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February 2022, Volume 18, Issue 2
- 1-25 Evaluating supervised and unsupervised background noise correction in human gut microbiome data
by Leah Briscoe & Brunilda Balliu & Sriram Sankararaman & Eran Halperin & Nandita R Garud - 1-26 Combination and competition between path integration and landmark navigation in the estimation of heading direction
by Sevan K Harootonian & Arne D Ekstrom & Robert C Wilson - 1-26 In silico prediction of HIV-1-host molecular interactions and their directionality
by Haiting Chai & Quan Gu & Joseph Hughes & David L Robertson - 1-27 Meta-control of social learning strategies
by Anil Yaman & Nicolas Bredeche & Onur Çaylak & Joel Z Leibo & Sang Wan Lee - 1-27 Shape analysis of gamma rhythm supports a superlinear inhibitory regime in an inhibition-stabilized network
by R Krishnakumaran & Mohammed Raees & Supratim Ray - 1-28 Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics
by Leonie van Steijn & Inge M N Wortel & Clément Sire & Loïc Dupré & Guy Theraulaz & Roeland M H Merks - 1-35 Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts
by Robert C Mines & Tomasz Lipniacki & Xiling Shen - 1-38 Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates
by Alessandra Løchen & James E Truscott & Nicholas J Croucher
January 2022, Volume 18, Issue 1
- 1-16 An initial ‘snapshot’ of sensory information biases the likelihood and speed of subsequent changes of mind
by William Turner & Daniel Feuerriegel & Robert Hester & Stefan Bode - 1-17 CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach
by Mengting Niu & Quan Zou & Chen Lin - 1-18 OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data
by Raga Krishnakumar & Anne M Ruffing - 1-19 Efficient ReML inference in variance component mixed models using a Min-Max algorithm
by Fabien Laporte & Alain Charcosset & Tristan Mary-Huard - 1-19 Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection
by Alasdair D F Clarke & Amelia R Hunt & Anna E Hughes - 1-20 Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution
by Tadamune Kaneko & Macoto Kikuchi - 1-21 Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods
by Richard Jiang & Prashant Singh & Fredrik Wrede & Andreas Hellander & Linda Petzold - 1-22 Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data
by Qi Jiang & Shuo Zhang & Lin Wan - 1-22 Fast and accurate influenza forecasting in the United States with Inferno
by Dave Osthus - 1-22 Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy
by Alexander B Brummer & Xin Yang & Eric Ma & Margarita Gutova & Christine E Brown & Russell C Rockne - 1-23 Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables
by Arno Strouwen & Bart M Nicolaï & Peter Goos - 1-23 Analytical kinetic model of native tandem promoters in E. coli
by Vatsala Chauhan & Mohamed N M Bahrudeen & Cristina S D Palma & Ines S C Baptista & Bilena L B Almeida & Suchintak Dash & Vinodh Kandavalli & Andre S Ribeiro - 1-24 Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach
by Marcell Miski & Bence Márk Keömley-Horváth & Dorina Rákóczi Megyeriné & Attila Csikász-Nagy & Zoltán Gáspári - 1-24 Formation, collective motion, and merging of macroscopic bacterial aggregates
by George Courcoubetis & Manasi S Gangan & Sean Lim & Xiaokan Guo & Stephan Haas & James Q Boedicker - 1-26 The evolutionary maintenance of Lévy flight foraging
by Winston Campeau & Andrew M Simons & Brett Stevens - 1-26 Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach
by Chen Jia & Abhyudai Singh & Ramon Grima - 1-27 Identification of periodic attractors in Boolean networks using a priori information
by Ulrike Münzner & Tomoya Mori & Marcus Krantz & Edda Klipp & Tatsuya Akutsu - 1-28 Discovering adaptation-capable biological network structures using control-theoretic approaches
by Priyan Bhattacharya & Karthik Raman & Arun K Tangirala - 1-29 A lexical approach for identifying behavioural action sequences
by Gautam Reddy & Laura Desban & Hidenori Tanaka & Julian Roussel & Olivier Mirat & Claire Wyart - 1-30 Interpretable machine learning for high-dimensional trajectories of aging health
by Spencer Farrell & Arnold Mitnitski & Kenneth Rockwood & Andrew D Rutenberg - 1-30 Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships
by Nina Kudryashova & Theoklitos Amvrosiadis & Nathalie Dupuy & Nathalie Rochefort & Arno Onken - 1-32 Optimism and pessimism in optimised replay
by Georgy Antonov & Christopher Gagne & Eran Eldar & Peter Dayan
December 2021, Volume 17, Issue 12
- 1-13 Ten simple rules for developing bioinformatics capacity at an academic institution
by Shaun Aron & C Victor Jongeneel & Paballo Abel Chauke & Melek Chaouch & Judit Kumuthini & Lyndon Zass & Fouzia Radouani & Samar Kamal Kassim & Faisal M Fadlelmola & Nicola Mulder - 1-13 Optimal vaccine allocation for COVID-19 in the Netherlands: A data-driven prioritization
by Fuminari Miura & Ka Yin Leung & Don Klinkenberg & Kylie E C Ainslie & Jacco Wallinga - 1-14 Development of an experiment-split method for benchmarking the generalization of a PTM site predictor: Lysine methylome as an example
by Guoyang Zou & Yang Zou & Chenglong Ma & Jiaojiao Zhao & Lei Li - 1-15 SWIFT: A deep learning approach to prediction of hypoxemic events in critically-Ill patients using SpO2 waveform prediction
by Akshaya V Annapragada & Joseph L Greenstein & Sanjukta N Bose & Bradford D Winters & Sridevi V Sarma & Raimond L Winslow - 1-17 Motif-pattern dependence of biomolecular phase separation driven by specific interactions
by Benjamin G Weiner & Andrew G T Pyo & Yigal Meir & Ned S Wingreen - 1-19 Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016–2018: A hidden Markov modelling study
by Deus Thindwa & Nicole Wolter & Amy Pinsent & Maimuna Carrim & John Ojal & Stefano Tempia & Jocelyn Moyes & Meredith McMorrow & Jackie Kleynhans & Anne von Gottberg & Neil French & PHIRST group & Cheryl Cohen & Stefan Flasche - 1-19 GCAEMDA: Predicting miRNA-disease associations via graph convolutional autoencoder
by Lei Li & Yu-Tian Wang & Cun-Mei Ji & Chun-Hou Zheng & Jian-Cheng Ni & Yan-Sen Su - 1-19 A systems genomics approach uncovers molecular associates of RSV severity
by Matthew N McCall & Chin-Yi Chu & Lu Wang & Lauren Benoodt & Juilee Thakar & Anthony Corbett & Jeanne Holden-Wiltse & Christopher Slaunwhite & Alex Grier & Steven R Gill & Ann R Falsey & David J Topham & Mary T Caserta & Edward E Walsh & Xing Qiu & Thomas J Mariani - 1-19 A spatio-temporal model to reveal oscillator phenotypes in molecular clocks: Parameter estimation elucidates circadian gene transcription dynamics in single-cells
by Måns Unosson & Marco Brancaccio & Michael Hastings & Adam M Johansen & Bärbel Finkenstädt - 1-20 Fine scale prediction of ecological community composition using a two-step sequential Machine Learning ensemble
by Icíar Civantos-Gómez & Javier García-Algarra & David García-Callejas & Javier Galeano & Oscar Godoy & Ignasi Bartomeus - 1-21 Dissociable influences of reward and punishment on adaptive cognitive control
by Xiamin Leng & Debbie Yee & Harrison Ritz & Amitai Shenhav - 1-21 One-carbon metabolism during the menstrual cycle and pregnancy
by Ruby Kim & H Frederik Nijhout & Michael C Reed - 1-22 Combination treatment optimization using a pan-cancer pathway model
by Robin Schmucker & Gabriele Farina & James Faeder & Fabian Fröhlich & Ali Sinan Saglam & Tuomas Sandholm - 1-22 Benchmarking of tools for axon length measurement in individually-labeled projection neurons
by Mario Rubio-Teves & Sergio Díez-Hermano & César Porrero & Abel Sánchez-Jiménez & Lucía Prensa & Francisco Clascá & María García-Amado & José Antonio Villacorta-Atienza - 1-22 Dynamic maximum entropy provides accurate approximation of structured population dynamics
by Katarína Bod’ová & Enikő Szép & Nicholas H Barton - 1-22 Internal state effects on behavioral shifts in freely behaving praying mantises (Tenodera sinensis)
by Shanel C Pickard & David J Bertsch & Zoe Le Garrec & Roy E Ritzmann & Roger D Quinn & Nicholas S Szczecinski - 1-23 DeepCME: A deep learning framework for computing solution statistics of the chemical master equation
by Ankit Gupta & Christoph Schwab & Mustafa Khammash - 1-23 Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?
by Juan Diaz-Colunga & Ramon Diaz-Uriarte - 1-24 Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes
by Lanxin Zhang & Junyu Wang & Max von Kleist - 1-28 Asymmetric and transient properties of reciprocal activity of antagonists during the paw-shake response in the cat
by Jessica R Parker & Alexander N Klishko & Boris I Prilutsky & Gennady S Cymbalyuk - 1-28 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant
by Joseph R Larsen & Margaret R Martin & John D Martin & James B Hicks & Peter Kuhn - 1-30 A data-informed mean-field approach to mapping of cortical parameter landscapes
by Zhuo-Cheng Xiao & Kevin K Lin & Lai-Sang Young - 1-31 Realistic retinal modeling unravels the differential role of excitation and inhibition to starburst amacrine cells in direction selectivity
by Elishai Ezra-Tsur & Oren Amsalem & Lea Ankri & Pritish Patil & Idan Segev & Michal Rivlin-Etzion - 1-38 Preparing to move: Setting initial conditions to simplify interactions with complex objects
by Rashida Nayeem & Salah Bazzi & Mohsen Sadeghi & Neville Hogan & Dagmar Sternad - 1-39 Decision prioritization and causal reasoning in decision hierarchies
by Ariel Zylberberg - 1-44 When shared concept cells support associations: Theory of overlapping memory engrams
by Chiara Gastaldi & Tilo Schwalger & Emanuela De Falco & Rodrigo Quian Quiroga & Wulfram Gerstner
November 2021, Volume 17, Issue 11
- 1-12 Identifying prognostic pairwise relationships among bacterial species in microbiome studies
by Sean M Devlin & Axel Martin & Irina Ostrovnaya - 1-14 Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data
by Tania Mendonca & Ana A Jones & Jose M Pozo & Sarah Baxendale & Tanya T Whitfield & Alejandro F Frangi - 1-16 Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling
by Danial Pourjafar-Dehkordi & Martin Zacharias - 1-16 The meaning of significant mean group differences for biomarker discovery
by Eva Loth & Jumana Ahmad & Chris Chatham & Beatriz López & Ben Carter & Daisy Crawley & Bethany Oakley & Hannah Hayward & Jennifer Cooke & Antonia San José Cáceres & Danilo Bzdok & Emily Jones & Tony Charman & Christian Beckmann & Thomas Bourgeron & Roberto Toro & Jan Buitelaar & Declan Murphy & Guillaume Dumas - 1-16 The role of competition versus cooperation in microbial community coalescence
by Pablo Lechón-Alonso & Tom Clegg & Jacob Cook & Thomas P Smith & Samraat Pawar - 1-18 Approximate distance correlation for selecting highly interrelated genes across datasets
by Qunlun Shen & Shihua Zhang - 1-19 Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data
by Pavel I Kos & Aleksandra A Galitsyna & Sergey V Ulianov & Mikhail S Gelfand & Sergey V Razin & Alexander V Chertovich - 1-21 Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data
by Torfinn S Madssen & Guro F Giskeødegård & Age K Smilde & Johan A Westerhuis - 1-21 Intriguing effects of selection intensity on the evolution of prosocial behaviors
by Alex McAvoy & Andrew Rao & Christoph Hauert - 1-23 Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT
by Shahab Sarmashghi & Metin Balaban & Eleonora Rachtman & Behrouz Touri & Siavash Mirarab & Vineet Bafna - 1-23 Cluster size distribution of cells disseminating from a primary tumor
by Mrinmoy Mukherjee & Herbert Levine - 1-23 Estimating the dimensionality of the manifold underlying multi-electrode neural recordings
by Ege Altan & Sara A Solla & Lee E Miller & Eric J Perreault - 1-24 Cross-population coupling of neural activity based on Gaussian process current source densities
by Natalie Klein & Joshua H Siegle & Tobias Teichert & Robert E Kass - 1-24 Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones
by Erik B Nordquist & Charles A English & Eugenia M Clerico & Woody Sherman & Lila M Gierasch & Jianhan Chen - 1-25 Comparison of metabolic states using genome-scale metabolic models
by Chaitra Sarathy & Marian Breuer & Martina Kutmon & Michiel E Adriaens & Chris T Evelo & Ilja C W Arts - 1-26 Optimizing network propagation for multi-omics data integration
by Konstantina Charmpi & Manopriya Chokkalingam & Ronja Johnen & Andreas Beyer - 1-26 Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance
by Mathurin Dorel & Bertram Klinger & Tommaso Mari & Joern Toedling & Eric Blanc & Clemens Messerschmidt & Michal Nadler-Holly & Matthias Ziehm & Anja Sieber & Falk Hertwig & Dieter Beule & Angelika Eggert & Johannes H Schulte & Matthias Selbach & Nils Blüthgen - 1-26 A gap-filling algorithm for prediction of metabolic interactions in microbial communities
by Dafni Giannari & Cleo Hanchen Ho & Radhakrishnan Mahadevan - 1-27 Multivariable association discovery in population-scale meta-omics studies
by Himel Mallick & Ali Rahnavard & Lauren J McIver & Siyuan Ma & Yancong Zhang & Long H Nguyen & Timothy L Tickle & George Weingart & Boyu Ren & Emma H Schwager & Suvo Chatterjee & Kelsey N Thompson & Jeremy E Wilkinson & Ayshwarya Subramanian & Yiren Lu & Levi Waldron & Joseph N Paulson & Eric A Franzosa & Hector Corrada Bravo & Curtis Huttenhower - 1-28 Crowd control: Reducing individual estimation bias by sharing biased social information
by Bertrand Jayles & Clément Sire & Ralf H J M Kurvers - 1-30 A confirmation bias in perceptual decision-making due to hierarchical approximate inference
by Richard D Lange & Ankani Chattoraj & Jeffrey M Beck & Jacob L Yates & Ralf M Haefner - 1-34 Protein domain-based prediction of drug/compound–target interactions and experimental validation on LIM kinases
by Tunca Doğan & Ece Akhan Güzelcan & Marcus Baumann & Altay Koyas & Heval Atas & Ian R Baxendale & Maria Martin & Rengul Cetin-Atalay - 1-35 Hybrid dedicated and distributed coding in PMd/M1 provides separation and interaction of bilateral arm signals
by Tanner C Dixon & Christina M Merrick & Joni D Wallis & Richard B Ivry & Jose M Carmena - 1-37 Causal inference regulates audiovisual spatial recalibration via its influence on audiovisual perception
by Fangfang Hong & Stephanie Badde & Michael S Landy - 1-38 Neural network features distinguish chemosensory stimuli in Caenorhabditis elegans
by Javier J How & Saket Navlakha & Sreekanth H Chalasani
October 2021, Volume 17, Issue 10
- 1-12 Ten simple rules for training yourself in an emerging field
by Whitney M Woelmer & L M Bradley & Lisa T Haber & David H Klinges & Abigail S L Lewis & Elizabeth J Mohr & Christa L Torrens & Kathryn I Wheeler & Alyssa M Willson - 1-15 A data-driven approach for constructing mutation categories for mutational signature analysis
by Gal Gilad & Mark D M Leiserson & Roded Sharan - 1-16 pyActigraphy: Open-source python package for actigraphy data visualization and analysis
by Grégory Hammad & Mathilde Reyt & Nikita Beliy & Marion Baillet & Michele Deantoni & Alexia Lesoinne & Vincenzo Muto & Christina Schmidt - 1-17 Estimating ectopic beat probability with simplified statistical models that account for experimental uncertainty
by Qingchu Jin & Joseph L Greenstein & Raimond L Winslow - 1-18 A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC
by Jason Bennett & Mikhail Pomaznoy & Akul Singhania & Bjoern Peters - 1-19 Improved prediction of smoking status via isoform-aware RNA-seq deep learning models
by Zifeng Wang & Aria Masoomi & Zhonghui Xu & Adel Boueiz & Sool Lee & Tingting Zhao & Russell Bowler & Michael Cho & Edwin K Silverman & Craig Hersh & Jennifer Dy & Peter J Castaldi - 1-19 RgCop-A regularized copula based method for gene selection in single-cell RNA-seq data
by Snehalika Lall & Sumanta Ray & Sanghamitra Bandyopadhyay - 1-20 Extended graphical lasso for multiple interaction networks for high dimensional omics data
by Yang Xu & Hongmei Jiang & Wenxin Jiang - 1-20 Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample’s infection concentration
by Daniel Cresta & Donald C Warren & Christian Quirouette & Amanda P Smith & Lindey C Lane & Amber M Smith & Catherine A A Beauchemin - 1-21 Steady-state measures of visual suppression
by Daniel H Baker & Greta Vilidaite & Alex R Wade - 1-21 Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities
by Yun Min Song & Hyukpyo Hong & Jae Kyoung Kim - 1-21 Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns
by Maxwell W Libbrecht & Rachel C W Chan & Michael M Hoffman - 1-21 Complexity and diversity in sparse code priors improve receptive field characterization of Macaque V1 neurons
by Ziniu Wu & Harold Rockwell & Yimeng Zhang & Shiming Tang & Tai Sing Lee - 1-22 PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes
by Charlie M Carpenter & Weiming Zhang & Lucas Gillenwater & Cameron Severn & Tusharkanti Ghosh & Russell Bowler & Katerina Kechris & Debashis Ghosh - 1-23 Building and experimenting with an agent-based model to study the population-level impact of CommunityRx, a clinic-based community resource referral intervention
by Stacy Tessler Lindau & Jennifer A Makelarski & Chaitanya Kaligotla & Emily M Abramsohn & David G Beiser & Chiahung Chou & Nicholson Collier & Elbert S Huang & Charles M Macal & Jonathan Ozik & Elizabeth L Tung - 1-24 Better tired than lost: Turtle ant trail networks favor coherence over short edges
by Arjun Chandrasekhar & James A R Marshall & Cortnea Austin & Saket Navlakha & Deborah M Gordon - 1-25 Tracking calcium dynamics from individual neurons in behaving animals
by Thibault Lagache & Alison Hanson & Jesús E Pérez-Ortega & Adrienne Fairhall & Rafael Yuste - 1-27 How conformity can lead to polarised social behaviour
by Folco Panizza & Alexander Vostroknutov & Giorgio Coricelli - 1-28 Atorvastatin-mediated rescue of cancer-related cognitive changes in combined anticancer therapies
by Junho Lee & Jin Su Kim & Yangjin Kim - 1-28 Visual perception of texture regularity: Conjoint measurements and a wavelet response-distribution model
by Hua-Chun Sun & David St-Amand & Curtis L Baker Jr. & Frederick A A Kingdom - 1-28 Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites
by Bikash K Bhandari & Chun Shen Lim & Daniela M Remus & Augustine Chen & Craig van Dolleweerd & Paul P Gardner - 1-28 Universal risk phenotype of US counties for flu-like transmission to improve county-specific COVID-19 incidence forecasts
by Yi Huang & Ishanu Chattopadhyay - 1-29 Point-estimating observer models for latent cause detection
by Jennifer Laura Lee & Wei Ji Ma - 1-31 Narrative event segmentation in the cortical reservoir
by Peter Ford Dominey - 1-32 Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity
by Daniel E Mattox & Chris Bailey-Kellogg - 1-32 Action planning and control under uncertainty emerge through a desirability-driven competition between parallel encoding motor plans
by Vince Enachescu & Paul Schrater & Stefan Schaal & Vassilios Christopoulos - 1-33 Choice history effects in mice and humans improve reward harvesting efficiency
by Junior Samuel López-Yépez & Juliane Martin & Oliver Hulme & Duda Kvitsiani - 1-35 Cortical feedback and gating in odor discrimination and generalization
by Gaia Tavoni & David E Chen Kersen & Vijay Balasubramanian - 1-38 Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans
by Yashika Arora & Pushpinder Walia & Mitsuhiro Hayashibe & Makii Muthalib & Shubhajit Roy Chowdhury & Stephane Perrey & Anirban Dutta
September 2021, Volume 17, Issue 9
- 1-5 Ten simple rules for avoiding predatory publishing scams
by Michelle Leonard & Suzanne Stapleton & Perry Collins & Terry Kit Selfe & Tara Cataldo - 1-6 Ten simple rules for being a faculty advocate of first-year graduate students
by Kevin A Janes - 1-8 Ten simple rules for choosing a PhD supervisor
by Loay Jabre & Catherine Bannon & J Scott P McCain & Yana Eglit - 1-12 Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment
by Sepideh Mazrouee & Susan J Little & Joel O Wertheim - 1-14 Hemodynamics-driven mathematical model of first and second heart sound generation
by Mehrdad Shahmohammadi & Hongxing Luo & Philip Westphal & Richard N Cornelussen & Frits W Prinzen & Tammo Delhaas - 1-16 Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections
by Thomas Beneteau & Christian Selinger & Mircea T Sofonea & Samuel Alizon - 1-16 Ten simple rules for supporting historically underrepresented students in science
by Suchinta Arif & Melanie Duc Bo Massey & Natalie Klinard & Julie Charbonneau & Loay Jabre & Ana Barbosa Martins & Danielle Gaitor & Rhiannon Kirton & Catalina Albury & Karma Nanglu - 1-19 ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves
by Eric D Musselman & Jake E Cariello & Warren M Grill & Nicole A Pelot - 1-20 Eliminating accidental deviations to minimize generalization error and maximize replicability: Applications in connectomics and genomics
by Eric W Bridgeford & Shangsi Wang & Zeyi Wang & Ting Xu & Cameron Craddock & Jayanta Dey & Gregory Kiar & William Gray-Roncal & Carlo Colantuoni & Christopher Douville & Stephanie Noble & Carey E Priebe & Brian Caffo & Michael Milham & Xi-Nian Zuo & Consortium for Reliability and Reproducibility & Joshua T Vogelstein - 1-20 Basis profile curve identification to understand electrical stimulation effects in human brain networks
by Kai J Miller & Klaus-Robert Müller & Dora Hermes - 1-21 Machine learning approach for automatic recognition of tomato-pollinating bees based on their buzzing-sounds
by Alison Pereira Ribeiro & Nádia Felix Felipe da Silva & Fernanda Neiva Mesquita & Priscila de Cássia Souza Araújo & Thierson Couto Rosa & José Neiva Mesquita-Neto - 1-21 Insights into the dynamic trajectories of protein filament division revealed by numerical investigation into the mathematical model of pure fragmentation
by Magali Tournus & Miguel Escobedo & Wei-Feng Xue & Marie Doumic - 1-21 XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers
by Jack B Maguire & Daniele Grattarola & Vikram Khipple Mulligan & Eugene Klyshko & Hans Melo - 1-22 Drug-induced resistance evolution necessitates less aggressive treatment
by Teemu Kuosmanen & Johannes Cairns & Robert Noble & Niko Beerenwinkel & Tommi Mononen & Ville Mustonen - 1-23 Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants
by Rui Yin & Johnathan D Guest & Ghazaleh Taherzadeh & Ragul Gowthaman & Ipsa Mittra & Jane Quackenbush & Brian G Pierce - 1-24 Personalized brain stimulation for effective neurointervention across participants
by Nienke E R van Bueren & Thomas L Reed & Vu Nguyen & James G Sheffield & Sanne H G van der Ven & Michael A Osborne & Evelyn H Kroesbergen & Roi Cohen Kadosh - 1-24 Optima TB: A tool to help optimally allocate tuberculosis spending
by Lara Goscé & Gerard J Abou Jaoude & David J Kedziora & Clemens Benedikt & Azfar Hussain & Sarah Jarvis & Alena Skrahina & Dzmitry Klimuk & Henadz Hurevich & Feng Zhao & Nicole Fraser-Hurt & Nejma Cheikh & Marelize Gorgens & David J Wilson & Romesh Abeysuriya & Rowan Martin-Hughes & Sherrie L Kelly & Anna Roberts & Robyn M Stuart & Tom Palmer & Jasmina Panovska-Griffiths & Cliff C Kerr & David P Wilson & Hassan Haghparast-Bidgoli & Jolene Skordis & Ibrahim Abubakar - 1-24 Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model
by Federica Gugole & Luc E Coffeng & Wouter Edeling & Benjamin Sanderse & Sake J de Vlas & Daan Crommelin - 1-25 Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C
by Susana Posada-Céspedes & Gert Van Zyl & Hesam Montazeri & Jack Kuipers & Soo-Yon Rhee & Roger Kouyos & Huldrych F Günthard & Niko Beerenwinkel - 1-25 Evaluating the effectiveness of ensemble voting in improving the accuracy of consensus signals produced by various DTWA algorithms from step-current signals generated during nanopore sequencing
by Michael Smith & Rachel Chan & Maaz Khurram & Paul M K Gordon - 1-25 Learning brain dynamics for decoding and predicting individual differences
by Joyneel Misra & Srinivas Govinda Surampudi & Manasij Venkatesh & Chirag Limbachia & Joseph Jaja & Luiz Pessoa - 1-25 Ergodicity-breaking reveals time optimal decision making in humans
by David Meder & Finn Rabe & Tobias Morville & Kristoffer H Madsen & Magnus T Koudahl & Ray J Dolan & Hartwig R Siebner & Oliver J Hulme - 1-26 Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome
by Ilario De Toma & Cesar Sierra & Mara Dierssen - 1-26 Neighbor-enhanced diffusivity in dense, cohesive cell populations
by Hyun Gyu Lee & Kyoung J Lee - 1-28 Latching dynamics as a basis for short-term recall
by Kwang Il Ryom & Vezha Boboeva & Oleksandra Soldatkina & Alessandro Treves - 1-28 Differences in olfactory bulb mitral cell spiking with ortho- and retronasal stimulation revealed by data-driven models
by Michelle F Craft & Andrea K Barreiro & Shree Hari Gautam & Woodrow L Shew & Cheng Ly - 1-28 Phenotypic-dependent variability and the emergence of tolerance in bacterial populations
by José Camacho Mateu & Matteo Sireci & Miguel A Muñoz - 1-29 Differential contribution to gene expression prediction of histone modifications at enhancers or promoters
by Mar González-Ramírez & Cecilia Ballaré & Francesca Mugianesi & Malte Beringer & Alexandra Santanach & Enrique Blanco & Luciano Di Croce - 1-29 An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City
by Sheng Zhang & Joan Ponce & Zhen Zhang & Guang Lin & George Karniadakis - 1-32 Envelope reconstruction of speech and music highlights stronger tracking of speech at low frequencies
by Nathaniel J Zuk & Jeremy W Murphy & Richard B Reilly & Edmund C Lalor - 1-35 Inter-trial effects in priming of pop-out: Comparison of computational updating models
by Fredrik Allenmark & Ahu Gokce & Thomas Geyer & Artyom Zinchenko & Hermann J Müller & Zhuanghua Shi - 1-39 On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo
by Charles-Elie Rabier & Vincent Berry & Marnus Stoltz & João D Santos & Wensheng Wang & Jean-Christophe Glaszmann & Fabio Pardi & Celine Scornavacca
August 2021, Volume 17, Issue 8
- 1-9 Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster
by Jamie J Alnasir - 1-10 Ten simple rules for aspiring graduate students
by Andrea I Luppi & Charlotte Coco Newton & Lynde Folsom & Elisa Galliano & Rafael Romero-Garcia - 1-12 Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries
by Benjamin Moore & Patricia Carvajal-López & Paballo Abel Chauke & Marco Cristancho & Victoria Dominguez Del Angel & Selene L Fernandez-Valverde & Amel Ghouila & Piraveen Gopalasingam & Fatma Zahra Guerfali & Alice Matimba & Sarah L Morgan & Guilherme Oliveira & Verena Ras & Alejandro Reyes & Javier De Las Rivas & Nicola Mulder - 1-13 SiGMoiD: A super-statistical generative model for binary data
by Xiaochuan Zhao & Germán Plata & Purushottam D Dixit - 1-13 Large-scale simulations of biological cell sorting driven by differential adhesion follow diffusion-limited domain coalescence regime
by Marc Durand - 1-17 An uncertainty-based model of the effects of fixation on choice
by Zhi-Wei Li & Wei Ji Ma - 1-18 Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base
by Tomasz Konopka & Sandra Ng & Damian Smedley - 1-18 Circadian rhythm shows potential for mRNA efficiency and self-organized division of labor in multinucleate cells
by Leif Zinn-Brooks & Marcus L Roper - 1-18 A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers
by Frances L Heredia & Abiel Roche-Lima & Elsie I Parés-Matos - 1-18 PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions
by Seyed Ziaeddin Alborzi & Amina Ahmed Nacer & Hiba Najjar & David W Ritchie & Marie-Dominique Devignes - 1-18 miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
by Ariel A Hippen & Matias M Falco & Lukas M Weber & Erdogan Pekcan Erkan & Kaiyang Zhang & Jennifer Anne Doherty & Anna Vähärautio & Casey S Greene & Stephanie C Hicks - 1-21 A large-scale brain network mechanism for increased seizure propensity in Alzheimer’s disease
by Luke Tait & Marinho A Lopes & George Stothart & John Baker & Nina Kazanina & Jiaxiang Zhang & Marc Goodfellow - 1-22 Unveiling functions of the visual cortex using task-specific deep neural networks
by Kshitij Dwivedi & Michael F Bonner & Radoslaw Martin Cichy & Gemma Roig - 1-22 Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations
by Jenny M Vo-Phamhi & Kevin A Yamauchi & Rafael Gómez-Sjöberg - 1-22 Review of machine learning methods for RNA secondary structure prediction
by Qi Zhao & Zheng Zhao & Xiaoya Fan & Zhengwei Yuan & Qian Mao & Yudong Yao - 1-23 Critical behaviour of the stochastic Wilson-Cowan model
by Antonio de Candia & Alessandro Sarracino & Ilenia Apicella & Lucilla de Arcangelis - 1-24 A multi-objective genetic algorithm to find active modules in multiplex biological networks
by Elva María Novoa-del-Toro & Efrén Mezura-Montes & Matthieu Vignes & Morgane Térézol & Frédérique Magdinier & Laurent Tichit & Anaïs Baudot - 1-24 Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread
by John R Giles & Derek A T Cummings & Bryan T Grenfell & Andrew J Tatem & Elisabeth zu Erbach-Schoenberg & CJE Metcalf & Amy Wesolowski - 1-24 A computational method for identifying an optimal combination of existing drugs to repair the action potentials of SQT1 ventricular myocytes
by Karoline Horgmo Jæger & Andrew G Edwards & Wayne R Giles & Aslak Tveito - 1-25 Using mobility data in the design of optimal lockdown strategies for the COVID-19 pandemic
by Ritabrata Dutta & Susana N Gomes & Dante Kalise & Lorenzo Pacchiardi - 1-25 The role of memory in non-genetic inheritance and its impact on cancer treatment resistance
by Tyler Cassidy & Daniel Nichol & Mark Robertson-Tessi & Morgan Craig & Alexander R A Anderson - 1-26 Identification of structures for ion channel kinetic models
by Kathryn E Mangold & Wei Wang & Eric K Johnson & Druv Bhagavan & Jonathan D Moreno & Jeanne M Nerbonne & Jonathan R Silva - 1-27 Computational identification and experimental characterization of preferred downstream positions in human core promoters
by René Dreos & Anna Sloutskin & Nati Malachi & Diana Ideses & Philipp Bucher & Tamar Juven-Gershon - 1-28 A hidden Markov model reliably characterizes ketamine-induced spectral dynamics in macaque local field potentials and human electroencephalograms
by Indie C Garwood & Sourish Chakravarty & Jacob Donoghue & Meredith Mahnke & Pegah Kahali & Shubham Chamadia & Oluwaseun Akeju & Earl K Miller & Emery N Brown - 1-28 Targeted modulation of protein liquid–liquid phase separation by evolution of amino-acid sequence
by Simon M Lichtinger & Adiran Garaizar & Rosana Collepardo-Guevara & Aleks Reinhardt - 1-29 Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters
by Natalie Schaworonkow & Bradley Voytek - 1-30 A probabilistic model for the ultradian timing of REM sleep in mice
by Sung-Ho Park & Justin Baik & Jiso Hong & Hanna Antila & Benjamin Kurland & Shinjae Chung & Franz Weber - 1-30 Comparative mapping of crawling-cell morphodynamics in deep learning-based feature space
by Daisuke Imoto & Nen Saito & Akihiko Nakajima & Gen Honda & Motohiko Ishida & Toyoko Sugita & Sayaka Ishihara & Koko Katagiri & Chika Okimura & Yoshiaki Iwadate & Satoshi Sawai - 1-33 Evaluation and comparison of multi-omics data integration methods for cancer subtyping
by Ran Duan & Lin Gao & Yong Gao & Yuxuan Hu & Han Xu & Mingfeng Huang & Kuo Song & Hongda Wang & Yongqiang Dong & Chaoqun Jiang & Chenxing Zhang & Songwei Jia - 1-33 Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows
by Daniel Schindler & Ted Moldenhawer & Maike Stange & Valentino Lepro & Carsten Beta & Matthias Holschneider & Wilhelm Huisinga - 1-35 Interspike interval correlations in neuron models with adaptation and correlated noise
by Lukas Ramlow & Benjamin Lindner
July 2021, Volume 17, Issue 7
- 1-12 Ten simple rules to improve academic work–life balance
by Michael John Bartlett & Feyza Nur Arslan & Adriana Bankston & Sarvenaz Sarabipour - 1-13 Ten simple rules for attending your first conference
by Elizabeth Leininger & Kelly Shaw & Niema Moshiri & Kelly Neiles & Getiria Onsongo & Anna Ritz - 1-15 POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis
by Pol Castellano-Escuder & Raúl González-Domínguez & Francesc Carmona-Pontaque & Cristina Andrés-Lacueva & Alex Sánchez-Pla - 1-16 Leveraging high-throughput screening data, deep neural networks, and conditional generative adversarial networks to advance predictive toxicology
by Adrian J Green & Martin J Mohlenkamp & Jhuma Das & Meenal Chaudhari & Lisa Truong & Robyn L Tanguay & David M Reif - 1-17 Elementary integrate-and-fire process underlies pulse amplitudes in Electrodermal activity
by Sandya Subramanian & Patrick L Purdon & Riccardo Barbieri & Emery N Brown - 1-17 The effect of natural selection on the propagation of protein expression noise to bacterial growth
by Laurens H J Krah & Rutger Hermsen - 1-18 Predicting seasonal influenza using supermarket retail records
by Ioanna Miliou & Xinyue Xiong & Salvatore Rinzivillo & Qian Zhang & Giulio Rossetti & Fosca Giannotti & Dino Pedreschi & Alessandro Vespignani - 1-18 A benchmark dataset for canopy crown detection and delineation in co-registered airborne RGB, LiDAR and hyperspectral imagery from the National Ecological Observation Network
by Ben G Weinstein & Sarah J Graves & Sergio Marconi & Aditya Singh & Alina Zare & Dylan Stewart & Stephanie A Bohlman & Ethan P White - 1-20 Accurate influenza forecasts using type-specific incidence data for small geographic units
by James Turtle & Pete Riley & Michal Ben-Nun & Steven Riley - 1-20 SCMFMDA: Predicting microRNA-disease associations based on similarity constrained matrix factorization
by Lei Li & Zhen Gao & Yu-Tian Wang & Ming-Wen Zhang & Jian-Cheng Ni & Chun-Hou Zheng & Yansen Su - 1-20 Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors
by Shirit Dvorkin & Reut Levi & Yoram Louzoun - 1-21 Accumulation of continuously time-varying sensory evidence constrains neural and behavioral responses in human collision threat detection
by Gustav Markkula & Zeynep Uludağ & Richard McGilchrist Wilkie & Jac Billington - 1-22 Risk sensitivity and theory of mind in human coordination
by Pedro L Ferreira & Francisco C Santos & Sérgio Pequito - 1-22 Bayesian back-calculation and nowcasting for line list data during the COVID-19 pandemic
by Tenglong Li & Laura F White - 1-22 ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements
by Xi Chen & Andrew F Neuwald & Leena Hilakivi-Clarke & Robert Clarke & Jianhua Xuan - 1-22 Computational Eurotransplant kidney allocation simulations demonstrate the feasibility and benefit of T-cell epitope matching
by Matthias Niemann & Nils Lachmann & Kirsten Geneugelijk & Eric Spierings - 1-22 Modeling changes in probabilistic reinforcement learning during adolescence
by Liyu Xia & Sarah L Master & Maria K Eckstein & Beth Baribault & Ronald E Dahl & Linda Wilbrecht & Anne Gabrielle Eva Collins - 1-22 Modelling locust foraging: How and why food affects group formation
by Fillipe Georgiou & Camille Buhl & J E F Green & Bishnu Lamichhane & Ngamta Thamwattana - 1-24 Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes
by Davin Lunz & Gregory Batt & Jakob Ruess & J Frédéric Bonnans - 1-24 Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure
by Toru Niina & Yasuhiro Matsunaga & Shoji Takada - 1-25 A Keller-Segel model for C elegans L1 aggregation
by Leon Avery & Brian Ingalls & Catherine Dumur & Alexander Artyukhin - 1-25 Noise suppression in stochastic genetic circuits using PID controllers
by Saurabh Modi & Supravat Dey & Abhyudai Singh - 1-25 Multitask learning over shared subspaces
by Nicholas Menghi & Kemal Kacar & Will Penny - 1-26 Neuron tracing and quantitative analyses of dendritic architecture reveal symmetrical three-way-junctions and phenotypes of git-1 in C. elegans
by Omer Yuval & Yael Iosilevskii & Anna Meledin & Benjamin Podbilewicz & Tom Shemesh - 1-28 Selection of stimulus parameters for enhancing slow wave sleep events with a neural-field theory thalamocortical model
by Felipe A Torres & Patricio Orio & María-José Escobar