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Content
September 2026, Volume 22, Issue 9
- 1-1 Quantification of beta-cell carrying capacity in prediabetes
by Aurore Woller & Yuval Tamir & Alon Bar & Avi Mayo & Michal Rein & Anastasia Godneva & Netta Mendelson Cohen & Eran Segal & Yoel Toledano & Smadar Shilo & Didier Gonze & Uri Alon - 1-7 When models choose metrics: Hidden geometry in computational biology
by Dillion M Fox - 1-8 Twelve quick tips for designing AI-driven HPC workflows
by Jamie J Alnasir - 1-12 Ten quick tips for spatial transcriptomics analysis
by Nagomi Kurogi & Koki Shimbara & Tatsuya Koreeda & Koki Tsuyuzaki - 1-13 malariasimple: An R package for fast simulations of malaria transmission
by Debbie Shackleton & Neil Ferguson & Lucy Okell & Tom Churcher & Pete Winskill - 1-17 A spectral framework for measuring diversity in multiple sequence alignments
by Vaitea Opuu - 1-17 Monte Carlo modeling of the formation and organization of ion channel clustering
by Nicolae Moise & Seth H Weinberg - 1-17 Inferring effective neuronal circuits via network flux counting
by Kevin S Chen & Ying-Jen Yang - 1-18 Exploring heterogeneity in mosquito exposure and attraction and its implications for malaria transmission
by Lars Kamber & Aurélien Cavelan & Melissa A Penny & Nakul Chitnis & Emma Louise Fairbanks - 1-19 Topologically-based parameter inference for agent-based model selection from spatiotemporal cellular data
by Alyssa R Wenzel & Patrick M Haughey & Kyle C Nguyen & John T Nardini & Jason M Haugh & Kevin B Flores - 1-19 Robust circular cluster-based statistics for respiration-brain coupling
by Teresa Berther & Elio Balestrieri & Martina Saltafossi & Laura Bock Paulsen & Lau M Andersen & Daniel S Kluger - 1-20 Coupling with opinion dynamics promotes prosocial behavior in multilayer networks
by Jnanajyoti Bhaumik & Naoki Masuda - 1-20 SmartHisto: Bayesian active learning for histology images
by Sriram Vijendran & Bailey Arruda & Tavis K Anderson & Oliver Eulenstein - 1-22 A real-time forecasting framework for emerging infectious diseases affecting animal populations
by Meryl Theng & Simin Lee & Andrew C Breed & Sharon Roche & Emily Sellens & Catherine Fraser & Kelly Wood & Chris P Jewell & Mark A Stevenson & Chris Baker & Simon M Firestone - 1-23 Topological potentials guiding protein self-assembly
by Ivan L A Spirandelli & Arnur Nigmetov & Dmitriy Morozov & Myfanwy E Evans - 1-24 Balanced DNA interpolation improves learning of genetic distance-informed embeddings in plants
by Lara M Kösters & Kevin Karbstein & Ladislav Hodač & Laura Albreht & Elvira Sahuquillo Balbuena & Daniel Botello & Olivier Hardy & Phebian Odufuwa & Eva Pardo Otero & Aireen Phang & Manuel Pimentel & Rosalía Piñeiro & James Smith & Peter Wilkie & Patrick Mäder & Jana Wäldchen - 1-24 Deterministic dynamics of distributional multi-agent reinforcement learning
by Clémence Bergerot & Pawel Romanczuk & Wolfram Barfuss - 1-25 R-package agentBayes: Likelihood-based statistical methods for agent-based models
by Niklas Moser & Dmitri Finkelshtein & Georgy Chargaziya & Stephen J Cornell & Sara Hamis & Jacob G Scott & Dagim Shiferaw Tadele & Otso Ovaskainen - 1-26 Sequence-free landscape inference for directed evolution
by Sebastian Towers & Jessica James & Harrison Steel & Idris Kempf - 1-26 Dynamic vibration-driven feedback shapes predator–prey interactions in an orb-weaving spider
by Hsin-Yi Hung & Abel Corver & Andrew Gordus - 1-27 A Bayesian framework for multivariate differential analysis
by Marie Chion & Arthur Leroy - 1-29 PanDelos-plus: A parallel algorithm for computing sequence homology in pangenomic analysis
by Simone Colli & Emiliano Maresi & Vincenzo Bonnici - 1-29 Data-driven modeling of spatiotemporal dynamics using multimodal imaging data
by Chunyan Li & Yutong Mao & Xiao Liu & Wenrui Hao - 1-29 Biomarker discovery and patient stratification in pancreatic cancer using incomplete multi-omics data
by Alejandra Paja-García & Rafael Romero-Becerra & Tero Aittokallio & Alberto López - 1-30 AET5: A transcriptome-guided molecular generation framework with contrastive self-supervised learning
by Zhikang Yuan & Xin Zhang & Gaoming Lin & Quan Zou & Subhashisa Swain & Yijie Ding & Prayag Tiwari & Shuofeng Yuan & Xiaoyi Guo - 1-31 Triplet-based species tree estimation: Sensitivity to gene tree rooting (or lack thereof)
by Tanjeem Azwad Zaman & Rabib Jahin Ibn Momin & Md Shamsuzzoha Bayzid - 1-35 Drift-diffusion dynamics of hippocampal replay
by Zhongxuan Wu & Xue-Xin Wei - 1-37 A unified framework for potency-oriented AMP discovery via multi-modal learning and guided sequence synthesis
by Wenyu Zhang & Yizheng Wang & Yixiao Zhai & Pinglu Zhang & Yijie Ding & Quan Zou
August 2026, Volume 22, Issue 8
- 1-1 Assessing the validity and reliability of computational phenotyping of mood
by Pablo Carrillo & Marc Benhamou & Roeland Heerema & Jean Daunizeau & Mathias Pessiglione & Fabien Vinckier - 1-7 The multi-omics fallacy in microbiome science
by Rebecca Lewandowski - 1-11 Eleven quick tips for Biomedical Federated Learning
by Kyle Ellrott & Venkat S Malladi & Jean-Christophe Bélisle-Pipon & Emek Demir & Yael Bensoussan & Serghei Mangul & Alex A T Bui & Paul C Boutros - 1-11 Ten quick tips for causal analysis of biomedical omics data
by Gleb Svinin & Rebecca Ting Jiin Loo & Nikhilesh Vasantha Kumar & Varsha Venkatesha Murthy & Dilara Uzuner Odongo & Ramón Díaz-Uriarte & Ana Conesa & Gianluca Bontempi & Susana Vinga & Ilaria Granata & Daniel Domingo-Fernández & Paola Lecca & Marieke L Kuijjer & Jesse H Krijthe & Ina Koch & Laurence Calzone & Simona Ester Rombo & Fátima Sánchez-Cabo & Enrico Glaab - 1-17 The perils of omitting omissions when modeling evidence accumulation
by Xiamin Leng & Alexander Fengler & Amitai Shenhav & Michael J Frank - 1-18 Stochastic modeling of long-legged ant A. gracilipes locomotion in laboratory experiments
by Jack Featherstone & Anouk Béraud & Meta Virant-Doberlet & Antonio Celani & Mahesh M Bandi - 1-19 Structure-aware deep learning enhances m6A prediction and reveals cell type-associated RNA structural signatures
by Mingze Sun & Di Zhang & Zhiyuan Li & Yihan Lin - 1-21 Collective posterior inference from highly variable empirical replicates
by Nadav Ben Nun & Saharon Rosset & David Gresham & Yoav Ram - 1-21 Decoding behavior with minimal and interpretable agent models
by Giorgio Nicoletti & Antonio Celani - 1-22 Mapping spatial colleague connectivity patterns from individual-level registry data to inform regional pandemic interventions
by PingPing Song & Sake J de Vlas & Tom Emery & Luc E Coffeng - 1-22 Noisy models of the ventral stream reveal the impact of recurrence and learned representations on information processing timescales
by Sara Varetti & Sebastian Goldt & Eugenio Piasini - 1-23 Simple birth-death-mutation models predict some—but not all—aspects of the experimental evolution of antibiotic resistance
by Elin Lilja & Rosalind J Allen & Bartlomiej Waclaw - 1-23 The genetic code at the balance point of error and demand
by Yudam Seo & Tsvi Tlusty & Junghyo Jo - 1-23 Non-Markovian dynamics and effective reproduction number in COVID-19: Evidence from Cyprus contact tracing data
by Pavlos Alexandros Dimitriou & Matteo D’Alessandro & Brian L Chang & Valentinos Silvestros & Elisavet Constantinou & Costas Pitris & Panayiotis Kolios & Piet Van Mieghem - 1-23 Evaluation of short-term multi-target respiratory forecasts over winter 2024-25 in England using sub-ensemble contribution analyses
by Jack Kennedy & William Ferguson & Owen Jones & Steven Riley & Thomas Ward & Maria L Tang & Jonathon Mellor - 1-23 ERFMTDA: Predicting tsRNA–disease associations using an enhanced rotative factorization machine
by Wei Lan & Dong Wang & Wenyi Chen & Xuhua Yan & Qingfeng Chen & Shirui Pan & Yi Pan - 1-23 Mechanical power output during stretch–shortening cycles of rat medial gastrocnemius muscle: Influence of various muscle length trajectories
by Edwin D H M Reuvers & Huub Maas & Wendy Noort & Maarten F Bobbert & Dinant A Kistemaker - 1-24 ScanNet: Single-cell annotation informed by transcriptional regulation Network via iterative heterogeneous graph learning
by Yongyu Long & Wenhao Zhang & Lan Cao & Xiaobing Huang & Ying Wang - 1-24 A fast numerical integration scheme for clonal expansion processes on graphs
by Chay Paterson & Miaomiao Gao & Joshua Hellier & Georg Luebeck & David C Wedge & Ivana Bozic - 1-24 CLASPP: A unified model for predicting post-translational modifications
by Nathan Gravel & Zhongliang Zhou & Ruili Fang & Austin Downes & Saber Soleymani & Natarajan Kannan - 1-25 Assessing the reliability of cellular decision making from noisy, multidimensional single-cell TNF–NF-κB signaling data
by Ali Emadi & Tomasz Lipniacki & Andre Levchenko & Ali Abdi - 1-26 Multiscale modeling of T cell exhaustion: A mathematical framework integrating continuous dynamics with spatial heterogeneity
by Chenghang Li & Yuhong Zhang & Xue Liu & Yipu Qu & Xiulan Lai & Jinzhi Lei - 1-26 Cerebellum-inspired neural network of supervised learning with tensor-based sparse coding for multi-class classification
by Runguang Zhou & Douglas Zhou & Songting Li & Xiaoyu Chen - 1-27 RareCapsNet: An explainable capsule network enables robust discovery of rare cell populations from large-scale single-cell transcriptomics
by Sumanta Ray & Snehalika Lall - 1-27 Modeling the influences of non-local connectomic projections on geometrically constrained cortical dynamics
by Rishikesan Maran & Eli J Müller & Ben D Fulcher - 1-27 Cell-specific Cahn-Hilliard models predict condensed fates of the chromosomal passenger complex
by Sarah M Groves & Min-Jhe Lu & Astrid Catalina Alvarez-Yela & Monserrat Gerardo-Ramírez & P Todd Stukenberg & John S Lowengrub & Kevin A Janes - 1-27 iDCF: Interpretable deconvolution of cell fractions via biologically-informed deep learning using scRNA-seq data
by Hongjiang Guo & Tingfang Wu & Wenzheng Wang & Yelu Jiang & Geng Li & Liangpeng Nie & Yunhua Jia & Lijun Quan & Moli Huang & Qiang Lyu - 1-28 Simulation and inference methods for non-Markovian stochastic reaction networks
by Thomas P Steele & David J Warne - 1-29 Leveraging synthetic and genetic data to improve epidemic forecasting
by Dave Osthus & Alexander C Murph & Emma E Goldberg & Lauren J Beesley & William M Fischer & Nidhi Parikh & Lauren A Castro - 1-30 Manifold-constrained plasticity enables stable learning in recurrent neural circuits
by Camille Godin & Jean-Philippe Thivierge - 1-30 Accurate de novo transcription unit annotation from run-on and sequencing data
by Paul R Munn & Jay Chia & Charles G Danko - 1-30 Improving the reliability of polygenic risk score-based prediction for cardiovascular and renal complications across ancestries in type 2 diabetes using Mondrian Cross-Conformal Prediction
by Edoh Kodji & Redha Attaoua & Mounsif Haloui & Camil Hishmih & Mirjam Seitz & Mark Woodward & Julie G Hussin & Pavel Hamet & Johanne Tremblay - 1-30 IBAS: Interaction-bridged association studies discovering novel genes underlying complex traits
by Dinghao Wang & Pathum Kossinna & Karen Ardila & Senitha Kumarapeli & M Ethan MacDonald & Jingjing Wu & Qingrun Zhang - 1-35 The SATvac model of CD8+ T cell expansion and contraction phases considering memory and effector cell differentiation
by Seyedeh Fatemeh Seyyedizadeh & David A Christian & Thomas A Adams II - 1-36 Theory and evidence of amplitude control by frequency detuning in a coupled neuronal oscillator system
by Adam C Lu & Seyed AmirHossein Ourang & Jeffrey D Moore - 1-37 Contrastive learning to fine-tune feature extraction models for the visual cortex
by Alex Mulrooney & Zhi Li & Austin J Brockmeier - 1-45 Reassessing adult surfactant replacement therapy with mechanics-informed reinforcement learning
by Philippe Meliga & Gregor Roncin & Alejandro Yepes Peñaranda & Elie Hachem
July 2026, Volume 22, Issue 7
- 1-6 Systems biology during 20 years of PLoS Computational Biology
by Mark Alber & Marc R Birtwistle & Stacey D Finley & Pedro Mendes - 1-10 ClusterApp to visualize, organize, and navigate metabolomics data
by Vinicius Hansel Figueiredo da Costa & Pothuvilage Karunarathne & Tiago Cabral Borelli & Isabela Victorino da Silva Amatto & Matheus de Lima Ortega & Robert A Quinn & Ricardo R da Silva - 1-13 CellExLink: End-to-end cell-type recognition and normalization in biomedical text
by Alimire Nabijiang & Leili Shahriyari - 1-14 htrSPRanalysis: An open source R package for expedited analysis of high-throughput binding kinetics data
by Janice M McCarthy & Kan Li & Georgia D Tomaras & S Moses Dennison - 1-16 TB-SERS analyzer: Analysis tool for tuberculosis prediction based on Raman spectroscopy with machine learning and convolutional neural network
by Jukgarin Eisiri & Chadatan Juntagran & Kanwara Trisakul & Benjawan Kaewseekhao & Noppadon Nuntawong & Chakchai So-In & Kiatichai Faksri - 1-16 A cost-optimized 5-protein panel revolutionizes systemic lupus erythematosus diagnosis
by Wenhua Lv & Zhenwei Shang & Chen Sun & Yuping Zou & Siyu Wei & Haiyan Chen & Junxian Tao & Hongsheng Tian & Yu Dong & Chen Zhang & Mingming Zhang & Hongchao Lv & Yongshuai Jiang - 1-17 Optimized phenotype definitions boost GWAS power
by Michael Zietz & Kathleen LaRow Brown & Undina Gisladottir & Nicholas P Tatonetti - 1-18 AgentBasedModeling.jl: A tool for stochastic simulation of structured population dynamics
by Paul Piho & Philipp Thomas - 1-21 Quantitative modelling of P-TEFb mediated CTD phosphorylation identifies local cooperativity
by Aaron Callenbach & Domagoj Dorešić & Robert Düster & Vanessa Nakonecnij & Erika Dudkin & Matthias Geyer & Jan Hasenauer - 1-21 HNPP: Higher-order network-based personalized PageRank for detecting critical phase in complex biological systems
by Jiayuan Zhong & Xuerong Gu & Dandan Ding & Qiao Wei & Bowen Niu & Ting Tao & Pei Chen & Rui Liu - 1-21 Ergodicity transformations predict human decision-making under risk
by Benjamin Skjold & Simon Richard Steinkamp & Colm Connaughton & Oliver James Hulme & Ole Peters - 1-21 Assessing scale and predictive diversity in models for single-cell transcriptomics based on Geneformer
by Junfan Chen & Fabian Schmidt & Ricardo Henao - 1-21 Combining sampling and attractor dynamics in spiking models of head direction systems
by Vojko Pjanovic & Jacob A Zavatone-Veth & Paul Masset & Sander W Keemink & Michele Nardin - 1-21 Whisker stimulation reinforces a resting-state network in the barrel cortex: Nested oscillations and avalanches
by Benedetta Mariani & Ramón Guevara & Mattia Tambaro & Marta Maschietto & Alessandro Leparulo & Stefano Vassanelli & Samir Suweis - 1-22 Sleep slow oscillation emergence on the scalp as a renewal point process
by Mahmoud Alipour & Sara C Mednick & Paola Malerba - 1-23 Revealing dichotomous prior biases in social anxiety through a social prism model
by Yuxi Wang & Qianqian Ju & Renhe Jia & Minghao Yuan & Yujia Peng - 1-24 Predictive coding explains asymmetric connectivity in the brain: A neural network study
by Romesa Khan & Hongsheng Zhong & Shuvam Das & Jack Cai & Matthias Niemeier - 1-24 Integrating multi-type features and knowledge graph for graded prediction of drug-induced liver injury in humans
by Ying Liu & Kaimiao Hu & Jie Geng & Qi Dai & Leyi Wei & Ran Su - 1-24 Analysis and design of disordered polypeptides with optimized sequence patterning properties
by Arjun Singh & Ali I Ukperaj & Gabriel F Porto & Gregory L Dignon - 1-25 Panorama: A robust pangenome-based method for predicting and comparing biological systems across species
by Jérôme Arnoux & Jean Mainguy & Laura Bry & Quentin Fernandez de Grado & Yazid Hoblos & David Vallenet & Alexandra Calteau - 1-26 Body surface potential driven personalisation of electrophysiological digital twins in hypertrophic cardiomyopathy
by Shambhavi Malik & Ludovica Cicci & Abdul Qayyum & Rahul Ghelani & Ji-jian Chow & Jagdeep Singh Mohal & Zachary I Whinnett & Amanda Varnava & Gernot Plank & Prapa Kanagaratnam & Steven A Niederer - 1-26 CPP2Vec: A representation learning approach for cell-penetrating peptides prediction
by Stavroula Svolou & Vasileios Konstantakos & Anastasia Krithara & Georgios Paliouras - 1-27 Mind the gap: An embedding guide to safely travel in sequence space
by Adam Wu & Jakub Lála & Quentin Trolliet & Abhinav Rajendran & Stefano Angioletti-Uberti - 1-29 Application of a uniaxial force by pulling the skin around the mammary gland may affect the orientation of the ducts and the length of the mammary ductal network: Findings from computational modeling and laboratory experiments
by Daisy Ulloa & Kelsey M Teeple & Sara B Scinto & Wonders O Ogundare & Deloris D Franklin & Theresa M Casey & Uduak Z George - 1-30 SynAPSeg: A novel dataset and image analysis framework for deep learning-based synapse detection and quantification
by Pascal Schamber & Sahana Darbhamulla & Molly Boyer & Madison Pelletier & Helene Hartman & Olivia Friedman & Shiyu Zhang & Allison Blais & Seyun Oh & Haining Zhong & Alexei M Bygrave - 1-30 NLCD: A method to discover nonlinear causal relations among genes
by Aravind Easwar & Manikandan Narayanan - 1-31 Uncertainty-aware quantitative analysis of high-throughput live cell migration data
by Simo Kitanovski & Shannon Conroy & Justin Sonneck & Lukas Claas & Madeleine Dorsch & Sebastian Urban & Jianxu Chen & Markus Kaiser & Barbara M Grüner & Daniel Hoffmann - 1-31 cpm: A python library for theory-driven modelling in computational psychiatry
by Lenard Dome & Frank H Hezemans & Kenza Kadri & Ben J Wagner & Andrew Webb & Tobias U Hauser - 1-40 Quantifying the spatiotemporal mechanical dynamics of engineered cardiac microbundles
by Hiba Kobeissi & Samuel J DePalma & Javiera Jilberto & David Nordsletten & Brendon M Baker & Emma Lejeune - 1-47 Molecular surveillance of multiplicity of infection, haplotype frequencies, and prevalence in infectious diseases
by Henri Christian Junior Tsoungui Obama & Kristan Alexander Schneider - 1-58 Population sparseness determines strength of Hebbian plasticity for maximal memory lifetime in associative networks
by Naomi Auer & Lars Chen & Jakob Stubenrauch & Benjamin Lindner & Richard Kempter
June 2026, Volume 22, Issue 6
- 1-1 Predicting continuous outcomes: Some new tests of associative approaches to contingency learning
by Julie Y L Chow & Hilary J Don & Ben Colagiuri & Evan J Livesey - 1-5 Predictive modeling in biology and medicine: Digital twins and multi-scale modeling
by Mark Alber & Amber Smith & Reinhard Laubenbacher & Roeland M H Merks - 1-8 Ten simple rules for making the supplement increase your paper’s impact
by Volker Grimm & Uta Berger & Stefano Mammola - 1-10 Ten simple rules for turning your qualifying exam into an NIH-style fellowship proposal: A guide for graduate students
by Courtney Peña-Lima & Cameron S Bader & Brendan K Ball & Troy C Dildine & Mekhala V Dissanayake & Iris van ‘t Erve & Albina Ibrayeva & Amy Nippert & MK Quinn & Chelse Spinner & Samuel Thompson & Antonio Tomasso & Crystal M Botham - 1-14 GrassSV – hybrid method to detect structural variants in high throughput DNA-seq data
by Dominik Witczak & Krzysztof Sychla & Julia Wysocka & Artur Laskowski & Wojciech Frohmberg & Marta Glowacka & Alicja Dzik & Piotr Lukasiak & Jacek Blazewicz & Aleksandra Swiercz - 1-15 A new method for augmenting short time series, with application to pain events in sickle cell disease
by Kumar Utkarsh & Nirmish R Shah & Tanvi Banerjee & Daniel M Abrams - 1-17 Heterogeneous suppressive effect of Wolbachia incompatible insect technique coupled with sterile insect technique across time and historical Ae. aegypti abundance - using distributional synthetic controls
by Yichen Zhai & Chia-Chen Chang & Zhiyong Xi & Cheong Huat Tan & Lee Ching Ng & Jue Tao Lim - 1-17 CoDaLoMic: An R package for modeling microbiome compositional and longitudinal data
by Irene Creus-Martí & Andrés Moya & Francisco J Santonja - 1-18 pyhgf: A neural network library for predictive coding
by Nicolas Legrand & Lilian Weber & Peter Thestrup Waade & Anna Hedvig Møller Daugaard & Mojtaba Khodadadi & Nace Mikuš & Christoph Mathys - 1-19 PepAnno: A structure-aware deep learning framework for bioactive peptide prediction, structural visualization, and physicochemical profiling
by Enyan Liu & Yueming Hu & Liya Liu & Yifan Chen & Shilong Zhang & Sida Li & Haoyu Chao & Luyao Xie & Yi Shen & Liangwei Wu & Julio Raúl Fernández Massó & Ming Chen - 1-19 Histology-informed spatial domain identification through multi-view graph convolutional networks
by Huihui Zhang & Jiaxing Chang & Zirong Li & Yue Sun & Pinli Hu & Haoxiu Wang & Hang Yang & Yonglin Ren & Xingtan Zhang & Zehua Chen & Kok Wai Wong & Haojing Shao - 1-20 Beyond the canonical: The role of post-transcriptional regulation in drug-target interaction prediction
by Md Istiaq Ansari & Khandakar Tanvir Ahmed & Debby D Wang & Kirill Medvedev & Wei Zhang - 1-20 Challenges and progress in RNA velocity: Comparative analysis across multiple biological contexts
by Sarah Ancheta & Leah Dorman & Guillaume Le Treut & Abel Gurung & Greg Huber & Loïc A Royer & Alejandro Granados & Merlin Lange - 1-22 Cell-type resolved transcriptional network analysis of in vivo cellular senescence following injury
by Alda Sabalic & Victoria Moiseeva & Andres Cisneros & Oleg Deryagin & Eusebio Perdiguero & Pura Muñoz-Cánoves & Jordi Garcia-Ojalvo - 1-22 scMagnifier: Resolving fine-grained cell subtypes via GRN-informed perturbations and consensus clustering
by Zhenhui He & Dong Kangning - 1-22 Heuristic multi-site optimization for protein sequence design using Masked Protein Language Models
by Lijuan Wang & Yuze Wang & Chen Qiu & Liwei Xiao & Xianliang Liu & Junjie Chen - 1-23 WormSORT: A detection-based multiple object tracking model for individual silkworms in breeding environments
by Hongkang Shi & Linbo Li & Shiping Zhu & Haibo He & Minghui Zhu & Jianfei Zhang - 1-24 On the conditions for shifts in metabolic strategies
by Maarten J Droste & Robert Planqué & Frank J Bruggeman - 1-24 MicroRNA target gene prediction model based on input-feature dependency and sample data expansion technique
by Yan Shao & Yazhou Li & Hexin Zhai & Shimin Dong - 1-24 On real-time calibrated prediction for complex model-based decision support in pandemics: Part 2
by Trevelyan J McKinley & Daniel B Williamson & Xiaoyu Xiong & James M Salter & Robert Challen & Leon Danon & Ben Youngman & Doug McNeall - 1-24 A multilevel hierarchical framework for quantification of experimental heterogeneity in population snapshot data
by David J Warne & Xiangrun Zhu & Thomas P Steele & Stuart T Johnston & Scott A Sisson & Matthew Faria & Ryan J Murphy & Alexander P Browning - 1-25 Neuronal excitability and parameter variability in the Hodgkin-Huxley model
by Alon Korngreen - 1-25 Machine learning-driven identification of virulence determinants in Borrelia burgdorferi associated with human dissemination
by Hoa Thanh Nguyen & Catherine A Brissette - 1-25 Delayed reward information is underweighted in reinforcement learning with dispersed feedback
by Miruna Cotet & David Poensgen & Ian Krajbich - 1-27 Data-driven model reveals increased stability of CAG-expanded huntingtin RNA due to MID1 binding
by Yuhong Liu & Annika Reisbitzer & Domagoj Dorešić & Jan Hasenauer & Sybille Krauß & Tatjana Tchumatchenko - 1-28 GHF-ACL: A novel contrastive learning framework with multi-order graph structures for herb-disease association prediction
by Yunmeng Zhang & Xiuhong Wu & Qiutong Wang & Lin Shi & Meiling Liu & Guohua Wang - 1-28 A mean-field model of neural networks with PV and SOM interneurons reveals connectivity-based mechanisms of gamma oscillations
by Farzin Tahvili & Martin Vinck & Matteo Di Volo - 1-31 CAdir: Joint clustering of cells and genes for single-cell transcriptomics with visualization-driven cluster quality assessment
by Clemens Kohl & Martin Vingron - 1-31 Variable selection-combined causal mediation analysis for continuous treatments with application to large-dimensional biomedical data
by Yajing Zhou & Kecheng Wei & Yahang Liu & Zhaoyang Li & Chen Huang & Guoyou Qin & Yongfu Yu - 1-34 A novel biclustering algorithm for mining m6A co-methylation patterns based on beta-binomial distribution and data screening strategy
by Zhaoyang Liu & Yuteng Xiao & Dao Xiang & Hao Shi & Kaijian Xia - 1-35 Evolution and the ultimatum game: An agent-based model with interbirth intervals and population structure
by Jeffrey C Schank & Matt L Miller
May 2026, Volume 22, Issue 5
- 1-1 MIAAIM: Multi-omics image integration with dimensional reduction for tissue state mapping
by Joshua M Hess & Richard K Dzeng & Iulian Ilieş & Denis Schapiro & John J Iskra & Divya Mirgh & John Nam & Erin H Seeley & David E Verrill & Walid M Abdelmoula & Michael S Regan & Georgios Theocharidis & Chin Lee Wu & Aristidis Veves & Nathalie Y R Agar & Ann E Sluder & Mark C Poznansky & Ruxandra F Sîrbulescu & Patrick M Reeves - 1-13 Ten simple rules for an effective mentor–mentee writing partnership
by Kristina Quynn & Megan J Hemmerlein & Alexandra H Keene-Snickers & Sarah M Howard & Mark D Stenglein & Kathryn Wilsterman & Carol J Wilusz - 1-15 Energy transfer leaves fingerprints in cyanine photoswitching behavior
by Vincent Ebert & Markus Sauer & Sören Doose - 1-16 Trial-level sequence modeling reveals hidden dynamics of dual-task interference
by Rick den Otter & Anna Dame & Sjoerd Stuit & Leendert van Maanen - 1-18 Dynamics of trachoma infection in West Africa revealed by a hidden state model
by Jake Carson & Thomas Crellen & Anna Borlase & Joaquin M Prada & Robin Bailey & T Déirdre Hollingsworth & Simon E F Spencer - 1-19 Multiplex networks-based directed graph neural network for cancer driver gene identification
by Pingting Li & Minzhu Xie - 1-19 Fast and interpretable quantification of biological shape heterogeneity via stratified Wasserstein kernel
by Wenjun Zhao & Danica J Sutherland & Khanh Dao Duc - 1-19 Limited ‘heft’ of weight-based outcomes in predicting influenza A virus disease severity in ferrets
by Troy J Kieran & Taronna R Maines & Jessica A Belser - 1-19 Network structure induced bias in estimates of intrinsic generation times
by Pratyush K Kollepara & Chiara Poletto & Joel C Miller - 1-20 A simple model captures key characteristics of biological non-deterministic genotype-phenotype maps
by Nora S Martin - 1-20 LSTM-attention-guided graph neural networks for integrated genotype–Environment modeling in maize yield prediction
by Amir Morshedian & Mike Domaratzki - 1-21 Exploring epidemic control policies using nonlinear programming and mathematical models
by Sandra Montes-Olivas & Adam J Kucharski & Michael B Gravenor & Simon DW Frost - 1-23 Extremal events dictate population growth rate inference
by Trevor GrandPre & Ethan Levien & Ariel Amir - 1-23 DREAMER-S: Deep leaRning-Enabled Attention-based Multiple-instance approaches with Explainable Representations for Spatial biology
by M Rifqi Rafsanjani & Alison Dooney & Rahul Suresh & Alice C O’Farrell & Monika A Jarzabek & Liam Shiels & Annette T Byrne & Jochen H M Prehn & Aidan D Meade - 1-24 Structural and dynamic basis of NOD2 tandem CARD association and NOD1/2–RIP2 signaling complexes
by Jitendra Maharana & Aritra Bej & Debasish Biswal & Debashis Panda & Arjun Sharma - 1-24 Efficient sequential Bayesian inference for state-space epidemic models using ensemble data assimilation
by Dhorasso Temfack & Jason Wyse - 1-25 Functional group classification using consensus clustering
by Pablo Ubilla Pavez & Andrea Paz & Daniel S Maynard - 1-28 FoMo: A unifying theory of visual foraging
by Alasdair D F Clarke & Anna E Hughes - 1-28 RNAprecis: Prediction of full-detail RNA conformation from the experimentally best-observed sparse parameters
by Henrik Wiechers & Christopher J Williams & Benjamin Eltzner & Franziska Hoppe & Michael G Prisant & Vincent B Chen & Ezra Miller & Kanti V Mardia & Jane S Richardson & Stephan F Huckemann - 1-28 PowerNovo2: A generative flow-based approach to non-autoregressive de novo peptide sequencing
by Denis V Petrovskiy & Kirill S Nikolsky & Vladimir R Rudnev & Liudmila I Kulikova & Tatiana V Butkova & Kristina A Malsagova & Arthur T Kopylov & Anna L Kaysheva - 1-28 Single-cell data integration across weakly linked modalities
by Zhipeng Zhou & Yang Zhang & Zhiming Dai - 1-28 Evaluating place cell detection methods in Rats and Humans: Implications for cross-species spatial coding
by Weijia Zhang & Thomas Donoghue & Salman E Qasim & Joshua Jacobs - 1-29 Hierarchical recurrent temporal prediction as a model of the mammalian dorsal visual pathway
by Sebastian Klavinskis-Whiting & Andrew J King & Nicol S Harper - 1-30 Fully synthetic replication of complex real biological cell clusters using a novel cluster-based ‘Rosetta-Routine’ computational modelling process
by Bradley Mason & Laura Justham & Liam Whitby & Alison Whitby & Stuart Scott & Samuel Nti & Jon Petzing - 1-34 Explainable AI-driven diagnosis model for early glaucoma detection using grey-wolf optimized extreme learning machine approach
by Debendra Muduli & Santosh Kumar Sharma & Sujata Dash & Bernardo Lemos & Saurav Mallik - 1-36 scHG: A supercell framework with high-order graph learning enables scalable multi-omics analysis
by Yixiang Huang & Yuan Gan & Xinqi Gong - 1-37 Decoupling between activation time and steady-state level in input-output responses
by Giorgio Ravanelli & Kee-Myoung Nam & Jeremy Gunawardena & Rosa Martinez-Corral - 1-46 Distilling noise characteristics and prior expectations in multisensory causal inference
by Shuze Liu & Trevor Holland & Wei Ji Ma & Luigi Acerbi
April 2026, Volume 22, Issue 4
- 1-1 Explaining attractive and repulsive biases in the subjective visual vertical
by Stefan Glasauer & W Pieter Medendorp - 1-8 Ten simple rules for postdoctoral mums to stay competitive in academia
by Belén Fadrique & Selene Báez - 1-9 Ten simple rules for organising an effective student-led writing retreat
by Nicholas W Daudt & Claudia Hird & Eleanor R M Kelly & Elli E Leinikki & Gretchen J McCarthy & Ian S Dixon-Anderson & Jackson E Beagley & Jessica B Moffitt & Joseph S Curtis & Lindsay M Wickman & Meghan L Duffy & Preston L Maluafiti & Saskia E Foreman & William Carome & Leah M Crowe - 1-10 Ten common mistakes that could ruin your enrichment analysis
by Anusuiya Bora & Matthew McKenzie & Mark Ziemann - 1-16 Semi-parametric empirical bayes method for multiplet detection in snATAC-seq with probabilistic multi-omic integration
by Yuntian Wu & Haoran Hu & Wei Chen & Johann E Gudjonsson & Lam C Tsoi & Xiaoquan Wen - 1-17 A multi-omics framework for survival mediation analysis of high-dimensional proteogenomic data
by Seungjun Ahn & Weijia Fu & Maaike van Gerwen & Lei Liu & Zhigang Li - 1-19 Rural-to-urban migrant worker mobility shaped measles epidemics in China
by Peihua Wang & Xianwen Wang & Wenyi Zhang & Yong Wang & Sen Pei & Xiao-Ke Xu & Wan Yang - 1-20 Clustering single-cell multi-omics data via weighted distance penalty and adaptive consistent graph regularization
by Wei Zhang & Yue Yu & Xiaoying Zheng & Juan Shen & Yuanyuan Li - 1-20 STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data
by Nicholas J Bradley & Sriram Pendyala & Katie Partington & Douglas M Fowler - 1-20 Efficiency, accuracy and robustness of probability generating function based parameter inference method for stochastic biochemical reactions
by Shiyue Li & Yiling Wang & Zhanpeng Shu & Ramon Grima & Qingchao Jiang & Zhixing Cao - 1-21 Forecastability of infectious disease time series: are some seasons and pathogens intrinsically more difficult to forecast?
by Lauren A White & Tomás M León - 1-21 Sharing the spotlight: Uncovering common attentional dynamics across species
by Mina Glukhova & Alejandro Tlaie & Robert Taylor & Pierre-Antoine Ferracci & Katharine Shapcott & Berkutay Mert & Olga Arne & Andrei Ciuparu & Raul C Muresan & Martha N Havenith & Marieke L Schölvinck - 1-22 Ensemble forecasts of COVID-19 activity to support Australia’s pandemic response: 2020–22
by Robert Moss & Ruarai J Tobin & Mitchell O’Hara-Wild & Adeshina I Adekunle & Dennis Liu & Tobin South & Dylan J Morris & Gerard E Ryan & Tianxiao Hao & Aarathy Babu & Katharine L Senior & James G Wood & Nick Golding & Joshua V Ross & Peter Dawson & Rob J Hyndman & David J Price & James M McCaw & Freya M Shearer - 1-22 Multidimensional scaling informed by F-statistic: Visualizing grouped microbiome data with inference
by Hyungseok Kim & Soobin Kim & Jeffrey A Kimbrel & Megan M Morris & Xavier Mayali & Cullen R Buie - 1-22 A framework for constructing insect steering circuits
by Robert Mitchell & Barbara Webb - 1-22 A Bayesian modelling framework for estimating tick-borne pathogen transmission dynamics at the host-tick interface
by Younjung Kim & Bruno Faivre & Thierry Boulinier & Célia Sineau & Clémence Galon & Sara Moutailler & Laure Bournez & Raphaëlle Métras - 1-22 Evolutionary Kuramoto dynamics unravels origins of chimera states in neural populations
by Thomas Zdyrski & Scott Pauls & Feng Fu - 1-22 Enhancing generalizability of model discovery across parameter space with multi-experiment equation learning for biological systems
by Maria-Veronica Ciocanel & John T Nardini & Kevin B Flores & Erica M Rutter & Suzanne S Sindi & Alexandria Volkening - 1-23 Leveraging mathematical models to predict and control T-cell activation
by Xabier Rey Barreiro & Jose Faro & Alejandro F Villaverde - 1-23 Learning the bistable cortical dynamics of the sleep-onset period
by Zhenxing Hu & Manaoj Aravind & Xu Lei & J Nathan Kutz & Jean-Julien Aucouturier - 1-23 Complexity of resting cortical activity predicts neurophysiological responses to theta-burst stimulation but fails to generalize: A rigorous machine-learning approach
by Matthew Herbert Ning & Haoqi Sun & Brice Passera & Duygu Bagci Das & Brandon Westover & Alvaro Pascual-Leone & Emiliano Santarnecchi & Mouhsin M Shafi & Recep A Ozdemir - 1-23 Coherent cross-modal generation of synthetic biomedical data to advance multimodal precision medicine
by Raffaele Marchesi & Nicolò Lazzaro & Walter Endrizzi & Gianluca Leonardi & Matteo Pozzi & Flavio Ragni & Stefano Bovo & Monica Moroni & Venet Osmani & Giuseppe Jurman - 1-24 How muscle ageing affects rapid goal-directed movement: mechanistic insights from a simple model
by Delyle T Polet & Christopher T Richards - 1-26 Developmental and aging changes in brain network switching dynamics revealed by EEG phase synchronization
by Dionysios Perdikis & Rita Sleimen-Malkoun & Viktor Müller & Viktor Jirsa - 1-28 Exploring neural manifolds across a wide range of intrinsic dimensions
by Jacopo Fadanni & Rosalba Pacelli & Alberto Zucchetta & Pietro Rotondo & Michele Allegra - 1-28 Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification
by Hannah Kockelbergh & Shelley C Evans & Liam Brierley & Peter L Green & Andrea L Jorgensen & Elizabeth J Soilleux & Anna Fowler - 1-33 One model to rule them all: Unification of voltage-gated potassium channel models via deep non-linear mixed effects modelling
by Domas Linkevicius & Angus Chadwick & Melanie I Stefan & David C Sterratt - 1-39 Unveiling gene perturbation effects through gene regulatory networks inference from single-cell transcriptomic data
by Clelia Corridori & Merrit Romeike & Giorgio Nicoletti & Christa Buecker & Samir Suweis & Sandro Azaele & Graziano Martello
March 2026, Volume 22, Issue 3
- 1-11 Online tutorial on survival analysis for biomarker discovery
by Jaka Kokošar & Ela Praznik & Martin Špendl & Nancy P Moreno & Alana Newell & Gad Shaulsky & Blaž Zupan - 1-14 Benchmarking spike source localization algorithms in high density probes
by Hao Zhao & Xinhe Zhang & Arnau Marin-Llobet & Xinyi Lin & Jia Liu - 1-15 napariTFM: An open-source tool for traction force microscopy and monolayer stress microscopy
by Artur Ruppel & Dennis Wörthmüller & Martial Balland & François Fagotto - 1-16 Free energy perturbations in enzyme kinetic models reveal cryptic epistasis
by Karol Buda & Nobuhiko Tokuriki - 1-18 Inverse game theory characterizes frequency-dependent selection driven by karyotypic diversity in triple negative breast cancer
by Thomas Veith & Richard J Beck & Joel S Brown & Noemi Andor - 1-18 Morphological determinants of glycosylation efficiency in Golgi cisternae
by Christopher K Revell & Martin Lowe & Nicola L Stevenson & Oliver E Jensen - 1-19 PepLM-GNN: A graph neural network framework leveraging pre-trained language models for peptide-protein binding prediction
by Ke Yan & Meijing Li & Shutao Chen & Tianyi Liu & Jing Hao & Bin Liu & Zhen Li - 1-19 ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries
by Moritz Hanke & Theresa Harten & Ronja Foraita - 1-20 Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries
by Konstantinos Antonopoulos & Olof Nordenstorm & Avlant Nilsson - 1-20 Functional bottlenecks can emerge from non-epistatic underlying traits
by Anna Ottavia Schulte & Samar Alqatari & Saverio Rossi & Francesco Zamponi - 1-21 Sub-national modelling of surveillance sensitivity to inform declaration of disease elimination: A retrospective validation against the elimination of wild poliovirus in Nigeria
by Emily S Nightingale & Ly Pham-Minh & Isah Mohammed Bello & Samuel Okrior & Tesfaye Bedada Erbeto & Marycelin Baba & Adekunle Adeneji & Megan Auzenbergs & W John Edmunds & Kathleen M O’Reilly - 1-21 Separating random and deterministic sources of computational noise in explore-exploit decisions
by Siyu Wang & Robert C Wilson - 1-21 An approximate-copula distribution for statistical modeling
by Sarah S Ji & Benjamin B Chu & Hua Zhou & Kenneth Lange - 1-21 Mechanism of Hsp70 activation: How J-domain proteins push for ATP hydrolysis
by Michał Olewniczak & Marcin Pitek & Jacek Czub & Jaroslaw Marszalek & Łukasz Nierzwicki & Bartlomiej Tomiczek - 1-21 Assessment of dispersion metrics for estimating single-cell transcriptional variability
by Tina Chen & Laurie A Boyer & Divyansh Agarwal - 1-21 Assessing the impact of climate and control interventions on spatio-temporal malaria dynamics using a stochastic metapopulation model
by Alexandros Angelakis & Anton Beloconi & Bryan O Nyawanda & Sammy Khagayi & Simon Kariuki & Stephen Munga & Patrick K Munywoki & Godfrey Bigogo & Penelope Vounatsou