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Content
December 2025, Volume 21, Issue 12
- 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 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 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 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 - 1-24 BAGEL: Protein engineering via exploration of an energy landscape
by Jakub Lála & Ayham Al-Saffar & Stefano Angioletti-Uberti - 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 - 1-38 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 - 1-44 Subthreshold moment analysis of neuronal populations driven by synchronous synaptic inputs
by Logan A Becker & Francois Baccelli & Thibaud Taillefumier
September 2025, Volume 21, Issue 9
- 1-7 Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings
by 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 & Daudi Jjingo - 1-13 Ten simple rules for training by researchers for researchers in a rapidly evolving workforce
by 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 & Amany Gouda-Vossos - 1-13 paramix: An R package for parameter discretisation in compartmental models, with application to calculating years of life lost
by Lucy Goodfellow & Carl A B Pearson & Simon R Procter - 1-15 A generalized theoretical framework to investigate multicomponent actin dynamics
by Mintu Nandi & Shashank Shekhar & Sandeep Choubey - 1-15 Adaptive algorithms for shaping behavior
by William L Tong & Venkatesh N Murthy & Gautam Reddy - 1-16 MRDtarget: A heuristic Gaussian approach for optimizing targeted capture regions to enhance Minimal Residual Disease detection
by Xuwen Wang & Yanfang Guan & Wei Gao & Xin Lai & Wuqiang Cao & Xiaoyan Zhu & Xiaoling Zeng & Yuqian Liu & Shenjie Wang & Ruoyu Liu & Xin Yi & Shuanying Yang & Jiayin Wang - 1-16 Generating correlated data for omics simulation
by Jianing Yang & Gregory R Grant & Thomas G Brooks - 1-16 Ten quick tips for protecting health data using de-identification and perturbation of structured datasets
by Tshikala Eddie Lulamba & Themba Mutemaringa & Nicki Tiffin - 1-17 Harmony-based data integration for distributed single-cell multi-omics data
by Ruizhi Yuan & Ziqi Rong & Haoran Hu & Tianhao Liu & Shiyue Tao & Wei Chen & Lu Tang - 1-17 Personalized pulse wave propagation modeling to improve vasopressor dosing management in patients with severe traumatic brain injury
by Kamil Wolos & Leszek Pstras & Urszula Bialonczyk & Malgorzata Debowska & Wojciech Dabrowski & Dorota Siwicka-Gieroba & Jan Poleszczuk - 1-17 Fast and exact stochastic simulations of epidemics on static and temporal networks
by Samuel Cure & Florian G Pflug & Simone Pigolotti - 1-18 Effects of segmentation errors on downstream-analysis in highly-multiplexed tissue imaging
by Matthias Bruhns & Jan T Schleicher & Maximilian Wirth & Marcello Zago & Sepideh Babaei & Manfred Claassen - 1-19 An explainable covariate compartmental model for predicting the spatio-temporal patterns of dengue in Sri Lanka
by Yichao Liu & Peter Fransson & Julian Heidecke & Prasad Liyanage & Jonas Wallin & Joacim Rocklöv - 1-19 Category-specific perceptual learning of robust object recognition modelled using deep neural networks
by Hojin Jang & Frank Tong - 1-19 SBMLNetwork: A framework for standards-based visualization of biochemical models
by Adel Heydarabadipour & Lucian Smith & Joseph L Hellerstein & Herbert M Sauro - 1-20 A graph neural network-based spatial multi-omics data integration method for deciphering spatial domains
by Congqiang Gao & Chenghui Yang & Lihua Zhang - 1-21 A history-dependent approach for accurate initial condition estimation in epidemic models
by Dongju Lim & Kyeong Tae Ko & Hyukpyo Hong & Hyojung Lee & Boseung Choi & Won Chang & Sunhwa Choi & Jae Kyoung Kim - 1-21 A nonlinear relationship between prediction errors and learning rates in human reinforcement-learning
by Boluwatife Ikwunne & Jolie Parham & Erdem Pulcu - 1-21 A physiologically inspired hybrid CPG/Reflex controller for cycling simulations that generalizes to walking
by Giacomo Severini & David Muñoz - 1-24 Clonal heterogeneity and antigenic stimulation shape persistence of the latent reservoir of HIV
by Marco Garcia Noceda & Gargi Kher & Shikhar Uttam & John P Barton - 1-24 Mathematical modeling of dopamine rhythms and timing of dopamine reuptake inhibitors
by Tianyong Yao & Ruby Kim - 1-25 Cortical networks with multiple interneuron types generate oscillatory patterns during predictive coding
by Kwangjun Lee & Cyriel M A Pennartz & Jorge F Mejias - 1-25 A computational framework for the investigation of phosphoinositide regulation
by Hilaire Yam Fung Cheung & Chukiat Tantiwong & Dipali Kale & Jonathan M Gibbins & Steve P Watson & Johan W M Heemskerk & Albert Sickmann & Robert Ahrends & Joanne L Dunster - 1-25 HyperACP: A cutting-edge hybrid framework for anticancer peptide classification via scalable feature extraction and adaptive neighbor-based synthesis
by Bangyi Zhang & Yun Zuo & Jun Wan & Jiayue Liu & Xiangrong Liu & Xiangxiang Zeng & Zhaohong Deng - 1-26 Human visual grouping based on within- and cross-area temporal correlations
by Yen-Ju Chen & Zitang Sun & Shin’ya Nishida - 1-26 Optimizing therapeutic outcomes with Mechanotherapy and Ultrasound Sonopermeation in solid tumors
by Marina Koutsi & Triantafyllos Stylianopoulos & Fotios Mpekris - 1-26 Effects of tDCS of the DLPFC on brain networks: A hybrid brain modeling study
by Yanqing Dong & Jing Wei & Songjun Peng & Xinran Wu & Yaru Xu & Jianfeng Feng & Jie Zhang & Viktor Jirsa & Jie Xiang - 1-26 Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations
by Jiancheng Zhang & Xiangting Li & Xiaolu Guo & Zhaoyi You & Lucas Böttcher & Alex Mogilner & Alexander Hoffmann & Tom Chou & Mingtao Xia - 1-27 Action subsampling supports policy compression in large action spaces
by Shuze Liu & Samuel Joseph Gershman - 1-30 Dynamical mean-field theory for a highly heterogeneous neural population with graded persistent activity of the entorhinal cortex
by Futa Tomita & Jun-nosuke Teramae - 1-31 Gene regulatory network structure informs the distribution of perturbation effects
by Matthew Aguirre & Jeffrey P Spence & Guy Sella & Jonathan K Pritchard - 1-35 Transcriptome-wide root causal inference
by Eric V Strobl & Eric R Gamazon - 1-42 A causal framework for the drivers of animal social network structure
by Ben Kawam & Julia Ostner & Richard McElreath & Oliver Schülke & Daniel Redhead
August 2025, Volume 21, Issue 8
- 1-10 Ten simple rules for being a co-author on a many-author non-empirical paper
by Friederike E Kohrs & Natascha Drude & Anita Bandrowski & Tracey L Weissgerber - 1-13 Emergence of a complex network structure on a Spatial Prisoner’s Dilemma
by Tomoko Sakiyama & Akihiro Takahara - 1-15 A neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens
by Weheliye H Weheliye & Javier Rodriguez & Luigi Feriani & Avelino Javer & Virginie Uhlmann & André E X Brown - 1-16 Ten simple rules for leading a many-author non-empirical paper
by Tracey L Weissgerber & Natascha Drude & Rima-Maria Rahal & Friederike E Kohrs - 1-17 Mathematical modeling suggests 14-3-3 proteins modulate RAF paradoxical activation
by Gaurav Mendiratta & Kodye Abbott & Yao-Cheng Li & Jingting Yu & Peter Carlip & Melinda Tong & Jianfeng Huang & Maxim N Shokhirev & Thomas McFall & Geoffrey M Wahl & Edward C Stites - 1-17 Does Zipf’s law of abbreviation shape birdsong?
by R Tucker Gilman & CD Durrant & Lucy Malpas & Rebecca N Lewis - 1-17 PLNMFG: Pseudo-label guided non-negative matrix factorization model with graph constraint for single-cell multi-omics data clustering
by Hui Yuan & Mingzhu Liu & Yushan Qiu & Wai-Ki Ching & Quan Zou - 1-18 Maynard Smith revisited: A multi-agent reinforcement learning approach to the coevolution of signalling behaviour
by Olivia Macmillan-Scott & Mirco Musolesi - 1-21 Emergence of cooperation promoted by higher-order strategy updates
by Dini Wang & Peng Yi & Yiguang Hong & Jie Chen & Gang Yan - 1-21 Modelling the effects of adult emergence on the surveillance and age distribution of medically important mosquitoes
by Isaac J Stopard & Ellie Sherrard-Smith & Hilary Ranson & Kobié Hyacinthe Toe & Jackie Cook & Joseph Biggs & Ben Lambert & Thomas S Churcher - 1-21 Nonparametric serial interval estimation with uniform mixtures
by Oswaldo Gressani & Niel Hens - 1-22 Data-driven analysis of fine-scale badger movement in the UK
by Jessica R Furber & Richard J Delahay & Ruth Cox & Rosie Woodroffe & Maria O’Hagan & Naratip Santitissadeekorn & Stefan Klus & Giovanni Lo Iacono & Mark A Chambers & David J B Lloyd - 1-22 Age polyethism can emerge from social learning: A game-theoretic investigation
by Moein Khajehnejad & Julian García & Bernd Meyer - 1-22 COEXIST: Coordinated single-cell integration of serial multiplexed tissue images
by Robert T Heussner & Cameron F Watson & Christopher Z Eddy & Kunlun Wang & Eric M Cramer & Allison L Creason & Gordon B Mills & Young Hwan Chang - 1-24 Stochastic model of IP3-induced Ca2+ spiking of HEK293 cells
by Caterina Azzoni & Rene Jüttner & Anje Sporbert & Michael Gotthardt & H Llewelyn Roderick & Martin Falcke - 1-25 Identification of the governing equation of stimulus-response data for run-and-tumble dynamics
by Shicong Lei & Yu’an Li & Zheng Ma & Hepeng Zhang & Min Tang - 1-25 Heterogeneous synaptic homeostasis: A novel mechanism boosting information propagation in the cortex
by Farhad Razi & Belén Sancristóbal - 1-25 Socioeconomic determinants of protective behaviors and contact patterns in the post-COVID-19 pandemic era: A cross-sectional study in Italy
by Michele Tizzani & Laetitia Gauvin - 1-28 A computational workflow for assessing drug effects on temporal signaling dynamics reveals robustness in stimulus-specific NFκB signaling
by Emily R Bozich & Xiaolu Guo & Jennifer L Wilson & Alexander Hoffmann - 1-28 IonBench: A benchmark of optimisation strategies for mathematical models of ion channel currents
by Matt J Owen & Gary R Mirams - 1-30 In silico modeling of directed differentiation of induced pluripotent stem cells to definitive endoderm
by Amirmahdi Mostofinejad & David A Romero & Dana Brinson & Thomas K Waddell & Golnaz Karoubi & Cristina H Amon - 1-33 A software ecosystem for brain tractometry processing, analysis, and insight
by 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 & Ariel Rokem - 1-35 Stochastic activity in low-rank recurrent neural networks
by Francesca Mastrogiuseppe & Joana Carmona & Christian K Machens
July 2025, Volume 21, Issue 7
- 1-6 Ten simple rules for developing a training program
by Leanna B Blevins & Amy M Harrigan & Kevin A Janes & Jason A Papin - 1-8 bmdrc: Python package for quantifying phenotypes from chemical exposures with benchmark dose modeling
by David J Degnan & Lisa M Bramer & Lisa Truong & Robyn L Tanguay & Sara M Gosline & Katrina M Waters - 1-10 Ten quick tips for navigating intellectual property in FAIR educational resources
by Eva Maria Funk & Ulf Toelch & Rebecca Ludwig & Silke Kniffert - 1-12 Ten simple rules for success as a trainee-led outreach organization in computational biology education
by Jennifer Blanc & Margaret C Steiner & Lauren E Blake & Elizabeth Gibbons & Mariadaria K Ianni-Ravn & Roxroy C Morgan & Suzanna Parkinson & Christian Porras & Ethan Zhong - 1-12 Ten simple rules for navigating AI in science
by 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 & Zhenzhu Li - 1-12 Time-series modeling of epidemics in complex populations: Detecting changes in incidence volatility over time
by Rachael Aber & Yanming Di & Benjamin D Dalziel - 1-14 Ten simple rules for thriving in a post-baccalaureate research program
by Michaelle E DiMaggio-Potter & Angelica Velosa & John C Brent IV & Osmar Del Rio & Eyerusalem F Abebaw & Fernando Aguilar-Ortega & Dante Rogers & Patrick E Rothwell & Angeline J Dukes - 1-18 Statistical analysis supports the size control mechanism of Chlamydia development
by Jinsu Kim & Christine Sütterlin & Ming Tan & German Enciso - 1-18 Tracking causal pathways in TMS-evoked brain responses
by 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 & Xujun Duan - 1-18 Ten simple rules for faculty members building just and equitable environments in academic science
by Veronica Martinez Acosta & Carlita Favero & Barbara Lom & Deanne Buffalari & Amy Jo Stavnezer & Leah Chase - 1-18 PoweREST: Statistical power estimation for spatial transcriptomics experiments to detect differentially expressed genes between two conditions
by Lan Shui & Anirban Maitra & Ying Yuan & Ken Lau & Harsimran Kaur & Liang Li & Ziyi Li & Translational and Basic Science Research in Early Lesions Research Consortia - 1-18 From imaging to computational domains for physics-driven molecular biology simulations: Hindered diffusion in platelet masses
by Catherine House & Ziyi Huang & Kaushik N Shankar & Sandra J Young & Meghan E Roberts & Scott L Diamond & Maurizio Tomaiuolo & Timothy J Stalker & Lu Lu & Talid Sinno - 1-18 Single-cell mutational burden distributions in birth–death processes
by Christo Morison & Dudley Stark & Weini Huang - 1-19 How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors
by Rui Wang & Tamar Schlick - 1-21 A Bayesian hierarchical model of trial-to-trial fluctuations in decision criterion
by Robin Vloeberghs & Anne E Urai & Kobe Desender & Scott W Linderman - 1-22 Identifying predictors and assessing causal effect on hypertension risk among adults using Double Machine Learning models: Insights from Bangladesh Demographic and Health Survey
by Probir Kumar Ghosh & Md Aminul Islam & Md Ahshanul Haque & Md Tariqujjaman & Novel Chandra Das & Mohammad Ali & Md Rasel Uddin & Md Golam Dostogir Harun - 1-23 EUP: Enhanced cross-species prediction of ubiquitination sites via a conditional variational autoencoder network based on ESM2
by Junhao Liu & Zeyu Luo & Rui Wang & Xin Li & Yawen Sun & Zongqing Chen & Yu-Juan Zhang - 1-23 Waveform distortion for temperature compensation and synchronization in circadian rhythms: An approach based on the renormalization group method
by Shingo Gibo & Teiji Kunihiro & Tetsuo Hatsuda & Gen Kurosawa - 1-24 Anatomical-electrical coupling of cardiac axes: Definitions and population variability for advancing personalised ECG interpretation
by Mohammad Kayyali & Ana Mincholé & Shuang Qian & Alistair Young & Devran Ugurlu & Elliot Fairweather & Steven Niederer & John Whitaker & Martin Bishop & Pablo Lamata - 1-25 Perceptual clustering in auditory streaming
by Nathanael Larigaldie & Tim Yates & Ulrik R Beierholm - 1-26 Analyzing greedy vaccine allocation algorithms for metapopulation disease models
by Jeffrey Keithley & Akash Choudhuri & Bijaya Adhikari & Sriram V Pemmaraju - 1-27 Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome
by Tarun Mahajan & Sergei Maslov - 1-33 Disentangling signal and noise in neural responses through generative modeling
by Kendrick Kay & Jacob S Prince & Thomas Gebhart & Greta Tuckute & Jingyang Zhou & Thomas Naselaris & Heiko H Schütt
June 2025, Volume 21, Issue 6
- 1-8 Ten simple rules for effectively assessing lab environments
by Kristen M Naegle & Jeffrey J Saucerman & Julie Leonard-Duke & Michael Rariden & Yonathan Tamrat Aberra - 1-13 Indirect punishment can outperform direct punishment in promoting cooperation in structured populations
by Yujia Wen & Zhixue He & Chen Shen & Jun Tanimoto - 1-16 Fusing multisensory signals across channels and time
by Swathi Anil & Dan F M Goodman & Marcus Ghosh - 1-17 Synthetic method of analogues for emerging infectious disease forecasting
by Alexander C Murph & G Casey Gibson & Elizabeth B Amona & Lauren J Beesley & Lauren A Castro & Sara Y Del Valle & Dave Osthus - 1-18 Predicting neuronal firing from calcium imaging using a control theoretic approach
by Nicholas A Rondoni & Fan Lu & Daniel B Turner-Evans & Marcella Gomez - 1-18 Features influencing the health and economic impact of preventing COVID-19 in immunocompromised individuals
by Siyu Chen & Sudhir Venkatesan & Sofie Arnetorp & Klas Bergenheim & Sabada Dube & Wilhelmine Meeraus & Cátia Ferreira & Sylvia Taylor & Lisa J White - 1-19 Nonequilibrium brain dynamics elicited as the origin of perturbative complexity
by Wiep Stikvoort & Eider Pérez-Ordoyo & Iván Mindlin & Anira Escrichs & Jacobo D Sitt & Morten L Kringelbach & Gustavo Deco & Yonatan Sanz Perl - 1-19 Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold
by Samuel Eriksson Lidbrink & Rebecca J Howard & Nandan Haloi & Erik Lindahl - 1-19 Uncovering the impact of randomness in HIV hotspot formation: A mathematical modeling study
by Nao Yamamoto & Daniel T Citron & Samuel M Mwalili & Duncan K Gathungu & Diego F Cuadros & Anna Bershteyn - 1-20 MVHGCN: Predicting circRNA-disease associations with multi-view heterogeneous graph convolutional neural networks
by Yan Miao & Xuan Tang & Chunyu Wang & Zhenyuan Sun & Guohua Wang & Shan Huang - 1-21 Computing generalized cophenetic distances under all Lp norms: A near-linear time algorithmic framework
by Paweł Górecki & Alexey Markin & Sriram Vijendran & Oliver Eulenstein - 1-21 Identifiability of phenotypic adaptation from low-cell-count experiments and a stochastic model
by Alexander P Browning & Rebecca M Crossley & Chiara Villa & Philip K Maini & Adrianne L Jenner & Tyler Cassidy & Sara Hamis - 1-21 Designing diverse and high-performance proteins with a large language model in the loop
by Carlos A Gomez-Uribe & Japheth Gado & Meiirbek Islamov - 1-22 GABAergic neurons can facilitate the propagation of cortical spreading depolarization: experiments in mouse neocortical slices and a novel neural field computational model
by Emre Baspinar & Martina Simonti & Hadi Srour & Mathieu Desroches & Daniele Avitabile & Massimo Mantegazza - 1-23 Multimodal CustOmics: A unified and interpretable multi-task deep learning framework for multimodal integrative data analysis in oncology
by Hakim Benkirane & Maria Vakalopoulou & David Planchard & Julien Adam & Ken Olaussen & Stefan Michiels & Paul-Henry Cournède - 1-23 Energy optimization induces predictive-coding properties in a multi-compartment spiking neural network model
by Mingfang Zhang & Raluca Chitic & Sander M Bohté - 1-23 Computations that sustain neural feature selectivity across processing stages
by Ryan J Rowekamp & Tatyana O Sharpee - 1-24 Stochastic gene expression in proliferating cells: Differing noise intensity in single-cell and population perspectives
by Zhanhao Zhang & Iryna Zabaikina & Cesar Nieto & Zahra Vahdat & Pavol Bokes & Abhyudai Singh - 1-26 The role of learned song in the evolution and speciation of Eastern and Spotted towhees
by Ximena León Du’Mottuchi & Nicole Creanza - 1-26 A mathematical model suggests collectivity and inconstancy enhance the efficiency of neuronal migration in the adult brain
by Daiki Wakita & Yuriko Sobu & Naoko Kaneko & Takeshi Kano - 1-26 Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology
by Yuxi Long & Bruce R Donald - 1-28 Variance in C. elegans gut bacterial load suggests complex host-microbe dynamics
by Satya Spandana Boddu & K Michael Martini & Ilya Nemenman & Nic M Vega - 1-29 OrgaCCC: Orthogonal graph autoencoders for constructing cell-cell communication networks on spatial transcriptomics data
by Xixuan Feng & Shuqin Zhang & Limin Li - 1-32 Uncertainty-aware traction force microscopy
by Adithan Kandasamy & Yi-Ting Yeh & Ricardo Serrano & Mark Mercola & Juan C del Alamo - 1-37 Impact of symmetry in local learning rules on predictive neural representations and generalization in spatial navigation
by Janis Keck & Caswell Barry & Christian F Doeller & Jürgen Jost
May 2025, Volume 21, Issue 5
- 1-5 Many roads to minimizing regret: A comparison of Wang et al (2024) and OpAL* models of adaptive striatal dopamine
by Joshua TS Hewson & Alana Jaskir & Michael J Frank - 1-12 Colonization times in Moran process on graphs
by Lenka Kopfová & Josef Tkadlec - 1-14 Optical Neuroimage Studio (OptiNiSt): Intuitive, scalable, extendable framework for optical neuroimage data analysis
by Yukako Yamane & Yuzhe Li & Keita Matsumoto & Ryota Kanai & Miles Desforges & Carlos Enrique Gutierrez & Kenji Doya - 1-15 Modeling opioid overdose events recurrence with a covariate-adjusted triggering point process
by Fenglian Pan & You Zhou & Carolina Vivas-Valencia & Nan Kong & Carol Ott & Mohammad S Jalali & Jian Liu