June 2023

With Bayesian inference and a pangenomic reference graph framework, HaploCart overcomes reference bias in mitochondrial haplogroup assignments, outperforming current tools. Robust to lower coverage sequences, it delivers phylogenetically-aware confidence scores, unbiased towards any haplogroup. A user-friendly tool accepting consensus FASTA, FASTQ, or GAM files. Ruben et al 2023

Image Credit: Gabriel Renaud, Midjourney

Education Articles

Teaching students to R³eason, not merely to solve problem sets: The role of philosophy and visual data communication in accessible data science education

Ilinca I. Ciubotariu, Gundula Bosch

PLOS Computational Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011160

Bioschemas training profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources

Leyla Jael Castro, Patricia M. Palagi, Niall Beard, Teresa K. Attwood, Michelle D. Brazas

PLOS Computational Biology: published June 15, 2023 | https://doi.org/10.1371/journal.pcbi.1011120

Ten simple rules for the sharing of bacterial genotype—Phenotype data on antimicrobial resistance

Leonid Chindelevitch, Maarten van Dongen, Heather Graz, Antonio Pedrotta, Anita Suresh, Swapna Uplekar, Elita Jauneikaite, Nicole Wheeler

PLOS Computational Biology: published June 22, 2023 | https://doi.org/10.1371/journal.pcbi.1011129

Perspective

Ten simple rules for organizations to support research data sharing

Robin Champieux, Anthony Solomonides, Marisa Conte, Svetlana Rojevsky, Jimmy Phuong, David A. Dorr, Elizabeth Zampino, Adam Wilcox, Matthew B. Carson, Kristi Holmes

PLOS Computational Biology: published June 15, 2023 | https://doi.org/10.1371/journal.pcbi.1011136

Research Articles

Humans decompose tasks by trading off utility and computational cost

Carlos G. Correa, Mark K. Ho, Frederick Callaway, Nathaniel D. Daw, Thomas L. Griffiths

PLOS Computational Biology: published June 1, 2023 | https://doi.org/10.1371/journal.pcbi.1011087

Disproportionate impacts of COVID-19 in a large US city

Spencer J. Fox, Emily Javan, Remy Pasco, Graham C. Gibson, Briana Betke, José L. Herrera-Diestra, Spencer Woody, Kelly Pierce, Kaitlyn E. Johnson, Maureen Johnson-León, Michael Lachmann, Lauren Ancel Meyers

PLOS Computational Biology: published June 1, 2023 | https://doi.org/10.1371/journal.pcbi.1011149

Modelling the spread and mitigation of an emerging vector-borne pathogen: Citrus greening in the U.S.

Viet-Anh Nguyen, David W. Bartels, Christopher A. Gilligan

PLOS Computational Biology: published June 2, 2023 | https://doi.org/10.1371/journal.pcbi.1010156

Patient groups in Rheumatoid arthritis identified by deep learning respond differently to biologic or targeted synthetic DMARDs

Maria Kalweit, Andrea M. Burden, Joschka Boedecker, Thomas Hügle, Theresa Burkard

PLOS Computational Biology: published June 2, 2023 | https://doi.org/10.1371/journal.pcbi.1011073

HAT: Hypergraph analysis toolbox

Joshua Pickard, Can Chen, Rahmy Salman, Cooper Stansbury, Sion Kim, Amit Surana, Anthony Bloch, Indika Rajapakse

PLOS Computational Biology: published June 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011190

Estimating fine age structure and time trends in human contact patterns from coarse contact data: The Bayesian rate consistency model

Shozen Dan, Yu Chen, Yining Chen, Melodie Monod, Veronika K. Jaeger, Samir Bhatt, André Karch, Oliver Ratmann, on behalf of the Machine Learning & Global Health network

PLOS Computational Biology: published June 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011191

A mutation-level covariate model for mutational signatures

Itay Kahane, Mark D. M. Leiserson, Roded Sharan

PLOS Computational Biology: published June 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011195

Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth

Hugo Dourado, Wolfram Liebermeister, Oliver Ebenhöh, Martin J. Lercher

PLOS Computational Biology: published June 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011156

Identifying properties of pattern completion neurons in a computational model of the visual cortex

Casey M. Baker, Yiyang Gong

PLOS Computational Biology: published June 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011167

Quantifying ecosystem states and state transitions of the Upper Mississippi River System using topological data analysis

Danelle Marie Larson, Wako Bungula, Casey McKean, Alaina Stockdill, Amber Lee, Frederick Forrest Miller, Killian Davis

PLOS Computational Biology: published June 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011147

Hebbian learning with elasticity explains how the spontaneous motor tempo affects music performance synchronization

Iran R. Roman, Adrian S. Roman, Ji Chul Kim, Edward W. Large

PLOS Computational Biology: published June 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011154

`HaploCart`: Human mtDNA haplogroup classification using a pangenomic reference graph

Joshua Daniel Rubin, Nicola Alexandra Vogel, Shyam Gopalakrishnan, Peter Wad Sackett, Gabriel Renaud

PLOS Computational Biology: published June 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011148

Computational simulations of tumor growth and treatment response: Benefits of high-frequency, low-dose drug regimens and concurrent vascular normalization

Mohammad R. Nikmaneshi, Rakesh K. Jain, Lance L. Munn

PLOS Computational Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011131

Environmental dynamics shape perceptual decision bias

Julie A. Charlton, Wiktor F. Młynarski, Yoon H. Bai, Ann M. Hermundstad, Robbe L. T. Goris

PLOS Computational Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011104

Latent Dirichlet Allocation modeling of environmental microbiomes

Anastasiia Kim, Sanna Sevanto, Eric R. Moore, Nicholas Lubbers

PLOS Computational Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011075

Mslar: Microbial synthetic lethal and rescue database

Sen-Bin Zhu, Qian-Hu Jiang, Zhi-Guo Chen, Xiang Zhou, Yan-ting Jin, Zixin Deng, Feng-Biao Guo

PLOS Computational Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011218

A dynamic calcium-force relationship model for sag behavior in fast skeletal muscle

Hojeong Kim, Charles J. Heckman

PLOS Computational Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011178

coiaf: Directly estimating complexity of infection with allele frequencies

Aris Paschalidis, Oliver J. Watson, Ozkan Aydemir, Robert Verity, Jeffrey A. Bailey

PLOS Computational Biology: published June 9, 2023 | https://doi.org/10.1371/journal.pcbi.1010247

Mechanisms of human dynamic object recognition revealed by sequential deep neural networks

Lynn K. A. Sörensen, Sander M. Bohté, Dorina de Jong, Heleen A. Slagter, H. Steven Scholte

PLOS Computational Biology: published June 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011169

Optimal density of bacterial cells

Tin Yau Pang, Martin J. Lercher

PLOS Computational Biology: published June 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011177

Spatial dynamics of malaria transmission

Sean L. Wu, John M. Henry, Daniel T. Citron, Doreen Mbabazi Ssebuliba, Juliet Nakakawa Nsumba, Héctor M. Sánchez C., Oliver J. Brady, Carlos A. Guerra, Guillermo A. García, Austin R. Carter, Heather M. Ferguson, Bakare Emmanuel Afolabi, Simon I. Hay, Robert C. Reiner Jr., Samson Kiware, David L. Smith

PLOS Computational Biology: published June 12, 2023 | https://doi.org/10.1371/journal.pcbi.1010684

An information theoretic method to resolve millisecond-scale spike timing precision in a comprehensive motor program

Joy Putney, Tobias Niebur, Leo Wood, Rachel Conn, Simon Sponberg

PLOS Computational Biology: published June 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011170

Recall DNA methylation levels at low coverage sites using a CNN model in WGBS

Ximei Luo, Yansu Wang, Quan Zou, Lei Xu

PLOS Computational Biology: published June 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011205

Stochastic simulations of self-organized elastogenesis in the developing lung

Xiru Fan, Cristian Valenzuela, Weijing Zhao, Zi Chen, Dong Wang, Steven J. Mentzer

PLOS Computational Biology: published June 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011219

A model of colour appearance based on efficient coding of natural images

Jolyon Troscianko, Daniel Osorio

PLOS Computational Biology: published June 15, 2023 | https://doi.org/10.1371/journal.pcbi.1011117

Optimizing tuberculosis treatment efficacy: Comparing the standard regimen with Moxifloxacin-containing regimens

Maral Budak, Joseph M. Cicchese, Pauline Maiello, H. Jacob Borish, Alexander G. White, Harris B. Chishti, Jaime Tomko, L. James Frye, Daniel Fillmore, Kara Kracinovsky, Jennifer Sakal, Charles A. Scanga, Philana Ling Lin, Véronique Dartois, Jennifer J. Linderman, JoAnne L. Flynn, Denise E. Kirschner

PLOS Computational Biology: published June 15, 2023 | https://doi.org/10.1371/journal.pcbi.1010823

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

Reo Sato, Kanji Shimomura, Kenji Morita

PLOS Computational Biology: published June 15, 2023 | https://doi.org/10.1371/journal.pcbi.1011206

MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets

Matthys G. Potgieter, Andrew J. M. Nel, Suereta Fortuin, Shaun Garnett, Jerome M. Wendoh, David L. Tabb, Nicola J. Mulder, Jonathan M. Blackburn

PLOS Computational Biology: published June 16, 2023 | https://doi.org/10.1371/journal.pcbi.1011163

Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses

Christopher J. Skalnik, Sean Y. Cheah, Mica Y. Yang, Mattheus B. Wolff, Ryan K. Spangler, Lee Talman, Jerry H. Morrison, Shayn M. Peirce, Eran Agmon, Markus W. Covert

PLOS Computational Biology: published June 16, 2023 | https://doi.org/10.1371/journal.pcbi.1011232

Distinguishing between different percolation regimes in noisy dynamic networks with an application to epileptic seizures

Xiaojing Zhu, Heather Shappell, Mark A. Kramer, Catherine J. Chu, Eric D. Kolaczyk

PLOS Computational Biology: published June 16, 2023 | https://doi.org/10.1371/journal.pcbi.1011188

BioSeq-Diabolo: Biological sequence similarity analysis using Diabolo

Hongliang Li, Bin Liu

PLOS Computational Biology: published June 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011214

Modeling the sequence dependence of differential antibody binding in the immune response to infectious disease

Robayet Chowdhury, Alexander T. Taguchi, Laimonas Kelbauskas, Phillip Stafford, Chris Diehnelt, Zhan-Gong Zhao, Phillip C. Williamson, Valerie Green, Neal W. Woodbury

PLOS Computational Biology: published June 20, 2023 | https://doi.org/10.1371/journal.pcbi.1010773

iPiDA-SWGCN: Identification of piRNA-disease associations based on Supplementarily Weighted Graph Convolutional Network

Jialu Hou, Hang Wei, Bin Liu

PLOS Computational Biology: published June 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011242

Grouping promotes both partnership and rivalry with long memory in direct reciprocity

Yohsuke Murase, Seung Ki Baek

PLOS Computational Biology: published June 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011228

Impact of variability in cell cycle periodicity on cell population dynamics

Chance M. Nowak, Tyler Quarton, Leonidas Bleris

PLOS Computational Biology: published June 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011080

Knowledge graph embedding for profiling the interaction between transcription factors and their target genes

Yang-Han Wu, Yu-An Huang, Jian-Qiang Li, Zhu-Hong You, Peng-Wei Hu, Lun Hu, Victor C. M. Leung, Zhi-Hua Du

PLOS Computational Biology: published June 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011207

Gain modulation and odor concentration invariance in early olfactory networks

Emiliano Marachlian, Ramón Huerta, Fernando F. Locatelli

PLOS Computational Biology: published June 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011176

Learning from the past: A short term forecast method for the COVID-19 incidence curve

Jean-David Morel, Jean-Michel Morel, Luis Alvarez

PLOS Computational Biology: published June 21, 2023 | https://doi.org/10.1371/journal.pcbi.1010790

The biomechanics of chewing and suckling in the infant: A potential mechanism for physiologic metopic suture closure

Pranav N. Haravu, Miguel Gonzalez, Shelby L. Nathan, Callum F. Ross, Olga Panagiotopoulou, Russell R. Reid

PLOS Computational Biology: published June 22, 2023 | https://doi.org/10.1371/journal.pcbi.1011227

Community detection in empirical kinase networks identifies new potential members of signalling pathways

Celia De Los Angeles Colomina Basanta, Marya Bazzi, Maruan Hijazi, Conrad Bessant, Pedro R. Cutillas

PLOS Computational Biology: published June 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010459

Analysis of high-dimensional metabolomics data with complex temporal dynamics using RM-ASCA+

Balázs Erdős, Johan A. Westerhuis, Michiel E. Adriaens, Shauna D. O’Donovan, Ren Xie, Cécile M. Singh-Povel, Age K. Smilde, Ilja C. W. Arts

PLOS Computational Biology: published June 23, 2023 | https://doi.org/10.1371/journal.pcbi.1011221

Deep learning approaches to landmark detection in tsetse wing images

Dylan S. Geldenhuys, Shane Josias, Willie Brink, Mulanga Makhubele, Cang Hui, Pietro Landi, Jeremy Bingham, John Hargrove, Marijn C. Hazelbag

PLOS Computational Biology: published June 26, 2023 | https://doi.org/10.1371/journal.pcbi.1011194

Cell to whole organ global sensitivity analysis on a four-chamber heart electromechanics model using Gaussian processes emulators

Marina Strocchi, Stefano Longobardi, Christoph M. Augustin, Matthias A. F. Gsell, Argyrios Petras, Christopher A. Rinaldi, Edward J. Vigmond, Gernot Plank, Chris J. Oates, Richard D. Wilkinson, Steven A. Niederer

PLOS Computational Biology: published June 26, 2023 | https://doi.org/10.1371/journal.pcbi.1011257

Individualized network analysis reveals a link between the gut microbiome, diet intervention and Gestational Diabetes Mellitus

Yimeng Liu, Guy Amit, Xiaolei Zhao, Na Wu, Daqing Li, Amir Bashan

PLOS Computational Biology: published June 29, 2023 | https://doi.org/10.1371/journal.pcbi.1011193

Corrections

Correction: Neural adaptation and fractional dynamics as a window to underlying neural excitability

Brian Nils Lundstrom, Thomas J. Richner

PLOS Computational Biology: published June 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011220

Correction: The contribution of the basal ganglia and cerebellum to motor learning: A neuro-computational approach

Javier Baladron, Julien Vitay, Torsten Fietzek, Fred H. Hamker

PLOS Computational Biology: published June 22, 2023 | https://doi.org/10.1371/journal.pcbi.1011243

Cover

HaploCart: Human mtDNA HaploGroup Classification using a Pangenomic Reference Graph

Education Articles

Perspective

Research Articles

Related Articles

Corrections

Related Articles

Related Articles