PLOS Computational Biology

2005 - 2025

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Volume 21, issue 12, 2025

Democratising high performance computing for bioinformatics through serverless cloud computing: A case study on CRISPR-Cas9 guide RNA design with Crackling Cloud pp. 1-11

Jacob Bradford, Divya Joy, Mattias Winsen, Nicholas Meurant, Mackenzie Wilkins, Laurence OW Wilson, Denis C Bauer and Dimitri Perrin

D3Impute: Dropout-aware discrimination, distribution-aware modeling, and density-guide imputation for scRNA-seq data pp. 1-38

Siyi Huang, Linfeng Jiang, Ming Yi and Yuan Zhu

Randomized Spatial PCA (RASP): A computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data pp. 1-28

Ian K Gingerich, Brittany A Goods and H Robert Frost

DDGWizard: Integration of feature calculation resources for analysis and prediction of changes in protein thermostability upon point mutations pp. 1-28

Mingkai Wang, Khaled Jumah, Qun Shao, Katarzyna Kamieniecka, Yihan Liu and Krzysztof Poterlowicz

LCMSpector: A simple open-source viewer for targeted hyphenated mass spectrometry analysis pp. 1-18

Mateusz Fido, Etienne Hoesli, Elisa Cappio Barazzone, Renato Zenobi and Emma Slack

Semi-supervised Bayesian integration of multiple spatial proteomics datasets pp. 1-26

Stephen Coleman, Lisa Breckels, Ross F Waller, Kathryn S Lilley, Chris Wallace, Oliver M Crook and Paul D W Kirk

ASPEN: Robust detection of allelic dynamics in single cell RNA-seq pp. 1-26

Veronika Petrova, Muqing Niu, Thomas S Vierbuchen and Emily S Wong

Whom do we prefer to learn from in observational reinforcement learning? pp. 1-21

Gota Morishita, Carsten Murawski, Nitin Yadav and Shinsuke Suzuki

Benchmarking interpretability of deep learning for predictive genomics: Recall, precision, and variability of feature attribution pp. 1-21

Justin Reynolds and Chongle Pan

Random time-shift approximation enables hierarchical Bayesian inference of mechanistic within-host viral dynamics models on large datasets pp. 1-23

Dylan J Morris, Lauren Kennedy and Andrew J Black

Do we advise as one likes? The alignment bias in social advice giving pp. 1-29

Xitong Luo, Lei Zhang and Yafeng Pan

Assessing the relative contributions of mosaic and regulatory developmental modes from single-cell trajectories pp. 1-19

Solène Song and Paul Villoutreix

Automated registration and clustering for enhanced localization atomic force microscopy of flexible membrane proteins pp. 1-19

Creighton M Lisowski, Gavin M King and Ioan Kosztin

Memory, innovation and vertical learning pp. 1-19

Madeleine Ammar, Laurel Fogarty and Anne Kandler

Comparing a computational model of visual problem solving with human vision on a difficult vision task pp. 1-20

Tarun Khajuria, Kadi Tulver and Jaan Aru

Receptor dimerization enables ligand discrimination through tunable response heterogeneity pp. 1-20

Assaf Biran and Yaron E Antebi

BAGEL: Protein engineering via exploration of an energy landscape pp. 1-24

Jakub Lála, Ayham Al-Saffar and Stefano Angioletti-Uberti

Sketch, capture and layout phylogenies pp. 1-13

Daniel H Huson

Identification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls pp. 1-22

Ana Paredes-Vázquez, Eva Balsa-Canto and Julio R Banga

Learning structured population models from data with WSINDy pp. 1-22

Rainey Lyons, Vanja Dukic and David M Bortz

Unsupervised detection and fitness estimation of emerging SARS-CoV-2 variants: Application to wastewater samples (ANRS0160) pp. 1-22

Alexandra Lefebvre, Vincent Maréchal, Arnaud Gloaguen, The Obépine Consortium, Amaury Lambert and Yvon Maday

ARTreeFormer: A faster attention-based autoregressive model for phylogenetic inference pp. 1-22

Tianyu Xie, Yicong Mao and Cheng Zhang

Decoupled contrastive multi-view clustering with adaptive false negative elimination for cancer subtyping pp. 1-27

Mengxiang Lin, Rongqi Fan, Saisai Zhu, Xiaoqiang Yan, Quan Zou and Zhen Tian

Volume 21, issue 11, 2025

Branch-specific gene discovery in cell differentiation using multi-omics graph attention pp. 1-17

Yihao Yin, Linzhi Zhuang, Yulei Wang, Yazhou Shi and Bengong Zhang

Splicing-aware scRNA-Seq resolution reveals execution-ready programs in effector Tregs pp. 1-17

Daniil K Lukyanov, Evgeniy S Egorov, Valeriia V Kriukova, Denis Syrko, Victor V Kotliar, Kristin Ladell, David A Price, Andre Franke and Dmitry M Chudakov

Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture pp. 1-15

Tien Comlekoglu, J Quetzalcóatl Toledo-Marín, Tina Comlekoglu, Douglas W DeSimone, Shayn M Peirce, Geoffrey Fox and James A Glazier

HAPP: High-accuracy pipeline for processing deep metabarcoding data pp. 1-23

John Sundh, Emma Granqvist, Ela Iwaszkiewicz-Eggebrecht, Lokeshwaran Manoharan, Laura J A van Dijk, Robert Goodsell, Nerivania N Godeiro, Bruno C Bellini, Johanna Orsholm, Piotr Łukasik, Andreia Miraldo, Tomas Roslin, Ayco J M Tack, Anders F Andersson and Fredrik Ronquist

Optimization of experimental designs for biological rhythm discovery pp. 1-23

Turner Silverthorne, Matthew Carlucci, Arturas Petronis and Adam R Stinchcombe

Spatial close-kin mark-recapture methods to estimate dispersal parameters and barrier strength for mosquitoes pp. 1-23

John M Marshall, Shuyi Yang, Jared B Bennett, Igor Filipović and Gordana Rašić

Ten simple rules for maximizing summer research experiences for students, mentors, and research groups pp. 1-7

Miriam B Goodman

Automated and modular protein binder design with BinderFlow pp. 1-14

Nayim González-Rodríguez, Carlos Chacón-Sánchez, Oscar Llorca and Rafael Fernández-Leiro

PathoRM: Computational inference of pathogenic RNA methylation sites by incorporating multi-view features pp. 1-20

Hui Liu, Jiani Ma, Xianjun Ma and Lin Zhang

Protein drift-diffusion in membranes with non-equilibrium fluctuations arising from gradients in concentration or temperature pp. 1-20

Dev Jasuja and Paul J Atzberger

Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations pp. 1-20

Yue Huang, Tianqi Tang, Xiaowu Dai and Fengzhu Sun

CrossLabFit: A novel framework for integrating qualitative and quantitative data across multiple labs for model calibration pp. 1-20

Rodolfo Blanco-Rodriguez, Tanya A Miura and Esteban Hernandez-Vargas

Prediction of graft loss in living donor liver transplantation during the early postoperative period pp. 1-20

Raiki Yoshimura, Naotoshi Nakamura, Takeru Matsuura, Takeo Toshima, Takasuke Fukuhara, Kazuyuki Aihara, Katsuhito Fujiu, Shingo Iwami and Tomoharu Yoshizumi

Real-time forecasting of data revisions in epidemic surveillance streams pp. 1-24

Jingjing Tang, Aaron Rumack, Bryan Wilder and Roni Rosenfeld

Ten simple rules for early-career researchers supervising short-term student projects pp. 1-8

Rebecca M Crossley and Philip K Maini

SpaMWGDA: Identifying spatial domains of spatial transcriptomes using multi-view weighted fusion graph convolutional network and data augmentation pp. 1-19

Lin Yuan, Boyuan Meng, Qingxiang Wang, Chunyu Hu, Cuihong Wang and Huang De-Shuang

Nash equilibrium of attack and defense behaviors between predators and prey pp. 1-30

Hiroyuki Ichijo, Yuichiro Kawamura and Tomoya Nakamura

Data-driven identification of biological systems using multi-scale analysis pp. 1-22

Ismaila Muhammed, Dimitris M Manias, Dimitris A Goussis and Haralampos Hatzikirou

The topology of synergy: Linking topological and information-theoretic approaches to higher-order interactions in complex systems pp. 1-22

Thomas F Varley, Pedro A M Mediano, Alice Patania and Josh Bongard

Null models for comparing information decomposition across complex systems pp. 1-25

Alberto Liardi, Fernando E Rosas, Robin L Carhart-Harris, George Blackburne, Daniel Bor and Pedro A M Mediano

A linear pathway for inositol pyrophosphate metabolism revealed by 18O labeling and model reduction pp. 1-25

Jacques Hermes, Geun-Don Kim, Guizhen Liu, Maria Giovanna De Leo, Andreas Mayer, Henning Jessen and Jens Timmer

OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders pp. 1-27

Klemens Flöge, Srisruthi Udayakumar, Johanna Sommer, Marie Piraud, Stefan Kesselheim, Vincent Fortuin, Stephan Günnemann, Karel J van der Weg, Holger Gohlke, Erinc Merdivan and Alina Bazarova

Federated learning for COVID-19 mortality prediction in a multicentric sample of 21 hospitals pp. 1-16

Roberta Moreira Wichmann, Murilo Afonso Robiati Bigoto and Alexandre Dias Porto Chiavegatto Filho

Library size-stabilized metacells construction enhances co-expression network analysis in single-cell data pp. 1-16

Tianjiao Zhang and Haibin Zhu

PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures pp. 1-9

Takumi Otagaki, Goro Terai, Kiyoshi Asai and Junichi Iwakiri

APDCA: An accurate and effective method for predicting associations between RBPs and AS-events during epithelial-mesenchymal transition pp. 1-18

Yangsong He, Zheng-Jian Bai, Wai-Ki Ching, Quan Zou and Yushan Qiu

Trial-by-trial learning of successor representations in human behavior pp. 1-18

Ari E Kahn, Dani S Bassett and Nathaniel D Daw

tvsfglasso: Time-varying scale-free graphical lasso for network estimation from time-series data pp. 1-18

Markku Kuismin and Mikko J Sillanpää

Epydemix: An open-source Python package for epidemic modeling with integrated approximate Bayesian calibration pp. 1-18

Nicoló Gozzi, Matteo Chinazzi, Jessica T Davis, Corrado Gioannini, Luca Rossi, Marco Ajelli, Nicola Perra and Alessandro Vespignani

Unlocking plant health survey data: An approach to quantify the sensitivity and specificity of visual inspections pp. 1-26

Matt Combes, Nathan Brown, Robin N Thompson, Alexander Mastin, Peter Crow and Stephen Parnell

Automated C. elegans behavior analysis via deep learning-based detection and tracking pp. 1-26

Xiaoke Liu, Jianming Liu, Wenjie Teng, Yuzhong Peng, Boao Li, Xiaoqing Han and Jing Huo

Universal scale-free representations in human visual cortex pp. 1-26

Raj Magesh Gauthaman, Brice Ménard and Michael F Bonner

Volume 21, issue 10, 2025

BMDD: A probabilistic framework for accurate imputation of zero-inflated microbiome sequencing data pp. 1-21

Huijuan Zhou, Jun Chen and Xianyang Zhang

Generalized contrastive PCA is equivalent to generalized eigendecomposition pp. 1-4

Joshua P Woller, David Menrath and Alireza Gharabaghi

Multivariate resilience indicators to anticipate vector-borne disease outbreaks: A West Nile virus case-study pp. 1-16

Clara Delecroix, Quirine ten Bosch, Egbert H Van Nes and Ingrid A van de Leemput

A semi-automated algorithm for image analysis of respiratory organoids pp. 1-16

Anna Demchenko, Maxim Balyasin, Elena Kondratyeva, Tatiana Kyian, Alyona Sorokina, Marina Loguinova and Svetlana Smirnikhina

Similarity-based transfer learning with deep learning networks for accurate CRISPR-Cas9 off-target prediction pp. 1-30

Jeremy Charlier, Zeinab Sherkatghanad and Vladimir Makarenkov

Simultaneously determining regional heterogeneity and connection directionality from neural activity and symmetric connection pp. 1-30

Jiawen Chang, Zhuda Yang and Changsong Zhou

Modelling plant disease spread and containment: Simulation and approximate Bayesian Computation for Xylella fastidiosa in Puglia, Italy pp. 1-19

Daniel Chapman, Flavia Occhibove, James M Bullock, Pieter S A Beck, Juan A Navas-Cortes and Steven M White

Drug-disease networks and drug repurposing pp. 1-19

Austin Polanco and Mark E J Newman

WormSNAP: A software for fast, accurate, and unbiased detection of fluorescent puncta in C. elegans pp. 1-19

Araven Tiroumalechetty, Elisa B Frankel and Peri T Kurshan

Improving policy design and epidemic response using integrated models of economic choice and disease dynamics with behavioral feedback pp. 1-24

Hongru Du, Matthew V Zahn, Sara L Loo, Tijs W Alleman, Shaun Truelove, Bryan Patenaude, Lauren M Gardner, Nicholas Papageorge and Alison L Hill

Inference of weak-form partial differential equations describing migration and proliferation mechanisms in wound healing experiments on cancer cells pp. 1-27

Siddhartha Srivastava, Patrick C Kinnunen, Zhenlin Wang, Kenneth KY Ho, Brock A Humphries, Siyi Chen, Jennifer J Linderman, Gary D Luker, Kathryn E Luker and Krishna Garikipati

HMFGraph: Novel Bayesian approach for recovering biological networks pp. 1-27

Aapo E Korhonen, Olli Sarala, Tuomas Hautamäki, Markku Kuismin and Mikko J Sillanpää

A Bayesian model of distance perception from ocular convergence pp. 1-25

Peter Scarfe and Paul B Hibbard

A mixture of attention experts-embedded flow-based generative model to create synthetic cells in single-cell RNA-Seq datasets pp. 1-25

Sultan Sevgi Turgut Ögme, Nizamettin Aydin and Zeyneb Kurt

A multi-layer encoder prediction model for individual sample specific gene combination effect (MLEC-iGeneCombo) pp. 1-15

Yun Shen, Kunjie Fan, Birkan Gökbağ, Nuo Sun, Chen Yang, Lijun Cheng and Lang Li

Impact of the COVID-19 pandemic on computational biology early career researchers: A global retrospective study pp. 1-15

Pradeep Eranti, Megha Hegde, Syed Muktadir Al Sium, R Gonzalo Parra, Alastair M Kilpatrick, Sayane Shome and Farzana Rahman

GeneDrive.jl: A decision tool to optimize biological vector control strategies under climate change pp. 1-15

Váleri N Vásquez, Erin A Mordecai and David Anthoff

Assessing parameter identifiability of a hemodynamics PDE model using spectral surrogates and dimension reduction pp. 1-33

Mitchel J Colebank

Spatial domain identification method based on multi-view graph convolutional network and contrastive learning pp. 1-17

Xikeng Liang, Shutong Xiao, Lu Ba, Yuhui Feng, Zhicheng Ma, Fatima Adilova, Jing Qi and Shuilin Jin

From ideal to practical: Heterogeneity of student-generated variant lists highlights hidden reproducibility gaps pp. 1-14

Rumeysa Aslıhan Ertürk, Abdullah Asım Emül, Büşra Nur Darendeli-Kiraz, Fatma Zehra Sarı, Mehmet Arif Ergün and Mehmet Baysan

Subthreshold moment analysis of neuronal populations driven by synchronous synaptic inputs pp. 1-44

Logan A Becker, Francois Baccelli and Thibaud Taillefumier

Inferring effective networks of spiking neurons using a continuous-time estimator of transfer entropy pp. 1-29

David P Shorten, Viola Priesemann, Michael Wibral and Joseph T Lizier

Multi-feature fusion network with marginal focal dice loss for multi-label therapeutic peptide prediction pp. 1-18

Yijun Mao, Yurong Weng, Jian Weng, Ming Li, Wanrong Gu, Rui Pang, Xudong Lin, Yunyan Xiong and Deyu Tang

A method for analysing tissue motion and deformation during mammalian organogenesis pp. 1-28

Morena Raiola, Isaac Esteban, Kenzo Ivanovitch, Miquel Sendra and Miguel Torres

Quantifying HiPSC-CM structural organization at scale with deep learning-enhanced SarcGraph pp. 1-28

Saeed Mohammadzadeh and Emma Lejeune

Response to comment on ”Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA” pp. 1-3

Eliezyer Fermino de Oliveira and Lucas Sjulson

Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches pp. 1-20

Javiera Cortés-Ríos, Maria Rodriguez-Fernandez, Peter Karl Sorger and Fabian Fröhlich

Analytical and computational solution for the estimation of SNP-heritability in biobank-scale and distributed datasets pp. 1-20

Guo-An Qi, Qi-Xin Zhang, Jingyu Kang, Tianyuan Li, Xiyun Xu, Zhe Zhang, Zhe Fan, Siyang Liu and Guo-Bo Chen

Social inequalities in vaccine coverage and their effects on epidemic spreading pp. 1-20

Adriana Manna, Marton Karsai and Nicola Perra

Synchrony, oscillations, and phase relationships in collective neuronal activity: A highly comparative overview of methods pp. 1-43

Fabiano Baroni and Ben D Fulcher

Statistical regularities in natural scenes that support figure-ground segregation by neural populations pp. 1-22

Clara T Friedman, Minqi Wang, Thomas Yerxa, Bryce A Arseneau, Xin Huang and Emily A Cooper

Nine quick tips for trustworthy machine learning in the biomedical sciences pp. 1-13

Luca Oneto and Davide Chicco

Adaptive proximity to criticality underlies amplification of ultra-slow fluctuations during free recall pp. 1-23

Dovi Yellin, Noam Siegel, Rafael Malach and Oren Shriki

Transmission thresholds for the spread of infections in healthcare facilities pp. 1-23

Damon J A Toth, Karim Khader, Christopher Mitchell and Matthew H Samore

Exact conditions for evolutionary stability in indirect reciprocity under noise pp. 1-23

Nikoleta E Glynatsi, Christian Hilbe and Yohsuke Murase

TastepepAI: An artificial intelligence platform for taste peptide de novo design pp. 1-23

Jianda Yue, Tingting Li, Jian Ouyang, Jiawei Xu, Hua Tan, Zihui Chen, Changsheng Han, Huanyu Li, Songping Liang, Zhonghua Liu, Zhonghua Liu and Ying Wang

Volume 21, issue 9, 2025

Optimizing therapeutic outcomes with Mechanotherapy and Ultrasound Sonopermeation in solid tumors pp. 1-26

Marina Koutsi, Triantafyllos Stylianopoulos and Fotios Mpekris

Human visual grouping based on within- and cross-area temporal correlations pp. 1-26

Yen-Ju Chen, Zitang Sun and Shin’ya Nishida

Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations pp. 1-26

Jiancheng Zhang, Xiangting Li, Xiaolu Guo, Zhaoyi You, Lucas Böttcher, Alex Mogilner, Alexander Hoffmann, Tom Chou and Mingtao Xia

Effects of tDCS of the DLPFC on brain networks: A hybrid brain modeling study pp. 1-26

Yanqing Dong, Jing Wei, Songjun Peng, Xinran Wu, Yaru Xu, Jianfeng Feng, Jie Zhang, Viktor Jirsa and Jie Xiang

A history-dependent approach for accurate initial condition estimation in epidemic models pp. 1-21

Dongju Lim, Kyeong Tae Ko, Hyukpyo Hong, Hyojung Lee, Boseung Choi, Won Chang, Sunhwa Choi and Jae Kyoung Kim

A nonlinear relationship between prediction errors and learning rates in human reinforcement-learning pp. 1-21

Boluwatife Ikwunne, Jolie Parham and Erdem Pulcu

A physiologically inspired hybrid CPG/Reflex controller for cycling simulations that generalizes to walking pp. 1-21

Giacomo Severini and David Muñoz

Effects of segmentation errors on downstream-analysis in highly-multiplexed tissue imaging pp. 1-18

Matthias Bruhns, Jan T Schleicher, Maximilian Wirth, Marcello Zago, Sepideh Babaei and Manfred Claassen

Gene regulatory network structure informs the distribution of perturbation effects pp. 1-31

Matthew Aguirre, Jeffrey P Spence, Guy Sella and Jonathan K Pritchard

Generating correlated data for omics simulation pp. 1-16

Jianing Yang, Gregory R Grant and Thomas G Brooks

MRDtarget: A heuristic Gaussian approach for optimizing targeted capture regions to enhance Minimal Residual Disease detection pp. 1-16

Xuwen Wang, Yanfang Guan, Wei Gao, Xin Lai, Wuqiang Cao, Xiaoyan Zhu, Xiaoling Zeng, Yuqian Liu, Shenjie Wang, Ruoyu Liu, Xin Yi, Shuanying Yang and Jiayin Wang

Ten quick tips for protecting health data using de-identification and perturbation of structured datasets pp. 1-16

Tshikala Eddie Lulamba, Themba Mutemaringa and Nicki Tiffin

Action subsampling supports policy compression in large action spaces pp. 1-27

Shuze Liu and Samuel Joseph Gershman

Transcriptome-wide root causal inference pp. 1-35

Eric V Strobl and Eric R Gamazon

Cortical networks with multiple interneuron types generate oscillatory patterns during predictive coding pp. 1-25

Kwangjun Lee, Cyriel M A Pennartz and Jorge F Mejias

A computational framework for the investigation of phosphoinositide regulation pp. 1-25

Hilaire Yam Fung Cheung, Chukiat Tantiwong, Dipali Kale, Jonathan M Gibbins, Steve P Watson, Johan W M Heemskerk, Albert Sickmann, Robert Ahrends and Joanne L Dunster

HyperACP: A cutting-edge hybrid framework for anticancer peptide classification via scalable feature extraction and adaptive neighbor-based synthesis pp. 1-25

Bangyi Zhang, Yun Zuo, Jun Wan, Jiayue Liu, Xiangrong Liu, Xiangxiang Zeng and Zhaohong Deng

Ten simple rules for training by researchers for researchers in a rapidly evolving workforce pp. 1-13

Meirian Lovelace-Tozer, John Brown, Robert Clemens, Kathryn Greenhill, Fathima Haseen, Danny Kingsley, Ellen A Lyrtzis, Katherine Mills, Giorgia Mori, Kathryn M Steel, Liz Stokes, Kathryn Unsworth, Adeline L H Wong and Amany Gouda-Vossos

paramix: An R package for parameter discretisation in compartmental models, with application to calculating years of life lost pp. 1-13

Lucy Goodfellow, Carl A B Pearson and Simon R Procter

Dynamical mean-field theory for a highly heterogeneous neural population with graded persistent activity of the entorhinal cortex pp. 1-30

Futa Tomita and Jun-nosuke Teramae

SBMLNetwork: A framework for standards-based visualization of biochemical models pp. 1-19

Adel Heydarabadipour, Lucian Smith, Joseph L Hellerstein and Herbert M Sauro

Category-specific perceptual learning of robust object recognition modelled using deep neural networks pp. 1-19

Hojin Jang and Frank Tong

An explainable covariate compartmental model for predicting the spatio-temporal patterns of dengue in Sri Lanka pp. 1-19

Yichao Liu, Peter Fransson, Julian Heidecke, Prasad Liyanage, Jonas Wallin and Joacim Rocklöv

A graph neural network-based spatial multi-omics data integration method for deciphering spatial domains pp. 1-20

Congqiang Gao, Chenghui Yang and Lihua Zhang

Clonal heterogeneity and antigenic stimulation shape persistence of the latent reservoir of HIV pp. 1-24

Marco Garcia Noceda, Gargi Kher, Shikhar Uttam and John P Barton

Mathematical modeling of dopamine rhythms and timing of dopamine reuptake inhibitors pp. 1-24

Tianyong Yao and Ruby Kim

Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings pp. 1-7

Ronald Galiwango, Christopher J Whalen, Grace Kebirungi, Mugume T Atwine, Rodgers Kimera, Alfred Ssekagiri, Timothy W Kimbowa, Edward Lukyamuzi, Mike Nsubuga, eLwazi Odsp, Lloyd Ssentongo, Henry Mutegeki, John M Fonner, Frank Wuerthwein, Ari Berman, Laura B Okalebo, Meghan McCarthy, Victor S Kramer, Mariam Quinones, Phillip Cruz, Darrell Hurt, Maria Y Giovanni, Nicola Mulder, Michael Tartakovsky, Jonathan Kayondo and Daudi Jjingo

A generalized theoretical framework to investigate multicomponent actin dynamics pp. 1-15

Mintu Nandi, Shashank Shekhar and Sandeep Choubey

Adaptive algorithms for shaping behavior pp. 1-15

William L Tong, Venkatesh N Murthy and Gautam Reddy

A causal framework for the drivers of animal social network structure pp. 1-42

Ben Kawam, Julia Ostner, Richard McElreath, Oliver Schülke and Daniel Redhead

Fast and exact stochastic simulations of epidemics on static and temporal networks pp. 1-17

Samuel Cure, Florian G Pflug and Simone Pigolotti

Personalized pulse wave propagation modeling to improve vasopressor dosing management in patients with severe traumatic brain injury pp. 1-17

Kamil Wolos, Leszek Pstras, Urszula Bialonczyk, Malgorzata Debowska, Wojciech Dabrowski, Dorota Siwicka-Gieroba and Jan Poleszczuk

Harmony-based data integration for distributed single-cell multi-omics data pp. 1-17

Ruizhi Yuan, Ziqi Rong, Haoran Hu, Tianhao Liu, Shiyue Tao, Wei Chen and Lu Tang

Volume 21, issue 8, 2025

Ten simple rules for being a co-author on a many-author non-empirical paper pp. 1-10

Friederike E Kohrs, Natascha Drude, Anita Bandrowski and Tracey L Weissgerber

A neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens pp. 1-15

Weheliye H Weheliye, Javier Rodriguez, Luigi Feriani, Avelino Javer, Virginie Uhlmann and André E X Brown

Does Zipf’s law of abbreviation shape birdsong? pp. 1-17

R Tucker Gilman, Durrant Cd, Lucy Malpas and Rebecca N Lewis

Mathematical modeling suggests 14-3-3 proteins modulate RAF paradoxical activation pp. 1-17

Gaurav Mendiratta, Kodye Abbott, Yao-Cheng Li, Jingting Yu, Peter Carlip, Melinda Tong, Jianfeng Huang, Maxim N Shokhirev, Thomas McFall, Geoffrey M Wahl and Edward C Stites

PLNMFG: Pseudo-label guided non-negative matrix factorization model with graph constraint for single-cell multi-omics data clustering pp. 1-17

Hui Yuan, Mingzhu Liu, Yushan Qiu, Wai-Ki Ching and Quan Zou

A software ecosystem for brain tractometry processing, analysis, and insight pp. 1-33

John Kruper, Adam Richie-Halford, Joanna Qiao, Asa Gilmore, Kelly Chang, Mareike Grotheer, Ethan Roy, Sendy Caffarra, Teresa Gomez, Sam Chou, Matthew Cieslak, Serge Koudoro, Eleftherios Garyfallidis, Theodore D Satthertwaite, Jason D Yeatman and Ariel Rokem

Stochastic activity in low-rank recurrent neural networks pp. 1-35

Francesca Mastrogiuseppe, Joana Carmona and Christian K Machens

COEXIST: Coordinated single-cell integration of serial multiplexed tissue images pp. 1-22

Robert T Heussner, Cameron F Watson, Christopher Z Eddy, Kunlun Wang, Eric M Cramer, Allison L Creason, Gordon B Mills and Young Hwan Chang

Data-driven analysis of fine-scale badger movement in the UK pp. 1-22

Jessica R Furber, Richard J Delahay, Ruth Cox, Rosie Woodroffe, Maria O’Hagan, Naratip Santitissadeekorn, Stefan Klus, Giovanni Lo Iacono, Mark A Chambers and David J B Lloyd

Age polyethism can emerge from social learning: A game-theoretic investigation pp. 1-22

Moein Khajehnejad, Julian García and Bernd Meyer

Socioeconomic determinants of protective behaviors and contact patterns in the post-COVID-19 pandemic era: A cross-sectional study in Italy pp. 1-25

Michele Tizzani and Laetitia Gauvin

Identification of the governing equation of stimulus-response data for run-and-tumble dynamics pp. 1-25

Shicong Lei, Yu’an Li, Zheng Ma, Hepeng Zhang and Min Tang

Heterogeneous synaptic homeostasis: A novel mechanism boosting information propagation in the cortex pp. 1-25

Farhad Razi and Belén Sancristóbal

Emergence of a complex network structure on a Spatial Prisoner’s Dilemma pp. 1-13

Tomoko Sakiyama and Akihiro Takahara

In silico modeling of directed differentiation of induced pluripotent stem cells to definitive endoderm pp. 1-30

Amirmahdi Mostofinejad, David A Romero, Dana Brinson, Thomas K Waddell, Golnaz Karoubi and Cristina H Amon

Stochastic model of IP3-induced Ca2+ spiking of HEK293 cells pp. 1-24

Caterina Azzoni, Rene Jüttner, Anje Sporbert, Michael Gotthardt, H Llewelyn Roderick and Martin Falcke

IonBench: A benchmark of optimisation strategies for mathematical models of ion channel currents pp. 1-28

Matt J Owen and Gary R Mirams

A computational workflow for assessing drug effects on temporal signaling dynamics reveals robustness in stimulus-specific NFκB signaling pp. 1-28

Emily R Bozich, Xiaolu Guo, Jennifer L Wilson and Alexander Hoffmann

Ten simple rules for leading a many-author non-empirical paper pp. 1-16

Tracey L Weissgerber, Natascha Drude, Rima-Maria Rahal and Friederike E Kohrs

Emergence of cooperation promoted by higher-order strategy updates pp. 1-21

Dini Wang, Peng Yi, Yiguang Hong, Jie Chen and Gang Yan

Modelling the effects of adult emergence on the surveillance and age distribution of medically important mosquitoes pp. 1-21

Isaac J Stopard, Ellie Sherrard-Smith, Hilary Ranson, Kobié Hyacinthe Toe, Jackie Cook, Joseph Biggs, Ben Lambert and Thomas S Churcher

Nonparametric serial interval estimation with uniform mixtures pp. 1-21

Oswaldo Gressani and Niel Hens

Maynard Smith revisited: A multi-agent reinforcement learning approach to the coevolution of signalling behaviour pp. 1-18

Olivia Macmillan-Scott and Mirco Musolesi

Volume 21, issue 7, 2025

Ten simple rules for developing a training program pp. 1-6

Leanna B Blevins, Amy M Harrigan, Kevin A Janes and Jason A Papin

From imaging to computational domains for physics-driven molecular biology simulations: Hindered diffusion in platelet masses pp. 1-18

Catherine House, Ziyi Huang, Kaushik N Shankar, Sandra J Young, Meghan E Roberts, Scott L Diamond, Maurizio Tomaiuolo, Timothy J Stalker, Lu Lu and Talid Sinno

Ten simple rules for faculty members building just and equitable environments in academic science pp. 1-18

Veronica Martinez Acosta, Carlita Favero, Barbara Lom, Deanne Buffalari, Amy Jo Stavnezer and Leah Chase

Statistical analysis supports the size control mechanism of Chlamydia development pp. 1-18

Jinsu Kim, Christine Sütterlin, Ming Tan and German Enciso

Single-cell mutational burden distributions in birth–death processes pp. 1-18

Christo Morison, Dudley Stark and Weini Huang

PoweREST: Statistical power estimation for spatial transcriptomics experiments to detect differentially expressed genes between two conditions pp. 1-18

Lan Shui, Anirban Maitra, Ying Yuan, Ken Lau, Harsimran Kaur, Liang Li, Ziyi Li and Translational and Basic Science Research in Early Lesions Research Consortia

Tracking causal pathways in TMS-evoked brain responses pp. 1-18

Jinming Xiao, Qing Yin, Lei Li, Yao Meng, Xiaobo Liu, Wanrou Hu, Xinyue Huang, Yu Feng, Xiaolong Shan, Weixing Zhao, Peng Wang, Xiaotian Wang, Youyi Li, Huafu Chen and Xujun Duan

Analyzing greedy vaccine allocation algorithms for metapopulation disease models pp. 1-26

Jeffrey Keithley, Akash Choudhuri, Bijaya Adhikari and Sriram V Pemmaraju

A Bayesian hierarchical model of trial-to-trial fluctuations in decision criterion pp. 1-21

Robin Vloeberghs, Anne E Urai, Kobe Desender and Scott W Linderman

Identifying predictors and assessing causal effect on hypertension risk among adults using Double Machine Learning models: Insights from Bangladesh Demographic and Health Survey pp. 1-22

Probir Kumar Ghosh, Md Aminul Islam, Md Ahshanul Haque, Md Tariqujjaman, Novel Chandra Das, Mohammad Ali, Md Rasel Uddin and Md Golam Dostogir Harun

Perceptual clustering in auditory streaming pp. 1-25

Nathanael Larigaldie, Tim Yates and Ulrik R Beierholm

Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome pp. 1-27

Tarun Mahajan and Sergei Maslov

Anatomical-electrical coupling of cardiac axes: Definitions and population variability for advancing personalised ECG interpretation pp. 1-24

Mohammad Kayyali, Ana Mincholé, Shuang Qian, Alistair Young, Devran Ugurlu, Elliot Fairweather, Steven Niederer, John Whitaker, Martin Bishop and Pablo Lamata

How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors pp. 1-19

Rui Wang and Tamar Schlick

bmdrc: Python package for quantifying phenotypes from chemical exposures with benchmark dose modeling pp. 1-8

David J Degnan, Lisa M Bramer, Lisa Truong, Robyn L Tanguay, Sara M Gosline and Katrina M Waters

Ten quick tips for navigating intellectual property in FAIR educational resources pp. 1-10

Eva Maria Funk, Ulf Toelch, Rebecca Ludwig and Silke Kniffert

Ten simple rules for thriving in a post-baccalaureate research program pp. 1-14

Michaelle E DiMaggio-Potter, Angelica Velosa, John C Brent Iv, Osmar Del Rio, Eyerusalem F Abebaw, Fernando Aguilar-Ortega, Dante Rogers, Patrick E Rothwell and Angeline J Dukes

Disentangling signal and noise in neural responses through generative modeling pp. 1-33

Kendrick Kay, Jacob S Prince, Thomas Gebhart, Greta Tuckute, Jingyang Zhou, Thomas Naselaris and Heiko H Schütt

Time-series modeling of epidemics in complex populations: Detecting changes in incidence volatility over time pp. 1-12

Rachael Aber, Yanming Di and Benjamin D Dalziel

Ten simple rules for navigating AI in science pp. 1-12

Aidan Crilly, Alice Malivert, Andreas Christ Sølvsten Jørgensen, Claire E Heaney, Gema I Vera Gonzalez, Marcus Ghosh, Manolo Fernandez Perez, Mikael M Mieskolainen, Mohammed Azzouzi and Zhenzhu Li

Ten simple rules for success as a trainee-led outreach organization in computational biology education pp. 1-12

Jennifer Blanc, Margaret C Steiner, Lauren E Blake, Elizabeth Gibbons, Mariadaria K Ianni-Ravn, Roxroy C Morgan, Suzanna Parkinson, Christian Porras and Ethan Zhong

Waveform distortion for temperature compensation and synchronization in circadian rhythms: An approach based on the renormalization group method pp. 1-23

Shingo Gibo, Teiji Kunihiro, Tetsuo Hatsuda and Gen Kurosawa

EUP: Enhanced cross-species prediction of ubiquitination sites via a conditional variational autoencoder network based on ESM2 pp. 1-23

Junhao Liu, Zeyu Luo, Rui Wang, Xin Li, Yawen Sun, Zongqing Chen and Yu-Juan Zhang

Volume 21, issue 6, 2025

Fusing multisensory signals across channels and time pp. 1-16

Swathi Anil, Dan F M Goodman and Marcus Ghosh

Variance in C. elegans gut bacterial load suggests complex host-microbe dynamics pp. 1-28

Satya Spandana Boddu, K Michael Martini, Ilya Nemenman and Nic M Vega

Predicting neuronal firing from calcium imaging using a control theoretic approach pp. 1-18

Nicholas A Rondoni, Fan Lu, Daniel B Turner-Evans and Marcella Gomez

Features influencing the health and economic impact of preventing COVID-19 in immunocompromised individuals pp. 1-18

Siyu Chen, Sudhir Venkatesan, Sofie Arnetorp, Klas Bergenheim, Sabada Dube, Wilhelmine Meeraus, Cátia Ferreira, Sylvia Taylor and Lisa J White

Computing generalized cophenetic distances under all Lp norms: A near-linear time algorithmic framework pp. 1-21

Paweł Górecki, Alexey Markin, Sriram Vijendran and Oliver Eulenstein

Designing diverse and high-performance proteins with a large language model in the loop pp. 1-21

Carlos A Gomez-Uribe, Japheth Gado and Meiirbek Islamov

Identifiability of phenotypic adaptation from low-cell-count experiments and a stochastic model pp. 1-21

Alexander P Browning, Rebecca M Crossley, Chiara Villa, Philip K Maini, Adrianne L Jenner, Tyler Cassidy and Sara Hamis

A mathematical model suggests collectivity and inconstancy enhance the efficiency of neuronal migration in the adult brain pp. 1-26

Daiki Wakita, Yuriko Sobu, Naoko Kaneko and Takeshi Kano

The role of learned song in the evolution and speciation of Eastern and Spotted towhees pp. 1-26

Ximena León Du’Mottuchi and Nicole Creanza

Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology pp. 1-26

Yuxi Long and Bruce R Donald

Synthetic method of analogues for emerging infectious disease forecasting pp. 1-17

Alexander C Murph, G Casey Gibson, Elizabeth B Amona, Lauren J Beesley, Lauren A Castro, Sara Y Del Valle and Dave Osthus

Multimodal CustOmics: A unified and interpretable multi-task deep learning framework for multimodal integrative data analysis in oncology pp. 1-23

Hakim Benkirane, Maria Vakalopoulou, David Planchard, Julien Adam, Ken Olaussen, Stefan Michiels and Paul-Henry Cournède

Computations that sustain neural feature selectivity across processing stages pp. 1-23

Ryan J Rowekamp and Tatyana O Sharpee

Energy optimization induces predictive-coding properties in a multi-compartment spiking neural network model pp. 1-23

Mingfang Zhang, Raluca Chitic and Sander M Bohté

OrgaCCC: Orthogonal graph autoencoders for constructing cell-cell communication networks on spatial transcriptomics data pp. 1-29

Xixuan Feng, Shuqin Zhang and Limin Li

MVHGCN: Predicting circRNA-disease associations with multi-view heterogeneous graph convolutional neural networks pp. 1-20

Yan Miao, Xuan Tang, Chunyu Wang, Zhenyuan Sun, Guohua Wang and Shan Huang

Stochastic gene expression in proliferating cells: Differing noise intensity in single-cell and population perspectives pp. 1-24

Zhanhao Zhang, Iryna Zabaikina, Cesar Nieto, Zahra Vahdat, Pavol Bokes and Abhyudai Singh

Ten simple rules for effectively assessing lab environments pp. 1-8

Kristen M Naegle, Jeffrey J Saucerman, Julie Leonard-Duke, Michael Rariden and Yonathan Tamrat Aberra

Nonequilibrium brain dynamics elicited as the origin of perturbative complexity pp. 1-19

Wiep Stikvoort, Eider Pérez-Ordoyo, Iván Mindlin, Anira Escrichs, Jacobo D Sitt, Morten L Kringelbach, Gustavo Deco and Yonatan Sanz Perl

Uncovering the impact of randomness in HIV hotspot formation: A mathematical modeling study pp. 1-19

Nao Yamamoto, Daniel T Citron, Samuel M Mwalili, Duncan K Gathungu, Diego F Cuadros and Anna Bershteyn

Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold pp. 1-19

Samuel Eriksson Lidbrink, Rebecca J Howard, Nandan Haloi and Erik Lindahl

GABAergic neurons can facilitate the propagation of cortical spreading depolarization: experiments in mouse neocortical slices and a novel neural field computational model pp. 1-22

Emre Baspinar, Martina Simonti, Hadi Srour, Mathieu Desroches, Daniele Avitabile and Massimo Mantegazza

Indirect punishment can outperform direct punishment in promoting cooperation in structured populations pp. 1-13

Yujia Wen, Zhixue He, Chen Shen and Jun Tanimoto

Impact of symmetry in local learning rules on predictive neural representations and generalization in spatial navigation pp. 1-37

Janis Keck, Caswell Barry, Christian F Doeller and Jürgen Jost

Uncertainty-aware traction force microscopy pp. 1-32

Adithan Kandasamy, Yi-Ting Yeh, Ricardo Serrano, Mark Mercola and Juan C del Alamo

Volume 21, issue 5, 2025

Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data pp. 1-24

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

Knowledge-aware contrastive heterogeneous molecular graph learning pp. 1-24

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

Optimization hardness constrains ecological transients pp. 1-24

William Gilpin

Parallel synapses with transmission nonlinearities enhance neuronal classification capacity pp. 1-20

Yuru Song and Marcus K Benna

Scoring protein-ligand binding structures through learning atomic graphs with inter-molecular adjacency pp. 1-20

Debby D Wang and Yuting Huang

Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation pp. 1-30

Wenjun Zhao, Erica Larschan, Björn Sandstede and Ritambhara Singh

Expectation generation and its effect on subsequent pain and visual perception pp. 1-30

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

Inferring synaptic transmission from the stochastic dynamics of the quantal content: An analytical approach pp. 1-22

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

Conformal prediction for uncertainty quantification in dynamic biological systems pp. 1-22

Alberto Portela, Julio R Banga and Marcos Matabuena

BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models pp. 1-25

Joseph James Tharayil, Jorge Blanco Alonso, Silvia Farcito, Bryn Lloyd, Armando Romani, Elvis Boci, Antonino Cassara, Felix Schürmann, Esra Neufeld, Niels Kuster and Michael Reimann

Stimulus uncertainty and relative reward rates determine adaptive responding in perceptual decision-making pp. 1-35

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

MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures pp. 1-27

Yuxiang Zhan, Francesco Musella and Frank Alber

Generative AI mitigates representation bias and improves model fairness through synthetic health data pp. 1-23

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

Colonization times in Moran process on graphs pp. 1-12

Lenka Kopfová and Josef Tkadlec

Modeling opioid overdose events recurrence with a covariate-adjusted triggering point process pp. 1-15

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

Building momentum: A computational account of persistence toward long-term goals pp. 1-39

Sneha Aenugu and John P O’Doherty

The effects of the post-delay epochs on working memory error reduction pp. 1-29

Zeyuan Ye, Haoran Li, Liang Tian and Changsong Zhou

Noise correlations and neuronal diversity may limit the utility of winner-take-all readout in a pop out visual search task pp. 1-29

Ori Hendler, Ronen Segev and Maoz Shamir

Optical Neuroimage Studio (OptiNiSt): Intuitive, scalable, extendable framework for optical neuroimage data analysis pp. 1-14

Yukako Yamane, Yuzhe Li, Keita Matsumoto, Ryota Kanai, Miles Desforges, Carlos Enrique Gutierrez and Kenji Doya

Ten quick tips to perform meaningful and reproducible molecular docking calculations pp. 1-18

Elvis A F Martis and Stéphane Téletchéa

OmniSegger: A time-lapse image analysis pipeline for bacterial cells pp. 1-18

Teresa W Lo, Kevin J Cutler, H James Choi and Paul A Wiggins

Capturing the emergent dynamical structure in biophysical neural models pp. 1-36

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

Many roads to minimizing regret: A comparison of Wang et al (2024) and OpAL* models of adaptive striatal dopamine pp. 1-5

Joshua TS Hewson, Alana Jaskir and Michael J Frank

Macroecological patterns in experimental microbial communities pp. 1-31

William R Shoemaker, Álvaro Sánchez and Jacopo Grilli

Mechanisms of mistrust: A Bayesian account of misinformation learning pp. 1-26

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

M-band wavelet-based multi-view clustering of cells pp. 1-16

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

Cellular morphodynamics as quantifiers for functional states of resident tissue macrophages in vivo pp. 1-28

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

Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells pp. 1-28

Owen M O’Connor and Mary J Dunlop

Volume 21, issue 4, 2025

The confidence-noise confidence-boost (CNCB) model of confidence rating data pp. 1-25

Pascal Mamassian and Vincent de Gardelle

Modeling diffusive search by non-adaptive sperm: Empirical and computational insights pp. 1-25

Benjamin M Brisard, Kylie D Cashwell, Stephanie M Stewart, Logan M Harrison, Aidan C Charles, Chelsea V Dennis, Ivie R Henslee, Ethan L Carrow, Heather A Belcher, Debajit Bhowmick, Paul W Vos, Maciej Majka, Martin Bier, David M Hart and Cameron A Schmidt

Quantifying expression and metabolic activity of genes regulated by pregnane X receptor in primary human hepatocyte spheroids pp. 1-25

Lukáš Lochman, Ellen Tanaka Kahiya, Bechara Saade, Tomáš Smutný, Jurjen Duintjer Tebbens, Petr Pávek and Veronika Bernhauerová

Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory pp. 1-19

Atsushi Matsuda and Mohammad R K Mofrad

Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2 pp. 1-19

Emma B Hodcroft, Martin S Wohlfender, Richard A Neher, Julien Riou and Christian L Althaus

On the validity of electric brain signal predictions based on population firing rates pp. 1-29

Torbjørn V Ness, Tom Tetzlaff, Gaute T Einevoll and David Dahmen

Quantifying the impact of contact tracing interview prioritisation strategies on disease transmission: A modelling study pp. 1-14

Logan Wu, Christopher M Baker, Nicholas Tierney, Kylie Carville, Jodie McVernon, Nick Golding, James M McCaw and Freya M Shearer

scPEDSSC: proximity enhanced deep sparse subspace clustering method for scRNA-seq data pp. 1-15

Xiaopeng Wei, Jingli Wu, Gaoshi Li, Jiafei Liu, Xi Wu and Chang He

A generalized higher-order correlation analysis framework for multi-omics network inference pp. 1-33

Weixuan Liu, Katherine A Pratte, Peter J Castaldi, Craig Hersh, Russell P Bowler, Farnoush Banaei-Kashani and Katerina J Kechris

Heuristic energy-based cyclic peptide design pp. 1-33

Qiyao Zhu, Vikram Khipple Mulligan and Dennis Shasha

Dynamic brain connectivity predicts emotional arousal during naturalistic movie-watching pp. 1-26

Jin Ke, Hayoung Song, Zihan Bai, Monica D Rosenberg and Yuan Chang Leong

Including population and environmental dynamic heterogeneities in continuum models of collective behaviour with applications to locust foraging and group structure pp. 1-21

Fillipe Georgiou, Camille Buhl, J E F Green, Bishnu Lamichhane and Ngamta Thamwattana

Federated epidemic surveillance pp. 1-21

Ruiqi Lyu, Roni Rosenfeld and Bryan Wilder

Balancing complexity, performance and plausibility to meta learn plasticity rules in recurrent spiking networks pp. 1-21

Basile Confavreux, Everton J Agnes, Friedemann Zenke, Henning Sprekeler and Tim P Vogels

A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes pp. 1-21

Ihab Hashem, Jian Wang and Jan FM Van Impe

Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City pp. 1-21

Renquan Zhang, Jilei Tai, Qing Yao, Wan Yang, Kai Ruggeri, Jeffrey Shaman and Sen Pei

Joint estimation of hand-foot-mouth disease model and prediction in korea using the ensemble kalman filter pp. 1-21

Wasim Abbas, Sieun Lee and Sangil Kim

Foraging animals use dynamic Bayesian updating to model meta-uncertainty in environment representations pp. 1-41

James Webb, Paul Steffan, Benjamin Y Hayden, Daeyeol Lee, Caleb Kemere and Matthew McGinley

A teaching proposal for a short course on biomedical data science pp. 1-16

Davide Chicco and Vasco Coelho

Ten quick tips to get you started with Bayesian statistics pp. 1-13

Olivier Gimenez, Andy Royle, Marc Kéry and Chloé R Nater

DelaySSA: stochastic simulation of biochemical systems and gene regulatory networks with or without time delays pp. 1-13

Ziyan Jin, Xinyi Zhou and Zhaoyuan Fang

Biases in neural population codes with a few active neurons pp. 1-13

Sander W Keemink and Mark CW van Rossum

TGF-M: Topology-augmented geometric features enhance molecular property prediction pp. 1-22

Wei He, Xu Tian, Xue Li, Peifu Han, Shuang Wang, Lin Liu and Tao Song

Simulating dynamic insecticide selection pressures for resistance management in mosquitoes assuming polygenic resistance pp. 1-37

Neil Philip Hobbs and Ian Hastings

Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model pp. 1-37

Ian Roberts, Richard G Everitt, Jere Koskela and Xavier Didelot

A computational account of multiple motives guiding context-dependent prosocial behavior pp. 1-34

Claire Lugrin, Jie Hu and Christian C Ruff

The multiscale self-similarity of the weighted human brain connectome pp. 1-20

Laia Barjuan, Muhua Zheng and M Ángeles Serrano

RMPJ: An ImageJ plugin for morphological information processing in biomedical images pp. 1-10

Yoshitaka Kimori

How distinct sources of nuisance variability in natural images and scenes limit human stereopsis pp. 1-42

David N White and Johannes Burge

An evolutionary model of rhythmic accelerando in animal vocal signalling pp. 1-12

Yannick Jadoul, Taylor A Hersh, Elias Fernández Domingos, Marco Gamba, Livio Favaro and Andrea Ravignani

A new paradigm considering multicellular adhesion, repulsion and attraction represent diverse cellular tile patterns pp. 1-23

Jose A Carrillo, Hideki Murakawa, Makoto Sato and Miaoxing Wang

Limitations and optimizations of cellular lineages tracking pp. 1-18

Nava Leibovich and Sidhartha Goyal

MINT: A toolbox for the analysis of multivariate neural information coding and transmission pp. 1-18

Gabriel Matías Lorenz, Nicola Marie Engel, Marco Celotto, Loren Koçillari, Sebastiano Curreli, Tommaso Fellin and Stefano Panzeri

Falsifying computational models of endothelial cell network formation through quantitative comparison with in vitro models pp. 1-18

Tessa M Vergroesen, Vincent Vermeulen and Roeland M H Merks

Meta-Reinforcement Learning reconciles surprise, value, and control in the anterior cingulate cortex pp. 1-18

Tim Vriens, Eliana Vassena, Giovanni Pezzulo, Gianluca Baldassarre and Massimo Silvetti

Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out pp. 1-18

Ben Williams, Santiago M Balvanera, Sarab S Sethi, Timothy AC Lamont, Jamaluddin Jompa, Mochyudho Prasetya, Laura Richardson, Lucille Chapuis, Emma Weschke, Andrew Hoey, Ricardo Beldade, Suzanne C Mills, Anne Haguenauer, Frederic Zuberer, Stephen D Simpson, David Curnick and Kate E Jones

Statistical signature of subtle behavioral changes in large-scale assays pp. 1-28

Alexandre Blanc, François Laurent, Alex Barbier-Chebbah, Hugues Van Assel, Benjamin T Cocanougher, Benjamin MW Jones, Peter Hague, Marta Zlatic, Rayan Chikhi, Christian L Vestergaard, Tihana Jovanic, Jean-Baptiste Masson and Chloé Barré

Dynamic modeling of EEG responses to natural speech reveals earlier processing of predictable words pp. 1-28

Jin Dou, Andrew J Anderson, Aaron S White, Samuel V Norman-Haignere and Edmund C Lalor

Volume 21, issue 3, 2025

DySCo: A general framework for dynamic functional connectivity pp. 1-32

Giuseppe de Alteriis, Oliver Sherwood, Alessandro Ciaramella, Robert Leech, Joana Cabral, Federico E Turkheimer and Paul Expert

GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data pp. 1-25

Simonida Zehr, Sebastian Wolf, Thomas Oellerich, Matthias S Leisegang, Ralf P Brandes, Marcel H Schulz and Timothy Warwick

Synthetic population generation with public health characteristics for spatial agent-based models pp. 1-22

Emma Von Hoene, Amira Roess, Hamdi Kavak and Taylor Anderson

Efficient numerosity estimation under limited time pp. 1-22

Joseph A Heng, Michael Woodford and Rafael Polania

Suprachiasmatic nucleus-wide estimation of oscillatory temporal dynamics pp. 1-22

Yifan Yao, Scott Pauls, Duncan Foley, Tomoko Yoshikawa, Sato Honma, Ken-Ichi Honma, Ellie McVeigh, Nicolas C Foley and Rae Silver

Computational studies reveal structural characterization and novel families of Puccinia striiformis f. sp. tritici effectors pp. 1-26

Raheel Asghar, Nan Wu, Noman Ali, Yulei Wang and Mahinur Akkaya

Gauge fixing for sequence-function relationships pp. 1-24

Anna Posfai, Juannan Zhou, David M McCandlish and Justin B Kinney

Post-processing and weighted combination of infectious disease nowcasts pp. 1-24

André Victor Ribeiro Amaral, Daniel Wolffram, Paula Moraga and Johannes Bracher

Exploring the transmission of cognitive task information through optimal brain pathways pp. 1-28

Zhengdong Wang, Yifeixue Yang, Ziyi Huang, Wanyun Zhao, Kaiqiang Su, Hengcheng Zhu and Dazhi Yin

Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills pp. 1-28

Russell Dinnage and Marian Kleineberg

Volume 21, issue 2, 2025

Early detection of disease outbreaks and non-outbreaks using incidence data: A framework using feature-based time series classification and machine learning pp. 1-21

Shan Gao, Amit K Chakraborty, Russell Greiner, Mark A Lewis and Hao Wang

Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities pp. 1-21

Lars Berling, Jonathan Klawitter, Remco Bouckaert, Dong Xie, Alex Gavryushkin and Alexei J Drummond

Nowcasting reported covid-19 hospitalizations using de-identified, aggregated medical insurance claims data pp. 1-26

Xueda Shen, Aaron Rumack, Bryan Wilder and Ryan J Tibshirani

Using a multi-strain infectious disease model with physical information neural networks to study the time dependence of SARS-CoV-2 variants of concern pp. 1-26

Wenxuan Li, Xu Chen, Suli Liu, Chiyu Zhang and Guyue Liu

Hexagons all the way down: grid cells as a conformal isometric map of space pp. 1-26

Vemund Sigmundson Schøyen, Kosio Beshkov, Markus Borud Pettersen, Erik Hermansen, Konstantin Holzhausen, Anders Malthe-Sørenssen, Marianne Fyhn and Mikkel Elle Lepperød

Identification of recurrent dynamics in distributed neural populations pp. 1-26

Rodrigo Osuna-Orozco, Edward Castillo, Kameron Decker Harris and Samantha R Santacruz

Information transmission in a cell monolayer: A numerical study pp. 1-24

Paweł Nałęcz-Jawecki, Przemysław Szyc, Frederic Grabowski, Marek Kochańczyk and Tomasz Lipniacki

A SuperLearner-based pipeline for the development of DNA methylation-derived predictors of phenotypic traits pp. 1-20

Dennis Khodasevich, Nina Holland, Lars van der Laan and Andres Cardenas

Compression-enabled interpretability of voxelwise encoding models pp. 1-20

Fatemeh Kamali, Amir Abolfazl Suratgar, Mohammadbagher Menhaj and Reza Abbasi-Asl

An application of nowcasting methods: Cases of norovirus during the winter 2023/2024 in England pp. 1-20

Jonathon Mellor, Maria L Tang, Emilie Finch, Rachel Christie, Oliver Polhill, Christopher E Overton, Ann Hoban, Amy Douglas, Sarah R Deeny and Thomas Ward

Repeated games with partner choice pp. 1-19

Christopher Graser, Takako Fujiwara-Greve, Julián García and Matthijs van Veelen

Reliability-enhanced data cleaning in biomedical machine learning using inductive conformal prediction pp. 1-27

Xianghao Zhan, Qinmei Xu, Yuanning Zheng, Guangming Lu and Olivier Gevaert

Bayesian classification of OXPHOS deficient skeletal myofibres pp. 1-22

Jordan Childs, Tiago Bernardino Gomes, Amy E Vincent, Andrew Golightly and Conor Lawless

SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data pp. 1-22

Shunsuke A Sakai, Ryosuke Nomura, Satoi Nagasawa, SungGi Chi, Ayako Suzuki, Yutaka Suzuki, Mitsuho Imai, Yoshiaki Nakamura, Takayuki Yoshino, Shumpei Ishikawa, Katsuya Tsuchihara, Shun-Ichiro Kageyama and Riu Yamashita

Optimal control prevents itself from eradicating stochastic disease epidemics pp. 1-25

Rachel Russell and Nik J Cunniffe

Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA pp. 1-23

Eliezyer Fermino de Oliveira, Pranjal Garg, Jens Hjerling-Leffler, Renata Batista-Brito and Lucas Sjulson

AWGE-ESPCA: An edge sparse PCA model based on adaptive noise elimination regularization and weighted gene network for Hermetia illucens genomic data analysis pp. 1-23

Rui Miao, Hao-Yang Yu, Bing-Jie Zhong, Hong-Xia Sun and Qiang Xia

ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature pp. 1-33

Luca Musella, Alejandro Afonso Castro, Xin Lai, Max Widmann and Julio Vera

Ten quick tips to build a Model Life Cycle pp. 1-10

Timothée Poisot, Daniel J Becker, Cole B Brookson, Ellie Graeden, Sadie J Ryan, Gemma Turon and Colin Carlson

Ten simple rules for fostering creativity in research labs pp. 1-7

Matthias C Rillig

Volume 21, issue 1, 2025

Multi-region infectious disease prediction modeling based on spatio-temporal graph neural network and the dynamic model pp. 1-26

Xiaoyi Wang and Zhen Jin

Integration of unpaired single cell omics data by deep transfer graph convolutional network pp. 1-21

Yulong Kan, Yunjing Qi, Zhongxiao Zhang, Xikeng Liang, Weihao Wang and Shuilin Jin

Ten simple rules for good model-sharing practices pp. 1-21

Ismael Kherroubi Garcia, Christopher Erdmann, Sandra Gesing, Michael Barton, Lauren Cadwallader, Geerten Hengeveld, Christine R Kirkpatrick, Kathryn Knight, Carsten Lemmen, Rebecca Ringuette, Qing Zhan, Melissa Harrison, Feilim Mac Gabhann, Natalie Meyers, Cailean Osborne, Charlotte Till, Paul Brenner, Matt Buys, Min Chen, Allen Lee, Jason Papin and Yuhan Rao

Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data pp. 1-21

Xu Shi, Xiao Wang, Lu Jin, Leena Halakivi-Clarke, Robert Clarke, Andrew F Neuwald and Jianhua Xuan

Extracting the fingerprints of sequences of random rhythmic auditory stimuli from electrophysiological data pp. 1-18

Fernando A Najman, Antonio Galves, Marcela Svarc and Claudia D Vargas

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data pp. 1-28

Evan Gorstein, Rosa Aghdam and Claudia Solís-Lemus

A robust transfer learning approach for high-dimensional linear regression to support integration of multi-source gene expression data pp. 1-16

Lulu Pan, Qian Gao, Kecheng Wei, Yongfu Yu, Guoyou Qin and Tong Wang

Sparse high-dimensional decomposition of non-primary auditory cortical receptive fields pp. 1-30

Shoutik Mukherjee, Behtash Babadi and Shihab Shamma

The calcitron: A simple neuron model that implements many learning rules via the calcium control hypothesis pp. 1-30

Toviah Moldwin, Li Shay Azran and Idan Segev

Benchmarking uncertainty quantification for protein engineering pp. 1-19

Kevin P Greenman, Ava P Amini and Kevin K Yang

Role and modulation of various spinal pathways for human upper limb control in different gravity conditions pp. 1-20

Alice Bruel, Lina Bacha, Emma Boehly, Constance De Trogoff, Luca Represa, Gregoire Courtine and Auke Ijspeert

Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers pp. 1-20

Kwang Su Kim, Masashi Iwamoto, Kosaku Kitagawa, Hyeongki Park, Sanae Hayashi, Senko Tsukuda, Takeshi Matsui, Masanori Atsukawa, Kentaro Matsuura, Natthaya Chuaypen, Pisit Tangkijvanich, Lena Allweiss, Takara Nishiyama, Naotoshi Nakamura, Yasuhisa Fujita, Eiryo Kawakami, Shinji Nakaoka, Masamichi Muramatsu, Kazuyuki Aihara, Takaji Wakita, Alan S Perelson, Maura Dandri, Koichi Watashi, Shingo Iwami and Yasuhito Tanaka

Optimal control of agent-based models via surrogate modeling pp. 1-27

Luis L Fonseca, Lucas Böttcher, Borna Mehrad and Reinhard C Laubenbacher

Mechanisms for dysregulation of excitatory-inhibitory balance underlying allodynia in dorsal horn neural subcircuits pp. 1-37

Alexander G Ginsberg, Scott F Lempka, Bo Duan, Victoria Booth and Jennifer Crodelle

Data-driven discovery and parameter estimation of mathematical models in biological pattern formation pp. 1-25

Hidekazu Hishinuma, Hisako Takigawa-Imamura and Takashi Miura

Eight quick tips for biologically and medically informed machine learning pp. 1-13

Luca Oneto and Davide Chicco

Bayesian active sound localisation: To what extent do humans perform like an ideal-observer? pp. 1-22

Glen McLachlan, Piotr Majdak, Jonas Reijniers, Michael Mihocic and Herbert Peremans

Exploiting the similarity of dissimilarities for biomedical applications and enhanced machine learning pp. 1-12

Mohammad Neamul Kabir, Li Rong Wang and Wilson Wen Bin Goh

Learning predictive signatures of HLA type from T-cell repertoires pp. 1-15

María Ruiz Ortega, Mikhail V Pogorelyy, Anastasia A Minervina, Paul G Thomas, Thierry Mora and Aleksandra M Walczak

Trajectory inference from single-cell genomics data with a process time model pp. 1-33

Meichen Fang, Gennady Gorin and Lior Pachter

Ten simple rules to complete successfully a computational MSc thesis project pp. 1-10

Edoardo Saccenti and Cristina Furlan

Deciphering the interplay between biology and physics with a finite element method-implemented vertex organoid model: A tool for the mechanical analysis of cell behavior on a spherical organoid shell pp. 1-29

Julien Laussu, Deborah Michel, Léa Magne, Stephane Segonds, Steven Marguet, Dimitri Hamel, Muriel Quaranta-Nicaise, Frederick Barreau, Emmanuel Mas, Vincent Velay, Florian Bugarin and Audrey Ferrand

Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense pp. 1-29

Nicole M Moody, Cole M Williams, Sohini Ramachandran and Matthew J Fuxjager