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Content
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 - 1-22 Large-scale paired chain BCR analysis reveals antibody clonal family inference bias and enhances resolution with machine learning
by Hao Wang & Kaixuan Wang & Qihang Xu & Linru Cai & Chuanxiang Huang & Linlin Chen & Yunliang Zang & Xihao Hu & Jian Zhang - 1-22 Epistasis mediates the role of negative frequency-dependent selection in bacterial strain structure
by Martin Guillemet & Sonja Lehtinen - 1-22 Fast and accessible morphology-free functional fluorescence imaging analysis
by Alejandro Estrada Berlanga & Gabrielle Y Kang & Amanda Kwok & Thomas Broggini & Jennifer Lawlor & Kishore V Kuchibhotla & David Kleinfeld & Gal Mishne & Adam S Charles - 1-22 Predicting viral sensitivity to antibodies using genetic sequences and antibody similarities
by Kai S Shimagaki & Gargi Kher & Rebecca M Lynch & John P Barton - 1-23 Overcoming extrapolation challenges of deep learning by incorporating physics in protein sequence-function modeling
by Shrishti Barethiya & Jian Huang & Clarice Stumpf & Xiao Liu & Hui Guan & Jianhan Chen - 1-23 Multi-ACPNet: A multi-scale sequence-structure feature fusion framework for anticancer peptide identification and functional prediction
by Lu Meng & Lijun Zhou - 1-23 MoCETSE: A mixture-of-convolutional experts and transformer-based model for predicting Gram-negative bacterial secreted effectors
by Hua Shi & Yihang Lin & Dachen Liu & Quan Zou - 1-23 D-LIM: A neural network for interpretable gene–gene interactions
by Shuhui Wang & Alexandre Allauzen & Philippe Nghe & Vaitea Opuu - 1-24 Approximate Bayesian inference of directed acyclic graphs in biology with flexible priors on edge states
by Evan A Martin & Venkata Patchigolla & Audrey Qiuyan Fu - 1-24 A reinforcement learning and sequential sampling model constrained by gaze data
by William M Hayes & Melanie J Touchard - 1-26 Metacognitive efficiency in learned value-based choice
by Sara Ershadmanesh & Ali Gholamzadeh & Kobe Desender & Peter Dayan - 1-27 Towards model-based characterization of individual electrically stimulated nerve fibers
by Rebecca C Felsheim & David J Sly & Stephen J O’Leary & Mathias Dietz - 1-28 Bayesian-calibrated global sensitivity analysis for mathematical models using generative AI
by Xuyuan Wang - 1-29 WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology
by Pranav Gangwar & Pratik Katte & Manu Bhat & Yatish Turakhia - 1-29 Enhancing anticancer peptide discovery: A fusion-centric framework with conditional diffusion for prediction and generation
by Binyu Li & Xin Zhang & Zhihua Huang & Prayag Tiwari & Quan Zou & Yijie Ding & Xiaoyi Guo - 1-29 Multi-omics and network pharmacology identify IGFBP1 as an m6A-Epigenetic target of pueraria in NSCLC therapy
by Rui Li & Dong-Mei Hu & Yong-Li Liu & Wei Zhao & Yu-Xin Zhang & Yi-Qing Qu - 1-30 iSTTC: A robust method for accurate estimation of intrinsic neural timescales from single-unit recordings
by Irina Pochinok & Ileana L Hanganu-Opatz & Mattia Chini - 1-37 From noise to models to numbers: Evaluating negative binomial models and parameter estimations in single-cell RNA-seq
by Yiling Wang & Zhanpeng Shu & Zhixing Cao & Ramon Grima - 1-42 Contextual inference through flexible integration of environmental features and behavioural outcomes
by Jessica Passlack & Andrew F MacAskill
February 2026, Volume 22, Issue 2
- 1-13 Coevolutionary dynamics of cooperation, risk, and cost in collective risk games
by Lichen Wang & Shijia Hua & Yuyuan Liu & Liang Zhang & Linjie Liu & Attila Szolnoki - 1-15 Learning genetic perturbation effects with variational causal inference
by Emily Liu & Jiaqi Zhang & Caroline Uhler - 1-16 SHADE: A multilevel Bayesian framework for modeling directional spatial interactions in tissue microenvironments
by Joel Eliason & Michele Peruzzi & Arvind Rao - 1-17 Controllable protein design via autoregressive direct coupling analysis conditioned on principal components
by Francesco Caredda & Lisa Gennai & Paolo De Los Rios & Andrea Pagnani - 1-17 Efficient Gaussian process-based motor hotspot hunting with concurrent optimization of TMS coil location and orientation
by David Luis Schultheiss & Zsolt Turi & Joschka Boedecker & Andreas Vlachos - 1-18 PON-Del predictor for sequence retaining protein deletions
by Haoyang Zhang & Muhammad Kabir & Mauno Vihinen - 1-18 Information theoretic measures of neural and behavioural coupling predict representational drift
by Kristine Heiney & Mónika Józsa & Michael E Rule & Henning Sprekeler & Stefano Nichele & Timothy O’Leary - 1-18 Cluster dispersal shapes microbial diversity during community assembly
by Loïc Marrec & Sonja Lehtinen - 1-19 A comparative study of statistical methods for identifying differentially expressed genes in spatial transcriptomics
by Yishan Wang & Chenxuan Zang & Ziyi Li & Charles C Guo & Dejian Lai & Peng Wei - 1-19 A framework for evaluating predicted sperm trajectories in crowded microscopy videos
by David Hart & Kylie Cashwell & Anita Bhandari & Jayath Premasinghe & Cameron Schmidt - 1-19 Introducing gold-standard essential gene datasets for Pseudomonas aeruginosa to enhance Tn-Seq analyses
by Cléophée Van Maele & Ségolène Caboche & Nathan Nicolau-Guillaumet & Anaëlle Muggeo & Thomas Guillard - 1-20 SpaLSTF: Diffusion-based generative model with BiLSTM and XCA-Transformer for spatial transcriptomics imputation
by Lin Yuan & Yufeng Jiang & Boyuan Meng & Qingxiang Wang & Cuihong Wang & De-Shuang Huang - 1-21 Degradation graphs reveal hidden proteolytic activity in peptidomes
by Erik Hartman & Johan Malmström & Jonas Wallin - 1-22 A 2D Gabor-wavelet baseline model out-performs a 3D surface model in scene-responsive cortex
by Anna Shafer-Skelton & Timothy F Brady & John T Serences - 1-23 Information uncertainty influences learning strategy from sequentially delayed rewards
by Sean R Maulhardt & Alec Solway & Caroline J Charpentier - 1-24 CA-CAE: A deep learning-based multi-omics model for pan-cancer subtype classification and prognosis prediction
by Shumei Zhang & Yicheng Lu & Peixian Li & Junxuan Wu & Guohua Wang & Wen Yang - 1-25 Paraplume: A fast and accurate antibody paratope prediction method provides insights into repertoire-scale binding dynamics
by Gabriel Athènes & Adam Woolfe & Thierry Mora & Aleksandra M Walczak - 1-27 Putting BASIL in a BLT: A Bayesian filtering method for estimating the fitness effects of nascent adaptive mutations
by Huan-Yu Kuo & Sergey Kryazhimskiy - 1-29 Start small: A model for tissue-wide planar cell polarity without morphogens
by Abhisha Thayambath & Julio M Belmonte - 1-29 FKSUDDAPre: A drug–disease association prediction framework based on F-TEST feature selection and AMDKSU resampling with interpretability analysis
by Yun Zuo & Chenyi Zhang & Ge Hua & Qiao Ning & Xiangrong Liu & Xiangxiang Zeng & Zhaohong Deng - 1-38 A theory for self-sustained balanced states in absence of strong external currents
by David Angulo-Garcia & Alessandro Torcini
January 2026, Volume 22, Issue 1
- 1-14 Exosome-mediated chemotaxis optimizes leader-follower cell migration
by Louis González & Andrew Mugler - 1-15 Peak strain dispersion as a nonlinear mediator in HFpEF: Unraveling subtype-specific pathways via SHAP-augmented ensemble modeling
by Mingming Lin & Kai Li & Xiaofan Wang & Juanjuan Sun & Kun Gong & Zhibin Wang & Pin Sun - 1-16 ShapeSpaceExplorer: Analysis of morphological transitions in migrating cells using similarity-based shape space mapping
by Samuel D R Jefferyes & Roswitha Gostner & Laura Cooper & Mohammed M Abdelsamea & Elly Straube & Nasir Rajpoot & David B A Epstein & Anne Straube - 1-17 Measuring real-time disease transmissibility with temperature-dependent generation intervals
by Esther Li Wen Choo & Kris V Parag & Jo Yi Chow & Jue Tao Lim - 1-18 Spatial variation in socio-economic vulnerability to Influenza-like Infection for the US population
by Shrabani S Tripathy & Joseph V Puthussery & Taveen S Kapoor & John R Cirrito & Rajan K Chakrabarty - 1-18 Hierarchical analysis of RNA secondary structures with pseudoknots based on sections
by Ryota Masuki & Donn Liew & Ee Hou Yong - 1-20 Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study
by Tanya T Karagiannis & Ye Chen & Sarah Bald & Albert Tai & Eric R Reed & Sofiya Milman & Stacy L Andersen & Thomas T Perls & Daniel Segrè & Paola Sebastiani & Meghan I Short - 1-21 Higher-level spatial prediction in natural vision across mouse visual cortex
by Micha Heilbron & Floris P de Lange - 1-21 PlasticEnz: An integrated database and screening tool combining homology and machine learning to identify plastic-degrading enzymes in meta-omics datasets
by Anna Krzynowek & Jasper Snoeks & Karoline Faust - 1-21 CoFormerSurv: Collaborative transformer for multi-omics survival analysis
by Gang Wen & Limin Li - 1-23 DSCA-HLAII: A dual-stream cross-attention model for predicting peptide–HLA class II interaction and presentation
by Ke Yan & Hongjun Yu & Shutao Chen & Alexey K Shaytan & Bin Liu & Youyu Wang - 1-23 Powerful large scale inference in high dimensional mediation analysis
by Asmita Roy & Xianyang Zhang - 1-25 Compaction of chromatin domains regulates target search times of proteins
by Shuvadip Dutta & Adarshkrishnan Rajakumar & Ranjith Padinhateeri & Mithun K Mitra - 1-25 Novel artificial selection method improves function of simulated microbial communities
by Björn Vessman & Pablo Guridi-Fernández & Flor Inés Arias-Sánchez & Sara Mitri - 1-26 Network models for bridging denoising and identifying spatial domains of spatially resolved transcriptomics
by Haiyue Wang & Wensheng Zhang & Zaiyi Liu & Xiaoke Ma - 1-27 Linking brain and behavior states in Zebrafish Larvae locomotion using hidden Markov models
by Mattéo Dommanget-Kott & Jorge Fernandez-de-Cossio-Diaz & Monica Coraggioso & Volker Bormuth & Rémi Monasson & Georges Debrégeas & Simona Cocco - 1-32 Persistence diagrams as morphological signatures of cells: A method to measure and compare cells within a population
by Yossi Bokor Bleile & Pooja Yadav & Patrice Koehl & Florian Rehfeldt
December 2025, Volume 21, Issue 12
- 1-9 Ten simple rules for running a virtual program to introduce computational biology at the high school level
by Hanako Osuga & Matthew C Chan & Katherine Brower & Liza J Ray & Jeanne T Chowning - 1-11 Democratising high performance computing for bioinformatics through serverless cloud computing: A case study on CRISPR-Cas9 guide RNA design with Crackling Cloud
by Jacob Bradford & Divya Joy & Mattias Winsen & Nicholas Meurant & Mackenzie Wilkins & Laurence OW Wilson & Denis C Bauer & Dimitri Perrin - 1-13 Sketch, capture and layout phylogenies
by Daniel H Huson - 1-18 LCMSpector: A simple open-source viewer for targeted hyphenated mass spectrometry analysis
by Mateusz Fido & Etienne Hoesli & Elisa Cappio Barazzone & Renato Zenobi & Emma Slack - 1-19 Automated registration and clustering for enhanced localization atomic force microscopy of flexible membrane proteins
by Creighton M Lisowski & Gavin M King & Ioan Kosztin - 1-19 Memory, innovation and vertical learning
by Madeleine Ammar & Laurel Fogarty & Anne Kandler - 1-19 Assessing the relative contributions of mosaic and regulatory developmental modes from single-cell trajectories
by Solène Song & Paul Villoutreix - 1-20 Receptor dimerization enables ligand discrimination through tunable response heterogeneity
by Assaf Biran & Yaron E Antebi - 1-20 Using artificial neural networks to reveal the human confidence computation
by Medha Shekhar & Herrick Fung & Krish Saxena & Farshad Rafiei & Dobromir Rahnev - 1-20 Comparing a computational model of visual problem solving with human vision on a difficult vision task
by Tarun Khajuria & Kadi Tulver & Jaan Aru - 1-21 Coancestry superposed on admixed populations yields measures of relatedness at individual-level resolution
by Danfeng Chen & John D Storey - 1-21 Benchmarking interpretability of deep learning for predictive genomics: Recall, precision, and variability of feature attribution
by Justin Reynolds & Chongle Pan - 1-21 Whom do we prefer to learn from in observational reinforcement learning?
by Gota Morishita & Carsten Murawski & Nitin Yadav & Shinsuke Suzuki - 1-22 ARTreeFormer: A faster attention-based autoregressive model for phylogenetic inference
by Tianyu Xie & Yicong Mao & Cheng Zhang - 1-22 Identification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls
by Ana Paredes-Vázquez & Eva Balsa-Canto & Julio R Banga - 1-22 Unsupervised detection and fitness estimation of emerging SARS-CoV-2 variants: Application to wastewater samples (ANRS0160)
by Alexandra Lefebvre & Vincent Maréchal & Arnaud Gloaguen & The Obépine Consortium & Amaury Lambert & Yvon Maday - 1-22 A game theoretic treatment of contagion in trade networks
by John S McAlister & Jesse L Brunner & Danielle J Galvin & Nina H Fefferman - 1-22 Learning structured population models from data with WSINDy
by Rainey Lyons & Vanja Dukic & David M Bortz - 1-23 Random time-shift approximation enables hierarchical Bayesian inference of mechanistic within-host viral dynamics models on large datasets
by Dylan J Morris & Lauren Kennedy & Andrew J Black - 1-23 Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy
by Théo Moutakanni & Camille Couprie & Seungeun Yi & Michael Doron & Zitong S Chen & Nikita Moshkov & Elouan Gardes & Mathilde Caron & Hugo Touvron & Armand Joulin & Piotr Bojanowski & Wolfgang M Pernice & Juan C Caicedo - 1-24 BAGEL: Protein engineering via exploration of an energy landscape
by Jakub Lála & Ayham Al-Saffar & Stefano Angioletti-Uberti - 1-25 When predict can also explain: Few-shot prediction to select better neural latents
by Kabir V Dabholkar & Omri Barak - 1-26 Semi-supervised Bayesian integration of multiple spatial proteomics datasets
by Stephen Coleman & Lisa Breckels & Ross F Waller & Kathryn S Lilley & Chris Wallace & Oliver M Crook & Paul D W Kirk - 1-26 ASPEN: Robust detection of allelic dynamics in single cell RNA-seq
by Veronika Petrova & Muqing Niu & Thomas S Vierbuchen & Emily S Wong - 1-27 Decoupled contrastive multi-view clustering with adaptive false negative elimination for cancer subtyping
by Mengxiang Lin & Rongqi Fan & Saisai Zhu & Xiaoqiang Yan & Quan Zou & Zhen Tian - 1-28 Randomized Spatial PCA (RASP): A computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data
by Ian K Gingerich & Brittany A Goods & H Robert Frost - 1-28 DDGWizard: Integration of feature calculation resources for analysis and prediction of changes in protein thermostability upon point mutations
by Mingkai Wang & Khaled Jumah & Qun Shao & Katarzyna Kamieniecka & Yihan Liu & Krzysztof Poterlowicz - 1-29 Do we advise as one likes? The alignment bias in social advice giving
by Xitong Luo & Lei Zhang & Yafeng Pan - 1-29 Long-term perceptual priors drive confidence bias that favors prior-congruent evidence
by Marika Constant & Elisa Filevich & Pascal Mamassian - 1-32 Neuronal identity is not static: An input-driven perspective
by Nishant Joshi & Sven van Der Burg & Tansu Celikel & Fleur Zeldenrust - 1-38 D3Impute: Dropout-aware discrimination, distribution-aware modeling, and density-guide imputation for scRNA-seq data
by Siyi Huang & Linfeng Jiang & Ming Yi & Yuan Zhu
November 2025, Volume 21, Issue 11
- 1-7 Ten simple rules for maximizing summer research experiences for students, mentors, and research groups
by Miriam B Goodman - 1-8 Ten simple rules for early-career researchers supervising short-term student projects
by Rebecca M Crossley & Philip K Maini - 1-9 PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures
by Takumi Otagaki & Goro Terai & Kiyoshi Asai & Junichi Iwakiri - 1-14 Automated and modular protein binder design with BinderFlow
by Nayim González-Rodríguez & Carlos Chacón-Sánchez & Oscar Llorca & Rafael Fernández-Leiro - 1-15 Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture
by Tien Comlekoglu & J Quetzalcóatl Toledo-Marín & Tina Comlekoglu & Douglas W DeSimone & Shayn M Peirce & Geoffrey Fox & James A Glazier - 1-16 Library size-stabilized metacells construction enhances co-expression network analysis in single-cell data
by Tianjiao Zhang & Haibin Zhu - 1-16 Federated learning for COVID-19 mortality prediction in a multicentric sample of 21 hospitals
by Roberta Moreira Wichmann & Murilo Afonso Robiati Bigoto & Alexandre Dias Porto Chiavegatto Filho - 1-17 Splicing-aware scRNA-Seq resolution reveals execution-ready programs in effector Tregs
by Daniil K Lukyanov & Evgeniy S Egorov & Valeriia V Kriukova & Denis Syrko & Victor V Kotliar & Kristin Ladell & David A Price & Andre Franke & Dmitry M Chudakov - 1-17 Branch-specific gene discovery in cell differentiation using multi-omics graph attention
by Yihao Yin & Linzhi Zhuang & Yulei Wang & Yazhou Shi & Bengong Zhang - 1-18 APDCA: An accurate and effective method for predicting associations between RBPs and AS-events during epithelial-mesenchymal transition
by Yangsong He & Zheng-Jian Bai & Wai-Ki Ching & Quan Zou & Yushan Qiu - 1-18 tvsfglasso: Time-varying scale-free graphical lasso for network estimation from time-series data
by Markku Kuismin & Mikko J Sillanpää - 1-18 Epydemix: An open-source Python package for epidemic modeling with integrated approximate Bayesian calibration
by Nicoló Gozzi & Matteo Chinazzi & Jessica T Davis & Corrado Gioannini & Luca Rossi & Marco Ajelli & Nicola Perra & Alessandro Vespignani - 1-18 Trial-by-trial learning of successor representations in human behavior
by Ari E Kahn & Dani S Bassett & Nathaniel D Daw - 1-19 SpaMWGDA: Identifying spatial domains of spatial transcriptomes using multi-view weighted fusion graph convolutional network and data augmentation
by Lin Yuan & Boyuan Meng & Qingxiang Wang & Chunyu Hu & Cuihong Wang & De-Shuang Huang - 1-20 Prediction of graft loss in living donor liver transplantation during the early postoperative period
by Raiki Yoshimura & Naotoshi Nakamura & Takeru Matsuura & Takeo Toshima & Takasuke Fukuhara & Kazuyuki Aihara & Katsuhito Fujiu & Shingo Iwami & Tomoharu Yoshizumi - 1-20 Protein drift-diffusion in membranes with non-equilibrium fluctuations arising from gradients in concentration or temperature
by Dev Jasuja & Paul J Atzberger - 1-20 Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations
by Yue Huang & Tianqi Tang & Xiaowu Dai & Fengzhu Sun - 1-20 CrossLabFit: A novel framework for integrating qualitative and quantitative data across multiple labs for model calibration
by Rodolfo Blanco-Rodriguez & Tanya A Miura & Esteban Hernandez-Vargas - 1-20 PathoRM: Computational inference of pathogenic RNA methylation sites by incorporating multi-view features
by Hui Liu & Jiani Ma & Xianjun Ma & Lin Zhang - 1-22 The topology of synergy: Linking topological and information-theoretic approaches to higher-order interactions in complex systems
by Thomas F Varley & Pedro A M Mediano & Alice Patania & Josh Bongard - 1-22 Data-driven identification of biological systems using multi-scale analysis
by Ismaila Muhammed & Dimitris M Manias & Dimitris A Goussis & Haralampos Hatzikirou - 1-23 HAPP: High-accuracy pipeline for processing deep metabarcoding data
by 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 & Fredrik Ronquist - 1-23 Spatial close-kin mark-recapture methods to estimate dispersal parameters and barrier strength for mosquitoes
by John M Marshall & Shuyi Yang & Jared B Bennett & Igor Filipović & Gordana Rašić - 1-23 Optimization of experimental designs for biological rhythm discovery
by Turner Silverthorne & Matthew Carlucci & Arturas Petronis & Adam R Stinchcombe - 1-24 Real-time forecasting of data revisions in epidemic surveillance streams
by Jingjing Tang & Aaron Rumack & Bryan Wilder & Roni Rosenfeld - 1-25 A linear pathway for inositol pyrophosphate metabolism revealed by 18O labeling and model reduction
by Jacques Hermes & Geun-Don Kim & Guizhen Liu & Maria Giovanna De Leo & Andreas Mayer & Henning Jessen & Jens Timmer - 1-25 Null models for comparing information decomposition across complex systems
by Alberto Liardi & Fernando E Rosas & Robin L Carhart-Harris & George Blackburne & Daniel Bor & Pedro A M Mediano - 1-26 Unlocking plant health survey data: An approach to quantify the sensitivity and specificity of visual inspections
by Matt Combes & Nathan Brown & Robin N Thompson & Alexander Mastin & Peter Crow & Stephen Parnell - 1-26 Automated C. elegans behavior analysis via deep learning-based detection and tracking
by Xiaoke Liu & Jianming Liu & Wenjie Teng & Yuzhong Peng & Boao Li & Xiaoqing Han & Jing Huo - 1-26 Universal scale-free representations in human visual cortex
by Raj Magesh Gauthaman & Brice Ménard & Michael F Bonner - 1-27 OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders
by Klemens Flöge & Srisruthi Udayakumar & Johanna Sommer & Marie Piraud & Stefan Kesselheim & Vincent Fortuin & Stephan Günnemann & Karel J van der Weg & Holger Gohlke & Erinc Merdivan & Alina Bazarova - 1-30 Nash equilibrium of attack and defense behaviors between predators and prey
by Hiroyuki Ichijo & Yuichiro Kawamura & Tomoya Nakamura
October 2025, Volume 21, Issue 10
- 1-3 Response to comment on ”Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA”
by Eliezyer Fermino de Oliveira & Lucas Sjulson - 1-4 Generalized contrastive PCA is equivalent to generalized eigendecomposition
by Joshua P Woller & David Menrath & Alireza Gharabaghi - 1-13 Nine quick tips for trustworthy machine learning in the biomedical sciences
by Luca Oneto & Davide Chicco - 1-14 From ideal to practical: Heterogeneity of student-generated variant lists highlights hidden reproducibility gaps
by Rumeysa Aslıhan Ertürk & Abdullah Asım Emül & Büşra Nur Darendeli-Kiraz & Fatma Zehra Sarı & Mehmet Arif Ergün & Mehmet Baysan - 1-15 Impact of the COVID-19 pandemic on computational biology early career researchers: A global retrospective study
by Pradeep Eranti & Megha Hegde & Syed Muktadir Al Sium & R Gonzalo Parra & Alastair M Kilpatrick & Sayane Shome & Farzana Rahman - 1-15 A multi-layer encoder prediction model for individual sample specific gene combination effect (MLEC-iGeneCombo)
by Yun Shen & Kunjie Fan & Birkan Gökbağ & Nuo Sun & Chen Yang & Lijun Cheng & Lang Li - 1-15 GeneDrive.jl: A decision tool to optimize biological vector control strategies under climate change
by Váleri N Vásquez & Erin A Mordecai & David Anthoff - 1-16 Multivariate resilience indicators to anticipate vector-borne disease outbreaks: A West Nile virus case-study
by Clara Delecroix & Quirine ten Bosch & Egbert H Van Nes & Ingrid A van de Leemput - 1-16 A semi-automated algorithm for image analysis of respiratory organoids
by Anna Demchenko & Maxim Balyasin & Elena Kondratyeva & Tatiana Kyian & Alyona Sorokina & Marina Loguinova & Svetlana Smirnikhina - 1-17 Spatial domain identification method based on multi-view graph convolutional network and contrastive learning
by Xikeng Liang & Shutong Xiao & Lu Ba & Yuhui Feng & Zhicheng Ma & Fatima Adilova & Jing Qi & Shuilin Jin - 1-18 Multi-feature fusion network with marginal focal dice loss for multi-label therapeutic peptide prediction
by Yijun Mao & Yurong Weng & Jian Weng & Ming Li & Wanrong Gu & Rui Pang & Xudong Lin & Yunyan Xiong & Deyu Tang - 1-19 Drug-disease networks and drug repurposing
by Austin Polanco & Mark E J Newman - 1-19 Modelling plant disease spread and containment: Simulation and approximate Bayesian Computation for Xylella fastidiosa in Puglia, Italy
by Daniel Chapman & Flavia Occhibove & James M Bullock & Pieter S A Beck & Juan A Navas-Cortes & Steven M White - 1-19 WormSNAP: A software for fast, accurate, and unbiased detection of fluorescent puncta in C. elegans
by Araven Tiroumalechetty & Elisa B Frankel & Peri T Kurshan - 1-20 Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches
by Javiera Cortés-Ríos & Maria Rodriguez-Fernandez & Peter Karl Sorger & Fabian Fröhlich - 1-20 Analytical and computational solution for the estimation of SNP-heritability in biobank-scale and distributed datasets
by Guo-An Qi & Qi-Xin Zhang & Jingyu Kang & Tianyuan Li & Xiyun Xu & Zhe Zhang & Zhe Fan & Siyang Liu & Guo-Bo Chen - 1-20 Social inequalities in vaccine coverage and their effects on epidemic spreading
by Adriana Manna & Marton Karsai & Nicola Perra - 1-21 BMDD: A probabilistic framework for accurate imputation of zero-inflated microbiome sequencing data
by Huijuan Zhou & Jun Chen & Xianyang Zhang - 1-22 Statistical regularities in natural scenes that support figure-ground segregation by neural populations
by Clara T Friedman & Minqi Wang & Thomas Yerxa & Bryce A Arseneau & Xin Huang & Emily A Cooper - 1-23 Adaptive proximity to criticality underlies amplification of ultra-slow fluctuations during free recall
by Dovi Yellin & Noam Siegel & Rafael Malach & Oren Shriki - 1-23 TastepepAI: An artificial intelligence platform for taste peptide de novo design
by Jianda Yue & Tingting Li & Jian Ouyang & Jiawei Xu & Hua Tan & Zihui Chen & Changsheng Han & Huanyu Li & Songping Liang & Zhonghua Liu & Zhonghua Liu & Ying Wang - 1-23 Transmission thresholds for the spread of infections in healthcare facilities
by Damon J A Toth & Karim Khader & Christopher Mitchell & Matthew H Samore - 1-23 Exact conditions for evolutionary stability in indirect reciprocity under noise
by Nikoleta E Glynatsi & Christian Hilbe & Yohsuke Murase - 1-24 Improving policy design and epidemic response using integrated models of economic choice and disease dynamics with behavioral feedback
by Hongru Du & Matthew V Zahn & Sara L Loo & Tijs W Alleman & Shaun Truelove & Bryan Patenaude & Lauren M Gardner & Nicholas Papageorge & Alison L Hill - 1-25 A Bayesian model of distance perception from ocular convergence
by Peter Scarfe & Paul B Hibbard - 1-25 A mixture of attention experts-embedded flow-based generative model to create synthetic cells in single-cell RNA-Seq datasets
by Sultan Sevgi Turgut Ögme & Nizamettin Aydin & Zeyneb Kurt - 1-27 HMFGraph: Novel Bayesian approach for recovering biological networks
by Aapo E Korhonen & Olli Sarala & Tuomas Hautamäki & Markku Kuismin & Mikko J Sillanpää - 1-27 Inference of weak-form partial differential equations describing migration and proliferation mechanisms in wound healing experiments on cancer cells
by Siddhartha Srivastava & Patrick C Kinnunen & Zhenlin Wang & Kenneth KY Ho & Brock A Humphries & Siyi Chen & Jennifer J Linderman & Gary D Luker & Kathryn E Luker & Krishna Garikipati - 1-28 Quantifying HiPSC-CM structural organization at scale with deep learning-enhanced SarcGraph
by Saeed Mohammadzadeh & Emma Lejeune - 1-28 A method for analysing tissue motion and deformation during mammalian organogenesis
by Morena Raiola & Isaac Esteban & Kenzo Ivanovitch & Miquel Sendra & Miguel Torres - 1-29 Inferring effective networks of spiking neurons using a continuous-time estimator of transfer entropy
by David P Shorten & Viola Priesemann & Michael Wibral & Joseph T Lizier - 1-30 Similarity-based transfer learning with deep learning networks for accurate CRISPR-Cas9 off-target prediction
by Jeremy Charlier & Zeinab Sherkatghanad & Vladimir Makarenkov - 1-30 Simultaneously determining regional heterogeneity and connection directionality from neural activity and symmetric connection
by Jiawen Chang & Zhuda Yang & Changsong Zhou - 1-33 Assessing parameter identifiability of a hemodynamics PDE model using spectral surrogates and dimension reduction
by Mitchel J Colebank - 1-43 Synchrony, oscillations, and phase relationships in collective neuronal activity: A highly comparative overview of methods
by Fabiano Baroni & Ben D Fulcher