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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 - 1-21 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 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 - 1-16 M-band wavelet-based multi-view clustering of cells
by Tong Liu & Zihuan Liu & Wenke Sun & Adeethyia Shankar & Yongzhong Zhao & Xiaodi Wang - 1-18 OmniSegger: A time-lapse image analysis pipeline for bacterial cells
by Teresa W Lo & Kevin J Cutler & H James Choi & Paul A Wiggins - 1-18 Ten quick tips to perform meaningful and reproducible molecular docking calculations
by Elvis A F Martis & Stéphane Téletchéa - 1-20 Parallel synapses with transmission nonlinearities enhance neuronal classification capacity
by Yuru Song & Marcus K Benna - 1-20 Scoring protein-ligand binding structures through learning atomic graphs with inter-molecular adjacency
by Debby D Wang & Yuting Huang - 1-22 Inferring synaptic transmission from the stochastic dynamics of the quantal content: An analytical approach
by Zahra Vahdat & Oliver Gambrell & Jonas Fisch & Eckhard Friauf & Abhyudai Singh - 1-22 Conformal prediction for uncertainty quantification in dynamic biological systems
by Alberto Portela & Julio R Banga & Marcos Matabuena - 1-23 Generative AI mitigates representation bias and improves model fairness through synthetic health data
by Raffaele Marchesi & Nicolo Micheletti & Nicholas I-Hsien Kuo & Sebastiano Barbieri & Giuseppe Jurman & Venet Osmani - 1-24 Knowledge-aware contrastive heterogeneous molecular graph learning
by Mukun Chen & Jia Wu & Shirui Pan & Fu Lin & Bo Du & Xiuwen Gong & Wenbin Hu - 1-24 Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data
by Quintin Pope & Rohan Varma & Christine Tataru & Maude M David & Xiaoli Fern - 1-24 Optimization hardness constrains ecological transients
by William Gilpin - 1-25 BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models
by Joseph James Tharayil & Jorge Blanco Alonso & Silvia Farcito & Bryn Lloyd & Armando Romani & Elvis Boci & Antonino Cassara & Felix Schürmann & Esra Neufeld & Niels Kuster & Michael Reimann - 1-26 Mechanisms of mistrust: A Bayesian account of misinformation learning
by Lion Schulz & Yannick Streicher & Eric Schulz & Rahul Bhui & Peter Dayan - 1-27 MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures
by Yuxiang Zhan & Francesco Musella & Frank Alber - 1-28 Cellular morphodynamics as quantifiers for functional states of resident tissue macrophages in vivo
by Miriam Schnitzerlein & Eric Greto & Anja Wegner & Anna Möller & Oliver Aust & Oumaima Ben Brahim & David B Blumenthal & Vasily Zaburdaev & Stefan Uderhardt - 1-28 Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells
by Owen M O’Connor & Mary J Dunlop - 1-29 Noise correlations and neuronal diversity may limit the utility of winner-take-all readout in a pop out visual search task
by Ori Hendler & Ronen Segev & Maoz Shamir - 1-29 The effects of the post-delay epochs on working memory error reduction
by Zeyuan Ye & Haoran Li & Liang Tian & Changsong Zhou - 1-30 Expectation generation and its effect on subsequent pain and visual perception
by Rotem Botvinik-Nezer & Stephan Geuter & Martin A Lindquist & Tor D Wager - 1-30 Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation
by Wenjun Zhao & Erica Larschan & Björn Sandstede & Ritambhara Singh - 1-31 Macroecological patterns in experimental microbial communities
by William R Shoemaker & Álvaro Sánchez & Jacopo Grilli - 1-35 Stimulus uncertainty and relative reward rates determine adaptive responding in perceptual decision-making
by Luis de la Cuesta-Ferrer & Christina Koß & Sarah Starosta & Nils Kasties & Daniel Lengersdorf & Frank Jäkel & Maik C Stüttgen - 1-36 Capturing the emergent dynamical structure in biophysical neural models
by Borjan Milinkovic & Lionel Barnett & Olivia Carter & Anil K Seth & Thomas Andrillon - 1-39 Building momentum: A computational account of persistence toward long-term goals
by Sneha Aenugu & John P O’Doherty
April 2025, Volume 21, Issue 4
- 1-10 RMPJ: An ImageJ plugin for morphological information processing in biomedical images
by Yoshitaka Kimori - 1-12 An evolutionary model of rhythmic accelerando in animal vocal signalling
by Yannick Jadoul & Taylor A Hersh & Elias Fernández Domingos & Marco Gamba & Livio Favaro & Andrea Ravignani - 1-13 Ten quick tips to get you started with Bayesian statistics
by Olivier Gimenez & Andy Royle & Marc Kéry & Chloé R Nater - 1-13 Biases in neural population codes with a few active neurons
by Sander W Keemink & Mark CW van Rossum - 1-13 DelaySSA: stochastic simulation of biochemical systems and gene regulatory networks with or without time delays
by Ziyan Jin & Xinyi Zhou & Zhaoyuan Fang - 1-14 Quantifying the impact of contact tracing interview prioritisation strategies on disease transmission: A modelling study
by Logan Wu & Christopher M Baker & Nicholas Tierney & Kylie Carville & Jodie McVernon & Nick Golding & James M McCaw & Freya M Shearer - 1-15 scPEDSSC: proximity enhanced deep sparse subspace clustering method for scRNA-seq data
by Xiaopeng Wei & Jingli Wu & Gaoshi Li & Jiafei Liu & Xi Wu & Chang He - 1-16 A teaching proposal for a short course on biomedical data science
by Davide Chicco & Vasco Coelho - 1-18 Limitations and optimizations of cellular lineages tracking
by Nava Leibovich & Sidhartha Goyal - 1-18 Meta-Reinforcement Learning reconciles surprise, value, and control in the anterior cingulate cortex
by Tim Vriens & Eliana Vassena & Giovanni Pezzulo & Gianluca Baldassarre & Massimo Silvetti - 1-18 MINT: A toolbox for the analysis of multivariate neural information coding and transmission
by Gabriel Matías Lorenz & Nicola Marie Engel & Marco Celotto & Loren Koçillari & Sebastiano Curreli & Tommaso Fellin & Stefano Panzeri - 1-18 Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out
by Ben Williams & Santiago M Balvanera & Sarab S Sethi & Timothy AC Lamont & Jamaluddin Jompa & Mochyudho Prasetya & Laura Richardson & Lucille Chapuis & Emma Weschke & Andrew Hoey & Ricardo Beldade & Suzanne C Mills & Anne Haguenauer & Frederic Zuberer & Stephen D Simpson & David Curnick & Kate E Jones - 1-18 Falsifying computational models of endothelial cell network formation through quantitative comparison with in vitro models
by Tessa M Vergroesen & Vincent Vermeulen & Roeland M H Merks - 1-19 Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2
by Emma B Hodcroft & Martin S Wohlfender & Richard A Neher & Julien Riou & Christian L Althaus - 1-19 Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory
by Atsushi Matsuda & Mohammad R K Mofrad - 1-20 The multiscale self-similarity of the weighted human brain connectome
by Laia Barjuan & Muhua Zheng & M Ángeles Serrano - 1-21 Including population and environmental dynamic heterogeneities in continuum models of collective behaviour with applications to locust foraging and group structure
by Fillipe Georgiou & Camille Buhl & J E F Green & Bishnu Lamichhane & Ngamta Thamwattana - 1-21 Joint estimation of hand-foot-mouth disease model and prediction in korea using the ensemble kalman filter
by Wasim Abbas & Sieun Lee & Sangil Kim - 1-21 Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City
by Renquan Zhang & Jilei Tai & Qing Yao & Wan Yang & Kai Ruggeri & Jeffrey Shaman & Sen Pei - 1-21 Federated epidemic surveillance
by Ruiqi Lyu & Roni Rosenfeld & Bryan Wilder - 1-21 A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes
by Ihab Hashem & Jian Wang & Jan FM Van Impe - 1-21 Balancing complexity, performance and plausibility to meta learn plasticity rules in recurrent spiking networks
by Basile Confavreux & Everton J Agnes & Friedemann Zenke & Henning Sprekeler & Tim P Vogels - 1-22 TGF-M: Topology-augmented geometric features enhance molecular property prediction
by Wei He & Xu Tian & Xue Li & Peifu Han & Shuang Wang & Lin Liu & Tao Song - 1-23 A new paradigm considering multicellular adhesion, repulsion and attraction represent diverse cellular tile patterns
by Jose A Carrillo & Hideki Murakawa & Makoto Sato & Miaoxing Wang - 1-25 The confidence-noise confidence-boost (CNCB) model of confidence rating data
by Pascal Mamassian & Vincent de Gardelle - 1-25 Quantifying expression and metabolic activity of genes regulated by pregnane X receptor in primary human hepatocyte spheroids
by Lukáš Lochman & Ellen Tanaka Kahiya & Bechara Saade & Tomáš Smutný & Jurjen Duintjer Tebbens & Petr Pávek & Veronika Bernhauerová - 1-25 Modeling diffusive search by non-adaptive sperm: Empirical and computational insights
by Benjamin M Brisard & Kylie D Cashwell & Stephanie M Stewart & Logan M Harrison & Aidan C Charles & Chelsea V Dennis & Ivie R Henslee & Ethan L Carrow & Heather A Belcher & Debajit Bhowmick & Paul W Vos & Maciej Majka & Martin Bier & David M Hart & Cameron A Schmidt - 1-26 Dynamic brain connectivity predicts emotional arousal during naturalistic movie-watching
by Jin Ke & Hayoung Song & Zihan Bai & Monica D Rosenberg & Yuan Chang Leong - 1-28 Dynamic modeling of EEG responses to natural speech reveals earlier processing of predictable words
by Jin Dou & Andrew J Anderson & Aaron S White & Samuel V Norman-Haignere & Edmund C Lalor - 1-28 Statistical signature of subtle behavioral changes in large-scale assays
by Alexandre Blanc & François Laurent & Alex Barbier-Chebbah & Hugues Van Assel & Benjamin T Cocanougher & Benjamin MW Jones & Peter Hague & Marta Zlatic & Rayan Chikhi & Christian L Vestergaard & Tihana Jovanic & Jean-Baptiste Masson & Chloé Barré - 1-29 On the validity of electric brain signal predictions based on population firing rates
by Torbjørn V Ness & Tom Tetzlaff & Gaute T Einevoll & David Dahmen - 1-33 Heuristic energy-based cyclic peptide design
by Qiyao Zhu & Vikram Khipple Mulligan & Dennis Shasha - 1-33 A generalized higher-order correlation analysis framework for multi-omics network inference
by Weixuan Liu & Katherine A Pratte & Peter J Castaldi & Craig Hersh & Russell P Bowler & Farnoush Banaei-Kashani & Katerina J Kechris - 1-34 A computational account of multiple motives guiding context-dependent prosocial behavior
by Claire Lugrin & Jie Hu & Christian C Ruff - 1-37 Simulating dynamic insecticide selection pressures for resistance management in mosquitoes assuming polygenic resistance
by Neil Philip Hobbs & Ian Hastings - 1-37 Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model
by Ian Roberts & Richard G Everitt & Jere Koskela & Xavier Didelot - 1-41 Foraging animals use dynamic Bayesian updating to model meta-uncertainty in environment representations
by James Webb & Paul Steffan & Benjamin Y Hayden & Daeyeol Lee & Caleb Kemere & Matthew McGinley - 1-42 How distinct sources of nuisance variability in natural images and scenes limit human stereopsis
by David N White & Johannes Burge
March 2025, Volume 21, Issue 3
- 1-22 Synthetic population generation with public health characteristics for spatial agent-based models
by Emma Von Hoene & Amira Roess & Hamdi Kavak & Taylor Anderson - 1-22 Efficient numerosity estimation under limited time
by Joseph A Heng & Michael Woodford & Rafael Polania - 1-22 Suprachiasmatic nucleus-wide estimation of oscillatory temporal dynamics
by Yifan Yao & Scott Pauls & Duncan Foley & Tomoko Yoshikawa & Sato Honma & Ken-Ichi Honma & Ellie McVeigh & Nicolas C Foley & Rae Silver - 1-24 Post-processing and weighted combination of infectious disease nowcasts
by André Victor Ribeiro Amaral & Daniel Wolffram & Paula Moraga & Johannes Bracher - 1-24 Gauge fixing for sequence-function relationships
by Anna Posfai & Juannan Zhou & David M McCandlish & Justin B Kinney - 1-25 GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data
by Simonida Zehr & Sebastian Wolf & Thomas Oellerich & Matthias S Leisegang & Ralf P Brandes & Marcel H Schulz & Timothy Warwick - 1-26 Computational studies reveal structural characterization and novel families of Puccinia striiformis f. sp. tritici effectors
by Raheel Asghar & Nan Wu & Noman Ali & Yulei Wang & Mahinur Akkaya - 1-28 Exploring the transmission of cognitive task information through optimal brain pathways
by Zhengdong Wang & Yifeixue Yang & Ziyi Huang & Wanyun Zhao & Kaiqiang Su & Hengcheng Zhu & Dazhi Yin - 1-28 Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills
by Russell Dinnage & Marian Kleineberg - 1-32 DySCo: A general framework for dynamic functional connectivity
by Giuseppe de Alteriis & Oliver Sherwood & Alessandro Ciaramella & Robert Leech & Joana Cabral & Federico E Turkheimer & Paul Expert
February 2025, Volume 21, Issue 2
- 1-7 Ten simple rules for fostering creativity in research labs
by Matthias C Rillig - 1-10 Ten quick tips to build a Model Life Cycle
by Timothée Poisot & Daniel J Becker & Cole B Brookson & Ellie Graeden & Sadie J Ryan & Gemma Turon & Colin Carlson - 1-19 Repeated games with partner choice
by Christopher Graser & Takako Fujiwara-Greve & Julián García & Matthijs van Veelen - 1-20 An application of nowcasting methods: Cases of norovirus during the winter 2023/2024 in England
by Jonathon Mellor & Maria L Tang & Emilie Finch & Rachel Christie & Oliver Polhill & Christopher E Overton & Ann Hoban & Amy Douglas & Sarah R Deeny & Thomas Ward - 1-20 Compression-enabled interpretability of voxelwise encoding models
by Fatemeh Kamali & Amir Abolfazl Suratgar & Mohammadbagher Menhaj & Reza Abbasi-Asl - 1-20 A SuperLearner-based pipeline for the development of DNA methylation-derived predictors of phenotypic traits
by Dennis Khodasevich & Nina Holland & Lars van der Laan & Andres Cardenas - 1-21 Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities
by Lars Berling & Jonathan Klawitter & Remco Bouckaert & Dong Xie & Alex Gavryushkin & Alexei J Drummond - 1-21 Early detection of disease outbreaks and non-outbreaks using incidence data: A framework using feature-based time series classification and machine learning
by Shan Gao & Amit K Chakraborty & Russell Greiner & Mark A Lewis & Hao Wang - 1-22 Bayesian classification of OXPHOS deficient skeletal myofibres
by Jordan Childs & Tiago Bernardino Gomes & Amy E Vincent & Andrew Golightly & Conor Lawless - 1-22 SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data
by Shunsuke A Sakai & Ryosuke Nomura & Satoi Nagasawa & SungGi Chi & Ayako Suzuki & Yutaka Suzuki & Mitsuho Imai & Yoshiaki Nakamura & Takayuki Yoshino & Shumpei Ishikawa & Katsuya Tsuchihara & Shun-Ichiro Kageyama & Riu Yamashita - 1-23 Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA
by Eliezyer Fermino de Oliveira & Pranjal Garg & Jens Hjerling-Leffler & Renata Batista-Brito & Lucas Sjulson - 1-23 AWGE-ESPCA: An edge sparse PCA model based on adaptive noise elimination regularization and weighted gene network for Hermetia illucens genomic data analysis
by Rui Miao & Hao-Yang Yu & Bing-Jie Zhong & Hong-Xia Sun & Qiang Xia - 1-24 Information transmission in a cell monolayer: A numerical study
by Paweł Nałęcz-Jawecki & Przemysław Szyc & Frederic Grabowski & Marek Kochańczyk & Tomasz Lipniacki - 1-25 Optimal control prevents itself from eradicating stochastic disease epidemics
by Rachel Russell & Nik J Cunniffe - 1-26 Nowcasting reported covid-19 hospitalizations using de-identified, aggregated medical insurance claims data
by Xueda Shen & Aaron Rumack & Bryan Wilder & Ryan J Tibshirani - 1-26 Identification of recurrent dynamics in distributed neural populations
by Rodrigo Osuna-Orozco & Edward Castillo & Kameron Decker Harris & Samantha R Santacruz - 1-26 Hexagons all the way down: grid cells as a conformal isometric map of space
by Vemund Sigmundson Schøyen & Kosio Beshkov & Markus Borud Pettersen & Erik Hermansen & Konstantin Holzhausen & Anders Malthe-Sørenssen & Marianne Fyhn & Mikkel Elle Lepperød - 1-26 Using a multi-strain infectious disease model with physical information neural networks to study the time dependence of SARS-CoV-2 variants of concern
by Wenxuan Li & Xu Chen & Suli Liu & Chiyu Zhang & Guyue Liu - 1-27 Reliability-enhanced data cleaning in biomedical machine learning using inductive conformal prediction
by Xianghao Zhan & Qinmei Xu & Yuanning Zheng & Guangming Lu & Olivier Gevaert - 1-33 ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature
by Luca Musella & Alejandro Afonso Castro & Xin Lai & Max Widmann & Julio Vera
January 2025, Volume 21, Issue 1
- 1-10 Ten simple rules to complete successfully a computational MSc thesis project
by Edoardo Saccenti & Cristina Furlan - 1-12 Exploiting the similarity of dissimilarities for biomedical applications and enhanced machine learning
by Mohammad Neamul Kabir & Li Rong Wang & Wilson Wen Bin Goh - 1-13 Eight quick tips for biologically and medically informed machine learning
by Luca Oneto & Davide Chicco - 1-15 Learning predictive signatures of HLA type from T-cell repertoires
by María Ruiz Ortega & Mikhail V Pogorelyy & Anastasia A Minervina & Paul G Thomas & Thierry Mora & Aleksandra M Walczak - 1-16 A robust transfer learning approach for high-dimensional linear regression to support integration of multi-source gene expression data
by Lulu Pan & Qian Gao & Kecheng Wei & Yongfu Yu & Guoyou Qin & Tong Wang - 1-18 Extracting the fingerprints of sequences of random rhythmic auditory stimuli from electrophysiological data
by Fernando A Najman & Antonio Galves & Marcela Svarc & Claudia D Vargas - 1-19 Benchmarking uncertainty quantification for protein engineering
by Kevin P Greenman & Ava P Amini & Kevin K Yang - 1-20 Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers
by Kwang Su Kim & Masashi Iwamoto & Kosaku Kitagawa & Hyeongki Park & Sanae Hayashi & Senko Tsukuda & Takeshi Matsui & Masanori Atsukawa & Kentaro Matsuura & Natthaya Chuaypen & Pisit Tangkijvanich & Lena Allweiss & Takara Nishiyama & Naotoshi Nakamura & Yasuhisa Fujita & Eiryo Kawakami & Shinji Nakaoka & Masamichi Muramatsu & Kazuyuki Aihara & Takaji Wakita & Alan S Perelson & Maura Dandri & Koichi Watashi & Shingo Iwami & Yasuhito Tanaka - 1-20 Role and modulation of various spinal pathways for human upper limb control in different gravity conditions
by Alice Bruel & Lina Bacha & Emma Boehly & Constance De Trogoff & Luca Represa & Gregoire Courtine & Auke Ijspeert - 1-21 Ten simple rules for good model-sharing practices
by Ismael Kherroubi Garcia & Christopher Erdmann & Sandra Gesing & Michael Barton & Lauren Cadwallader & Geerten Hengeveld & Christine R Kirkpatrick & Kathryn Knight & Carsten Lemmen & Rebecca Ringuette & Qing Zhan & Melissa Harrison & Feilim Mac Gabhann & Natalie Meyers & Cailean Osborne & Charlotte Till & Paul Brenner & Matt Buys & Min Chen & Allen Lee & Jason Papin & Yuhan Rao - 1-21 Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data
by Xu Shi & Xiao Wang & Lu Jin & Leena Halakivi-Clarke & Robert Clarke & Andrew F Neuwald & Jianhua Xuan - 1-21 Integration of unpaired single cell omics data by deep transfer graph convolutional network
by Yulong Kan & Yunjing Qi & Zhongxiao Zhang & Xikeng Liang & Weihao Wang & Shuilin Jin - 1-22 Bayesian active sound localisation: To what extent do humans perform like an ideal-observer?
by Glen McLachlan & Piotr Majdak & Jonas Reijniers & Michael Mihocic & Herbert Peremans - 1-25 Data-driven discovery and parameter estimation of mathematical models in biological pattern formation
by Hidekazu Hishinuma & Hisako Takigawa-Imamura & Takashi Miura - 1-26 Multi-region infectious disease prediction modeling based on spatio-temporal graph neural network and the dynamic model
by Xiaoyi Wang & Zhen Jin - 1-27 Optimal control of agent-based models via surrogate modeling
by Luis L Fonseca & Lucas Böttcher & Borna Mehrad & Reinhard C Laubenbacher - 1-28 HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data
by Evan Gorstein & Rosa Aghdam & Claudia Solís-Lemus - 1-29 Deciphering the interplay between biology and physics with a finite element method-implemented vertex organoid model: A tool for the mechanical analysis of cell behavior on a spherical organoid shell
by Julien Laussu & Deborah Michel & Léa Magne & Stephane Segonds & Steven Marguet & Dimitri Hamel & Muriel Quaranta-Nicaise & Frederick Barreau & Emmanuel Mas & Vincent Velay & Florian Bugarin & Audrey Ferrand - 1-29 Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense
by Nicole M Moody & Cole M Williams & Sohini Ramachandran & Matthew J Fuxjager - 1-30 The calcitron: A simple neuron model that implements many learning rules via the calcium control hypothesis
by Toviah Moldwin & Li Shay Azran & Idan Segev - 1-30 Sparse high-dimensional decomposition of non-primary auditory cortical receptive fields
by Shoutik Mukherjee & Behtash Babadi & Shihab Shamma - 1-33 Trajectory inference from single-cell genomics data with a process time model
by Meichen Fang & Gennady Gorin & Lior Pachter - 1-37 Mechanisms for dysregulation of excitatory-inhibitory balance underlying allodynia in dorsal horn neural subcircuits
by Alexander G Ginsberg & Scott F Lempka & Bo Duan & Victoria Booth & Jennifer Crodelle
December 2024, Volume 20, Issue 12
- 1-9 Hands-on training about data clustering with orange data mining toolbox
by Janez Demšar & Blaž Zupan - 1-10 Randomness as a driver of inactivity in social groups
by Abel Bernadou & Raphaël Jeanson - 1-11 ClustAll: An R package for patient stratification in complex diseases
by Asier Ortega-Legarreta & Sara Palomino-Echeverria & Estefania Huergo & Vincenzo Lagani & Narsis A Kiani & Pierre-Emmanuel Rautou & Nuria Planell Picola & Jesper Tegner & David Gomez-Cabrero - 1-17 Therapeutic dose prediction of α5-GABA receptor modulation from simulated EEG of depression severity
by Alexandre Guet-McCreight & Frank Mazza & Thomas D Prevot & Etienne Sibille & Etay Hay - 1-17 Mechanical network equivalence between the katydid and mammalian inner ears
by Emine Celiker & Charlie Woodrow & Òscar Guadayol & Leonidas-Romanos Davranoglou & Christian M Schlepütz & Beth Mortimer & Graham K Taylor & Stuart Humphries & Fernando Montealegre-Z - 1-18 Optimisation strategies for directed evolution without sequencing
by Jessica James & Sebastian Towers & Jakob Foerster & Harrison Steel - 1-19 Properties of winning Iterated Prisoner’s Dilemma strategies
by Nikoleta E Glynatsi & Vincent Knight & Marc Harper - 1-19 Machine learning mathematical models for incidence estimation during pandemics
by Oscar Fajardo-Fontiveros & Mattia Mattei & Giulio Burgio & Clara Granell & Sergio Gómez & Alex Arenas & Marta Sales-Pardo & Roger Guimerà - 1-19 Adapting to time: Why nature may have evolved a diverse set of neurons
by Karim G Habashy & Benjamin D Evans & Dan F M Goodman & Jeffrey S Bowers - 1-20 Preserving friendships in school contacts: An algorithm to construct synthetic temporal networks for epidemic modelling
by Lucille Calmon & Elisabetta Colosi & Giulia Bassignana & Alain Barrat & Vittoria Colizza - 1-20 A mathematical model of plasmin-mediated fibrinolysis of single fibrin fibers
by Roukayatou R Ouedraogo & Hannah K Sowers & Spencer R Lynch & Nathan E Hudson & Brittany E Bannish - 1-21 scMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum
by Yuqian Liu & Yan Chen & Huanwen Wu & Xuanping Zhang & Yuqi Wang & Xin Yi & Zhiyong Liang & Jiayin Wang