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Content
November 2023, Volume 19, Issue 11
- 1-13 Ten simple rules for students navigating summer research experiences for undergraduates (REU) programs: From application to program completion
by Maria Manzanares & Courtney Peña & Kayla C Kobak & Miranda B Stratton - 1-15 GENERALIST: A latent space based generative model for protein sequence families
by Hoda Akl & Brooke Emison & Xiaochuan Zhao & Arup Mondal & Alberto Perez & Purushottam D Dixit - 1-16 Addressing erroneous scale assumptions in microbe and gene set enrichment analysis
by Kyle C McGovern & Michelle Pistner Nixon & Justin D Silverman - 1-17 A data-driven semi-parametric model of SARS-CoV-2 transmission in the United States
by John M Drake & Andreas Handel & Éric Marty & Eamon B O’Dea & Tierney O’Sullivan & Giovanni Righi & Andrew T Tredennick - 1-18 Assessing the importance of demographic risk factors across two waves of SARS-CoV-2 using fine-scale case data
by Anthony J Wood & Aeron R Sanchez & Paul R Bessell & Rebecca Wightman & Rowland R Kao - 1-19 Attention-based deep clustering method for scRNA-seq cell type identification
by Shenghao Li & Hui Guo & Simai Zhang & Yizhou Li & Menglong Li - 1-20 On convolutional neural networks for selection inference: Revealing the effect of preprocessing on model learning and the capacity to discover novel patterns
by Ryan M Cecil & Lauren A Sugden - 1-21 Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data
by Javier Kipen & Joakim Jaldén - 1-25 Adaptive oscillators support Bayesian prediction in temporal processing
by Keith B Doelling & Luc H Arnal & M Florencia Assaneo - 1-26 BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale
by Tyler W H Backman & Christina Schenk & Tijana Radivojevic & David Ando & Jahnavi Singh & Jeffrey J Czajka & Zak Costello & Jay D Keasling & Yinjie Tang & Elena Akhmatskaya & Hector Garcia Martin - 1-26 Interaction between decision-making and motor learning when selecting reach targets in the presence of bias and noise
by Tianyao Zhu & Jason P Gallivan & Daniel M Wolpert & J Randall Flanagan - 1-27 External mechanical loading overrules cell-cell mechanical communication in sprouting angiogenesis during early bone regeneration
by Chiara Dazzi & Julia Mehl & Mounir Benamar & Holger Gerhardt & Petra Knaus & Georg N Duda & Sara Checa - 1-27 Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany
by Elisabeth K Brockhaus & Daniel Wolffram & Tanja Stadler & Michael Osthege & Tanmay Mitra & Jonas M Littek & Ekaterina Krymova & Anna J Klesen & Jana S Huisman & Stefan Heyder & Laura M Helleckes & Matthias an der Heiden & Sebastian Funk & Sam Abbott & Johannes Bracher - 1-27 The mechanism of MinD stability modulation by MinE in Min protein dynamics
by William C Carlquist & Eric N Cytrynbaum - 1-27 Tuning social interactions’ strength drives collective response to light intensity in schooling fish
by Tingting Xue & Xu Li & GuoZheng Lin & Ramón Escobedo & Zhangang Han & Xiaosong Chen & Clément Sire & Guy Theraulaz - 1-28 Learning efficient representations of environmental priors in working memory
by Tahra L Eissa & Zachary P Kilpatrick - 1-29 Exploring strategy differences between humans and monkeys with recurrent neural networks
by Ben Tsuda & Barry J Richmond & Terrence J Sejnowski - 1-31 Modeling the diverse effects of divisive normalization on noise correlations
by Oren Weiss & Hayley A Bounds & Hillel Adesnik & Ruben Coen-Cagli - 1-32 Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation
by Sarvesh Nikumbh & Boris Lenhard
October 2023, Volume 19, Issue 10
- 1-16 Inference of transmission dynamics and retrospective forecast of invasive meningococcal disease
by Jaime Cascante-Vega & Marta Galanti & Katharina Schley & Sen Pei & Jeffrey Shaman - 1-16 Establishing brain states in neuroimaging data
by Zalina Dezhina & Jonathan Smallwood & Ting Xu & Federico E Turkheimer & Rosalyn J Moran & Karl J Friston & Robert Leech & Erik D Fagerholm - 1-17 Bayesian modeling of the impact of antibiotic resistance on the efficiency of MRSA decolonization
by Fanni Ojala & Mohamad R Abdul Sater & Loren G Miller & James A McKinnell & Mary K Hayden & Susan S Huang & Yonatan H Grad & Pekka Marttinen - 1-18 Mechanistic characterization of oscillatory patterns in unperturbed tumor growth dynamics: The interplay between cancer cells and components of tumor microenvironment
by Aymara Sancho-Araiz & Zinnia P Parra-Guillen & Jean Bragard & Sergio Ardanza & Victor Mangas-Sanjuan & Iñaki F Trocóniz - 1-19 Circadian distribution of epileptiform discharges in epilepsy: Candidate mechanisms of variability
by Isabella Marinelli & Jamie J Walker & Udaya Seneviratne & Wendyl D’Souza & Mark J Cook & Clare Anderson & Andrew P Bagshaw & Stafford L Lightman & Wessel Woldman & John R Terry - 1-19 Lévy movements and a slowly decaying memory allow efficient collective learning in groups of interacting foragers
by Andrea Falcón-Cortés & Denis Boyer & Maximino Aldana & Gabriel Ramos-Fernández - 1-21 Deep convolutional and conditional neural networks for large-scale genomic data generation
by Burak Yelmen & Aurélien Decelle & Leila Lea Boulos & Antoine Szatkownik & Cyril Furtlehner & Guillaume Charpiat & Flora Jay - 1-21 A 2D model to study how secondary growth affects the self-supporting behaviour of climbing plants
by Giacomo Vecchiato & Tom Hattermann & Michele Palladino & Fabio Tedone & Patrick Heuret & Nick P Rowe & Pierangelo Marcati - 1-22 Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data
by Lorenzo Posani & Francesca Rizzato & Rémi Monasson & Simona Cocco - 1-22 Modeling functional cell types in spike train data
by Daniel N Zdeblick & Eric T Shea-Brown & Daniela M Witten & Michael A Buice - 1-23 Combining the dynamic model and deep neural networks to identify the intensity of interventions during COVID-19 pandemic
by Mengqi He & Sanyi Tang & Yanni Xiao - 1-23 Temperature sensitive contact modes allosterically gate TRPV3
by Daniel Burns & Vincenzo Venditti & Davit A Potoyan - 1-24 Rational social distancing policy during epidemics with limited healthcare capacity
by Simon K Schnyder & John J Molina & Ryoichi Yamamoto & Matthew S Turner - 1-26 Natural variability in bee brain size and symmetry revealed by micro-CT imaging and deep learning
by Philipp D Lösel & Coline Monchanin & Renaud Lebrun & Alejandra Jayme & Jacob J Relle & Jean-Marc Devaud & Vincent Heuveline & Mathieu Lihoreau - 1-26 Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Tracker
by Oliver J Meacock & William M Durham - 1-27 Distilling identifiable and interpretable dynamic models from biological data
by Gemma Massonis & Alejandro F Villaverde & Julio R Banga - 1-29 Recognition and reconstruction of cell differentiation patterns with deep learning
by Robin Dirk & Jonas L Fischer & Simon Schardt & Markus J Ankenbrand & Sabine C Fischer - 1-29 Spatial Configurations of 3D Extracellular Matrix Collagen Density and Anisotropy Simultaneously Guide Angiogenesis
by Steven A LaBelle & A Marsh Poulson IV & Steve A Maas & Adam Rauff & Gerard A Ateshian & Jeffrey A Weiss - 1-30 Phi fluctuates with surprisal: An empirical pre-study for the synthesis of the free energy principle and integrated information theory
by Christoffer Lundbak Olesen & Peter Thestrup Waade & Larissa Albantakis & Christoph Mathys - 1-32 Rapid runtime learning by curating small datasets of high-quality items obtained from memory
by Joseph Scott German & Guofeng Cui & Chenliang Xu & Robert A Jacobs - 1-35 Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies
by Yilin Gao & Fengzhu Sun - 1-39 Objects guide human gaze behavior in dynamic real-world scenes
by Nicolas Roth & Martin Rolfs & Olaf Hellwich & Klaus Obermayer - 1-45 Integrated information theory (IIT) 4.0: Formulating the properties of phenomenal existence in physical terms
by Larissa Albantakis & Leonardo Barbosa & Graham Findlay & Matteo Grasso & Andrew M Haun & William Marshall & William G P Mayner & Alireza Zaeemzadeh & Melanie Boly & Bjørn E Juel & Shuntaro Sasai & Keiko Fujii & Isaac David & Jeremiah Hendren & Jonathan P Lang & Giulio Tononi
September 2023, Volume 19, Issue 9
- 1-13 Ten simple rules for interpreting and evaluating a meta-analysis
by Rebecca B Carlson & Jennifer R Martin & Robert D Beckett - 1-17 An automated interface for sedimentation velocity analysis in SEDFIT
by Peter Schuck & Samuel C To & Huaying Zhao - 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