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Content
September 2020, Volume 16, Issue 9
- 1-25 Identifying locations of re-entrant drivers from patient-specific distribution of fibrosis in the left atrium
by Aditi Roy & Marta Varela & Henry Chubb & Robert MacLeod & Jules C Hancox & Tobias Schaeffter & Oleg Aslanidi - 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 Short-term depression and long-term plasticity together tune sensitive range of synaptic plasticity
by Nicolas Deperrois & Michael Graupner - 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 - 1-27 A compiler for biological networks on silicon chips
by J Kyle Medley & Jonathan Teo & Sung Sik Woo & Joseph Hellerstein & Rahul Sarpeshkar & Herbert M Sauro - 1-28 Buffering and total calcium levels determine the presence of oscillatory regimes in cardiac cells
by Miquel Marchena & Blas Echebarria & Yohannes Shiferaw & Enrique Alvarez-Lacalle - 1-28 Domino-like transient dynamics at seizure onset in epilepsy
by Jennifer Creaser & Congping Lin & Thomas Ridler & Jonathan T Brown & Wendyl D’Souza & Udaya Seneviratne & Mark Cook & John R Terry & Krasimira Tsaneva-Atanasova - 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
- 1-7 Ten simple rules to increase computational skills among biologists with Code Clubs
by Ada K Hagan & Nicholas A Lesniak & Marcy J Balunas & Lucas Bishop & William L Close & Matthew D Doherty & Amanda G Elmore & Kaitlin J Flynn & Geoffrey D Hannigan & Charlie C Koumpouras & Matthew L Jenior & Ariangela J Kozik & Kathryn McBride & Samara B Rifkin & Joshua M A Stough & Kelly L Sovacool & Marc A Sze & Sarah Tomkovich & Begum D Topcuoglu & Patrick D Schloss - 1-15 Achieving stable dynamics in neural circuits
by Leo Kozachkov & Mikael Lundqvist & Jean-Jacques Slotine & Earl K Miller - 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 Vector genetics, insecticide resistance and gene drives: An agent-based modeling approach to evaluate malaria transmission and elimination
by Prashanth Selvaraj & Edward A Wenger & Daniel Bridenbecker & Nikolai Windbichler & Jonathan R Russell & Jaline Gerardin & Caitlin A Bever & Milen Nikolov - 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 Engineering recurrent neural networks from task-relevant manifolds and dynamics
by Eli Pollock & Mehrdad Jazayeri - 1-23 Simulating flow induced migration in vascular remodelling
by Ashkan Tabibian & Siavash Ghaffari & Diego A Vargas & Hans Van Oosterwyck & Elizabeth A V Jones - 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 - 1-36 Mathematical model and tool to explore shorter multi-drug therapy options for active pulmonary tuberculosis
by John Fors & Natasha Strydom & William S Fox & Ron J Keizer & Radojka M Savic - 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 - 1-10 Nine quick tips for efficient bioinformatics curriculum development and training
by Susan McClatchy & Kristin M Bass & Daniel M Gatti & Adam Moylan & Gary Churchill - 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 - 1-16 Is mammography screening beneficial: An individual-based stochastic model for breast cancer incidence and mortality
by Thuy T T Le & Frederick R Adler - 1-18 Bayesian modelling of high-throughput sequencing assays with malacoda
by Andrew R Ghazi & Xianguo Kong & Ed S Chen & Leonard C Edelstein & Chad A Shaw - 1-18 OSS-DBS: Open-source simulation platform for deep brain stimulation with a comprehensive automated modeling
by Konstantin Butenko & Christian Bahls & Max Schröder & Rüdiger Köhling & Ursula van Rienen - 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 Quorum sensing via dynamic cytokine signaling comprehensively explains divergent patterns of effector choice among helper T cells
by Edward C Schrom II & Simon A Levin & Andrea L Graham - 1-21 Mathematical modeling of plant cell fate transitions controlled by hormonal signals
by Filip Z Klawe & Thomas Stiehl & Peter Bastian & Christophe Gaillochet & Jan U Lohmann & Anna Marciniak-Czochra - 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 - 1-24 Heart failure-induced atrial remodelling promotes electrical and conduction alternans
by Na Zhao & Qince Li & Kevin Zhang & Kuanquan Wang & Runnan He & Yongfeng Yuan & Henggui Zhang - 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 - 1-26 Perturbation biology links temporal protein changes to drug responses in a melanoma cell line
by Elin Nyman & Richard R Stein & Xiaohong Jing & Weiqing Wang & Benjamin Marks & Ioannis K Zervantonakis & Anil Korkut & Nicholas P Gauthier & Chris Sander - 1-27 Cross-species regulatory sequence activity prediction
by David R Kelley - 1-29 Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator
by Mariam Ordyan & Tom Bartol & Mary Kennedy & Padmini Rangamani & Terrence Sejnowski - 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
- 1-6 10 simple rules for teaching wet-lab experimentation to computational biology students, i.e., turning computer mice into lab rats
by Joseph C Ayoob & Joshua D Kangas - 1-7 HemoMIPs—Automated analysis and result reporting pipeline for targeted sequencing data
by Philip Kleinert & Beth Martin & Martin Kircher - 1-8 The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies
by Aleksey V Zimin & Steven L Salzberg - 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 - 1-19 Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment
by Alexey Savelyev & Gary E Gorbet & Amy Henrickson & Borries Demeler - 1-19 Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers
by Yu Hu & Kai Wang & Mingyao Li - 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 bigPint: A Bioconductor visualization package that makes big data pint-sized
by Lindsay Rutter & Dianne Cook - 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 Mechanobiological model for simulation of injured cartilage degradation via pro-inflammatory cytokines and mechanical stimulus
by Atte S A Eskelinen & Petri Tanska & Cristina Florea & Gustavo A Orozco & Petro Julkunen & Alan J Grodzinsky & Rami K Korhonen - 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 Multiplexing rhythmic information by spike timing dependent plasticity
by Nimrod Sherf & Shamir Maoz - 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 Stochastic dynamics of Francisella tularensis infection and replication
by Jonathan Carruthers & Grant Lythe & Martín López-García & Joseph Gillard & Thomas R Laws & Roman Lukaszewski & Carmen Molina-París - 1-26 Natural scene statistics predict how humans pool information across space in surface tilt estimation
by Seha Kim & Johannes Burge - 1-26 Modelling the effects of ephaptic coupling on selectivity and response patterns during artificial stimulation of peripheral nerves
by Miguel Capllonch-Juan & Francisco Sepulveda - 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 - 1-31 A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks
by Víctor A López-Agudelo & Tom A Mendum & Emma Laing & HuiHai Wu & Andres Baena & Luis F Barrera & Dany J V Beste & Rigoberto Rios-Estepa - 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
- 1-3 Improving reproducibility in computational biology research
by Jason A Papin & Feilim Mac Gabhann & Herbert M Sauro & David Nickerson & Anand Rampadarath - 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 - 1-9 Ten simple rules for making training materials FAIR
by Leyla Garcia & Bérénice Batut & Melissa L Burke & Mateusz Kuzak & Fotis Psomopoulos & Ricardo Arcila & Teresa K Attwood & Niall Beard & Denise Carvalho-Silva & Alexandros C Dimopoulos & Victoria Dominguez del Angel & Michel Dumontier & Kim T Gurwitz & Roland Krause & Peter McQuilton & Loredana Le Pera & Sarah L Morgan & Päivi Rauste & Allegra Via & Pascal Kahlem & Gabriella Rustici & Celia W G van Gelder & Patricia M Palagi - 1-12 Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles
by Alastair M Kilpatrick & Audra Anjum & Lonnie Welch - 1-14 Complex interactions can create persistent fluctuations in high-diversity ecosystems
by Felix Roy & Matthieu Barbier & Giulio Biroli & Guy Bunin - 1-15 A unifying model for the propagation of prion proteins in yeast brings insight into the [PSI+] prion
by Paul Lemarre & Laurent Pujo-Menjouet & Suzanne S Sindi - 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 Conservation laws by virtue of scale symmetries in neural systems
by Erik D Fagerholm & W M C Foulkes & Yasir Gallero-Salas & Fritjof Helmchen & Karl J Friston & Rosalyn J Moran & Robert Leech - 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 - 1-20 Modeling the temporal network dynamics of neuronal cultures
by Jose Cadena & Ana Paula Sales & Doris Lam & Heather A Enright & Elizabeth K Wheeler & Nicholas O Fischer - 1-21 In silico analysis of hypoxia activated prodrugs in combination with anti angiogenic therapy through nanocell delivery
by Cameron Meaney & Sander Rhebergen & Mohammad Kohandel - 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 Chloride dynamics alter the input-output properties of neurons
by Christopher B Currin & Andrew J Trevelyan & Colin J Akerman & Joseph V Raimondo - 1-22 Self-organization in brain tumors: How cell morphology and cell density influence glioma pattern formation
by Sara Jamous & Andrea Comba & Pedro R Lowenstein & Sebastien Motsch - 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 - 1-23 Estimating a novel stochastic model for within-field disease dynamics of banana bunchy top virus via approximate Bayesian computation
by Abhishek Varghese & Christopher Drovandi & Antonietta Mira & Kerrie Mengersen - 1-23 Ranbow: A fast and accurate method for polyploid haplotype reconstruction
by M-Hossein Moeinzadeh & Jun Yang & Evgeny Muzychenko & Giuseppe Gallone & David Heller & Knut Reinert & Stefan Haas & Martin Vingron - 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 - 1-25 The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth
by Juami Hermine Mariama van Gils & Erik van Dijk & Alessia Peduzzo & Alexander Hofmann & Nicola Vettore & Marie P Schützmann & Georg Groth & Halima Mouhib & Daniel E Otzen & Alexander K Buell & Sanne Abeln - 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 - 1-33 Modeling the effects of motivation on choice and learning in the basal ganglia
by Maaike M H van Swieten & Rafal Bogacz - 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 - 1-11 Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions
by Gregory L Medlock & Thomas J Moutinho & Jason A Papin - 1-12 Ten simple rules for innovative dissemination of research
by Tony Ross-Hellauer & Jonathan P Tennant & Viltė Banelytė & Edit Gorogh & Daniela Luzi & Peter Kraker & Lucio Pisacane & Roberta Ruggieri & Electra Sifacaki & Michela Vignoli - 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 High-dimensional mediation analysis in survival models
by Chengwen Luo & Botao Fa & Yuting Yan & Yang Wang & Yiwang Zhou & Yue Zhang & Zhangsheng Yu - 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 - 1-18 DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning
by Jean-Baptiste Lugagne & Haonan Lin & Mary J Dunlop - 1-18 Information integration and collective motility in phototactic cyanobacteria
by Shakti N Menon & P Varuni & Gautam I Menon - 1-18 ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks
by Pierre Millard & Uwe Schmitt & Patrick Kiefer & Julia A Vorholt & Stéphanie Heux & Jean-Charles Portais - 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 Robustness of the Dorsal morphogen gradient with respect to morphogen dosage
by Hadel Al Asafen & Prasad U Bandodkar & Sophia Carrell-Noel & Allison E Schloop & Jeramey Friedman & Gregory T Reeves - 1-21 Improving the coverage of credible sets in Bayesian genetic fine-mapping
by Anna Hutchinson & Hope Watson & Chris Wallace - 1-21 Inferring the immune response from repertoire sequencing
by Maximilian Puelma Touzel & Aleksandra M Walczak & Thierry Mora - 1-22 Dysregulated biodynamics in metabolic attractor systems precede the emergence of amyotrophic lateral sclerosis
by Paul Curtin & Christine Austin & Austen Curtin & Chris Gennings & Claudia Figueroa-Romero & Kristen A Mikhail & Tatiana M Botero & Stephen A Goutman & Eva L Feldman & Manish Arora - 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 Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation
by Luis Busto-Moner & Julien Morival & Honglei Ren & Arjang Fahim & Zachary Reitz & Timothy L Downing & Elizabeth L Read - 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 - 1-24 A three-dimensional phase-field model for multiscale modeling of thrombus biomechanics in blood vessels
by Xiaoning Zheng & Alireza Yazdani & He Li & Jay D Humphrey & George E Karniadakis - 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 - 1-28 Humans adapt their anticipatory eye movements to the volatility of visual motion properties
by Chloé Pasture & Anna Montagnini & Laurent Udo Perrinet - 1-28 Optimizing the deployment of ultra-low volume and indoor residual spraying for dengue outbreak response
by Sean M Cavany & Guido España & Alun L Lloyd & Lance A Waller & Uriel Kitron & Helvio Astete & William H Elson & Gonzalo M Vazquez-Prokopec & Thomas W Scott & Amy C Morrison & Robert C Reiner Jr. & T Alex Perkins - 1-29 Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution
by Andreas Haahr Larsen & Yong Wang & Sandro Bottaro & Sergei Grudinin & Lise Arleth & Kresten Lindorff-Larsen - 1-30 Learning action-oriented models through active inference
by Alexander Tschantz & Anil K Seth & Christopher L Buckley - 1-31 Ensemble modeling of auditory streaming reveals potential sources of bistability across the perceptual hierarchy
by David F Little & Joel S Snyder & Mounya Elhilali - 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 - 1-36 An electrodiffusive, ion conserving Pinsky-Rinzel model with homeostatic mechanisms
by Marte J Sætra & Gaute T Einevoll & Geir Halnes - 1-39 The research and development process for multiscale models of infectious disease systems
by Winston Garira - 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
- 1-10 Ten simple rules for providing effective bioinformatics research support
by Judit Kumuthini & Michael Chimenti & Sven Nahnsen & Alexander Peltzer & Rebone Meraba & Ross McFadyen & Gordon Wells & Deanne Taylor & Mark Maienschein-Cline & Jian-Liang Li & Jyothi Thimmapuram & Radha Murthy-Karuturi & Lyndon Zass - 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 ProteinVR: Web-based molecular visualization in virtual reality
by Kevin C Cassidy & Jan Šefčík & Yogindra Raghav & Alexander Chang & Jacob D Durrant - 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 - 1-18 The influence of red blood cell deformability on hematocrit profiles and platelet margination
by Benjamin Czaja & Mario Gutierrez & Gábor Závodszky & David de Kanter & Alfons Hoekstra & Omolola Eniola-Adefeso - 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 - 1-20 Tracking progress towards malaria elimination in China: Individual-level estimates of transmission and its spatiotemporal variation using a diffusion network approach
by Isobel Routledge & Shengjie Lai & Katherine E Battle & Azra C Ghani & Manuel Gomez-Rodriguez & Kyle B Gustafson & Swapnil Mishra & Juliette Unwin & Joshua L Proctor & Andrew J Tatem & Zhongjie Li & Samir Bhatt - 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