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September 2020, Volume 16, Issue 9
- 1-24 Classification of estrogenic compounds by coupling high content analysis and machine learning algorithms
by Rajib Mukherjee & Burcu Beykal & Adam T Szafran & Melis Onel & Fabio Stossi & Maureen G Mancini & Dillon Lloyd & Fred A Wright & Lan Zhou & Michael A Mancini & Efstratios N Pistikopoulos - 1-24 Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data
by Camila P. E. de Souza & Mirela Andronescu & Tehmina Masud & Farhia Kabeer & Justina Biele & Emma Laks & Daniel Lai & Patricia Ye & Jazmine Brimhall & Beixi Wang & Edmund Su & Tony Hui & Qi Cao & Marcus Wong & Michelle Moksa & Richard A Moore & Martin Hirst & Samuel Aparicio & Sohrab P Shah - 1-25 Shape-to-graph mapping method for efficient characterization and classification of complex geometries in biological images
by William Pilcher & Xingyu Yang & Anastasia Zhurikhina & Olga Chernaya & Yinghan Xu & Peng Qiu & Denis Tsygankov - 1-25 Efficient sensory coding of multidimensional stimuli
by Thomas E Yerxa & Eric Kee & Michael R DeWeese & Emily A Cooper - 1-25 The relative contributions of infectious and mitotic spread to HTLV-1 persistence
by Daniel J Laydon & Vikram Sunkara & Lies Boelen & Charles R M Bangham & Becca Asquith - 1-27 Response nonlinearities in networks of spiking neurons
by Alessandro Sanzeni & Mark H Histed & Nicolas Brunel - 1-27 Inferring a complete genotype-phenotype map from a small number of measured phenotypes
by Zachary R Sailer & Sarah H Shafik & Robert L Summers & Alex Joule & Alice Patterson-Robert & Rowena E Martin & Michael J Harms - 1-27 Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention
by Yunjun Zhang & Thomas Leitner & Jan Albert & Tom Britton - 1-28 Similarities and differences in spatial and non-spatial cognitive maps
by Charley M Wu & Eric Schulz & Mona M Garvert & Björn Meder & Nicolas W Schuck - 1-29 Uncertainty-driven regulation of learning and exploration in adolescents: A computational account
by Marieke Jepma & Jessica V Schaaf & Ingmar Visser & Hilde M Huizenga - 1-39 Fast estimation of time-varying infectious disease transmission rates
by Mikael Jagan & Michelle S deJonge & Olga Krylova & David J D Earn
August 2020, Volume 16, Issue 8
- 1-16 Information transmission from NFkB signaling dynamics to gene expression
by Alok Maity & Roy Wollman - 1-17 Deconvolving the contributions of cell-type heterogeneity on cortical gene expression
by Ellis Patrick & Mariko Taga & Ayla Ergun & Bernard Ng & William Casazza & Maria Cimpean & Christina Yung & Julie A Schneider & David A Bennett & Chris Gaiteri & Philip L De Jager & Elizabeth M Bradshaw & Sara Mostafavi - 1-18 Multiplexing information flow through dynamic signalling systems
by Giorgos Minas & Dan J Woodcock & Louise Ashall & Claire V Harper & Michael R H White & David A Rand - 1-20 Template-based mapping of dynamic motifs in tissue morphogenesis
by Tomer Stern & Stanislav Y Shvartsman & Eric F Wieschaus - 1-20 A novel single-cell based method for breast cancer prognosis
by Xiaomei Li & Lin Liu & Gregory J Goodall & Andreas Schreiber & Taosheng Xu & Jiuyong Li & Thuc D Le - 1-20 Optimising efficacy of antibiotics against systemic infection by varying dosage quantities and times
by Andy Hoyle & David Cairns & Iona Paterson & Stuart McMillan & Gabriela Ochoa & Andrew P Desbois - 1-21 JBrowse Connect: A server API to connect JBrowse instances and users
by Eric Yao & Robert Buels & Lincoln Stein & Taner Z Sen & Ian Holmes - 1-21 Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits
by Craig A Glastonbury & Sara L Pulit & Julius Honecker & Jenny C Censin & Samantha Laber & Hanieh Yaghootkar & Nilufer Rahmioglu & Emilie Pastel & Katerina Kos & Andrew Pitt & Michelle Hudson & Christoffer Nellåker & Nicola L Beer & Hans Hauner & Christian M Becker & Krina T Zondervan & Timothy M Frayling & Melina Claussnitzer & Cecilia M Lindgren - 1-22 Inferring the ancestry of parents and grandparents from genetic data
by Jingwen Pei & Yiming Zhang & Rasmus Nielsen & Yufeng Wu - 1-23 Order matters: How covert value updating during sequential option sampling shapes economic preference
by Chen Hu & Philippe Domenech & Mathias Pessiglione - 1-26 Effect of magnitude and variability of energy of activation in multisite ultrasensitive biochemical processes
by Leonila Lagunes & Lee Bardwell & German A Enciso - 1-27 A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis
by Amrit Dhar & Duncan K Ralph & Vladimir N Minin & Frederick A Matsen IV - 1-27 Drug-target binding quantitatively predicts optimal antibiotic dose levels in quinolones
by Fabrizio Clarelli & Adam Palmer & Bhupender Singh & Merete Storflor & Silje Lauksund & Ted Cohen & Sören Abel & Pia Abel zur Wiesch - 1-28 Dynamic estimation of auditory temporal response functions via state-space models with Gaussian mixture process noise
by Sina Miran & Alessandro Presacco & Jonathan Z Simon & Michael C Fu & Steven I Marcus & Behtash Babadi - 1-29 Reliable estimation of membrane curvature for cryo-electron tomography
by Maria Salfer & Javier F Collado & Wolfgang Baumeister & Rubén Fernández-Busnadiego & Antonio Martínez-Sánchez - 1-29 Understanding multivariate brain activity: Evaluating the effect of voxelwise noise correlations on population codes in functional magnetic resonance imaging
by Ru-Yuan Zhang & Xue-Xin Wei & Kendrick Kay - 1-29 Modeling time-varying brain networks with a self-tuning optimized Kalman filter
by D Pascucci & M Rubega & G Plomp - 1-34 Buildup and bistability in auditory streaming as an evidence accumulation process with saturation
by Quynh-Anh Nguyen & John Rinzel & Rodica Curtu - 1-39 Task-evoked activity quenches neural correlations and variability across cortical areas
by Takuya Ito & Scott L Brincat & Markus Siegel & Ravi D Mill & Biyu J He & Earl K Miller & Horacio G Rotstein & Michael W Cole
July 2020, Volume 16, Issue 7
- 1-6 Ten simple rules for reading a scientific paper
by Maureen A Carey & Kevin L Steiner & William A Petri Jr - 1-10 Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices
by Joe Hilton & Matt J Keeling - 1-12 A framework to assess the quality and impact of bioinformatics training across ELIXIR
by Kim T Gurwitz & Prakash Singh Gaur & Louisa J Bellis & Lee Larcombe & Eva Alloza & Balint Laszlo Balint & Alexander Botzki & Jure Dimec & Victoria Dominguez del Angel & Pedro L Fernandes & Eija Korpelainen & Roland Krause & Mateusz Kuzak & Loredana Le Pera & Brane Leskošek & Jessica M Lindvall & Diana Marek & Paula A Martinez & Tuur Muyldermans & Ståle Nygård & Patricia M Palagi & Hedi Peterson & Fotis Psomopoulos & Vojtech Spiwok & Celia W G van Gelder & Allegra Via & Marko Vidak & Daniel Wibberg & Sarah L Morgan & Gabriella Rustici - 1-14 Multidimensional phenotyping predicts lifespan and quantifies health in Caenorhabditis elegans
by Céline N Martineau & André E X Brown & Patrick Laurent - 1-19 Socioeconomic bias in influenza surveillance
by Samuel V Scarpino & James G Scott & Rosalind M Eggo & Bruce Clements & Nedialko B Dimitrov & Lauren Ancel Meyers - 1-20 A practical application of generative adversarial networks for RNA-seq analysis to predict the molecular progress of Alzheimer's disease
by Jinhee Park & Hyerin Kim & Jaekwang Kim & Mookyung Cheon - 1-20 iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding
by Huiyuan Chen & Feixiong Cheng & Jing Li - 1-20 Beyond ranking nodes: Predicting epidemic outbreak sizes by network centralities
by Doina Bucur & Petter Holme - 1-20 Using information theory to optimise epidemic models for real-time prediction and estimation
by Kris V Parag & Christl A Donnelly - 1-21 Immunization strategies in networks with missing data
by Samuel F Rosenblatt & Jeffrey A Smith & G Robin Gauthier & Laurent Hébert-Dufresne - 1-21 A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms
by August George & Paola Bisignano & John M Rosenberg & Michael Grabe & Daniel M Zuckerman - 1-22 Estimation of neuron parameters from imperfect observations
by Joseph D Taylor & Samuel Winnall & Alain Nogaret - 1-22 Predicting lymphatic filariasis elimination in data-limited settings: A reconstructive computational framework for combining data generation and model discovery
by Morgan E Smith & Emily Griswold & Brajendra K Singh & Emmanuel Miri & Abel Eigege & Solomon Adelamo & John Umaru & Kenrick Nwodu & Yohanna Sambo & Jonathan Kadimbo & Jacob Danyobi & Frank O Richards & Edwin Michael - 1-23 A novel riboswitch classification based on imbalanced sequences achieved by machine learning
by Solomon Shiferaw Beyene & Tianyi Ling & Blagoj Ristevski & Ming Chen - 1-23 Cortical ignition dynamics is tightly linked to the core organisation of the human connectome
by Samy Castro & Wael El-Deredy & Demian Battaglia & Patricio Orio - 1-24 Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data
by Xian F Mallory & Mohammadamin Edrisi & Nicholas Navin & Luay Nakhleh - 1-24 An in vitro quantitative systems pharmacology approach for deconvolving mechanisms of drug-induced, multilineage cytopenias
by Jennifer L Wilson & Dan Lu & Nick Corr & Aaron Fullerton & James Lu - 1-25 Heterogeneous, delayed-onset killing by multiple-hitting T cells: Stochastic simulations to assess methods for analysis of imaging data
by Richard J Beck & Dario I Bijker & Joost B Beltman - 1-26 A simple model for learning in volatile environments
by Payam Piray & Nathaniel D Daw - 1-27 Cross-species regulatory sequence activity prediction
by David R Kelley - 1-34 Brain-optimized extraction of complex sound features that drive continuous auditory perception
by Julia Berezutskaya & Zachary V Freudenburg & Umut Güçlü & Marcel A J van Gerven & Nick F Ramsey
June 2020, Volume 16, Issue 6
- 1-13 Measurable health effects associated with the daylight saving time shift
by Hanxin Zhang & Torsten Dahlén & Atif Khan & Gustaf Edgren & Andrey Rzhetsky - 1-15 XDream: Finding preferred stimuli for visual neurons using generative networks and gradient-free optimization
by Will Xiao & Gabriel Kreiman - 1-15 Assessing predictors for new post translational modification sites: A case study on hydroxylation
by Damiano Piovesan & Andras Hatos & Giovanni Minervini & Federica Quaglia & Alexander Miguel Monzon & Silvio C E Tosatto - 1-17 Forecasting unprecedented ecological fluctuations
by Samuel R Bray & Bo Wang - 1-17 Sample-based modeling reveals bidirectional interplay between cell cycle progression and extrinsic apoptosis
by Dirke Imig & Nadine Pollak & Frank Allgöwer & Markus Rehm - 1-17 Disease evolution in reaction networks: Implications for a diagnostic problem
by Abolfazl Ramezanpour & Alireza Mashaghi - 1-18 A validation framework for neuroimaging software: The case of population receptive fields
by Garikoitz Lerma-Usabiaga & Noah Benson & Jonathan Winawer & Brian A Wandell - 1-21 Discriminating between negative cooperativity and ligand binding to independent sites using pre-equilibrium properties of binding curves
by Federico Sevlever & Juan Pablo Di Bella & Alejandra C Ventura - 1-21 Kilohertz waveforms optimized to produce closed-state Na+ channel inactivation eliminate onset response in nerve conduction block
by Guosheng Yi & Warren M Grill - 1-22 Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data
by Nima Nouri & Steven H Kleinstein - 1-22 Resilience of three-dimensional sinusoidal networks in liver tissue
by Jens Karschau & André Scholich & Jonathan Wise & Hernán Morales-Navarrete & Yannis Kalaidzidis & Marino Zerial & Benjamin M Friedrich - 1-24 Emergence of cooperative bistability and robustness of gene regulatory networks
by Shintaro Nagata & Macoto Kikuchi - 1-25 Combined model-free and model-sensitive reinforcement learning in non-human primates
by Bruno Miranda & W M Nishantha Malalasekera & Timothy E Behrens & Peter Dayan & Steven W Kennerley - 1-25 Realistic modeling of mesoscopic ephaptic coupling in the human brain
by Giulio Ruffini & Ricardo Salvador & Ehsan Tadayon & Roser Sanchez-Todo & Alvaro Pascual-Leone & Emiliano Santarnecchi - 1-26 Natural scene statistics predict how humans pool information across space in surface tilt estimation
by Seha Kim & Johannes Burge - 1-27 Classifying sex and strain from mouse ultrasonic vocalizations using deep learning
by A Ivanenko & P Watkins & M A J van Gerven & K Hammerschmidt & B Englitz - 1-27 A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data
by David Lamparter & Rajat Bhatnagar & Katja Hebestreit & T Grant Belgard & Alice Zhang & Victor Hanson-Smith - 1-27 Brain dynamics for confidence-weighted learning
by Florent Meyniel - 1-27 Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface
by Anna U Lowegard & Marcel S Frenkel & Graham T Holt & Jonathan D Jou & Adegoke A Ojewole & Bruce R Donald - 1-28 Multiscale modeling of human cerebrovasculature: A hybrid approach using image-based geometry and a mathematical algorithm
by Satoshi Ii & Hiroki Kitade & Shunichi Ishida & Yohsuke Imai & Yoshiyuki Watanabe & Shigeo Wada - 1-29 It’s about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology
by Niklas Korsbo & Henrik Jönsson - 1-29 Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites
by Ethan D Evans & Chengzhen Dai & Siavash Isazadeh & Shinkyu Park & Carlo Ratti & Eric J Alm - 1-34 Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model
by Sandra Mayr & Fabian Hauser & Sujitha Puthukodan & Markus Axmann & Janett Göhring & Jaroslaw Jacak
May 2020, Volume 16, Issue 5
- 1-9 Ten Simple Rules for a successful remote postdoc
by Kevin R Burgio & Caitlin McDonough MacKenzie & Stephanie B Borrelle & S K Morgan Ernest & Jacquelyn L Gill & Kurt E Ingeman & Amy Teffer & Ethan P White - 1-9 Ten simple rules for running a successful women-in-STEM organization on an academic campus
by Deborah D Rupert & Alexandra C Nowlan & Oliver H Tam & Molly Gale Hammell - 1-12 Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles
by Alastair M Kilpatrick & Audra Anjum & Lonnie Welch - 1-15 Inference on dengue epidemics with Bayesian regime switching models
by Jue Tao Lim & Borame Sue Dickens & Sun Haoyang & Ng Lee Ching & Alex R Cook - 1-16 Early warning signals in motion inference
by Yuval Hart & Maryam Vaziri-Pashkam & L Mahadevan - 1-17 Calibration of individual-based models to epidemiological data: A systematic review
by C Marijn Hazelbag & Jonathan Dushoff & Emanuel M Dominic & Zinhle E Mthombothi & Wim Delva - 1-17 Microbial communities display alternative stable states in a fluctuating environment
by Clare I Abreu & Vilhelm L Andersen Woltz & Jonathan Friedman & Jeff Gore - 1-18 Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system
by Sinu Paul & Nathan P Croft & Anthony W Purcell & David C Tscharke & Alessandro Sette & Morten Nielsen & Bjoern Peters - 1-18 Ad hoc efforts for advancing data science education
by Orianna DeMasi & Alexandra Paxton & Kevin Koy - 1-19 Towards a data-driven characterization of behavioral changes induced by the seasonal flu
by Nicolò Gozzi & Daniela Perrotta & Daniela Paolotti & Nicola Perra - 1-19 GCNCDA: A new method for predicting circRNA-disease associations based on Graph Convolutional Network Algorithm
by Lei Wang & Zhu-Hong You & Yang-Ming Li & Kai Zheng & Yu-An Huang - 1-21 A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type
by Alan Le Goallec & Braden T Tierney & Jacob M Luber & Evan M Cofer & Aleksandar D Kostic & Chirag J Patel - 1-22 Compositional Lotka-Volterra describes microbial dynamics in the simplex
by Tyler A Joseph & Liat Shenhav & Joao B Xavier & Eran Halperin & Itsik Pe’er - 1-22 iCDA-CGR: Identification of circRNA-disease associations based on Chaos Game Representation
by Kai Zheng & Zhu-Hong You & Jian-Qiang Li & Lei Wang & Zhen-Hao Guo & Yu-An Huang - 1-23 Bayesian regression explains how human participants handle parameter uncertainty
by Jannes Jegminat & Maya A Jastrzębowska & Matthew V Pachai & Michael H Herzog & Jean-Pascal Pfister - 1-23 Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis
by Amanda Brucker & Wenbin Lu & Rachel Marceau West & Qi-You Yu & Chuhsing Kate Hsiao & Tzu-Hung Hsiao & Ching-Heng Lin & Patrik K E Magnusson & Patrick F Sullivan & Jin P Szatkiewicz & Tzu-Pin Lu & Jung-Ying Tzeng - 1-24 Scale free topology as an effective feedback system
by Alexander Rivkind & Hallel Schreier & Naama Brenner & Omri Barak - 1-24 Shape-preserving elastic solid models of macromolecules
by Guang Song - 1-25 Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease
by Christine A Tataru & Maude M David - 1-27 The Affective Ising Model: A computational account of human affect dynamics
by Tim Loossens & Merijn Mestdagh & Egon Dejonckheere & Peter Kuppens & Francis Tuerlinckx & Stijn Verdonck - 1-27 Path integration in large-scale space and with novel geometries: Comparing vector addition and encoding-error models
by Sevan K Harootonian & Robert C Wilson & Lukáš Hejtmánek & Eli M Ziskin & Arne D Ekstrom - 1-29 Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry
by Andrew J Bernoff & Michael Culshaw-Maurer & Rebecca A Everett & Maryann E Hohn & W Christopher Strickland & Jasper Weinburd - 1-44 Autonomous emergence of connectivity assemblies via spike triplet interactions
by Lisandro Montangie & Christoph Miehl & Julijana Gjorgjieva - 1-50 Robustness and parameter geography in post-translational modification systems
by Kee-Myoung Nam & Benjamin M Gyori & Silviana V Amethyst & Daniel J Bates & Jeremy Gunawardena
April 2020, Volume 16, Issue 4
- 1-5 Ten Simple Rules for landing on the right job after your PhD or postdoc
by Kuan-lin Huang - 1-5 Ten Simple Rules for writing algorithmic bioinformatics conference papers
by Paul Medvedev - 1-7 Ten simple rules for more objective decision-making
by Anthony C Fletcher & Georges A Wagner & Philip E Bourne - 1-13 On the choice of metric in gradient-based theories of brain function
by Simone Carlo Surace & Jean-Pascal Pfister & Wulfram Gerstner & Johanni Brea - 1-15 Telling ecological networks apart by their structure: An environment-dependent approach
by Chuliang Song & Serguei Saavedra - 1-16 Climbing Escher’s stairs: A way to approximate stability landscapes in multidimensional systems
by Pablo Rodríguez-Sánchez & Egbert H van Nes & Marten Scheffer - 1-18 Deep reinforcement learning for the control of microbial co-cultures in bioreactors
by Neythen J Treloar & Alex J H Fedorec & Brian Ingalls & Chris P Barnes - 1-18 A powerful and versatile colocalization test
by Yangqing Deng & Wei Pan - 1-19 DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data
by Yi Jiang & Gina Giase & Kay Grennan & Annie W Shieh & Yan Xia & Lide Han & Quan Wang & Qiang Wei & Rui Chen & Sihan Liu & Kevin P White & Chao Chen & Bingshan Li & Chunyu Liu - 1-20 Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking
by Sarah F McGough & Michael A Johansson & Marc Lipsitch & Nicolas A Menzies - 1-20 Predicting cell lineages using autoencoders and optimal transport
by Karren Dai Yang & Karthik Damodaran & Saradha Venkatachalapathy & Ali C Soylemezoglu & G V Shivashankar & Caroline Uhler - 1-20 MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
by Avtar Roopra - 1-21 Inferring the immune response from repertoire sequencing
by Maximilian Puelma Touzel & Aleksandra M Walczak & Thierry Mora - 1-22 Comparison of methods for rhythm analysis of complex animals’ acoustic signals
by Lara S Burchardt & Mirjam Knörnschild - 1-22 LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer
by Junpeng Zhang & Taosheng Xu & Lin Liu & Wu Zhang & Chunwen Zhao & Sijing Li & Jiuyong Li & Nini Rao & Thuc Duy Le - 1-23 Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE
by Lisa-Katrin Schätzle & Ali Hadizadeh Esfahani & Andreas Schuppert - 1-24 Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis
by Yuanchao Zhang & Man S Kim & Erin R Reichenberger & Ben Stear & Deanne M Taylor - 1-25 DOT: Gene-set analysis by combining decorrelated association statistics
by Olga A Vsevolozhskaya & Min Shi & Fengjiao Hu & Dmitri V Zaykin - 1-25 The drift diffusion model as the choice rule in inter-temporal and risky choice: A case study in medial orbitofrontal cortex lesion patients and controls
by Jan Peters & Mark D’Esposito - 1-26 Multiview learning for understanding functional multiomics
by Nam D Nguyen & Daifeng Wang - 1-28 Multiple-target tracking in human and machine vision
by Shiva Kamkar & Fatemeh Ghezloo & Hamid Abrishami Moghaddam & Ali Borji & Reza Lashgari - 1-30 Learning action-oriented models through active inference
by Alexander Tschantz & Anil K Seth & Christopher L Buckley - 1-32 Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology
by Sean L Wu & Héctor M Sánchez C. & John M Henry & Daniel T Citron & Qian Zhang & Kelly Compton & Biyonka Liang & Amit Verma & Derek A T Cummings & Arnaud Le Menach & Thomas W Scott & Anne L Wilson & Steven W Lindsay & Catherine L Moyes & Penny A Hancock & Tanya L Russell & Thomas R Burkot & John M Marshall & Samson Kiware & Robert C Reiner Jr & David L Smith - 1-33 Generalizing to generalize: Humans flexibly switch between compositional and conjunctive structures during reinforcement learning
by Nicholas T Franklin & Michael J Frank - 1-34 eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
by Augusto Anguita-Ruiz & Alberto Segura-Delgado & Rafael Alcalá & Concepción M Aguilera & Jesús Alcalá-Fdez - 1-35 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
by Christopher T Lee & Justin G Laughlin & Nils Angliviel de La Beaumelle & Rommie E Amaro & J Andrew McCammon & Ravi Ramamoorthi & Michael Holst & Padmini Rangamani - 1-42 Discovery of hierarchical representations for efficient planning
by Momchil S Tomov & Samyukta Yagati & Agni Kumar & Wanqian Yang & Samuel J Gershman - 1-44 Striatal network modeling in Huntington’s Disease
by Adam Ponzi & Scott J Barton & Kendra D Bunner & Claudia Rangel-Barajas & Emily S Zhang & Benjamin R Miller & George V Rebec & James Kozloski
March 2020, Volume 16, Issue 3
- 1-12 ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data
by Lisa M Bramer & Amanda M White & Kelly G Stratton & Allison M Thompson & Daniel Claborne & Kirsten Hofmockel & Lee Ann McCue - 1-14 Quantifying the roles of vomiting, diarrhea, and residents vs. staff in norovirus transmission in U.S. nursing home outbreaks
by Carly Adams & David Young & Paul A Gastañaduy & Prabasaj Paul & Zach Marsh & Aron J Hall & Benjamin A Lopman - 1-14 A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015
by Ellen Brooks-Pollock & Leon Danon & Hester Korthals Altes & Jennifer A Davidson & Andrew M T Pollock & Dick van Soolingen & Colin Campbell & Maeve K Lalor - 1-16 The use of mixture density networks in the emulation of complex epidemiological individual-based models
by Christopher N Davis & T Deirdre Hollingsworth & Quentin Caudron & Michael A Irvine - 1-17 Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex
by Dmitrii S Shcherbinin & Vlad A Belousov & Mikhail Shugay - 1-19 Detecting critical slowing down in high-dimensional epidemiological systems
by Tobias Brett & Marco Ajelli & Quan-Hui Liu & Mary G Krauland & John J Grefenstette & Willem G van Panhuis & Alessandro Vespignani & John M Drake & Pejman Rohani - 1-20 CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data
by Thilde Terkelsen & Anders Krogh & Elena Papaleo - 1-21 Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines
by Elba Raimúndez & Simone Keller & Gwen Zwingenberger & Karolin Ebert & Sabine Hug & Fabian J Theis & Dieter Maier & Birgit Luber & Jan Hasenauer - 1-21 The spread of a wild plant pathogen is driven by the road network
by Elina Numminen & Anna-Liisa Laine - 1-22 Parallel Tempering with Lasso for model reduction in systems biology
by Sanjana Gupta & Robin E C Lee & James R Faeder - 1-24 Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating
by Keri A McKiernan & Anna K Koster & Merritt Maduke & Vijay S Pande - 1-25 Modeling binary and graded cone cell fate patterning in the mouse retina
by Kiara C Eldred & Cameron Avelis & Robert J Johnston Jr & Elijah Roberts - 1-25 Deconvolution of calcium imaging data using marked point processes
by Ryohei Shibue & Fumiyasu Komaki - 1-26 Mechanisms underlying attraction to odors in walking Drosophila
by Liangyu Tao & Siddhi Ozarkar & Vikas Bhandawat - 1-27 PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
by Guillaume Gautreau & Adelme Bazin & Mathieu Gachet & Rémi Planel & Laura Burlot & Mathieu Dubois & Amandine Perrin & Claudine Médigue & Alexandra Calteau & Stéphane Cruveiller & Catherine Matias & Christophe Ambroise & Eduardo P C Rocha & David Vallenet - 1-34 A simplified modelling framework facilitates more complex representations of plant circadian clocks
by Mathias Foo & Declan G Bates & Ozgur E Akman
February 2020, Volume 16, Issue 2
- 1-9 Ten simple rules for getting started on Twitter as a scientist
by Veronika Cheplygina & Felienne Hermans & Casper Albers & Natalia Bielczyk & Ionica Smeets - 1-13 Ten Simple Rules to becoming a principal investigator
by John S Tregoning & Jason E McDermott - 1-17 RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method
by Kosuke Hamazaki & Hiroyoshi Iwata - 1-18 Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells
by Toshinori Namba & Shuji Ishihara - 1-18 Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies
by Shuang Song & Wei Jiang & Lin Hou & Hongyu Zhao - 1-19 Orbit Image Analysis: An open-source whole slide image analysis tool
by Manuel Stritt & Anna K Stalder & Enrico Vezzali - 1-19 Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network
by Andrei Zinovyev & Urszula Czerwinska & Laura Cantini & Emmanuel Barillot & Klaus M Frahm & Dima L Shepelyansky - 1-19 Inferring TF activation order in time series scRNA-Seq studies
by Chieh Lin & Jun Ding & Ziv Bar-Joseph - 1-20 Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice
by Aleksandr Kovaltsuk & Matthew I J Raybould & Wing Ki Wong & Claire Marks & Sebastian Kelm & James Snowden & Johannes Trück & Charlotte M Deane - 1-20 Navigable maps of structural brain networks across species
by Antoine Allard & M Ángeles Serrano - 1-21 Surprise response as a probe for compressed memory states
by Hadar Levi-Aharoni & Oren Shriki & Naftali Tishby - 1-21 Bayesian inference and comparison of stochastic transcription elongation models
by Jordan Douglas & Richard Kingston & Alexei J Drummond - 1-23 Early prediction of antigenic transitions for influenza A/H3N2
by Lauren A Castro & Trevor Bedford & Lauren Ancel Meyers - 1-23 A generative growth model for thalamocortical axonal branching in primary visual cortex
by Pegah Kassraian-Fard & Michael Pfeiffer & Roman Bauer - 1-23 Predicting colorectal cancer risk from adenoma detection via a two-type branching process model
by Brian M Lang & Jack Kuipers & Benjamin Misselwitz & Niko Beerenwinkel - 1-24 The relation between crosstalk and gene regulation form revisited
by Rok Grah & Tamar Friedlander - 1-26 Doubting what you already know: Uncertainty regarding state transitions is associated with obsessive compulsive symptoms
by Isaac Fradkin & Casimir Ludwig & Eran Eldar & Jonathan D Huppert - 1-27 Dynamic integration of forward planning and heuristic preferences during multiple goal pursuit
by Florian Ott & Dimitrije Marković & Alexander Strobel & Stefan J Kiebel - 1-28 Stochastic optimal open-loop control as a theory of force and impedance planning via muscle co-contraction
by Bastien Berret & Frédéric Jean - 1-29 Multi-state design of flexible proteins predicts sequences optimal for conformational change
by Marion F Sauer & Alexander M Sevy & James E Crowe Jr. & Jens Meiler
January 2020, Volume 16, Issue 1
- 1-11 Collaboration leads to cooperation on sparse networks
by Simon D Angus & Jonathan Newton - 1-12 BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis
by Manoj Kumar & Cameron T Ellis & Qihong Lu & Hejia Zhang & Mihai Capotă & Theodore L Willke & Peter J Ramadge & Nicholas B Turk-Browne & Kenneth A Norman - 1-13 Limits on amplifiers of natural selection under death-Birth updating
by Josef Tkadlec & Andreas Pavlogiannis & Krishnendu Chatterjee & Martin A Nowak - 1-16 The Dynamic Shift Detector: An algorithm to identify changes in parameter values governing populations
by Christie A Bahlai & Elise F Zipkin - 1-17 Interpreting neural decoding models using grouped model reliance
by Simon Valentin & Maximilian Harkotte & Tzvetan Popov - 1-17 Learning from animals: How to Navigate Complex Terrains
by Henghui Zhu & Hao Liu & Armin Ataei & Yonatan Munk & Thomas Daniel & Ioannis Ch Paschalidis - 1-17 VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning
by Jiwoong Kim & David E Greenberg & Reed Pifer & Shuang Jiang & Guanghua Xiao & Samuel A Shelburne & Andrew Koh & Yang Xie & Xiaowei Zhan - 1-18 A single reaction-diffusion equation for the multifarious eruptions of urticaria
by Sungrim Seirin-Lee & Yuhki Yanase & Shunsuke Takahagi & Michihiro Hide - 1-19 Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power
by Vaitea Opuu & Giuliano Nigro & Thomas Gaillard & Emmanuelle Schmitt & Yves Mechulam & Thomas Simonson - 1-20 Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs
by Benjamin Allen & Christine Sample & Robert Jencks & James Withers & Patricia Steinhagen & Lori Brizuela & Joshua Kolodny & Darren Parke & Gabor Lippner & Yulia A Dementieva - 1-21 Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming
by Jake P Taylor-King & Asbjørn N Riseth & Will Macnair & Manfred Claassen - 1-22 Tissue-guided LASSO for prediction of clinical drug response using preclinical samples
by Edward W Huang & Ameya Bhope & Jing Lim & Saurabh Sinha & Amin Emad - 1-23 Computational optimization of associative learning experiments
by Filip Melinscak & Dominik R Bach - 1-24 A new method for inferring timetrees from temporally sampled molecular sequences
by Sayaka Miura & Koichiro Tamura & Qiqing Tao & Louise A Huuki & Sergei L Kosakovsky Pond & Jessica Priest & Jiamin Deng & Sudhir Kumar - 1-24 A system for tracking whisker kinematics and whisker shape in three dimensions
by Rasmus S Petersen & Andrea Colins Rodriguez & Mathew H Evans & Dario Campagner & Michaela S E Loft - 1-25 Emergence of social inequality in the spatial harvesting of renewable public goods
by Jaideep Joshi & Åke Brännström & Ulf Dieckmann - 1-31 Notch signaling and taxis mechanisms regulate early stage angiogenesis: A mathematical and computational model
by Rocío Vega & Manuel Carretero & Rui D M Travasso & Luis L Bonilla - 1-32 Emergence and suppression of cooperation by action visibility in transparent games
by Anton M Unakafov & Thomas Schultze & Alexander Gail & Sebastian Moeller & Igor Kagan & Stephan Eule & Fred Wolf
December 2019, Volume 15, Issue 12
- 1-10 Nine quick tips for analyzing network data
by Vincent Miele & Catherine Matias & Stéphane Robin & Stéphane Dray - 1-14 Benchmarking network algorithms for contextualizing genes of interest
by Abby Hill & Scott Gleim & Florian Kiefer & Frederic Sigoillot & Joseph Loureiro & Jeremy Jenkins & Melody K Morris - 1-16 Motion prediction enables simulated MR-imaging of freely moving model organisms
by Markus Reischl & Mazin Jouda & Neil MacKinnon & Erwin Fuhrer & Natalia Bakhtina & Andreas Bartschat & Ralf Mikut & Jan G Korvink - 1-16 Statistical inference in ensemble modeling of cellular metabolism
by Tuure Hameri & Marc-Olivier Boldi & Vassily Hatzimanikatis - 1-17 Representation learning of genomic sequence motifs with convolutional neural networks
by Peter K Koo & Sean R Eddy - 1-18 Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15
by Akira Endo & Mitsuo Uchida & Adam J Kucharski & Sebastian Funk - 1-18 CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data
by Kai Kang & Qian Meng & Igor Shats & David M Umbach & Melissa Li & Yuanyuan Li & Xiaoling Li & Leping Li - 1-19 Statistics of correlated percolation in a bacterial community
by Xiaoling Zhai & Joseph W Larkin & Kaito Kikuchi & Samuel E Redford & Ushasi Roy & Gürol M Süel & Andrew Mugler - 1-19 Stochasticity of replication forks’ speeds plays a key role in the dynamics of DNA replication
by Razie Yousefi & Maga Rowicka - 1-21 Overlap matrix completion for predicting drug-associated indications
by Mengyun Yang & Huimin Luo & Yaohang Li & Fang-Xiang Wu & Jianxin Wang - 1-21 The effect of inhibition on rate code efficiency indicators
by Tomas Barta & Lubomir Kostal - 1-21 Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models
by Colette Mair & Sema Nickbakhsh & Richard Reeve & Jim McMenamin & Arlene Reynolds & Rory N Gunson & Pablo R Murcia & Louise Matthews - 1-23 Incomplete information about the partner affects the development of collaborative strategies in joint action
by Vinil T Chackochan & Vittorio Sanguineti - 1-23 From energy to cellular forces in the Cellular Potts Model: An algorithmic approach
by Elisabeth G Rens & Leah Edelstein-Keshet - 1-23 Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
by Giacomo Janson & Alessandro Grottesi & Marco Pietrosanto & Gabriele Ausiello & Giulia Guarguaglini & Alessandro Paiardini - 1-24 Regulatory context drives conservation of glycine riboswitch aptamers
by Matt Crum & Nikhil Ram-Mohan & Michelle M Meyer - 1-25 Inferring reaction network structure from single-cell, multiplex data, using toric systems theory
by Shu Wang & Jia-Ren Lin & Eduardo D Sontag & Peter K Sorger - 1-25 Stability of spontaneous, correlated activity in mouse auditory cortex
by Richard F Betzel & Katherine C Wood & Christopher Angeloni & Maria Neimark Geffen & Danielle S Bassett