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Current Issue of PLoSBiology


Current Issue | PLOS Computational Biology
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Table of Contents

November 2024

A key facet of both natural and artificial intelligence lies in their predictive potential. The last decade offered a mere glimpse of AI's revolutionary potential in predicting protein structures. AI's impact on predictability and understanding in biology is destined to expand towards phenomena such as intracellular protein sorting. We outline a roadmap for next-generation algorithms emphasizing the integration of evolutionary and experimental diversity in training data and model parameters inspired by evolutionary cell biology. With the prevalence of advanced machine learning increasing, our analyses exemplify how diversity can bridge AI and biology, fostering novel insights and breakthroughs. Gould et al

Image Credit: Parth K. Raval

Education

Eleven quick tips for properly handling tabular data

Marla I. Hertz, Ashley S. McNeill

Research Articles

A mechanistic model of in vitro plasma activation to evaluate therapeutic kallikrein-kinin system inhibitors

Alireza Rezvani-Sharif, Hadi Lioe, Steven K. Dower, Matthias Pelzing, Con Panousis, Dalton J. E. Harvie, Ineke L. Muir

Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes

Zahra Razaghi-Moghadam, Fayaz Soleymani Babadi, Zoran Nikoloski

A computational analysis of the oncogenic and anti-tumor immunity role of P4HA3 in human cancers

Hong Yan Huang, Fu Wei Zhang, Jie Yu, Yan Hong Xiao, Di Zhu, XiaoLin Yi, XiaoHua Lin, Ming Jin, Hai Yun Jin, Yong Sheng Huang, Shu Wei Ren

Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal

John H. Tay, Arthur Kocher, Sebastian Duchene

During haptic communication, the central nervous system compensates distinctly for delay and noise

Jonathan Eden, Ekaterina Ivanova, Etienne Burdet

Beyond IC50—A computational dynamic model of drug resistance in enzyme inhibition treatment

J. Roadnight Sheehan, Astrid S. de Wijn, Thales Souza Freire, Ran Friedman

A deep learning model for prediction of autism status using whole-exome sequencing data

Qing Wu, Eric M. Morrow, Ece D. Gamsiz Uzun

A computational algorithm for optimal design of a bioartificial organ scaffold architecture

Martina Bukač, Sunčica Čanić, Boris Muha, Yifan Wang

Molecular dynamics simulations of a multicellular model with cell-cell interactions and Hippo signaling pathway

Toshihito Umegaki, Hisashi Moriizumi, Fumiko Ogushi, Mutsuhiro Takekawa, Takashi Suzuki

Reliability of plastid and mitochondrial localisation prediction declines rapidly with the evolutionary distance to the training set increasing

Sven B. Gould, Jonas Magiera, Carolina García García, Parth K. Raval

Teaching deep networks to see shape: Lessons from a simplified visual world

Christian Jarvers, Heiko Neumann

A modular protein language modelling approach to immunogenicity prediction

Hugh O’Brien, Max Salm, Laura T. Morton, Maciej Szukszto, Felix O’Farrell, Charlotte Boulton, Laurence King, Supreet Kaur Bola, Pablo D. Becker, Andrew Craig, Morten Nielsen, Yardena Samuels, Charles Swanton, Marc R. Mansour, Sine Reker Hadrup, Sergio A. Quezada

Approximate planning in spatial search

Marta Kryven, Suhyoun Yu, Max Kleiman-Weiner, Tomer Ullman, Joshua Tenenbaum

Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations

Aylin Bircan, Nurdan Kuru, Onur Dereli, Berkay Selçuk, Ogün Adebali

Human-like dissociations between confidence and accuracy in convolutional neural networks

Medha Shekhar, Dobromir Rahnev

AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis

Michael Alexander Ramirez Sierra, Thomas R. Sokolowski

GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies

Lin Lin, Rachel L. Spreng, Kelly E. Seaton, S. Moses Dennison, Lindsay C. Dahora, Daniel J. Schuster, Sheetal Sawant, Peter B. Gilbert, Youyi Fong, Neville Kisalu, Andrew J. Pollard, Georgia D. Tomaras, Jia Li

A new look at TFPI inhibition of factor X activation

Fabian Santiago, Amandeep Kaur, Shannon Bride, Dougald Monroe, Karin Leiderman, Suzanne Sindi

Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation

Jørgen Ankill, Zhi Zhao, Xavier Tekpli, Elin H. Kure, Vessela N. Kristensen, Anthony Mathelier, Thomas Fleischer

Simplified internal models in human control of complex objects

Salah Bazzi, Stephan Stansfield, Neville Hogan, Dagmar Sternad

Human perception of self-motion and orientation during galvanic vestibular stimulation and physical motion

Aaron R. Allred, Caroline R. Austin, Lanna Klausing, Nicholas Boggess, Torin K. Clark

A dynamical systems model for the total fission rate in Drp1-dependent mitochondrial fission

Anna K. Leinheiser, Colleen C. Mitchell, Ethan Rooke, Stefan Strack, Chad E. Grueter

SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects

Baptiste Ruiz, Arnaud Belcour, Samuel Blanquart, Sylvie Buffet-Bataillon, Isabelle Le Huërou-Luron, Anne Siegel, Yann Le Cunff

Prediction of virus-host associations using protein language models and multiple instance learning

Dan Liu, Francesca Young, Kieran D. Lamb, David L. Robertson, Ke Yuan

Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers

Evandro Konzen, Richard J. Delahay, Dave J. Hodgson, Robbie A. McDonald, Ellen Brooks Pollock, Simon E. F. Spencer, Trevelyan J. McKinley

Reward Bases: A simple mechanism for adaptive acquisition of multiple reward types

Beren Millidge, Yuhang Song, Armin Lak, Mark E. Walton, Rafal Bogacz

A framework for counterfactual analysis, strategy evaluation, and control of epidemics using reproduction number estimates

Baike She, Rebecca Lee Smith, Ian Pytlarz, Shreyas Sundaram, Philip E. Paré

Upstream open reading frames may contain hundreds of novel human exons

Hyun Joo Ji, Steven L. Salzberg

Co-contraction embodies uncertainty: An optimal feedforward strategy for robust motor control

Bastien Berret, Dorian Verdel, Etienne Burdet, Frédéric Jean

Learning patterns of HIV-1 resistance to broadly neutralizing antibodies with reduced subtype bias using multi-task learning

Aime Bienfait Igiraneza, Panagiota Zacharopoulou, Robert Hinch, Chris Wymant, Lucie Abeler-Dörner, John Frater, Christophe Fraser

An off-lattice discrete model to characterise filamentous yeast colony morphology

Kai Li, J. Edward F. Green, Hayden Tronnolone, Alexander K. Y. Tam, Andrew J. Black, Jennifer M. Gardner, Joanna F. Sundstrom, Vladimir Jiranek, Benjamin J. Binder

Deep neural networks for endemic measles dynamics: Comparative analysis and integration with mechanistic models

Wyatt G. Madden, Wei Jin, Benjamin Lopman, Andreas Zufle, Benjamin Dalziel, C. Jessica E. Metcalf, Bryan T. Grenfell, Max S. Y. Lau

Competition for resources can reshape the evolutionary properties of spatial structure

Anush Devadhasan, Oren Kolodny, Oana Carja

Socially driven negative feedback regulates activity and energy use in ant colonies

Maurizio Porfiri, Nicole Abaid, Simon Garnier

scGRN-Entropy: Inferring cell differentiation trajectories using single-cell data and gene regulation network-based transfer entropy

Rui Sun, Wenjie Cao, ShengXuan Li, Jian Jiang, Yazhou Shi, Bengong Zhang

An inductive bias for slowly changing features in human reinforcement learning

Noa L. Hedrich, Eric Schulz, Sam Hall-McMaster, Nicolas W. Schuck

Mathematical modeling suggests heterogeneous replication of Mycobacterium tuberculosis in rabbits

Vitaly V. Ganusov, Afsal Kolloli, Selvakumar Subbian

Methods

Structure-aware annotation of leucine-rich repeat domains

Boyan Xu, Alois Cerbu, Christopher J. Tralie, Daven Lim, Ksenia Krasileva

EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering

Ciara Judge, Timothy Vaughan, Timothy Russell, Sam Abbott, Louis du Plessis, Tanja Stadler, Oliver Brady, Sarah Hill

Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics

Alexandria M. Jensen, Peter DeWitt, Brianne M. Bettcher, Julia Wrobel, Katerina Kechris, Debashis Ghosh

Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning

Robert van Dijk, John Arevalo, Mehrtash Babadi, Anne E. Carpenter, Shantanu Singh