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Current Issue of PLoSBiology

Current Issue | PLOS Computational Biology
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Table of Contents

July 2024

Cover

AI-powered Immune Repertoire Analysis: Enhancing Diagnostic Precision and Unveiling Disease Insights
Issue Image

Integrating AI with next-generation sequencing (NGS) of human immune repertoires has transformative potential for clinical diagnostics. By leveraging machine learning, AI improves diagnostic precision through accurate disease classification, subtype identification, and discovery of immune markers, paving the way for personalized treatment strategies.

Image Credit: Paul Schmidt-Barbo

Education Articles

Ten simple rules for building and maintaining a responsible data science workflow

Sara Stoudt, Yacine Jernite, Brandeis Marshall, Ben Marwick, Malvika Sharan, Kirstie Whitaker, Valentin Danchev

PLOS Computational Biology: published July 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012232

Nine quick tips for open meta-analyses

David Moreau, Kristina Wiebels

PLOS Computational Biology: published July 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012252

Research Articles

Model-based analysis of the acute effects of transcutaneous magnetic spinal cord stimulation on micturition after spinal cord injury in humans

Mahshid Fardadi, J. C. Leiter, Daniel C. Lu, Tetsuya Iwasaki

PLOS Computational Biology: published July 1, 2024 | https://doi.org/10.1371/journal.pcbi.1012237

Co-existence of synaptic plasticity and metastable dynamics in a spiking model of cortical circuits

Xiaoyu Yang, Giancarlo La Camera

PLOS Computational Biology: published July 1, 2024 | https://doi.org/10.1371/journal.pcbi.1012220

Compressive instabilities enable cell-induced extreme densification patterns in the fibrous extracellular matrix: Discrete model predictions

Chrysovalantou Kalaitzidou, Georgios Grekas, Andreas Zilian, Charalambos Makridakis, Phoebus Rosakis

PLOS Computational Biology: published July 1, 2024 | https://doi.org/10.1371/journal.pcbi.1012238

Detection of disease-specific signatures in B cell repertoires of lymphomas using machine learning

Paul Schmidt-Barbo, Gabriel Kalweit, Mehdi Naouar, Lisa Paschold, Edith Willscher, Christoph Schultheiß, Bruno Märkl, Stefan Dirnhofer, Alexandar Tzankov, Mascha Binder, Maria Kalweit

PLOS Computational Biology: published July 2, 2024 | https://doi.org/10.1371/journal.pcbi.1011570

A variational autoencoder trained with priors from canonical pathways increases the interpretability of transcriptome data

Bin Liu, Bodo Rosenhahn, Thomas Illig, David S. DeLuca

PLOS Computational Biology: published July 3, 2024 | https://doi.org/10.1371/journal.pcbi.1011198

Modeling the impact of neuromorphological alterations in Down syndrome on fast neural oscillations

Pau Clusella, Linus Manubens-Gil, Jordi Garcia-Ojalvo, Mara Dierssen

PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012259

Joint modeling of choices and reaction times based on Bayesian contextual behavioral control

Sarah Schwöbel, Dimitrije Marković, Michael N. Smolka, Stefan Kiebel

PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012228

Nonlinear fusion is optimal for a wide class of multisensory tasks

Marcus Ghosh, Gabriel Béna, Volker Bormuth, Dan F. M. Goodman

PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012246

scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics

Gustavo Magaña-López, Laurence Calzone, Andrei Zinovyev, Loïc Paulevé

PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011620

Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM

Jesper J. Madsen, Y. Zenmei Ohkubo

PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011421

Phenotypic memory in quorum sensing

Ghazaleh Ostovar, James Q. Boedicker

PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011696

Kernel Bayesian logistic tensor decomposition with automatic rank determination for predicting multiple types of miRNA-disease associations

Yingjun Ma, Yuanyuan Ma

PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012287

Competitive advantages of T-even phage lysis inhibition in response to secondary infection

Ulrik Hvid, Namiko Mitarai

PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012242

Synaptic reorganization of synchronized neuronal networks with synaptic weight and structural plasticity

Kanishk Chauhan, Alexander B. Neiman, Peter A. Tass

PLOS Computational Biology: published July 9, 2024 | https://doi.org/10.1371/journal.pcbi.1012261

Jointly efficient encoding and decoding in neural populations

Simone Blanco Malerba, Aurora Micheli, Michael Woodford, Rava Azeredo da Silveira

PLOS Computational Biology: published July 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012240

PARE: A framework for removal of confounding effects from any distance-based dimension reduction method

Andrew A. Chen, Kelly Clark, Blake E. Dewey, Anna DuVal, Nicole Pellegrini, Govind Nair, Youmna Jalkh, Samar Khalil, Jon Zurawski, Peter A. Calabresi, Daniel S. Reich, Rohit Bakshi, Haochang Shou, Russell T. Shinohara, Alzheimer’s Disease Neuroimaging Initiative, and North American Imaging in Multiple Sclerosis Cooperative

PLOS Computational Biology: published July 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012241

Reinforcement learning of altruistic punishment differs between cultures and across the lifespan

Ziyan Guo, Jialu Yu, Wenxin Wang, Patricia Lockwood, Zhen Wu

PLOS Computational Biology: published July 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012274

An integrative approach to protein sequence design through multiobjective optimization

Lu Hong, Tanja Kortemme

PLOS Computational Biology: published July 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011953

Role of diffusion and reaction of the constituents in spreading of histone modification marks

Vinoth Manivannan, Mandar M. Inamdar, Ranjith Padinhateeri

PLOS Computational Biology: published July 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012235

Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers

David R. Penas, Meysam Hashemi, Viktor K. Jirsa, Julio R. Banga

PLOS Computational Biology: published July 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011642

Identifying cell states in single-cell RNA-seq data at statistically maximal resolution

Pascal Grobecker, Thomas Sakoparnig, Erik van Nimwegen

PLOS Computational Biology: published July 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012224

Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission

Elias Rosenblatt, Jonathan D. Cook, Graziella V. DiRenzo, Evan H. Campbell Grant, Fernando Arce, Kim M. Pepin, F. Javiera Rudolph, Michael C. Runge, Susan Shriner, Daniel P. Walsh, Brittany A. Mosher

PLOS Computational Biology: published July 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012263

Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma

Alexa Petrucciani, Alexis Hoerter, Leigh Kotze, Nelita Du Plessis, Elsje Pienaar

PLOS Computational Biology: published July 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012266

Identifying topologically associating domains using differential kernels

Luka Maisuradze, Megan C. King, Ivan V. Surovtsev, Simon G. J. Mochrie, Mark D. Shattuck, Corey S. O’Hern

PLOS Computational Biology: published July 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012221

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference

Samuel E. Hoff, F. Emil Thomasen, Kresten Lindorff-Larsen, Massimiliano Bonomi

PLOS Computational Biology: published July 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012180

Convergence, sampling and total order estimator effects on parameter orthogonality in global sensitivity analysis

Harry Saxton, Xu Xu, Torsten Schenkel, Richard H. Clayton, Ian Halliday

PLOS Computational Biology: published July 17, 2024 | https://doi.org/10.1371/journal.pcbi.1011946

When should lockdown be implemented? Devising cost-effective strategies for managing epidemics amid vaccine uncertainty

Nathan J. Doyle, Fergus Cumming, Robin N. Thompson, Michael J. Tildesley

PLOS Computational Biology: published July 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012010

Fixation times on directed graphs

David A. Brewster, Martin A. Nowak, Josef Tkadlec

PLOS Computational Biology: published July 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012299

Emergent effects of synaptic connectivity on the dynamics of global and local slow waves in a large-scale thalamocortical network model of the human brain

Brianna Marsh, M. Gabriela Navas-Zuloaga, Burke Q. Rosen, Yury Sokolov, Jean Erik Delanois, Oscar C. Gonzalez, Giri P. Krishnan, Eric Halgren, Maxim Bazhenov

PLOS Computational Biology: published July 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012245

Simulation of Soluble and Bound VEGF-stimulated in vitro Capillary-like Network Formation on Deformed Substrate

Hsun Chiang, Chih-Ang Chung

PLOS Computational Biology: published July 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012281

Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Simon K. S. Chu, Kush Narang, Justin B. Siegel

PLOS Computational Biology: published July 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012248

Quantifying massively parallel microbial growth with spatially mediated interactions

Florian Borse, Dovydas Kičiatovas, Teemu Kuosmanen, Mabel Vidal, Guillermo Cabrera-Vives, Johannes Cairns, Jonas Warringer, Ville Mustonen

PLOS Computational Biology: published July 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011585

Spatial information allows inference of the prevalence of direct cell–to–cell viral infection

Thomas Williams, James M. McCaw, James M. Osborne

PLOS Computational Biology: published July 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012264

Generating information-dense promoter sequences with optimal string packing

Virgile Andreani, Eric J. South, Mary J. Dunlop

PLOS Computational Biology: published July 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012276

A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures

Noah B. Herrington, Yan Chak Li, David Stein, Gaurav Pandey, Avner Schlessinger

PLOS Computational Biology: published July 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012302

A low-dimensional approximation of optimal confidence

Pierre Le Denmat, Tom Verguts, Kobe Desender

PLOS Computational Biology: published July 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012273

FedGMMAT: Federated generalized linear mixed model association tests

Wentao Li, Han Chen, Xiaoqian Jiang, Arif Harmanci

PLOS Computational Biology: published July 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012142

Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile

Patrick Bryant, Frank Noé

PLOS Computational Biology: published July 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012253

Spatial inequities in access to medications for treatment of opioid use disorder highlight scarcity of methadone providers under counterfactual scenarios

Eric Tatara, Qinyun Lin, Jonathan Ozik, Marynia Kolak, Nicholson Collier, Dylan Halpern, Luc Anselin, Harel Dahari, Basmattee Boodram, John Schneider

PLOS Computational Biology: published July 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012307

A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression

Matthieu Bouguéon, Vincent Legagneux, Octave Hazard, Jérémy Bomo, Anne Siegel, Jérôme Feret, Nathalie Théret

PLOS Computational Biology: published July 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011858

Reassessing the modularity of gene co-expression networks using the Stochastic Block Model

Diogo Melo, Luisa F. Pallares, Julien F. Ayroles

PLOS Computational Biology: published July 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012300

Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment

Vivienne Leech, Fiona N. Kenny, Stefania Marcotti, Tanya J. Shaw, Brian M. Stramer, Angelika Manhart

PLOS Computational Biology: published July 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011879

Using deep learning to decipher the impact of telomerase promoter mutations on the dynamic metastatic morpholome

Andres J. Nevarez, Anusorn Mudla, Sabrina A. Diaz, Nan Hao

PLOS Computational Biology: published July 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012271

Population bursts in a modular neural network as a mechanism for synchronized activity in KNDy neurons

Wilfredo Blanco, Joel Tabak, Richard Bertram

PLOS Computational Biology: published July 31, 2024 | https://doi.org/10.1371/journal.pcbi.1011820

Forecasting of influenza activity and associated hospital admission burden and estimating the impact of COVID-19 pandemic on 2019/20 winter season in Hong Kong

Yiu-Chung Lau, Songwei Shan, Dong Wang, Dongxuan Chen, Zhanwei Du, Eric H. Y. Lau, Daihai He, Linwei Tian, Peng Wu, Benjamin J. Cowling, Sheikh Taslim Ali

PLOS Computational Biology: published July 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012311

Multitask learning of a biophysically-detailed neuron model

Jonas Verhellen, Kosio Beshkov, Sebastian Amundsen, Torbjørn V. Ness, Gaute T. Einevoll

PLOS Computational Biology: published July 31, 2024 | https://doi.org/10.1371/journal.pcbi.1011728

Probabilistic neural transfer function estimation with Bayesian system identification

Nan Wu, Isabel Valera, Fabian Sinz, Alexander Ecker, Thomas Euler, Yongrong Qiu

PLOS Computational Biology: published July 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012354

Methods

NeuroMotion: Open-source platform with neuromechanical and deep network modules to generate surface EMG signals during voluntary movement

Shihan Ma, Irene Mendez Guerra, Arnault Hubert Caillet, Jiamin Zhao, Alexander Kenneth Clarke, Kostiantyn Maksymenko, Samuel Deslauriers-Gauthier, Xinjun Sheng, Xiangyang Zhu, Dario Farina

PLOS Computational Biology: published July 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012257

Estimating error rates for single molecule protein sequencing experiments

Matthew Beauregard Smith, Kent VanderVelden, Thomas Blom, Heather D. Stout, James H. Mapes, Tucker M. Folsom, Christopher Martin, Angela M. Bardo, Edward M. Marcotte

PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012258

Modeling soybean growth: A mixed model approach

Maud Delattre, Yusuke Toda, Jessica Tressou, Hiroyoshi Iwata

PLOS Computational Biology: published July 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011258

Achieving Occam’s razor: Deep learning for optimal model reduction

Botond B. Antal, Anthony G. Chesebro, Helmut H. Strey, Lilianne R. Mujica-Parodi, Corey Weistuch

PLOS Computational Biology: published July 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012283

Detecting and quantifying heterogeneity in susceptibility using contact tracing data

Beth M. Tuschhoff, David A. Kennedy

PLOS Computational Biology: published July 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012310

Software

ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture

Xun Fu, Jack Withers, Juri A. Miyamae, Talia Y. Moore

PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012243

HPVsim: An agent-based model of HPV transmission and cervical disease

Robyn M. Stuart, Jamie A. Cohen, Cliff C. Kerr, Prashant Mathur, National Disease Modelling Consortium of India, Romesh G. Abeysuriya, Marita Zimmermann, Darcy W. Rao, Mariah C. Boudreau, Serin Lee, Luojun Yang, Daniel J. Klein

PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012181

BCI Toolbox: An open-source python package for the Bayesian causal inference model

Haocheng Zhu, Ulrik Beierholm, Ladan Shams

PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011791

NRV: An open framework for in silico evaluation of peripheral nerve electrical stimulation strategies

Thomas Couppey, Louis Regnacq, Roland Giraud, Olivier Romain, Yannick Bornat, Florian Kolbl

PLOS Computational Biology: published July 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011826

nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework

Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Y. Lee, Cole G. Jensen, David Ladd, Mark Polster, Friederike Hanssen, Simon Heumos, nf-core community, Gur Yaari, Markus C. Kowarik, Sven Nahnsen, Steven H. Kleinstein

PLOS Computational Biology: published July 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012265