March 2023

Morphologies of select neuron models from the NeuroML Database. Animated 3-D renderings depicting the morphology and electrical activity of each model in the database with more than one compartment are shared at https://neuroml-db.org, along with quantitative characterizations of the morphological properties. Birgiolas et al 2023

Image Credit: Justas Birgiolas, Vergil Haynes, Padraig Gleeson, Richard C. Gerkin, Suzanne W. Dietrich, Sharon Crook

Education Articles

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

Ryan R. Wick, Louise M. Judd, Kathryn E. Holt

PLOS Computational Biology: published March 2, 2023 | https://doi.org/10.1371/journal.pcbi.1010905

A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya

Ruth Nanjala, Festus Nyasimi, Daniel Masiga, Caleb Kipkurui Kibet

PLOS Computational Biology: published March 2, 2023 | https://doi.org/10.1371/journal.pcbi.1010904

Ten simple rules for serving as an editor

Cameron Mura, Philip E. Bourne

PLOS Computational Biology: published March 2, 2023 | https://doi.org/10.1371/journal.pcbi.1010911

Ten simple rules for designing and conducting undergraduate replication projects

David Moreau, Kristina Wiebels

PLOS Computational Biology: published March 16, 2023 | https://doi.org/10.1371/journal.pcbi.1010957

Ten simple rules for socially responsible science

Alon Zivony, Rasha Kardosh, Liadh Timmins, Niv Reggev

PLOS Computational Biology: published March 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010954

Perspective

An implementation framework to improve the transparency and reproducibility of computational models of infectious diseases

Darya Pokutnaya, Bruce Childers, Alice E. Arcury-Quandt, Harry Hochheiser, Willem G. Van Panhuis

PLOS Computational Biology: published March 16, 2023 | https://doi.org/10.1371/journal.pcbi.1010856

Review

Ten (not so) simple rules for clinical trial data-sharing

Claude Pellen, Anne Le Louarn, Gilliosa Spurrier-Bernard, Evelyne Decullier, Jean-Marie Chrétien, Eric Rosenthal, Gérard Le Goff, David Moher, John P. A. Ioannidis, Florian Naudet

PLOS Computational Biology: published March 9, 2023 | https://doi.org/10.1371/journal.pcbi.1010879

Research Articles

Modelling daily weight variation in honey bee hives

Karina Arias-Calluari, Theotime Colin, Tanya Latty, Mary Myerscough, Eduardo G. Altmann

PLOS Computational Biology: published March 1, 2023 | https://doi.org/10.1371/journal.pcbi.1010880

Inferring protein fitness landscapes from laboratory evolution experiments

Sameer D’Costa, Emily C. Hinds, Chase R. Freschlin, Hyebin Song, Philip A. Romero

PLOS Computational Biology: published March 1, 2023 | https://doi.org/10.1371/journal.pcbi.1010956

Personality variation is eroded by simple social behaviours in collective foragers

Sean A. Rands, Christos C. Ioannou

PLOS Computational Biology: published March 2, 2023 | https://doi.org/10.1371/journal.pcbi.1010908

Coding of object location by heterogeneous neural populations with spatially dependent correlations in weakly electric fish

Myriah Haggard, Maurice J. Chacron

PLOS Computational Biology: published March 3, 2023 | https://doi.org/10.1371/journal.pcbi.1010938

Spatial and temporal correlations in human cortex are inherently linked and predicted by functional hierarchy, vigilance state as well as antiepileptic drug load

Paul Manuel Müller, Christian Meisel

PLOS Computational Biology: published March 3, 2023 | https://doi.org/10.1371/journal.pcbi.1010919

NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML

Justas Birgiolas, Vergil Haynes, Padraig Gleeson, Richard C. Gerkin, Suzanne W. Dietrich, Sharon Crook

PLOS Computational Biology: published March 3, 2023 | https://doi.org/10.1371/journal.pcbi.1010941

MGAE-DC: Predicting the synergistic effects of drug combinations through multi-channel graph autoencoders

Peng Zhang, Shikui Tu

PLOS Computational Biology: published March 3, 2023 | https://doi.org/10.1371/journal.pcbi.1010951

Predicting functional effects of ion channel variants using new phenotypic machine learning methods

Christian Malte Boßelmann, Ulrike B. S. Hedrich, Holger Lerche, Nico Pfeifer

PLOS Computational Biology: published March 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010959

Physics-based tissue simulator to model multicellular systems: A study of liver regeneration and hepatocellular carcinoma recurrence

Luciana Melina Luque, Carlos Manuel Carlevaro, Camilo Julio Llamoza Torres, Enrique Lomba

PLOS Computational Biology: published March 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010920

Macroscopic resting state model predicts theta burst stimulation response: A randomized trial

Neda Kaboodvand, Behzad Iravani, Martijn P. van den Heuvel, Jonas Persson, Robert Boden

PLOS Computational Biology: published March 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010958

CustOmics: A versatile deep-learning based strategy for multi-omics integration

Hakim Benkirane, Yoann Pradat, Stefan Michiels, Paul-Henry Cournède

PLOS Computational Biology: published March 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010921

Particle-based model shows complex rearrangement of tissue mechanical properties are needed for roots to grow in hard soil

Matthias Mimault, Mariya Ptashnyk, Lionel X. Dupuy

PLOS Computational Biology: published March 7, 2023 | https://doi.org/10.1371/journal.pcbi.1010916

Detection of genes with differential expression dispersion unravels the role of autophagy in cancer progression

Christophe Le Priol, Chloé-Agathe Azencott, Xavier Gidrol

PLOS Computational Biology: published March 9, 2023 | https://doi.org/10.1371/journal.pcbi.1010342

Mechano-biological and bio-mechanical pathways in cutaneous wound healing

Marco Pensalfini, Adrian Buganza Tepole

PLOS Computational Biology: published March 9, 2023 | https://doi.org/10.1371/journal.pcbi.1010902

G4mismatch: Deep neural networks to predict G-quadruplex propensity based on G4-seq data

Mira Barshai, Barak Engel, Idan Haim, Yaron Orenstein

PLOS Computational Biology: published March 10, 2023 | https://doi.org/10.1371/journal.pcbi.1010948

OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer

Anni S. Halkola, Kaisa Joki, Tuomas Mirtti, Marko M. Mäkelä, Tero Aittokallio, Teemu D. Laajala

PLOS Computational Biology: published March 10, 2023 | https://doi.org/10.1371/journal.pcbi.1010333

First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer

Magnus J. Haughey, Aleix Bassolas, Sandro Sousa, Ann-Marie Baker, Trevor A. Graham, Vincenzo Nicosia, Weini Huang

PLOS Computational Biology: published March 13, 2023 | https://doi.org/10.1371/journal.pcbi.1010952

Towards self-describing and FAIR bulk formats for biomedical data

Michael Lukowski, Andrew Prokhorenkov, Robert L. Grossman

PLOS Computational Biology: published March 13, 2023 | https://doi.org/10.1371/journal.pcbi.1010944

Hindcasts and forecasts of suicide mortality in US: A modeling study

Sasikiran Kandula, Mark Olfson, Madelyn S. Gould, Katherine M. Keyes, Jeffrey Shaman

PLOS Computational Biology: published March 13, 2023 | https://doi.org/10.1371/journal.pcbi.1010945

Predicting the causative pathogen among children with pneumonia using a causal Bayesian network

Yue Wu, Steven Mascaro, Mejbah Bhuiyan, Parveen Fathima, Ariel O. Mace, Mark P. Nicol, Peter C. Richmond, Lea-Ann Kirkham, Michael Dymock, David A. Foley, Charlie McLeod, Meredith L. Borland, Andrew Martin, Phoebe C. M. Williams, Julie A. Marsh, Thomas L. Snelling, Christopher C. Blyth

PLOS Computational Biology: published March 13, 2023 | https://doi.org/10.1371/journal.pcbi.1010967

Inferring feature importance with uncertainties with application to large genotype data

Pål Vegard Johnsen, Inga Strümke, Mette Langaas, Andrew Thomas DeWan, Signe Riemer-Sørensen

PLOS Computational Biology: published March 14, 2023 | https://doi.org/10.1371/journal.pcbi.1010963

ProInfer: An interpretable protein inference tool leveraging on biological networks

Hui Peng, Limsoon Wong, Wilson Wen Bin Goh

PLOS Computational Biology: published March 17, 2023 | https://doi.org/10.1371/journal.pcbi.1010961

PCB: A pseudotemporal causality-based Bayesian approach to identify EMT-associated regulatory relationships of AS events and RBPs during breast cancer progression

Liangjie Sun, Yushan Qiu, Wai-Ki Ching, Pu Zhao, Quan Zou

PLOS Computational Biology: published March 17, 2023 | https://doi.org/10.1371/journal.pcbi.1010939

Large eddy simulation of droplet transport and deposition in the human respiratory tract to evaluate inhalation risk

Alicia Murga, Rahul Bale, Chung-Gang Li, Kazuhide Ito, Makoto Tsubokura

PLOS Computational Biology: published March 20, 2023 | https://doi.org/10.1371/journal.pcbi.1010972

Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments

Dohoon Lee, Bonil Koo, Jeewon Yang, Sun Kim

PLOS Computational Biology: published March 20, 2023 | https://doi.org/10.1371/journal.pcbi.1010946

adaPop: Bayesian inference of dependent population dynamics in coalescent models

Lorenzo Cappello, Jaehee Kim, Julia A. Palacios

PLOS Computational Biology: published March 20, 2023 | https://doi.org/10.1371/journal.pcbi.1010897

Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning

Bercem Dutagaci, Bingbing Duan, Chenxi Qiu, Craig D. Kaplan, Michael Feig

PLOS Computational Biology: published March 22, 2023 | https://doi.org/10.1371/journal.pcbi.1010999

A real data-driven simulation strategy to select an imputation method for mixed-type trait data

Jacqueline A. May, Zeny Feng, Sarah J. Adamowicz

PLOS Computational Biology: published March 22, 2023 | https://doi.org/10.1371/journal.pcbi.1010154

New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells

Nantia Leonidou, Alina Renz, Reihaneh Mostolizadeh, Andreas Dräger

PLOS Computational Biology: published March 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010903

Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers

Sean B. King, Mona Singh

PLOS Computational Biology: published March 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010966

A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer

Delora Baptista, Pedro G. Ferreira, Miguel Rocha

PLOS Computational Biology: published March 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010200

Mitochondrial network structure controls cell-to-cell mtDNA variability generated by cell divisions

Robert C. Glastad, Iain G. Johnston

PLOS Computational Biology: published March 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010953

In vitro–in silico correlation of three-dimensional turbulent flows in an idealized mouth-throat model

Eliram Nof, Saurabh Bhardwaj, Pantelis Koullapis, Ron Bessler, Stavros Kassinos, Josué Sznitman

PLOS Computational Biology: published March 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010537

Theta-gamma phase amplitude coupling in a hippocampal CA1 microcircuit

Adam Ponzi, Salvador Dura-Bernal, Michele Migliore

PLOS Computational Biology: published March 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010942

Topological descriptors of the parameter region of multistationarity: Deciding upon connectivity

Máté László Telek, Elisenda Feliu

PLOS Computational Biology: published March 24, 2023 | https://doi.org/10.1371/journal.pcbi.1010970

Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates

Christoffer Norn, Ingemar André

PLOS Computational Biology: published March 24, 2023 | https://doi.org/10.1371/journal.pcbi.1010262

Modeling bee movement shows how a perceptual masking effect can influence flower discovery

Ana Morán, Mathieu Lihoreau, Alfonso Pérez-Escudero, Jacques Gautrais

PLOS Computational Biology: published March 24, 2023 | https://doi.org/10.1371/journal.pcbi.1010558

Global nonlinear approach for mapping parameters of neural mass models

Dominic M. Dunstan, Mark P. Richardson, Eugenio Abela, Ozgur E. Akman, Marc Goodfellow

PLOS Computational Biology: published March 24, 2023 | https://doi.org/10.1371/journal.pcbi.1010985

A real-time feedback system stabilises the regulation of worker reproduction under various colony sizes

Simeon Adejumo, Tomonori Kikuchi, Kazuki Tsuji, Kana Maruyama-Onda, Ken Sugawara, Yoshikatsu Hayashi

PLOS Computational Biology: published March 24, 2023 | https://doi.org/10.1371/journal.pcbi.1010840

Docking cholesterol to integral membrane proteins with Rosetta

Brennica Marlow, Georg Kuenze, Jens Meiler, Julia Koehler Leman

PLOS Computational Biology: published March 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010947

The effect of non-linear signal in classification problems using gene expression

Benjamin J. Heil, Jake Crawford, Casey S. Greene

PLOS Computational Biology: published March 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010984

An associative memory Hamiltonian model for DNA and nucleosomes

Weiqi Lu, José N. Onuchic, Michele Di Pierro

PLOS Computational Biology: published March 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011013

One model fits all: Combining inference and simulation of gene regulatory networks

Elias Ventre, Ulysse Herbach, Thibault Espinasse, Gérard Benoit, Olivier Gandrillon

PLOS Computational Biology: published March 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010962

Robust deep learning object recognition models rely on low frequency information in natural images

Zhe Li, Josue Ortega Caro, Evgenia Rusak, Wieland Brendel, Matthias Bethge, Fabio Anselmi, Ankit B. Patel, Andreas S. Tolias, Xaq Pitkow

PLOS Computational Biology: published March 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010932

Quantification of spatial and phenotypic heterogeneity in an agent-based model of tumour-macrophage interactions

Joshua A. Bull, Helen M. Byrne

PLOS Computational Biology: published March 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010994

The evolution of behavioral cues and signaling in displaced communication

Arthur Bernard, Steffen Wischmann, Dario Floreano, Laurent Keller

PLOS Computational Biology: published March 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010487

A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses

William T. Harvey, Vinny Davies, Rodney S. Daniels, Lynne Whittaker, Victoria Gregory, Alan J. Hay, Dirk Husmeier, John W. McCauley, Richard Reeve

PLOS Computational Biology: published March 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010885

Modelling quantitative fungicide resistance and breakdown of resistant cultivars: Designing integrated disease management strategies for Septoria of winter wheat

Nick P. Taylor, Nik J. Cunniffe

PLOS Computational Biology: published March 28, 2023 | https://doi.org/10.1371/journal.pcbi.1010969

Validation framework for epidemiological models with application to COVID-19 models

Kimberly A. Dautel, Ephraim Agyingi, Pras Pathmanathan

PLOS Computational Biology: published March 29, 2023 | https://doi.org/10.1371/journal.pcbi.1010968

Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer

Karen E. Ross, Guolin Zhang, Cuneyt Akcora, Yu Lin, Bin Fang, John Koomen, Eric B. Haura, Mark Grimes

PLOS Computational Biology: published March 30, 2023 | https://doi.org/10.1371/journal.pcbi.1010690

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

Carlos A. Gandarilla-Pérez, Sergio Pinilla, Anne-Florence Bitbol, Martin Weigt

PLOS Computational Biology: published March 30, 2023 | https://doi.org/10.1371/journal.pcbi.1011010

Development of a scoring function for comparing simulated and experimental tumor spheroids

Julian Herold, Eric Behle, Jakob Rosenbauer, Jacopo Ferruzzi, Alexander Schug

PLOS Computational Biology: published March 30, 2023 | https://doi.org/10.1371/journal.pcbi.1010471

A new method for the joint estimation of instantaneous reproductive number and serial interval during epidemics

Chenxi Dai, Dongsheng Zhou, Bo Gao, Kaifa Wang

PLOS Computational Biology: published March 31, 2023 | https://doi.org/10.1371/journal.pcbi.1011021

BiComp-DTA: Drug-target binding affinity prediction through complementary biological-related and compression-based featurization approach

Mahmood Kalemati, Mojtaba Zamani Emani, Somayyeh Koohi

PLOS Computational Biology: published March 31, 2023 | https://doi.org/10.1371/journal.pcbi.1011036

JASPER: A fast genome polishing tool that improves accuracy of genome assemblies

Alina Guo, Steven L. Salzberg, Aleksey V. Zimin

PLOS Computational Biology: published March 31, 2023 | https://doi.org/10.1371/journal.pcbi.1011032

chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling

Maxx H. Tessmer, Stefan Stoll

PLOS Computational Biology: published March 31, 2023 | https://doi.org/10.1371/journal.pcbi.1010834

Predicting regrowth of low-grade gliomas after radiotherapy

Stéphane Plaszczynski, Basile Grammaticos, Johan Pallud, Jean-Eric Campagne, Mathilde Badoual

PLOS Computational Biology: published March 31, 2023 | https://doi.org/10.1371/journal.pcbi.1011002

Corrections

Correction: Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses

Wendi Bacon, Alexandra Holinski, Marina Pujol, Meredith Wilmott, Sarah L Morgan, on behalf of the European Molecular Biology Laboratory—European Bioinformatics Institute Training Team

PLOS Computational Biology: published March 7, 2023 | https://doi.org/10.1371/journal.pcbi.1010964

Correction: Constructing Benchmark Test Sets for Biological Sequence Analysis Using Independent Set Algorithms

Samantha Petti, Sean R Eddy

PLOS Computational Biology: published March 8, 2023 | https://doi.org/10.1371/journal.pcbi.1010971

Correction: Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection

Alasdair D. F. Clarke, Amelia R. Hunt, Anna E. Hughes

PLOS Computational Biology: published March 17, 2023 | https://doi.org/10.1371/journal.pcbi.1010997

Correction: A musculoskeletal finite element model of rat knee joint for evaluating cartilage biomechanics during gait

Gustavo A. Orozco, Kalle Karjalainen, Eng Kuan Moo, Lauri Stenroth, Petri Tanska, Jaqueline Lourdes Rios, Teemu V. Tuomainen, Mikko J. Nissi, Hanna Isaksson, Walter Herzog, Rami K. Korhonen

PLOS Computational Biology: published March 29, 2023 | https://doi.org/10.1371/journal.pcbi.1011025

Cover

Visualizations of computational models of neurons available at the NeuroML Database

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