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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 - 1-15 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 - 1-18 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 - 1-24 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 - 1-26 Mechanisms of mistrust: A Bayesian account of misinformation learning
by Lion Schulz & Yannick Streicher & Eric Schulz & Rahul Bhui & Peter Dayan - 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 - 1-30 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 - 1-36 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 - 1-22 Mapping genes for human face shape: Exploration of univariate phenotyping strategies
by Meng Yuan & Seppe Goovaerts & Michiel Vanneste & Harold Matthews & Hanne Hoskens & Stephen Richmond & Ophir D Klein & Richard A Spritz & Benedikt Hallgrimsson & Susan Walsh & Mark D Shriver & John R Shaffer & Seth M Weinberg & Hilde Peeters & Peter Claes - 1-22 Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform
by Xavier Escriba-Montagut & Yannick Marcon & Augusto Anguita-Ruiz & Demetris Avraam & Jose Urquiza & Andrei S Morgan & Rebecca C Wilson & Paul Burton & Juan R Gonzalez - 1-22 The Burr distribution as a model for the delay between key events in an individual’s infection history
by Nyall Jamieson & Christiana Charalambous & David M Schultz & Ian Hall - 1-22 Estimating the distribution of parameters in differential equations with repeated cross-sectional data
by Hyeontae Jo & Sung Woong Cho & Hyung Ju Hwang - 1-24 A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors
by Henri Schmidt & Benjamin J Raphael - 1-24 A multi-scale study of thalamic state-dependent responsiveness
by Jorin Overwiening & Federico Tesler & Domenico Guarino & Alain Destexhe - 1-25 Estimating the time-varying effective reproduction number via Cycle Threshold-based Transformer
by Xin-Yu Zhang & Lan-Lan Yu & Wei-Yi Wang & Gui-Quan Sun & Jian-Cheng Lv & Tao Zhou & Quan-Hui Liu - 1-26 Evolution of cooperation in multichannel games on multiplex networks
by Amit Basak & Supratim Sengupta - 1-27 A framework for modelling desert locust population dynamics and large-scale dispersal
by Renata Retkute & William Thurston & Keith Cressman & Christopher A Gilligan - 1-29 Integration of partially observed multimodal and multiscale neural signals for estimating a neural circuit using dynamic causal modeling
by Jiyoung Kang & Hae-Jeong Park - 1-31 Marked point process variational autoencoder with applications to unsorted spiking activities
by Ryohei Shibue & Tomoharu Iwata - 1-31 Mathematical basis and toolchain for hierarchical optimization of biochemical networks
by Nisha Ann Viswan & Alexandre Tribut & Manvel Gasparyan & Ovidiu Radulescu & Upinder S Bhalla - 1-32 Neuro-cognitive multilevel causal modeling: A framework that bridges the explanatory gap between neuronal activity and cognition
by Moritz Grosse-Wentrup & Akshey Kumar & Anja Meunier & Manuel Zimmer - 1-37 Parallel development of object recognition in newborn chicks and deep neural networks
by Lalit Pandey & Donsuk Lee & Samantha M W Wood & Justin N Wood - 1-39 Uncovering population contributions to the extracellular potential in the mouse visual system using Laminar Population Analysis
by Atle E Rimehaug & Anders M Dale & Anton Arkhipov & Gaute T Einevoll - 1-43 Evaluation and comparison of methods for neuronal parameter optimization using the Neuroptimus software framework
by Máté Mohácsi & Márk Patrik Török & Sára Sáray & Luca Tar & Gábor Farkas & Szabolcs Káli - 1-44 Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction
by Akash Bahai & Chee Keong Kwoh & Yuguang Mu & Yinghui Li - 1-46 Extracting interpretable signatures of whole-brain dynamics through systematic comparison
by Annie G Bryant & Kevin Aquino & Linden Parkes & Alex Fornito & Ben D Fulcher
November 2024, Volume 20, Issue 11
- 1-10 Eleven quick tips for properly handling tabular data
by Marla I Hertz & Ashley S McNeill - 1-17 MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm
by Chao Wang & Quan Zou - 1-17 Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function
by Yuanchen Zhao & Otto X Cordero & Mikhail Tikhonov - 1-17 Deep neural networks for endemic measles dynamics: Comparative analysis and integration with mechanistic models
by Wyatt G Madden & Wei Jin & Benjamin Lopman & Andreas Zufle & Benjamin Dalziel & C Jessica E. Metcalf & Bryan T Grenfell & Max S Y Lau - 1-18 The evolutionary cost of homophily: Social stratification facilitates stable variant coexistence and increased rates of evolution in host-associated pathogens
by Shuanger Li & Davorka Gulisija & Oana Carja - 1-19 Socially driven negative feedback regulates activity and energy use in ant colonies
by Maurizio Porfiri & Nicole Abaid & Simon Garnier - 1-21 A new look at TFPI inhibition of factor X activation
by Fabian Santiago & Amandeep Kaur & Shannon Bride & Dougald Monroe & Karin Leiderman & Suzanne Sindi - 1-21 Approximate planning in spatial search
by Marta Kryven & Suhyoun Yu & Max Kleiman-Weiner & Tomer Ullman & Joshua Tenenbaum - 1-21 scGRN-Entropy: Inferring cell differentiation trajectories using single-cell data and gene regulation network-based transfer entropy
by Rui Sun & Wenjie Cao & ShengXuan Li & Jian Jiang & Yazhou Shi & Bengong Zhang - 1-23 A mechanistic model of in vitro plasma activation to evaluate therapeutic kallikrein-kinin system inhibitors
by Alireza Rezvani-Sharif & Hadi Lioe & Steven K Dower & Matthias Pelzing & Con Panousis & Dalton J E Harvie & Ineke L Muir - 1-23 Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning
by Robert van Dijk & John Arevalo & Mehrtash Babadi & Anne E Carpenter & Shantanu Singh - 1-23 GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies
by Lin Lin & Rachel L Spreng & Kelly E Seaton & S Moses Dennison & Lindsay C Dahora & Daniel J Schuster & Sheetal Sawant & Peter B Gilbert & Youyi Fong & Neville Kisalu & Andrew J Pollard & Georgia D Tomaras & Jia Li - 1-23 Reliability of plastid and mitochondrial localisation prediction declines rapidly with the evolutionary distance to the training set increasing
by Sven B Gould & Jonas Magiera & Carolina García García & Parth K Raval - 1-24 Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics
by Alexandria M Jensen & Peter DeWitt & Brianne M Bettcher & Julia Wrobel & Katerina Kechris & Debashis Ghosh - 1-25 Human perception of self-motion and orientation during galvanic vestibular stimulation and physical motion
by Aaron R Allred & Caroline R Austin & Lanna Klausing & Nicholas Boggess & Torin K Clark - 1-25 Mathematical modeling suggests heterogeneous replication of Mycobacterium tuberculosis in rabbits
by Vitaly V Ganusov & Afsal Kolloli & Selvakumar Subbian - 1-27 Co-contraction embodies uncertainty: An optimal feedforward strategy for robust motor control
by Bastien Berret & Dorian Verdel & Etienne Burdet & Frédéric Jean - 1-30 An inductive bias for slowly changing features in human reinforcement learning
by Noa L Hedrich & Eric Schulz & Sam Hall-McMaster & Nicolas W Schuck - 1-30 A framework for counterfactual analysis, strategy evaluation, and control of epidemics using reproduction number estimates
by Baike She & Rebecca Lee Smith & Ian Pytlarz & Shreyas Sundaram & Philip E Paré - 1-32 Teaching deep networks to see shape: Lessons from a simplified visual world
by Christian Jarvers & Heiko Neumann - 1-33 Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations
by Aylin Bircan & Nurdan Kuru & Onur Dereli & Berkay Selçuk & Ogün Adebali
October 2024, Volume 20, Issue 10
- 1-10 Gene signatures for cancer research: A 25-year retrospective and future avenues
by Wei Liu & Huaqin He & Davide Chicco - 1-17 EEG microstate transition cost correlates with task demands
by Giacomo Barzon & Ettore Ambrosini & Antonino Vallesi & Samir Suweis - 1-17 Integrating information from historical data into mechanistic models for influenza forecasting
by Alessio Andronico & Juliette Paireau & Simon Cauchemez - 1-19 Enhancing insights in sexually transmitted infection mapping: Syphilis in Forsyth County, North Carolina, a case study
by Lani Fox & William C Miller & Dionne Gesink & Irene Doherty & Marc Serre - 1-20 IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation
by Haolin Jiang & Yulian Xu & Yunguang Tong & Dong Zhang & Ruhong Zhou - 1-20 Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals
by Michele Gentili & Kimberly Glass & Enrico Maiorino & Brian D Hobbs & Zhonghui Xu & Peter J Castaldi & Michael H Cho & Craig P Hersh & Dandi Qiao & Jarrett D Morrow & Vincent J Carey & John Platig & Edwin K Silverman - 1-21 Best practices for estimating and reporting epidemiological delay distributions of infectious diseases
by Kelly Charniga & Sang Woo Park & Andrei R Akhmetzhanov & Anne Cori & Jonathan Dushoff & Sebastian Funk & Katelyn M Gostic & Natalie M Linton & Adrian Lison & Christopher E Overton & Juliet R C Pulliam & Thomas Ward & Simon Cauchemez & Sam Abbott - 1-21 PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites
by Yun Zuo & Xingze Fang & Jiayong Wan & Wenying He & Xiangrong Liu & Xiangxiang Zeng & Zhaohong Deng - 1-24 Building, benchmarking, and exploring perturbative maps of transcriptional and morphological data
by Safiye Celik & Jan-Christian Hütter & Sandra Melo Carlos & Nathan H Lazar & Rahul Mohan & Conor Tillinghast & Tommaso Biancalani & Marta M Fay & Berton A Earnshaw & Imran S Haque - 1-24 Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer
by Lianghong Chen & Zi Huai Huang & Yan Sun & Mike Domaratzki & Qian Liu & Pingzhao Hu - 1-25 A Computational Framework for Understanding the Impact of Prior Experiences on Pain Perception and Neuropathic Pain
by Malin Ramne & Jon Sensinger - 1-25 Regularizing hyperparameters of interacting neural signals in the mouse cortex reflect states of arousal
by Dmitry R Lyamzin & Andrea Alamia & Mohammad Abdolrahmani & Ryo Aoki & Andrea Benucci - 1-27 Computational joint action: Dynamical models to understand the development of joint coordination
by Cecilia De Vicariis & Vinil T Chackochan & Laura Bandini & Eleonora Ravaschio & Vittorio Sanguineti - 1-27 Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history
by Gabriel A A Silva & Avril M Harder & Kenneth B Kirksey & Samarth Mathur & Janna R Willoughby - 1-28 The optimal spatially-dependent control measures to effectively and economically eliminate emerging infectious diseases
by Fan Xia & Yanni Xiao & Junling Ma - 1-29 Compression-based inference of network motif sets
by Alexis Bénichou & Jean-Baptiste Masson & Christian L Vestergaard - 1-29 Why aphid virus retention needs more attention: Modelling aphid behaviour and virus manipulation in non-persistent plant virus transmission
by Elin K Falla & Nik J Cunniffe - 1-32 Roles and interplay of reinforcement-based and error-based processes during reaching and gait in neurotypical adults and individuals with Parkinson’s disease
by Adam M Roth & John H Buggeln & Joanna E Hoh & Jonathan M Wood & Seth R Sullivan & Truc T Ngo & Jan A Calalo & Rakshith Lokesh & Susanne M Morton & Stephen Grill & John J Jeka & Michael J Carter & Joshua G A Cashaback - 1-34 Learning probability distributions of sensory inputs with Monte Carlo predictive coding
by Gaspard Oliviers & Rafal Bogacz & Alexander Meulemans - 1-38 Bayesian polynomial neural networks and polynomial neural ordinary differential equations
by Colby Fronk & Jaewoong Yun & Prashant Singh & Linda Petzold - 1-39 Mcadet: A feature selection method for fine-resolution single-cell RNA-seq data based on multiple correspondence analysis and community detection
by Saishi Cui & Sina Nassiri & Issa Zakeri - 1-45 A flexible generative algorithm for growing in silico placentas
by Diana C de Oliveira & Hani Cheikh Sleiman & Kelly Payette & Jana Hutter & Lisa Story & Joseph V Hajnal & Daniel C Alexander & Rebecca J Shipley & Paddy J Slator
September 2024, Volume 20, Issue 9
- 1-9 Ten simple rules for successfully carrying out funded research projects
by Diego A Forero & Walter H Curioso & Wei Wang - 1-11 Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting
by Anis Ur Rahman & Gleb Tikhonov & Jari Oksanen & Tuomas Rossi & Otso Ovaskainen - 1-12 Ten quick tips for ensuring machine learning model validity
by Wilson Wen Bin Goh & Mohammad Neamul Kabir & Sehwan Yoo & Limsoon Wong - 1-17 Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies
by Adrian J Green & Lisa Truong & Preethi Thunga & Connor Leong & Melody Hancock & Robyn L Tanguay & David M Reif - 1-17 Bayesian clustering with uncertain data
by Kath Nicholls & Paul D W Kirk & Chris Wallace - 1-18 Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases
by Joseph Shingleton & David Mustard & Steven Dyke & Hannah Williams & Emma Bennett & Thomas Finnie - 1-19 Calibrating dimension reduction hyperparameters in the presence of noise
by Justin Lin & Julia Fukuyama - 1-20 Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency
by Eslam Abousamra & Marlin Figgins & Trevor Bedford - 1-20 Construct prognostic models of multiple myeloma with pathway information incorporated
by Shuo Wang & ShanJin Wang & Wei Pan & YuYang Yi & Junyan Lu - 1-21 A hierarchy of metabolite exchanges in metabolic models of microbial species and communities
by Ylva Katarina Wedmark & Jon Olav Vik & Ove Øyås - 1-22 HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures
by Olav N L Aga & Morten Brun & Kazeem A Dauda & Ramon Diaz-Uriarte & Konstantinos Giannakis & Iain G Johnston - 1-23 Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter
by Jolanda Malamud & Sinan Guloksuz & Ruud van Winkel & Philippe Delespaul & Marc A F De Hert & Catherine Derom & Evert Thiery & Nele Jacobs & Bart P F Rutten & Quentin J M Huys - 1-23 Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data
by Michiel Stock & Wim Van Criekinge & Dimitri Boeckaerts & Steff Taelman & Maxime Van Haeverbeke & Pieter Dewulf & Bernard De Baets - 1-23 HELP: A computational framework for labelling and predicting human common and context-specific essential genes
by Ilaria Granata & Lucia Maddalena & Mario Manzo & Mario Rosario Guarracino & Maurizio Giordano - 1-23 The primacy model and the structure of olfactory space
by Hamza Giaffar & Sergey Shuvaev & Dmitry Rinberg & Alexei A Koulakov - 1-24 Overcoming CRISPR-Cas9 off-target prediction hurdles: A novel approach with ESB rebalancing strategy and CRISPR-MCA model
by Yanpeng Yang & Yanyi Zheng & Quan Zou & Jian Li & Hailin Feng - 1-24 SEMbap: Bow-free covariance search and data de-correlation
by Mario Grassi & Barbara Tarantino - 1-24 Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments
by Janice Yang & Neil J Daily & Taylor K Pullinger & Tetsuro Wakatsuki & Eric A Sobie