Current Issue | PLOS Computational Biology

Ecosystems consist of diverse mixtures of cooperating and competing species, which cause these systems to take a long time to reach stable equilibrium states. Here, we borrow tools from computational complexity theory to frame complex ecosystems as optimization problems, and we derive scaling laws for the time that it takes ecosystems to equilibrate. This image shows transient chaos in a model ecosystem, in which the equilibration time strongly varies as the initial species densities change. Gilpin et al. 2025

Image Credit: William Gilpin

Education Articles

Ten quick tips to perform meaningful and reproducible molecular docking calculations

Elvis A. F. Martis, Stéphane Téletchéa

PLOS Computational Biology: published May 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013030

Ten simple rules for queer data collection and analysis by STEM researchers

Dori M. Grijseels, M. Banqueri, Keerthana Iyer, Lee Hanlin, Melanie Ortiz Alvarez de la Campa, David Pagliaccio, Bittu K. Rajaraman, Eitan Schechtman, On behalf of ALBA Network Gender & Sexual Diversity Working Group

PLOS Computational Biology: published May 28, 2025 | https://doi.org/10.1371/journal.pcbi.1013091

Perspective

Dual-use capabilities of concern of biological AI models

Jaspreet Pannu, Doni Bloomfield, Robert MacKnight, Moritz S. Hanke, Alex Zhu, Gabe Gomes, Anita Cicero, Thomas V. Inglesby

PLOS Computational Biology: published May 8, 2025 | https://doi.org/10.1371/journal.pcbi.1012975

Review

Vertex models capturing subcellular scales in epithelial tissues

Zoë Lange, Franziska Matthäus, Mingfeng Qiu

PLOS Computational Biology: published May 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012993

Research Articles

The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut

Anastasia Galperina, Gabriele Andrea Lugli, Christian Milani, Willem M. De Vos, Marco Ventura, Anne Salonen, Bonnie Hurwitz, Alise Jany Ponsero

PLOS Computational Biology: published May 2, 2025 | https://doi.org/10.1371/journal.pcbi.1012268

A kinetic model for USP14 regulated substrate degradation in 26S proteasome

Di Wu, Qi Ouyang, Hongli Wang, Youdong Mao

PLOS Computational Biology: published May 2, 2025 | https://doi.org/10.1371/journal.pcbi.1012761

Structural and mechanistic diversity in p53-mediated regulation of organismal longevity across taxonomical orders

Romani Osbourne, Kelly M. Thayer

PLOS Computational Biology: published May 2, 2025 | https://doi.org/10.1371/journal.pcbi.1012382

Filter-based models of suppression in retinal ganglion cells: Comparison and generalization across species and stimuli

Neda Shahidi, Fernando Rozenblit, Mohammad H. Khani, Helene M. Schreyer, Matthias Mietsch, Dario A. Protti, Tim Gollisch

PLOS Computational Biology: published May 2, 2025 | https://doi.org/10.1371/journal.pcbi.1013031

Replicability of bulk RNA-Seq differential expression and enrichment analysis results for small cohort sizes

Peter Methys Degen, Matúš Medo

PLOS Computational Biology: published May 5, 2025 | https://doi.org/10.1371/journal.pcbi.1011630

Colonization times in Moran process on graphs

Lenka Kopfová, Josef Tkadlec

PLOS Computational Biology: published May 5, 2025 | https://doi.org/10.1371/journal.pcbi.1012868

Optimization hardness constrains ecological transients

William Gilpin

PLOS Computational Biology: published May 5, 2025 | https://doi.org/10.1371/journal.pcbi.1013051

Modeling opioid overdose events recurrence with a covariate-adjusted triggering point process

Fenglian Pan, You Zhou, Carolina Vivas-Valencia, Nan Kong, Carol Ott, Mohammad S Jalali, Jian Liu

PLOS Computational Biology: published May 5, 2025 | https://doi.org/10.1371/journal.pcbi.1012889

Accounting for reporting delays in real-time phylodynamic analyses with preferential sampling

Catalina M. Medina, Julia A. Palacios, Volodymyr M. Minin

PLOS Computational Biology: published May 6, 2025 | https://doi.org/10.1371/journal.pcbi.1012970

Multiscale simulations that incorporate patient-specific neural network models of platelet calcium signaling predict diverse thrombotic outcomes under flow

Kaushik N. Shankar, Talid Sinno, Scott L. Diamond

PLOS Computational Biology: published May 6, 2025 | https://doi.org/10.1371/journal.pcbi.1013085

A multiscale model of the action of a capsid assembly modulator for the treatment of chronic hepatitis B

Sarafa A. Iyaniwura, Tyler Cassidy, Ruy M. Ribeiro, Alan S. Perelson

PLOS Computational Biology: published May 6, 2025 | https://doi.org/10.1371/journal.pcbi.1012322

scSDNE: A semi-supervised method for inferring cell-cell interactions based on graph embedding

Chenchen Jia, Haiyun Wang, Jianping Zhao, Junfeng Xia, Chunhou Zheng

PLOS Computational Biology: published May 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013027

Distinguishing multiple roles of T cell and macrophage involvement in determining lymph node fates during Mycobacterium tuberculosis infection

Kathryn C. Krupinsky, Christian T. Michael, Pariksheet Nanda, Joshua T. Mattila, Denise Kirschner

PLOS Computational Biology: published May 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013033

Noise correlations and neuronal diversity may limit the utility of winner-take-all readout in a pop out visual search task

Ori Hendler, Ronen Segev, Maoz Shamir

PLOS Computational Biology: published May 7, 2025 | https://doi.org/10.1371/journal.pcbi.1013092

Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data

Quintin Pope, Rohan Varma, Christine Tataru, Maude M David, Xiaoli Fern

PLOS Computational Biology: published May 7, 2025 | https://doi.org/10.1371/journal.pcbi.1011353

Nuclear deformation by microtubule molecular motors

Naruemon Rueangkham, Miguel Valle-Inclán Cabello, Franziska Lautenschläger, Rhoda J. Hawkins

PLOS Computational Biology: published May 8, 2025 | https://doi.org/10.1371/journal.pcbi.1012305

Smart epidemic control: A hybrid model blending ODEs and agent-based simulations for optimal, real-world intervention planning

Péter Polcz, István Z. Reguly, Kálmán Tornai, János Juhász, Sándor Pongor, Attila Csikász-Nagy, Gábor Szederkényi

PLOS Computational Biology: published May 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013028

Macroecological patterns in experimental microbial communities

William R. Shoemaker, Álvaro Sánchez, Jacopo Grilli

PLOS Computational Biology: published May 8, 2025 | https://doi.org/10.1371/journal.pcbi.1013044

A model of thalamo-cortical interaction for incremental binding in mental contour-tracing

Daniel Schmid, Heiko Neumann

PLOS Computational Biology: published May 8, 2025 | https://doi.org/10.1371/journal.pcbi.1012835

Scoring protein-ligand binding structures through learning atomic graphs with inter-molecular adjacency

Debby D. Wang, Yuting Huang

PLOS Computational Biology: published May 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013074

Success-efficient/failure-safe strategy for hierarchical reinforcement motor learning

Jan Babič, Tjasa Kunavar, Erhan Oztop, Mitsuo Kawato

PLOS Computational Biology: published May 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013089

Human impedance modulation to improve visuo-haptic perception

Xiaoxiao Cheng, Shixian Shen, Ekaterina Ivanova, Gerolamo Carboni, Atsushi Takagi, Etienne Burdet

PLOS Computational Biology: published May 9, 2025 | https://doi.org/10.1371/journal.pcbi.1013042

Parallel synapses with transmission nonlinearities enhance neuronal classification capacity

Yuru Song, Marcus K. Benna

PLOS Computational Biology: published May 9, 2025 | https://doi.org/10.1371/journal.pcbi.1012285

Conformal prediction for uncertainty quantification in dynamic biological systems

Alberto Portela, Julio R. Banga, Marcos Matabuena

PLOS Computational Biology: published May 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013098

The geometry of efficient codes: How rate-distortion trade-offs distort the latent representations of generative models

Leo D’Amato, Gian Luca Lancia, Giovanni Pezzulo

PLOS Computational Biology: published May 12, 2025 | https://doi.org/10.1371/journal.pcbi.1012952

Mathematical modeling of malaria vaccination with seasonality and immune feedback

Zhuolin Qu, Denis Patterson, Lihong Zhao, Joan Ponce, Christina J. Edholm, Olivia F. Prosper Feldman, Lauren M. Childs

PLOS Computational Biology: published May 12, 2025 | https://doi.org/10.1371/journal.pcbi.1012988

How are estimated cellular turnover rates influenced by the dynamics of a source population?

Arpit C. Swain, José A. M. Borghans, Rob J. de Boer

PLOS Computational Biology: published May 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013052

Integrated mathematical and experimental modeling uncovers enhanced EMT plasticity upon loss of the DLC1 tumor suppressor

Sebastian Höpfl, Merih Özverin, Helena Nowack, Raluca Tamas, Andrew G. Clark, Nicole Radde, Monilola A. Olayioye

PLOS Computational Biology: published May 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013076

Knowledge-aware contrastive heterogeneous molecular graph learning

Mukun Chen, Jia Wu, Shirui Pan, Fu Lin, Bo Du, Xiuwen Gong, Wenbin Hu

PLOS Computational Biology: published May 12, 2025 | https://doi.org/10.1371/journal.pcbi.1013008

The effects of the post-delay epochs on working memory error reduction

Zeyuan Ye, Haoran Li, Liang Tian, Changsong Zhou

PLOS Computational Biology: published May 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013083

Inferring synaptic transmission from the stochastic dynamics of the quantal content: An analytical approach

Zahra Vahdat, Oliver Gambrell, Jonas Fisch, Eckhard Friauf, Abhyudai Singh

PLOS Computational Biology: published May 13, 2025 | https://doi.org/10.1371/journal.pcbi.1013067

Identifying the DNA methylation preference of transcription factors using ProtBERT and SVM

Yanchao Li, Quan Zou, Qi Dai, Antony Stalin, Ximei Luo

PLOS Computational Biology: published May 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012513

Building momentum: A computational account of persistence toward long-term goals

Sneha Aenugu, John P. O’Doherty

PLOS Computational Biology: published May 14, 2025 | https://doi.org/10.1371/journal.pcbi.1013054

Mechanisms of mistrust: A Bayesian account of misinformation learning

Lion Schulz, Yannick Streicher, Eric Schulz, Rahul Bhui, Peter Dayan

PLOS Computational Biology: published May 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012814

How swarming bats can use the collective soundscape for obstacle avoidance

Dieter Vanderelst, Herbert Peremans

PLOS Computational Biology: published May 15, 2025 | https://doi.org/10.1371/journal.pcbi.1013013

Generative AI mitigates representation bias and improves model fairness through synthetic health data

Raffaele Marchesi, Nicolo Micheletti, Nicholas I-Hsien Kuo, Sebastiano Barbieri, Giuseppe Jurman, Venet Osmani

PLOS Computational Biology: published May 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013080

Uncovering the impact of infection routes on within-host MPXV dynamics: Insights from a mathematical modeling study

Qi Deng, Woldegebriel Assefa Woldegerima, Wenjing Zhang, Ali Asgary, Jude Dzevela Kong, Sarah Flicker, Nicholas H. Ogden, James Orbinski, Nicola Luigi Bragazzi, Jianhong Wu

PLOS Computational Biology: published May 19, 2025 | https://doi.org/10.1371/journal.pcbi.1013073

A multiscale electro-metabolic model of a rat neocortical circuit reveals the impact of ageing on central cortical layers

Sofia Farina, Alessandro Cattabiani, Darshan Mandge, Polina Shichkova, James B. Isbister, Jean Jacquemier, James G. King, Henry Markram, Daniel Keller

PLOS Computational Biology: published May 20, 2025 | https://doi.org/10.1371/journal.pcbi.1013070

Modelling motility of Trypanosoma brucei

Florian A. Overberg, Narges Jamshidi Khameneh, Timothy Krüger, Markus Engstler, Gerhard Gompper, Dmitry A. Fedosov

PLOS Computational Biology: published May 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013111

Balancing prior knowledge and sensory data in a predictive coding model of coherent motion detection

Elnaz Nemati, David B. Grayden, Anthony N. Burkitt, Parvin Zarei Eskikand

PLOS Computational Biology: published May 21, 2025 | https://doi.org/10.1371/journal.pcbi.1013116

Interleaved single and bursting spiking resonance in neurons

Cesar C. Ceballos, Nourdin Chadly, Eric Lowet, Rodrigo F. O. Pena

PLOS Computational Biology: published May 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013126

Expectation generation and its effect on subsequent pain and visual perception

Rotem Botvinik-Nezer, Stephan Geuter, Martin A. Lindquist, Tor D. Wager

PLOS Computational Biology: published May 22, 2025 | https://doi.org/10.1371/journal.pcbi.1013053

Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells

Owen M. O’Connor, Mary J. Dunlop

PLOS Computational Biology: published May 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013071

MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures

Yuxiang Zhan, Francesco Musella, Frank Alber

PLOS Computational Biology: published May 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013114

Geometric and mechanical guidance: Role of stigmatic epidermis in early pollen tube pathfinding in arabidopsis

Lucie Riglet, Catherine Quilliet, Christophe Godin, Karin John, Isabelle Fobis-Loisy

PLOS Computational Biology: published May 27, 2025 | https://doi.org/10.1371/journal.pcbi.1013077

Relating sparse and predictive coding to divisive normalization

Yanbo Lian, Anthony N. Burkitt

PLOS Computational Biology: published May 27, 2025 | https://doi.org/10.1371/journal.pcbi.1013059

Stimulus uncertainty and relative reward rates determine adaptive responding in perceptual decision-making

Luis de la Cuesta-Ferrer, Christina Koß, Sarah Starosta, Nils Kasties, Daniel Lengersdorf, Frank Jäkel, Maik C. Stüttgen

PLOS Computational Biology: published May 27, 2025 | https://doi.org/10.1371/journal.pcbi.1012636

The respiratory cycle modulates distinct dynamics of affective and perceptual decision-making

Malthe Brændholt, Niia Nikolova, Melina Vejlø, Leah Banellis, Francesca Fardo, Daniel S. Kluger, Micah Allen

PLOS Computational Biology: published May 27, 2025 | https://doi.org/10.1371/journal.pcbi.1013086

RETINA: Reconstruction-based pre-trained enhanced TransUNet for electron microscopy segmentation on the CEM500K dataset

Cheng Xing, Ronald Xie, Gary D. Bader

PLOS Computational Biology: published May 28, 2025 | https://doi.org/10.1371/journal.pcbi.1013115

Cellular morphodynamics as quantifiers for functional states of resident tissue macrophages in vivo

Miriam Schnitzerlein, Eric Greto, Anja Wegner, Anna Möller, Oliver Aust, Oumaima Ben Brahim, David B. Blumenthal, Vasily Zaburdaev, Stefan Uderhardt

PLOS Computational Biology: published May 29, 2025 | https://doi.org/10.1371/journal.pcbi.1011859

Accounting for contact tracing in epidemiological birth-death models

Anna Zhukova, Olivier Gascuel

PLOS Computational Biology: published May 29, 2025 | https://doi.org/10.1371/journal.pcbi.1012461

Understanding the hemodynamic changes in fetuses with coarctation of the aorta using a lumped model of fetal circulation

Inmaculada Villanueva-Baxarias, Anna Pellisé-Tintoré, María Pérez-Rodríguez, Laura Nogué, Pooja Vaziraani, Iris Soveral, Fàtima Crispi, Olga Gómez, Patricia Garcia-Canadilla, Oscar Camara, Bart Bijnens, Gabriel Bernardino

PLOS Computational Biology: published May 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013096

Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data

Katharina Waury, Stefan Lelieveld, Sanne Abeln, Henk-Jan van den Ham

PLOS Computational Biology: published May 30, 2025 | https://doi.org/10.1371/journal.pcbi.1013057

Formal Comment

Many roads to minimizing regret: A comparison of Wang et al (2024) and OpAL* models of adaptive striatal dopamine

Joshua T.S. Hewson, Alana Jaskir, Michael J. Frank

PLOS Computational Biology: published May 8, 2025 | https://doi.org/10.1371/journal.pcbi.1012920

Methods

Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation

Wenjun Zhao, Erica Larschan, Björn Sandstede, Ritambhara Singh

PLOS Computational Biology: published May 8, 2025 | https://doi.org/10.1371/journal.pcbi.1012476

Capturing the emergent dynamical structure in biophysical neural models

Borjan Milinkovic, Lionel Barnett, Olivia Carter, Anil K. Seth, Thomas Andrillon

PLOS Computational Biology: published May 12, 2025 | https://doi.org/10.1371/journal.pcbi.1012572

M-band wavelet-based multi-view clustering of cells

Tong Liu, Zihuan Liu, Wenke Sun, Adeethyia Shankar, Yongzhong Zhao, Xiaodi Wang

PLOS Computational Biology: published May 23, 2025 | https://doi.org/10.1371/journal.pcbi.1013060

Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM)

Miriam Goldman, Chunyu Zhao, Katherine S. Pollard

PLOS Computational Biology: published May 27, 2025 | https://doi.org/10.1371/journal.pcbi.1012277

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May 2025

Cover

Computational complexity in a random ecosystem