November 2023

Ctenophores (comb jellies) are the largest organisms which locomote using cilia, with body lengths on the order of centimeters. Flat, paddle-like bundles of millimeter-long cilia (ctenes) are arranged in rows and beat sequentially in metachronal waves to create the fluid flows that enable swimming and feeding. Using behavioral experiments and mathematical modeling, we show that the unique distribution of the ctenes and independent frequency control between paired rows allow ctenophores to reorient in almost any direction within a small space (omnidirectional swimming). This image shows a still frame from a high speed video of a freely swimming adult lobate ctenophore (Bolinopsis vitrea), with metachronal waves clearly present on the ctene rows. Herrera-Amaya, Byron 2023.

Image Credit: 2018 by M.L. Byron

Education

Ten simple rules for students navigating summer research experiences for undergraduates (REU) programs: From application to program completion

Maria Manzanares, Courtney Peña, Kayla C. Kobak, Miranda B. Stratton

PLOS Computational Biology: published November 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011573

Research Articles

Interaction between decision-making and motor learning when selecting reach targets in the presence of bias and noise

Tianyao Zhu, Jason P. Gallivan, Daniel M. Wolpert, J. Randall Flanagan

PLOS Computational Biology: published November 2, 2023 | https://doi.org/10.1371/journal.pcbi.1011596

A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing

Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto D’Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna

PLOS Computational Biology: published November 2, 2023 | https://doi.org/10.1371/journal.pcbi.1011557

Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data

Javier Kipen, Joakim Jaldén

PLOS Computational Biology: published November 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011345

Rhythmic modulation of prediction errors: A top-down gating role for the beta-range in speech processing

Sevada Hovsepyan, Itsaso Olasagasti, Anne-Lise Giraud

PLOS Computational Biology: published November 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011595

Quantitative mechanistic model reveals key determinants of placental IgG transfer and informs prenatal immunization strategies

Remziye E. Wessel, Sepideh Dolatshahi

PLOS Computational Biology: published November 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011109

Inferring causal connectivity from pairwise recordings and optogenetics

Mikkel Elle Lepperød, Tristan Stöber, Torkel Hafting, Marianne Fyhn, Konrad Paul Kording

PLOS Computational Biology: published November 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011574

Modeling cell populations metabolism and competition under maximum power constraints

Luigi Conte, Francesco Gonella, Andrea Giansanti, Axel Kleidon, Alessandra Romano

PLOS Computational Biology: published November 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011607

A data-driven semi-parametric model of SARS-CoV-2 transmission in the United States

John M. Drake, Andreas Handel, Éric Marty, Eamon B. O’Dea, Tierney O’Sullivan, Giovanni Righi, Andrew T. Tredennick

PLOS Computational Biology: published November 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011610

MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images

Yuyang Huang, Gufeng Yu, Yang Yang

PLOS Computational Biology: published November 8, 2023 | https://doi.org/10.1371/journal.pcbi.1011623

Using normative modeling and machine learning for detecting mild traumatic brain injury from magnetoencephalography data

Veera Itälinna, Hanna Kaltiainen, Nina Forss, Mia Liljeström, Lauri Parkkonen

PLOS Computational Biology: published November 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011613

Geometric and topological characterization of the cytoarchitecture of islets of Langerhans

Manu Aggarwal, Deborah A. Striegel, Manami Hara, Vipul Periwal

PLOS Computational Biology: published November 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011617

A zero-agnostic model for copy number evolution in cancer

Henri Schmidt, Palash Sashittal, Benjamin J. Raphael

PLOS Computational Biology: published November 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011590

Learning efficient representations of environmental priors in working memory

Tahra L. Eissa, Zachary P. Kilpatrick

PLOS Computational Biology: published November 9, 2023 | https://doi.org/10.1371/journal.pcbi.1011622

The limitations of phenotype prediction in metabolism

Pablo Yubero, Alvar A. Lavin, Juan F. Poyatos

PLOS Computational Biology: published November 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011631

Attention-based deep clustering method for scRNA-seq cell type identification

Shenghao Li, Hui Guo, Simai Zhang, Yizhou Li, Menglong Li

PLOS Computational Biology: published November 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011641

Architecture of the brain’s visual system enhances network stability and performance through layers, delays, and feedback

Osvaldo Matias Velarde, Hernán A. Makse, Lucas C. Parra

PLOS Computational Biology: published November 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011078

BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale

Tyler W. H. Backman, Christina Schenk, Tijana Radivojevic, David Ando, Jahnavi Singh, Jeffrey J. Czajka, Zak Costello, Jay D. Keasling, Yinjie Tang, Elena Akhmatskaya, Hector Garcia Martin

PLOS Computational Biology: published November 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011111

A general hypergraph learning algorithm for drug multi-task predictions in micro-to-macro biomedical networks

Shuting Jin, Yue Hong, Li Zeng, Yinghui Jiang, Yuan Lin, Leyi Wei, Zhuohang Yu, Xiangxiang Zeng, Xiangrong Liu

PLOS Computational Biology: published November 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011597

Folding kinetics of an entangled protein

Leonardo Salicari, Marco Baiesi, Enzo Orlandini, Antonio Trovato

PLOS Computational Biology: published November 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011107

Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy

Erik Hallström, Vinodh Kandavalli, Petter Ranefall, Johan Elf, Carolina Wählby

PLOS Computational Biology: published November 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011181

Repetitive transcranial magnetic stimulation (rTMS) triggers dose-dependent homeostatic rewiring in recurrent neuronal networks

Swathi Anil, Han Lu, Stefan Rotter, Andreas Vlachos

PLOS Computational Biology: published November 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011027

External mechanical loading overrules cell-cell mechanical communication in sprouting angiogenesis during early bone regeneration

Chiara Dazzi, Julia Mehl, Mounir Benamar, Holger Gerhardt, Petra Knaus, Georg N. Duda, Sara Checa

PLOS Computational Biology: published November 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011647

Understanding heterogeneous mechanisms of heart failure with preserved ejection fraction through cardiorenal mathematical modeling

Sanchita Basu, Hongtao Yu, Jonathan R. Murrow, K. Melissa Hallow

PLOS Computational Biology: published November 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011598

Bayesian spatial modelling of localised SARS-CoV-2 transmission through mobility networks across England

Thomas Ward, Mitzi Morris, Andrew Gelman, Bob Carpenter, William Ferguson, Christopher Overton, Martyn Fyles

PLOS Computational Biology: published November 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011580

FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi

Ananthan Nambiar, Veronika Dubinkina, Simon Liu, Sergei Maslov

PLOS Computational Biology: published November 16, 2023 | https://doi.org/10.1371/journal.pcbi.1011563

Tuning social interactions’ strength drives collective response to light intensity in schooling fish

Tingting Xue, Xu Li, GuoZheng Lin, Ramón Escobedo, Zhangang Han, Xiaosong Chen, Clément Sire, Guy Theraulaz

PLOS Computational Biology: published November 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011636

Information-theoretic analyses of neural data to minimize the effect of researchers’ assumptions in predictive coding studies

Patricia Wollstadt, Daniel L. Rathbun, W. Martin Usrey, André Moraes Bastos, Michael Lindner, Viola Priesemann, Michael Wibral

PLOS Computational Biology: published November 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011567

Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment

Cyril Malbranke, William Rostain, Florence Depardieu, Simona Cocco, Rémi Monasson, David Bikard

PLOS Computational Biology: published November 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011621

AimSeg: A machine-learning-aided tool for axon, inner tongue and myelin segmentation

Pau Carrillo-Barberà, Ana Maria Rondelli, Jose Manuel Morante-Redolat, Bertrand Vernay, Anna Williams, Peter Bankhead

PLOS Computational Biology: published November 17, 2023 | https://doi.org/10.1371/journal.pcbi.1010845

The mechanism of MinD stability modulation by MinE in Min protein dynamics

William C. Carlquist, Eric N. Cytrynbaum

PLOS Computational Biology: published November 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011615

Omnidirectional propulsion in a metachronal swimmer

Adrian Herrera-Amaya, Margaret L. Byron

PLOS Computational Biology: published November 17, 2023 | https://doi.org/10.1371/journal.pcbi.1010891

Imaging with spatio-temporal modelling to characterize the dynamics of plant-pathogen lesions

Melen Leclerc, Stéphane Jumel, Frédéric M. Hamelin, Rémi Treilhaud, Nicolas Parisey, Youcef Mammeri

PLOS Computational Biology: published November 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011627

Exploring strategy differences between humans and monkeys with recurrent neural networks

Ben Tsuda, Barry J. Richmond, Terrence J. Sejnowski

PLOS Computational Biology: published November 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011618

Addressing erroneous scale assumptions in microbe and gene set enrichment analysis

Kyle C. McGovern, Michelle Pistner Nixon, Justin D. Silverman

PLOS Computational Biology: published November 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011659

Overcoming chemotherapy resistance in low-grade gliomas: A computational approach

Thibault Delobel, Luis E. Ayala-Hernández, Jesús J. Bosque, Julián Pérez-Beteta, Salvador Chulián, Manuel García-Ferrer, Pilar Piñero, Philippe Schucht, Michael Murek, Víctor M. Pérez-García

PLOS Computational Biology: published November 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011208

Neural network models for sequence-based TCR and HLA association prediction

Si Liu, Philip Bradley, Wei Sun

PLOS Computational Biology: published November 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011664

Bayesian accounts of perceptual decisions in the nonclinical continuum of psychosis: Greater imprecision in both top-down and bottom-up processes

Isabella Goodwin, Joshua Kugel, Robert Hester, Marta I. Garrido

PLOS Computational Biology: published November 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011670

IDP-LM: Prediction of protein intrinsic disorder and disorder functions based on language models

Yihe Pang, Bin Liu

PLOS Computational Biology: published November 22, 2023 | https://doi.org/10.1371/journal.pcbi.1011657

Network analysis of patterns and relevance of enteric pathogen co-infections among infants in a diarrhea-endemic setting

E. Ross Colgate, Connor Klopfer, Dorothy M. Dickson, Benjamin Lee, Matthew J. Wargo, Ashraful Alam, Beth D. Kirkpatrick, Laurent Hébert-Dufresne

PLOS Computational Biology: published November 22, 2023 | https://doi.org/10.1371/journal.pcbi.1011624

A multiscale model of the role of microenvironmental factors in cell segregation and heterogeneity in breast cancer development

J. Roberto Romero-Arias, Carlos A. González-Castro, Guillermo Ramírez-Santiago

PLOS Computational Biology: published November 22, 2023 | https://doi.org/10.1371/journal.pcbi.1011673

Biased placement of Mitochondria fission facilitates asymmetric inheritance of protein aggregates during yeast cell division

Gordon Sun, Christine Hwang, Tony Jung, Jian Liu, Rong Li

PLOS Computational Biology: published November 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011588

Adaptive oscillators support Bayesian prediction in temporal processing

Keith B. Doelling, Luc H. Arnal, M. Florencia Assaneo

PLOS Computational Biology: published November 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011669

A simulation-based method to inform serosurvey design for estimating the force of infection using existing blood samples

Anna Vicco, Clare P. McCormack, Belen Pedrique, John H. Amuasi, Anthony Afum-Adjei Awuah, Christian Obirikorang, Nicole S. Struck, Eva Lorenz, Jürgen May, Isabela Ribeiro, Gathsaurie Neelika Malavige, Christl A. Donnelly, Ilaria Dorigatti

PLOS Computational Biology: published November 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011666

The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement

Arron Bale, Robert Rambo, Christopher Prior

PLOS Computational Biology: published November 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011248

Assessing the importance of demographic risk factors across two waves of SARS-CoV-2 using fine-scale case data

Anthony J. Wood, Aeron R. Sanchez, Paul R. Bessell, Rebecca Wightman, Rowland R. Kao

PLOS Computational Biology: published November 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011611

How effective were Australian Quarantine Stations in mitigating transmission aboard ships during the influenza pandemic of 1918-19?

Punya Alahakoon, Peter G. Taylor, James M. McCaw

PLOS Computational Biology: published November 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011656

On convolutional neural networks for selection inference: Revealing the effect of preprocessing on model learning and the capacity to discover novel patterns

Ryan M. Cecil, Lauren A. Sugden

PLOS Computational Biology: published November 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010979

A Bayesian inference method to estimate transmission trees with multiple introductions; applied to SARS-CoV-2 in Dutch mink farms

Bastiaan R. Van der Roest, Martin C. J. Bootsma, Egil A. J. Fischer, Don Klinkenberg, Mirjam E. E. Kretzschmar

PLOS Computational Biology: published November 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010928

GENERALIST: A latent space based generative model for protein sequence families

Hoda Akl, Brooke Emison, Xiaochuan Zhao, Arup Mondal, Alberto Perez, Purushottam D. Dixit

PLOS Computational Biology: published November 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011655

Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany

Elisabeth K. Brockhaus, Daniel Wolffram, Tanja Stadler, Michael Osthege, Tanmay Mitra, Jonas M. Littek, Ekaterina Krymova, Anna J. Klesen, Jana S. Huisman, Stefan Heyder, Laura M. Helleckes, Matthias an der Heiden, Sebastian Funk, Sam Abbott, Johannes Bracher

PLOS Computational Biology: published November 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011653

The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples

Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

PLOS Computational Biology: published November 29, 2023 | https://doi.org/10.1371/journal.pcbi.1011648

Predicting lncRNA-disease associations based on heterogeneous graph convolutional generative adversarial network

Zhonghao Lu, Hua Zhong, Lin Tang, Jing Luo, Wei Zhou, Lin Liu

PLOS Computational Biology: published November 29, 2023 | https://doi.org/10.1371/journal.pcbi.1011634

Contributions of cell behavior to geometric order in embryonic cartilage

Sonja Mathias, Igor Adameyko, Andreas Hellander, Jochen Kursawe

PLOS Computational Biology: published November 29, 2023 | https://doi.org/10.1371/journal.pcbi.1011658

Fluctuations in auxin levels depend upon synchronicity of cell divisions in a one-dimensional model of auxin transport

Simon Bellows, George Janes, Daniele Avitabile, John R. King, Anthony Bishopp, Etienne Farcot

PLOS Computational Biology: published November 30, 2023 | https://doi.org/10.1371/journal.pcbi.1011646

Metamodelling of a two-population spiking neural network

Jan-Eirik W. Skaar, Nicolai Haug, Alexander J. Stasik, Gaute T. Einevoll, Kristin Tøndel

PLOS Computational Biology: published November 30, 2023 | https://doi.org/10.1371/journal.pcbi.1011625

Modeling the diverse effects of divisive normalization on noise correlations

Oren Weiss, Hayley A. Bounds, Hillel Adesnik, Ruben Coen-Cagli

PLOS Computational Biology: published November 30, 2023 | https://doi.org/10.1371/journal.pcbi.1011667

Correction

Correction: AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK

Derek J. Essegian, Valery Chavez, Rabia Khurshid, Jaime R. Merchan, Stephan C. Schürer

PLOS Computational Biology: published November 22, 2023 | https://doi.org/10.1371/journal.pcbi.1011672

Formal Comment

Only a topological method can identify all possible network structures capable of Robust Perfect Adaptation

Robyn P. Araujo, Lance A. Liotta

PLOS Computational Biology: published November 22, 2023 | https://doi.org/10.1371/journal.pcbi.1011638

Methods

Inferring microbial interactions with their environment from genomic and metagenomic data

James D. Brunner, Laverne A. Gallegos-Graves, Marie E. Kroeger

PLOS Computational Biology: published November 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011661

Gene communities in co-expression networks across different tissues

Madison Russell, Alber Aqil, Marie Saitou, Omer Gokcumen, Naoki Masuda

PLOS Computational Biology: published November 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011616

Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation

Sarvesh Nikumbh, Boris Lenhard

PLOS Computational Biology: published November 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011491

Software

CGG toolkit: Software components for computational genomics

Dimitrios Vasileiou, Christos Karapiperis, Ismini Baltsavia, Anastasia Chasapi, Dag Ahrén, Paul J. Janssen, Ioannis Iliopoulos, Vasilis J. Promponas, Anton J. Enright, Christos A. Ouzounis

PLOS Computational Biology: published November 7, 2023 | https://doi.org/10.1371/journal.pcbi.1011498

Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay

Christopher R. Keefe, Matthew R. Dillon, Elizabeth Gehret, Chloe Herman, Mary Jewell, Colin V. Wood, Evan Bolyen, J. Gregory Caporaso

PLOS Computational Biology: published November 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011676

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