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September 2023, Volume 19, Issue 9
- 1-18 Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics
by Serena Aneli & Piero Fariselli & Elena Chierto & Carla Bini & Carlo Robino & Giovanni Birolo - 1-18 Uncovering specific mechanisms across cell types in dynamical models
by Adrian L Hauber & Marcus Rosenblatt & Jens Timmer - 1-19 Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony
by Seirana Hashemi & Zahra Razaghi-Moghadam & Zoran Nikoloski - 1-20 iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease
by Ziheng Duan & Yi Dai & Ahyeon Hwang & Cheyu Lee & Kaichi Xie & Chutong Xiao & Min Xu & Matthew J Girgenti & Jing Zhang - 1-21 Beyond ℓ1 sparse coding in V1
by Ilias Rentzeperis & Luca Calatroni & Laurent U Perrinet & Dario Prandi - 1-22 Identifying a developmental transition in honey bees using gene expression data
by Bryan C Daniels & Ying Wang & Robert E Page Jr & Gro V Amdam - 1-22 Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England
by James D Munday & Sam Abbott & Sophie Meakin & Sebastian Funk - 1-22 Human-environment feedback and the consistency of proenvironmental behavior
by Claire Ecotière & Sylvain Billiard & Jean-Baptiste André & Pierre Collet & Régis Ferrière & Sylvie Méléard - 1-23 Nowcasting the 2022 mpox outbreak in England
by Christopher E Overton & Sam Abbott & Rachel Christie & Fergus Cumming & Julie Day & Owen Jones & Rob Paton & Charlie Turner & Thomas Ward - 1-24 Measuring uncertainty in human visual segmentation
by Jonathan Vacher & Claire Launay & Pascal Mamassian & Ruben Coen-Cagli - 1-24 Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches
by Zheng Jiang & Yue-Yue Shen & Rong Liu - 1-24 Fixation dynamics on hypergraphs
by Ruodan Liu & Naoki Masuda - 1-26 A role for cortical interneurons as adversarial discriminators
by Ari S Benjamin & Konrad P Kording - 1-26 Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data
by Simon Boutry & Raphaël Helaers & Tom Lenaerts & Miikka Vikkula - 1-27 What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases
by Francis Banville & Dominique Gravel & Timothée Poisot - 1-27 Mate selection: A useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding
by Billy Tchounke & Leopoldo Sanchez & Joseph Martin Bell & David Cros - 1-27 Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels
by Erik Nordquist & Guohui Zhang & Shrishti Barethiya & Nathan Ji & Kelli M White & Lu Han & Zhiguang Jia & Jingyi Shi & Jianmin Cui & Jianhan Chen - 1-28 Mixtures of strategies underlie rodent behavior during reversal learning
by Nhat Minh Le & Murat Yildirim & Yizhi Wang & Hiroki Sugihara & Mehrdad Jazayeri & Mriganka Sur - 1-28 Simulation-based inference for efficient identification of generative models in computational connectomics
by Jan Boelts & Philipp Harth & Richard Gao & Daniel Udvary & Felipe Yáñez & Daniel Baum & Hans-Christian Hege & Marcel Oberlaender & Jakob H Macke - 1-29 iCVS—Inferring Cardio-Vascular hidden States from physiological signals available at the bedside
by Neta Ravid Tannenbaum & Omer Gottesman & Azadeh Assadi & Mjaye Mazwi & Uri Shalit & Danny Eytan - 1-31 Personalized prediction for multiple chronic diseases by developing the multi-task Cox learning model
by Shuaijie Zhang & Fan Yang & Lijie Wang & Shucheng Si & Jianmei Zhang & Fuzhong Xue - 1-31 Profile-Wise Analysis: A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models
by Matthew J Simpson & Oliver J Maclaren - 1-32 The inhibitory control of traveling waves in cortical networks
by Grishma Palkar & Jian-young Wu & Bard Ermentrout - 1-32 Self-loops in evolutionary graph theory: Friends or foes?
by Nikhil Sharma & Sedigheh Yagoobi & Arne Traulsen - 1-36 Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models
by Christian Tönsing & Bernhard Steiert & Jens Timmer & Clemens Kreutz - 1-45 Error-independent effect of sensory uncertainty on motor learning when both feedforward and feedback control processes are engaged
by Christopher L Hewitson & David M Kaplan & Matthew J Crossley
August 2023, Volume 19, Issue 8
- 1-6 Ten simple rules for writing a technical book
by Jess Haberman & Greg Wilson - 1-12 Ten simple rules for a mom-friendly Academia
by Esther Sebastián-González & Eva Graciá & Alejandra Morán-Ordóñez & Irene Pérez-Ibarra & Ana Sanz-Aguilar & Mar Sobral - 1-14 Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool
by Rebecca K Nash & Samir Bhatt & Anne Cori & Pierre Nouvellet - 1-15 A new method for the analysis of access period experiments, illustrated with whitefly-borne cassava mosaic begomovirus
by Ruairí Donnelly & Christopher A Gilligan - 1-18 Practical sampling of constraint-based models: Optimized thinning boosts CHRR performance
by Johann F Jadebeck & Wolfgang Wiechert & Katharina Nöh - 1-18 Synaptic weights that correlate with presynaptic selectivity increase decoding performance
by Júlia V Gallinaro & Benjamin Scholl & Claudia Clopath - 1-18 Ensemble inference of unobserved infections in networks using partial observations
by Renquan Zhang & Jilei Tai & Sen Pei - 1-19 E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction
by Rahmatullah Roche & Bernard Moussad & Md Hossain Shuvo & Debswapna Bhattacharya - 1-19 Evolutionary dynamics on sequential temporal networks
by Anzhi Sheng & Aming Li & Long Wang - 1-20 Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network
by Wenxing Hu & Lixin Guan & Mengshan Li - 1-20 The specious art of single-cell genomics
by Tara Chari & Lior Pachter - 1-21 Disentangling Abstraction from Statistical Pattern Matching in Human and Machine Learning
by Sreejan Kumar & Ishita Dasgupta & Nathaniel D Daw & Jonathan D Cohen & Thomas L Griffiths - 1-22 iCircDA-NEAE: Accelerated attribute network embedding and dynamic convolutional autoencoder for circRNA-disease associations prediction
by Lin Yuan & Jiawang Zhao & Zhen Shen & Qinhu Zhang & Yushui Geng & Chun-Hou Zheng & De-Shuang Huang - 1-23 Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model
by Shawn A Means & Mathias W Roesler & Amy S Garrett & Leo Cheng & Alys R Clark - 1-23 In-silico and in-vitro morphometric analysis of intestinal organoids
by Sandra Montes-Olivas & Danny Legge & Abbie Lund & Alexander G Fletcher & Ann C Williams & Lucia Marucci & Martin Homer - 1-23 Scoring epidemiological forecasts on transformed scales
by Nikos I Bosse & Sam Abbott & Anne Cori & Edwin van Leeuwen & Johannes Bracher & Sebastian Funk - 1-23 An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space
by Bastian Volker Helmut Hornung & Nicolas Terrapon - 1-23 Neural network models for influenza forecasting with associated uncertainty using Web search activity trends
by Michael Morris & Peter Hayes & Ingemar J Cox & Vasileios Lampos - 1-24 Curated single cell multimodal landmark datasets for R/Bioconductor
by Kelly B Eckenrode & Dario Righelli & Marcel Ramos & Ricard Argelaguet & Christophe Vanderaa & Ludwig Geistlinger & Aedin C Culhane & Laurent Gatto & Vincent Carey & Martin Morgan & Davide Risso & Levi Waldron - 1-24 STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring
by Azka Javaid & Hildreth Robert Frost - 1-24 Functional and spatial rewiring principles jointly regulate context-sensitive computation
by Jia Li & Ilias Rentzeperis & Cees van Leeuwen - 1-25 Mathematical modeling indicates that regulatory inhibition of CD8+ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load
by Jonathan W Cody & Amy L Ellis-Connell & Shelby L O’Connor & Elsje Pienaar - 1-25 Receptive field sizes and neuronal encoding bandwidth are constrained by axonal conduction delays
by Tim C Hladnik & Jan Grewe - 1-26 From time-series transcriptomics to gene regulatory networks: A review on inference methods
by Malvina Marku & Vera Pancaldi - 1-28 Efficient sampling-based Bayesian Active Learning for synaptic characterization
by Camille Gontier & Simone Carlo Surace & Igor Delvendahl & Martin Müller & Jean-Pascal Pfister - 1-28 Mathematical models of developmental vascular remodelling: A review
by Jessica R Crawshaw & Jennifer A Flegg & Miguel O Bernabeu & James M Osborne - 1-28 VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
by Guillermo Rangel-Pineros & Alexandre Almeida & Martin Beracochea & Ekaterina Sakharova & Manja Marz & Alejandro Reyes Muñoz & Martin Hölzer & Robert D Finn - 1-29 Automatic extraction of actin networks in plants
by Jordan Hembrow & Michael J Deeks & David M Richards - 1-31 Enhancing reinforcement learning models by including direct and indirect pathways improves performance on striatal dependent tasks
by Kim T Blackwell & Kenji Doya - 1-31 Hybrid predictive coding: Inferring, fast and slow
by Alexander Tscshantz & Beren Millidge & Anil K Seth & Christopher L Buckley - 1-31 Redundant representations are required to disambiguate simultaneously presented complex stimuli
by W Jeffrey Johnston & David J Freedman - 1-31 Inferring gene regulatory networks using transcriptional profiles as dynamical attractors
by Ruihao Li & Jordan C Rozum & Morgan M Quail & Mohammad N Qasim & Suzanne S Sindi & Clarissa J Nobile & Réka Albert & Aaron D Hernday - 1-31 Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration
by Caetano Souto-Maior & Yazmin L Serrano Negron & Susan T Harbison - 1-33 Structural identifiability of biomolecular controller motifs with and without flow measurements as model output
by Eivind S Haus & Tormod Drengstig & Kristian Thorsen - 1-34 Geometry of population activity in spiking networks with low-rank structure
by Ljubica Cimeša & Lazar Ciric & Srdjan Ostojic - 1-41 Switching state-space modeling of neural signal dynamics
by Mingjian He & Proloy Das & Gladia Hotan & Patrick L Purdon
July 2023, Volume 19, Issue 7
- 1-16 LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses
by Alexei J Drummond & Kylie Chen & Fábio K Mendes & Dong Xie - 1-17 LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity
by Juan Xie & Hyeongseon Jeon & Gang Xin & Qin Ma & Dongjun Chung - 1-17 Network feature-based phenotyping of leaf venation robustly reconstructs the latent space
by Kohei Iwamasa & Koji Noshita - 1-19 RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure
by Elena Rivas - 1-20 Monte Carlo samplers for efficient network inference
by Zeliha Kilic & Max Schweiger & Camille Moyer & Steve Pressé - 1-20 Continuous action with a neurobiologically inspired computational approach reveals the dynamics of selection history
by Mukesh Makwana & Fan Zhang & Dietmar Heinke & Joo-Hyun Song - 1-21 Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection
by Alain J Mbebi & Zoran Nikoloski - 1-21 The interplay between age structure and cultural transmission
by Anne Kandler & Laurel Fogarty & Folgert Karsdorp - 1-22 Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants
by Ahmed Taha & Mauricio Patón & David R Penas & Julio R Banga & Jorge Rodríguez - 1-22 Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach
by Christian Blau & Linnea Yvonnesdotter & Erik Lindahl - 1-23 Mapping the semi-nested community structure of 3D chromosome contact networks
by Dolores Bernenko & Sang Hoon Lee & Per Stenberg & Ludvig Lizana - 1-24 Biological complexity facilitates tuning of the neuronal parameter space
by Marius Schneider & Alexander D Bird & Albert Gidon & Jochen Triesch & Peter Jedlicka & Hermann Cuntz - 1-25 Indirect reciprocity with stochastic and dual reputation updates
by Yohsuke Murase & Christian Hilbe - 1-26 A multi-scale clutch model for adhesion complex mechanics
by Chiara Venturini & Pablo Sáez - 1-29 SpikeShip: A method for fast, unsupervised discovery of high-dimensional neural spiking patterns
by Boris Sotomayor-Gómez & Francesco P Battaglia & Martin Vinck - 1-32 Sequential mutations in exponentially growing populations
by Michael D Nicholson & David Cheek & Tibor Antal - 1-33 Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment
by Roger Vargas & Liam Abbott & Daniel Bower & Nicole Frahm & Mike Shaffer & Wen-Han Yu - 1-39 Mechanisms of sensorimotor adaptation in a hierarchical state feedback control model of speech
by Kwang S Kim & Jessica L Gaines & Benjamin Parrell & Vikram Ramanarayanan & Srikantan S Nagarajan & John F Houde - 1-39 Modality independent or modality specific? Common computations underlie confidence judgements in visual and auditory decisions
by Rebecca K West & William J Harrison & Natasha Matthews & Jason B Mattingley & David K Sewell - 1-39 Unified tumor growth mechanisms from multimodel inference and dataset integration
by Samantha P Beik & Leonard A Harris & Michael A Kochen & Julien Sage & Vito Quaranta & Carlos F Lopez
June 2023, Volume 19, Issue 6
- 1-7 HAT: Hypergraph analysis toolbox
by Joshua Pickard & Can Chen & Rahmy Salman & Cooper Stansbury & Sion Kim & Amit Surana & Anthony Bloch & Indika Rajapakse - 1-10 A mutation-level covariate model for mutational signatures
by Itay Kahane & Mark D M Leiserson & Roded Sharan - 1-12 Teaching students to R3eason, not merely to solve problem sets: The role of philosophy and visual data communication in accessible data science education
by Ilinca I Ciubotariu & Gundula Bosch - 1-14 Recall DNA methylation levels at low coverage sites using a CNN model in WGBS
by Ximei Luo & Yansu Wang & Quan Zou & Lei Xu - 1-16 Stochastic simulations of self-organized elastogenesis in the developing lung
by Xiru Fan & Cristian Valenzuela & Weijing Zhao & Zi Chen & Dong Wang & Steven J Mentzer - 1-17 Patient groups in Rheumatoid arthritis identified by deep learning respond differently to biologic or targeted synthetic DMARDs
by Maria Kalweit & Andrea M Burden & Joschka Boedecker & Thomas Hügle & Theresa Burkard - 1-18 Analysis of high-dimensional metabolomics data with complex temporal dynamics using RM-ASCA+
by Balázs Erdős & Johan A Westerhuis & Michiel E Adriaens & Shauna D O’Donovan & Ren Xie & Cécile M Singh-Povel & Age K Smilde & Ilja C W Arts - 1-19 Supervised learning and model analysis with compositional data
by Shimeng Huang & Elisabeth Ailer & Niki Kilbertus & Niklas Pfister - 1-19 BioSeq-Diabolo: Biological sequence similarity analysis using Diabolo
by Hongliang Li & Bin Liu - 1-20 Nonlinear eco-evolutionary games with global environmental fluctuations and local environmental feedbacks
by Yishen Jiang & Xin Wang & Longzhao Liu & Ming Wei & Jingwu Zhao & Zhiming Zheng & Shaoting Tang - 1-20 Knowledge graph embedding for profiling the interaction between transcription factors and their target genes
by Yang-Han Wu & Yu-An Huang & Jian-Qiang Li & Zhu-Hong You & Peng-Wei Hu & Lun Hu & Victor C M Leung & Zhi-Hua Du - 1-20 Learning from the past: A short term forecast method for the COVID-19 incidence curve
by Jean-David Morel & Jean-Michel Morel & Luis Alvarez - 1-20 Environmental dynamics shape perceptual decision bias
by Julie A Charlton & Wiktor F Młynarski & Yoon H Bai & Ann M Hermundstad & Robbe L T Goris - 1-22 Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state
by Tobias S Brett & Shweta Bansal & Pejman Rohani - 1-22 Distinguishing between different percolation regimes in noisy dynamic networks with an application to epileptic seizures
by Xiaojing Zhu & Heather Shappell & Mark A Kramer & Catherine J Chu & Eric D Kolaczyk - 1-23 Hebbian learning with elasticity explains how the spontaneous motor tempo affects music performance synchronization
by Iran R Roman & Adrian S Roman & Ji Chul Kim & Edward W Large - 1-23 Grouping promotes both partnership and rivalry with long memory in direct reciprocity
by Yohsuke Murase & Seung Ki Baek - 1-26 The biomechanics of chewing and suckling in the infant: A potential mechanism for physiologic metopic suture closure
by Pranav N Haravu & Miguel Gonzalez & Shelby L Nathan & Callum F Ross & Olga Panagiotopoulou & Russell R Reid - 1-26 Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth
by Hugo Dourado & Wolfram Liebermeister & Oliver Ebenhöh & Martin J Lercher - 1-27 HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph
by Joshua Daniel Rubin & Nicola Alexandra Vogel & Shyam Gopalakrishnan & Peter Wad Sackett & Gabriel Renaud - 1-30 Estimating fine age structure and time trends in human contact patterns from coarse contact data: The Bayesian rate consistency model
by Shozen Dan & Yu Chen & Yining Chen & Melodie Monod & Veronika K Jaeger & Samir Bhatt & André Karch & Oliver Ratmann & on behalf of the Machine Learning & Global Health network - 1-30 Identifying properties of pattern completion neurons in a computational model of the visual cortex
by Casey M Baker & Yiyang Gong - 1-31 Adaptive dynamics of memory-one strategies in the repeated donation game
by Philip LaPorte & Christian Hilbe & Martin A Nowak - 1-31 Humans decompose tasks by trading off utility and computational cost
by Carlos G Correa & Mark K Ho & Frederick Callaway & Nathaniel D Daw & Thomas L Griffiths
May 2023, Volume 19, Issue 5
- 1-13 Four guiding principles for effective trainee-led STEM community engagement through high school outreach
by Stefanie Luecke & Allison Schiffman & Apeksha Singh & Helen Huang & Barbara Shannon & Catera L Wilder - 1-18 Random walk informed heterogeneity detection reveals how the lymph node conduit network influences T cells collective exploration behavior
by Solène Song & Malek Senoussi & Paul Escande & Paul Villoutreix - 1-18 Identifying prognostic subgroups of luminal-A breast cancer using deep autoencoders and gene expressions
by Seunghyun Wang & Doheon Lee - 1-19 Matrix prior for data transfer between single cell data types in latent Dirichlet allocation
by Alan Min & Timothy Durham & Louis Gevirtzman & William Stafford Noble - 1-20 ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning
by Olga Mineeva & Daniel Danciu & Bernhard Schölkopf & Ruth E Ley & Gunnar Rätsch & Nicholas D Youngblut - 1-20 Predicting anti-cancer drug combination responses with a temporal cell state network model
by Deepraj Sarmah & Wesley O Meredith & Ian K Weber & Madison R Price & Marc R Birtwistle - 1-21 An approximate diffusion process for environmental stochasticity in infectious disease transmission modelling
by Sanmitra Ghosh & Paul J Birrell & Daniela De Angelis - 1-22 Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression
by Kexin Huang & Yun Zhang & Haoran Gong & Zhengzheng Qiao & Tiangang Wang & Weiling Zhao & Liyu Huang & Xiaobo Zhou - 1-23 A unitary mechanism underlies adaptation to both local and global environmental statistics in time perception
by Tianhe Wang & Yingrui Luo & Richard B Ivry & Jonathan S Tsay & Ernst Pöppel & Yan Bao - 1-23 Tight basis cycle representatives for persistent homology of large biological data sets
by Manu Aggarwal & Vipul Periwal - 1-24 Enabling interpretable machine learning for biological data with reliability scores
by K D Ahlquist & Lauren A Sugden & Sohini Ramachandran - 1-25 Targeting operational regimes of interest in recurrent neural networks
by Pierre Ekelmans & Nataliya Kraynyukova & Tatjana Tchumatchenko - 1-25 Canonical Response Parameterization: Quantifying the structure of responses to single-pulse intracranial electrical brain stimulation
by Kai J Miller & Klaus-Robert Müller & Gabriela Ojeda Valencia & Harvey Huang & Nicholas M Gregg & Gregory A Worrell & Dora Hermes - 1-26 Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier
by Matthew Beauregard Smith & Zack Booth Simpson & Edward M Marcotte - 1-29 Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data
by David Augustin & Ben Lambert & Ken Wang & Antje-Christine Walz & Martin Robinson & David Gavaghan - 1-31 Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths
by Jean-Michel Arbona & Hadi Kabalane & Jeremy Barbier & Arach Goldar & Olivier Hyrien & Benjamin Audit - 1-36 Data-driven segmentation of cortical calcium dynamics
by Sydney C Weiser & Brian R Mullen & Desiderio Ascencio & James B Ackman
April 2023, Volume 19, Issue 4
- 1-6 Establishing effective cross-disciplinary collaboration: Combining simple rules for reproducible computational research, a good data management plan, and good research practice
by Bogna Stawarczyk & Małgorzata Roos - 1-13 Calibrating agent-based models to tumor images using representation learning
by Colin G Cess & Stacey D Finley - 1-14 Rare-event sampling analysis uncovers the fitness landscape of the genetic code
by Yuji Omachi & Nen Saito & Chikara Furusawa - 1-16 Bridging the gap between mechanistic biological models and machine learning surrogates
by Ioana M Gherman & Zahraa S Abdallah & Wei Pang & Thomas E Gorochowski & Claire S Grierson & Lucia Marucci - 1-18 Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data
by Krystian Zieliński & Sebastian Pukszta & Małgorzata Mickiewicz & Marta Kotlarz & Piotr Wygocki & Marcin Zieleń & Dominika Drzewiecka & Damian Drzyzga & Anna Kloska & Joanna Jakóbkiewicz-Banecka - 1-20 Fidelity of hyperbolic space for Bayesian phylogenetic inference
by Matthew Macaulay & Aaron Darling & Mathieu Fourment - 1-20 Shape-driven deep neural networks for fast acquisition of aortic 3D pressure and velocity flow fields
by Endrit Pajaziti & Javier Montalt-Tordera & Claudio Capelli & Raphaël Sivera & Emilie Sauvage & Michael Quail & Silvia Schievano & Vivek Muthurangu - 1-20 Gate-based quantum computing for protein design
by Mohammad Hassan Khatami & Udson C Mendes & Nathan Wiebe & Philip M Kim - 1-21 Fusing an agent-based model of mosquito population dynamics with a statistical reconstruction of spatio-temporal abundance patterns
by Sean M Cavany & Guido España & Alun L Lloyd & Gonzalo M Vazquez-Prokopec & Helvio Astete & Lance A Waller & Uriel Kitron & Thomas W Scott & Amy C Morrison & Robert C Reiner Jr & T Alex Perkins - 1-21 Multi-view clustering by CPS-merge analysis with application to multimodal single-cell data
by Lixiang Zhang & Lin Lin & Jia Li - 1-23 High rifampicin peak plasma concentrations accelerate the slow phase of bacterial decline in tuberculosis patients: Evidence for heteroresistance
by Antal Martinecz & Martin J Boeree & Andreas H Diacon & Rodney Dawson & Colin Hemez & Rob E Aarnoutse & Pia Abel zur Wiesch - 1-24 Minor variations in multicellular life cycles have major effects on adaptation
by Hanna Isaksson & Åke Brännström & Eric Libby - 1-27 Recurrent predictive coding models for associative memory employing covariance learning
by Mufeng Tang & Tommaso Salvatori & Beren Millidge & Yuhang Song & Thomas Lukasiewicz & Rafal Bogacz - 1-28 Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference
by Aidan B Estelle & August George & Elisar J Barbar & Daniel M Zuckerman - 1-29 Efficient coding of natural scenes improves neural system identification
by Yongrong Qiu & David A Klindt & Klaudia P Szatko & Dominic Gonschorek & Larissa Hoefling & Timm Schubert & Laura Busse & Matthias Bethge & Thomas Euler - 1-31 Model certainty in cellular network-driven processes with missing data
by Michael W Irvin & Arvind Ramanathan & Carlos F Lopez
March 2023, Volume 19, Issue 3
- 1-7 Ten simple rules for serving as an editor
by Cameron Mura & Philip E Bourne - 1-10 Ten (not so) simple rules for clinical trial data-sharing
by Claude Pellen & Anne Le Louarn & Gilliosa Spurrier-Bernard & Evelyne Decullier & Jean-Marie Chrétien & Eric Rosenthal & Gérard Le Goff & David Moher & John P A Ioannidis & Florian Naudet - 1-12 The effect of non-linear signal in classification problems using gene expression
by Benjamin J Heil & Jake Crawford & Casey S Greene - 1-13 A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya
by Ruth Nanjala & Festus Nyasimi & Daniel Masiga & Caleb Kipkurui Kibet - 1-15 Robust deep learning object recognition models rely on low frequency information in natural images
by Zhe Li & Josue Ortega Caro & Evgenia Rusak & Wieland Brendel & Matthias Bethge & Fabio Anselmi & Ankit B Patel & Andreas S Tolias & Xaq Pitkow - 1-16 Predicting functional effects of ion channel variants using new phenotypic machine learning methods
by Christian Malte Boßelmann & Ulrike B S Hedrich & Holger Lerche & Nico Pfeifer - 1-17 Ten simple rules for socially responsible science
by Alon Zivony & Rasha Kardosh & Liadh Timmins & Niv Reggev - 1-18 Spatial and temporal correlations in human cortex are inherently linked and predicted by functional hierarchy, vigilance state as well as antiepileptic drug load
by Paul Manuel Müller & Christian Meisel - 1-18 Hindcasts and forecasts of suicide mortality in US: A modeling study
by Sasikiran Kandula & Mark Olfson & Madelyn S Gould & Katherine M Keyes & Jeffrey Shaman - 1-19 Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates
by Christoffer Norn & Ingemar André - 1-19 Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins
by Carlos A Gandarilla-Pérez & Sergio Pinilla & Anne-Florence Bitbol & Martin Weigt - 1-19 CustOmics: A versatile deep-learning based strategy for multi-omics integration
by Hakim Benkirane & Yoann Pradat & Stefan Michiels & Paul-Henry Cournède - 1-19 MGAE-DC: Predicting the synergistic effects of drug combinations through multi-channel graph autoencoders
by Peng Zhang & Shikui Tu - 1-21 Inferring protein fitness landscapes from laboratory evolution experiments
by Sameer D’Costa & Emily C Hinds & Chase R Freschlin & Hyebin Song & Philip A Romero - 1-21 Macroscopic resting state model predicts theta burst stimulation response: A randomized trial
by Neda Kaboodvand & Behzad Iravani & Martijn P van den Heuvel & Jonas Persson & Robert Boden - 1-22 Inferring feature importance with uncertainties with application to large genotype data
by Pål Vegard Johnsen & Inga Strümke & Mette Langaas & Andrew Thomas DeWan & Signe Riemer-Sørensen - 1-22 Modelling daily weight variation in honey bee hives
by Karina Arias-Calluari & Theotime Colin & Tanya Latty & Mary Myerscough & Eduardo G Altmann - 1-24 Detection of genes with differential expression dispersion unravels the role of autophagy in cancer progression
by Christophe Le Priol & Chloé-Agathe Azencott & Xavier Gidrol - 1-24 Validation framework for epidemiological models with application to COVID-19 models
by Kimberly A Dautel & Ephraim Agyingi & Pras Pathmanathan - 1-25 A new method for the joint estimation of instantaneous reproductive number and serial interval during epidemics
by Chenxi Dai & Dongsheng Zhou & Bo Gao & Kaifa Wang - 1-26 A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer
by Delora Baptista & Pedro G Ferreira & Miguel Rocha - 1-27 Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning
by Bercem Dutagaci & Bingbing Duan & Chenxi Qiu & Craig D Kaplan & Michael Feig - 1-28 One model fits all: Combining inference and simulation of gene regulatory networks
by Elias Ventre & Ulysse Herbach & Thibault Espinasse & Gérard Benoit & Olivier Gandrillon - 1-28 BiComp-DTA: Drug-target binding affinity prediction through complementary biological-related and compression-based featurization approach
by Mahmood Kalemati & Mojtaba Zamani Emani & Somayyeh Koohi - 1-28 Global nonlinear approach for mapping parameters of neural mass models
by Dominic M Dunstan & Mark P Richardson & Eugenio Abela & Ozgur E Akman & Marc Goodfellow - 1-29 Coding of object location by heterogeneous neural populations with spatially dependent correlations in weakly electric fish
by Myriah Haggard & Maurice J Chacron - 1-31 OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer
by Anni S Halkola & Kaisa Joki & Tuomas Mirtti & Marko M Mäkelä & Tero Aittokallio & Teemu D Laajala - 1-38 Topological descriptors of the parameter region of multistationarity: Deciding upon connectivity
by Máté László Telek & Elisenda Feliu
February 2023, Volume 19, Issue 2
- 1-13 A linear discriminant analysis model of imbalanced associative learning in the mushroom body compartment
by David Lipshutz & Aneesh Kashalikar & Shiva Farashahi & Dmitri B Chklovskii - 1-14 Forecasting upper respiratory tract infection burden using high-dimensional time series data and forecast combinations
by Jue Tao Lim & Kelvin Bryan Tan & John Abisheganaden & Borame L Dickens - 1-17 Neural adaptation and fractional dynamics as a window to underlying neural excitability
by Brian Nils Lundstrom & Thomas J Richner - 1-20 Interpreting T-cell search “strategies” in the light of evolution under constraints
by Inge M N Wortel & Johannes Textor - 1-20 iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures
by Joris J R Louwen & Satria A Kautsar & Sven van der Burg & Marnix H Medema & Justin J J van der Hooft - 1-23 Evolutionary dynamics of hyperbolic language
by Madison S Krieger - 1-23 Contact networks have small metric backbones that maintain community structure and are primary transmission subgraphs
by Rion Brattig Correia & Alain Barrat & Luis M Rocha - 1-24 Functional duality in group criticality via ambiguous interactions
by Takayuki Niizato & Hisashi Murakami & Takuya Musha - 1-24 Simulation-based inference for non-parametric statistical comparison of biomolecule dynamics
by Hippolyte Verdier & François Laurent & Alhassan Cassé & Christian L Vestergaard & Christian G Specht & Jean-Baptiste Masson - 1-24 AI reveals insights into link between CD33 and cognitive impairment in Alzheimer’s Disease
by Tamara Raschka & Meemansa Sood & Bruce Schultz & Aybuge Altay & Christian Ebeling & Holger Fröhlich - 1-28 Temporal progression along discrete coding states during decision-making in the mouse gustatory cortex
by Liam Lang & Giancarlo La Camera & Alfredo Fontanini - 1-29 LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics
by Giulio Ruffini & Giada Damiani & Diego Lozano-Soldevilla & Nikolas Deco & Fernando E Rosas & Narsis A Kiani & Adrián Ponce-Alvarez & Morten L Kringelbach & Robin Carhart-Harris & Gustavo Deco - 1-31 Non-destructive classification of unlabeled cells: Combining an automated benchtop magnetic resonance scanner and artificial intelligence
by Philipp Fey & Daniel Ludwig Weber & Jannik Stebani & Philipp Mörchel & Peter Jakob & Jan Hansmann & Karl-Heinz Hiller & Daniel Haddad - 1-31 Unsupervised learning reveals interpretable latent representations for translucency perception
by Chenxi Liao & Masataka Sawayama & Bei Xiao - 1-41 Criticality in probabilistic models of spreading dynamics in brain networks: Epileptic seizures
by S Amin Moosavi & Wilson Truccolo
January 2023, Volume 19, Issue 1
- 1-4 Ten simple rules for defining a computational biology project
by William Stafford Noble - 1-11 Ten simple rules for implementing open and reproducible research practices after attending a training course
by Verena Heise & Constance Holman & Hung Lo & Ekaterini Maria Lyras & Mark Christopher Adkins & Maria Raisa Jessica Aquino & Konstantinos I Bougioukas & Katherine O Bray & Martyna Gajos & Xuanzong Guo & Corinna Hartling & Rodrigo Huerta-Gutierrez & Miroslava Jindrová & Joanne P M Kenney & Adrianna P Kępińska & Laura Kneller & Elena Lopez-Rodriguez & Felix Mühlensiepen & Angela Richards & Gareth Richards & Maximilian Siebert & James A Smith & Natalie Smith & Nicolai Stransky & Sirpa Tarvainen & Daniela Sofia Valdes & Kayleigh L Warrington & Nina-Maria Wilpert & Disa Witkowska & Mirela Zaneva & Jeanette Zanker & Tracey L Weissgerber - 1-19 Surround suppression in mouse auditory cortex underlies auditory edge detection
by Omri David Gilday & Benedikt Praegel & Ido Maor & Tav Cohen & Israel Nelken & Adi Mizrahi - 1-19 Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks
by Polina Lakrisenko & Paul Stapor & Stephan Grein & Łukasz Paszkowski & Dilan Pathirana & Fabian Fröhlich & Glenn Terje Lines & Daniel Weindl & Jan Hasenauer - 1-20 A dual graph neural network for drug–drug interactions prediction based on molecular structure and interactions
by Mei Ma & Xiujuan Lei - 1-20 Interspecific comparison of gene expression profiles using machine learning
by Artem S Kasianov & Anna V Klepikova & Alexey V Mayorov & Gleb S Buzanov & Maria D Logacheva & Aleksey A Penin - 1-23 Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit
by Yibo Zhao & Nikoleta Vavouraki & Ruth C Lovering & Valentina Escott-Price & Kirsten Harvey & Patrick A Lewis & Claudia Manzoni - 1-26 RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks
by Souvik Seal & Qunhua Li & Elle Butler Basner & Laura M Saba & Katerina Kechris - 1-26 Mapping of morpho-electric features to molecular identity of cortical inhibitory neurons
by Yann Roussel & Csaba Verasztó & Dimitri Rodarie & Tanguy Damart & Michael Reimann & Srikanth Ramaswamy & Henry Markram & Daniel Keller - 1-26 Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering
by Theresa Ullmann & Stefanie Peschel & Philipp Finger & Christian L Müller & Anne-Laure Boulesteix - 1-27 Bayesian reconstruction of memories stored in neural networks from their connectivity
by Sebastian Goldt & Florent Krzakala & Lenka Zdeborová & Nicolas Brunel - 1-27 One dimensional approximations of neuronal dynamics reveal computational strategy
by Connor Brennan & Adeeti Aggarwal & Rui Pei & David Sussillo & Alex Proekt - 1-28 Towards integration of time-resolved confocal microscopy of a 3D in vitro microfluidic platform with a hybrid multiscale model of tumor angiogenesis
by Caleb M Phillips & Ernesto A B F Lima & Manasa Gadde & Angela M Jarrett & Marissa Nichole Rylander & Thomas E Yankeelov - 1-28 Skilled motor control of an inverted pendulum implies low entropy of states but high entropy of actions
by Nicola Catenacci Volpi & Martin Greaves & Dari Trendafilov & Christoph Salge & Giovanni Pezzulo & Daniel Polani - 1-29 Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates
by Alexander P Browning & Matthew J Simpson - 1-29 Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability
by Ryan J Murphy & Gency Gunasingh & Nikolas K Haass & Matthew J Simpson