sandel, Heather Jordan, Mark Eric Benbow, Jean-François Guégan

PLOS Computational Biology: published September 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012435

Antiviral capacity of the early CD8 T-cell response is predictive of natural control of SIV infection: Learning in vivo dynamics using ex vivo data

Bharadwaj Vemparala, Vincent Madelain, Caroline Passaes, Antoine Millet, Véronique Avettand-Fenoel, Ramsès Djidjou-Demasse, Nathalie Dereuddre-Bosquet, Roger Le Grand, Christine Rouzioux, Bruno Vaslin, Asier Sáez-Cirión, Jérémie Guedj, Narendra M. Dixit

PLOS Computational Biology: published September 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012434

Construct prognostic models of multiple myeloma with pathway information incorporated

Shuo Wang, ShanJin Wang, Wei Pan, YuYang Yi, Junyan Lu

PLOS Computational Biology: published September 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012444

SEMbap: Bow-free covariance search and data de-correlation

Mario Grassi, Barbara Tarantino

PLOS Computational Biology: published September 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012448

Oscillations in an artificial neural network convert competing inputs into a temporal code

Katharina Duecker, Marco Idiart, Marcel van Gerven, Ole Jensen

PLOS Computational Biology: published September 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012429

Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments

Janice Yang, Neil J. Daily, Taylor K. Pullinger, Tetsuro Wakatsuki, Eric A. Sobie

PLOS Computational Biology: published September 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011806

An exploration into CTEPH medications: Combining natural language processing, embedding learning, in vitro models, and real-world evidence for drug repurposing

Daniel Steiert, Corey Wittig, Priyanka Banerjee, Robert Preissner, Robert Szulcek

PLOS Computational Biology: published September 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012417

Comparison and benchmark of deep learning methods for non-coding RNA classification

Constance Creux, Farida Zehraoui, François Radvanyi, Fariza Tahi

PLOS Computational Biology: published September 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012446

Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803

Tobias Pfennig, Elena Kullmann, Tomáš Zavřel, Andreas Nakielski, Oliver Ebenhöh, Jan Červený, Gábor Bernát, Anna Barbara Matuszyńska

PLOS Computational Biology: published September 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012445

Calibrating dimension reduction hyperparameters in the presence of noise

Justin Lin, Julia Fukuyama

PLOS Computational Biology: published September 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012427

Noise leads to the perceived increase in evolutionary rates over short time scales

Brian C. O’Meara, Jeremy M. Beaulieu

PLOS Computational Biology: published September 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012458

Insights into muscle metabolic energetics: Modelling muscle-tendon mechanics and metabolic rates during walking across speeds

Israel Luis, Maarten Afschrift, Friedl De Groote, Elena M. Gutierrez-Farewik

PLOS Computational Biology: published September 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012411

The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes

Anibal S. Amaral, Damien P. Devos

PLOS Computational Biology: published September 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012459

Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data

Silja Tammi, Satu Koskela, Blood Service Biobank, Kati Hyvärinen, Jukka Partanen, Jarmo Ritari

PLOS Computational Biology: published September 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011718

Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections

Ke Li, Chrispin Chaguza, Julian Stamp, Yi Ting Chew, Nicholas F. G. Chen, David Ferguson, Sameer Pandya, Nick Kerantzas, Wade Schulz, Yale SARS-CoV-2 Genomic Surveillance Initiative, Anne M. Hahn, C. Brandon Ogbunugafor, Virginia E. Pitzer, Lorin Crawford, Daniel M. Weinberger, Nathan D. Grubaugh

PLOS Computational Biology: published September 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012469

Measuring and understanding information storage and transfer in a simulated human gut microbiome

Hannah Zoller, Carlos Garcia Perez, Javier Betel Geijo Fernández, Wolfgang zu Castell

PLOS Computational Biology: published September 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012359

Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex

Nafiseh Atapour, Marcello G. P. Rosa, Shi Bai, Sylwia Bednarek, Agata Kulesza, Gabriela Saworska, Sadaf Teymornejad, Katrina H. Worthy, Piotr Majka

PLOS Computational Biology: published September 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012428

Impact of phylogeny on the inference of functional sectors from protein sequence data

Nicola Dietler, Alia Abbara, Subham Choudhury, Anne-Florence Bitbol

PLOS Computational Biology: published September 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012091

A retrospective assessment of forecasting the peak of the SARS-CoV-2 Omicron BA.1 wave in England

Matt J. Keeling, Louise Dyson

PLOS Computational Biology: published September 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012452

The neural dynamics associated with computational complexity

Juan Pablo Franco, Peter Bossaerts, Carsten Murawski

PLOS Computational Biology: published September 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012447

Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter

Jolanda Malamud, Sinan Guloksuz, Ruud van Winkel, Philippe Delespaul, Marc A. F. De Hert, Catherine Derom, Evert Thiery, Nele Jacobs, Bart P. F. Rutten, Quentin J. M. Huys

PLOS Computational Biology: published September 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012457

Language models outperform cloze predictability in a cognitive model of reading

Adrielli Tina Lopes Rego, Joshua Snell, Martijn Meeter

PLOS Computational Biology: published September 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012117

A hierarchy of metabolite exchanges in metabolic models of microbial species and communities

Ylva Katarina Wedmark, Jon Olav Vik, Ove Øyås

PLOS Computational Biology: published September 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012472

Impact of occluder device configurations in in-silico left atrial hemodynamics for the analysis of device-related thrombus

Carlos Albors, Jordi Mill, Andy L. Olivares, Xavier Iriart, Hubert Cochet, Oscar Camara

PLOS Computational Biology: published September 26, 2024 | https://doi.org/10.1371/journal.pcbi.1011546

The refinement paradox and cumulative cultural evolution: Complex products of collective improvement favor conformist outcomes, blind copying, and hyper-credulity

Elena Miu, Luke Rendell, Sam Bowles, Rob Boyd, Daniel Cownden, Magnus Enquist, Kimmo Eriksson, Marcus W. Feldman, Timothy Lillicrap, Richard McElreath, Stuart Murray, James Ounsley, Kevin N. Lala

PLOS Computational Biology: published September 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012436

HELP: A computational framework for labelling and predicting human common and context-specific essential genes

Ilaria Granata, Lucia Maddalena, Mario Manzo, Mario Rosario Guarracino, Maurizio Giordano

PLOS Computational Biology: published September 27, 2024 | https://doi.org/10.1371/journal.pcbi.1012076

The role of training variability for model-based and model-free learning of an arbitrary visuomotor mapping

Carlos A. Velázquez-Vargas, Nathaniel D. Daw, Jordan A. Taylor

PLOS Computational Biology: published September 27, 2024 | https://doi.org/10.1371/journal.pcbi.1012471

Effect of aberrant fructose metabolism following SARS-CoV-2 infection on colorectal cancer patients’ poor prognosis

Jiaxin Jiang, Xiaona Meng, Yibo Wang, Ziqian Zhuang, Ting Du, Jing Yan

PLOS Computational Biology: published September 27, 2024 | https://doi.org/10.1371/journal.pcbi.1012412

Emergent ecological patterns and modelling of gut microbiomes in health and in disease

Jacopo Pasqualini, Sonia Facchin, Andrea Rinaldo, Amos Maritan, Edoardo Savarino, Samir Suweis

PLOS Computational Biology: published September 27, 2024 | https://doi.org/10.1371/journal.pcbi.1012482

Integrating dynamic models and neural networks to discover the mechanism of meteorological factors on Aedes population

Mengze Zhang, Xia Wang, Sanyi Tang

PLOS Computational Biology: published September 27, 2024 | https://doi.org/10.1371/journal.pcbi.1012499

Exploring the potential of structure-based deep learning approaches for T cell receptor design

Helder V. Ribeiro-Filho, Gabriel E. Jara, João V. S. Guerra, Melyssa Cheung, Nathaniel R. Felbinger, José G. C. Pereira, Brian G. Pierce, Paulo S. Lopes-de-Oliveira

PLOS Computational Biology: published September 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012489

A new approach to Health Benefits Package design: an application of the Thanzi La Onse model in Malawi

Margherita Molaro, Sakshi Mohan, Bingling She, Martin Chalkley, Tim Colbourn, Joseph H. Collins, Emilia Connolly, Matthew M. Graham, Eva Janoušková, Ines Li Lin, Gerald Manthalu, Emmanuel Mnjowe, Dominic Nkhoma, Pakwanja D. Twea, Andrew N. Phillips, Paul Revill, Asif U. Tamuri, Joseph Mfutso-Bengo, Tara D. Mangal, Timothy B. Hallett

PLOS Computational Biology: published September 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012462

BootCellNet, a resampling-based procedure, promotes unsupervised identification of cell populations via robust inference of gene regulatory networks

Yutaro Kumagai

PLOS Computational Biology: published September 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012480

HIPI: Spatially resolved multiplexed protein expression inferred from H&E WSIs

Ron Zeira, Leon Anavy, Zohar Yakhini, Ehud Rivlin, Daniel Freedman

PLOS Computational Biology: published September 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012501

Study of impacts of two types of cellular aging on the yeast bud morphogenesis

Kevin Tsai, Zhen Zhou, Jiadong Yang, Zhiliang Xu, Shixin Xu, Roya Zandi, Nan Hao, Weitao Chen, Mark Alber

PLOS Computational Biology: published September 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012491

Managing spatio-temporal heterogeneity of susceptibles by embedding it into an homogeneous model: A mechanistic and deep learning study

Biao Tang, Kexin Ma, Yan Liu, Xia Wang, Sanyi Tang, Yanni Xiao, Robert A. Cheke

PLOS Computational Biology: published September 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012497

Correction

Correction: Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era

Kiesha Prem, Kevin van Zandvoort, Petra Klepac, Rosalind M. Eggo, Nicholas G. Davies, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Alex R. Cook, Mark Jit

PLOS Computational Biology: published September 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012454

Software

Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting

Anis Ur Rahman, Gleb Tikhonov, Jari Oksanen, Tuomas Rossi, Otso Ovaskainen

PLOS Computational Biology: published September 3, 2024 | https://doi.org/10.1371/journal.pcbi.1011914

AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact

Monica Golumbeanu, Olivier Briët, Clara Champagne, Jeanne Lemant, Munir Winkel, Barnabas Zogo, Maximilian Gerhards, Marianne Sinka, Nakul Chitnis, Melissa Penny, Emilie Pothin, Tom Smith

PLOS Computational Biology: published September 13, 2024 | https://doi.org/10.1371/journal.pcbi.1011609

Facilitating pathway and network based analysis of RNA-Seq data with pathlinkR

Travis M. Blimkie, Andy An, Robert E. W. Hancock

PLOS Computational Biology: published September 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012422

This page is brought to you by Brian Golding (Golding@McMaster.CA) and is copied locally here to speed your access. To go to the original page (should you find something interesting or should you wish to follow links) click on Current Issue of PLoSBiology

September 2024

Cover

Synthetic "dead-leaves" image

Editorial

Education Articles

Review

Research Articles

Correction

Related Articles

Methods

Software

This page is brought to you by Brian Golding (Golding@McMaster.CA) and is copied locally here to speed your access. To go to the original page (should you find something interesting or should you wish to follow links) click on

Current Issue of PLoSBiology