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Content
October 2018, Volume 14, Issue 10
- 1-4 Ten simple rules for developing good reading habits during graduate school and beyond
by Marcos Méndez - 1-4 Ten simple rules when considering retirement
by Philip E Bourne - 1-7 What to know before forecasting the flu
by Prithwish Chakraborty & Bryan Lewis & Stephen Eubank & John S Brownstein & Madhav Marathe & Naren Ramakrishnan - 1-8 Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor
by Richard A Erickson & Michael N Fienen & S Grace McCalla & Emily L Weiser & Melvin L Bower & Jonathan M Knudson & Greg Thain - 1-15 Modeling effects of voltage dependent properties of the cardiac muscarinic receptor on human sinus node function
by Robin Moss & Frank B Sachse & Eloy G Moreno-Galindo & Ricardo A Navarro-Polanco & Martin Tristani-Firouzi & Gunnar Seemann - 1-17 A k -mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria
by Erki Aun & Age Brauer & Veljo Kisand & Tanel Tenson & Maido Remm - 1-19 Virus and CTL dynamics in the extrafollicular and follicular tissue compartments in SIV-infected macaques
by Dominik Wodarz & Pamela J Skinner & David N Levy & Elizabeth Connick - 1-20 meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays
by Sahar Gelfman & Quanli Wang & Yi-Fan Lu & Diana Hall & Christopher D Bostick & Ryan Dhindsa & Matt Halvorsen & K Melodi McSweeney & Ellese Cotterill & Tom Edinburgh & Michael A Beaumont & Wayne N Frankel & Slavé Petrovski & Andrew S Allen & Michael J Boland & David B Goldstein & Stephen J Eglen - 1-21 Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals
by Iksoo Huh & Isabel Mendizabal & Taesung Park & Soojin V Yi - 1-21 Ten quick tips for getting the most scientific value out of numerical data
by Lars Ole Schwen & Sabrina Rueschenbaum - 1-22 Modeling sensory-motor decisions in natural behavior
by Ruohan Zhang & Shun Zhang & Matthew H Tong & Yuchen Cui & Constantin A Rothkopf & Dana H Ballard & Mary M Hayhoe - 1-23 Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data
by Misbah Razzaq & Loïc Paulevé & Anne Siegel & Julio Saez-Rodriguez & Jérémie Bourdon & Carito Guziolowski - 1-24 Predicting B cell receptor substitution profiles using public repertoire data
by Amrit Dhar & Kristian Davidsen & Frederick A Matsen IV & Vladimir N Minin - 1-24 Seizure pathways: A model-based investigation
by Philippa J Karoly & Levin Kuhlmann & Daniel Soudry & David B Grayden & Mark J Cook & Dean R Freestone - 1-28 Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells
by Ernest C Y Ho & Juan Nicolas Malagón & Abha Ahuja & Rama Singh & Ellen Larsen - 1-28 State dependence of stimulus-induced variability tuning in macaque MT
by Joseph A Lombardo & Matthew V Macellaio & Bing Liu & Stephanie E Palmer & Leslie C Osborne - 1-30 A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments
by Katharina Nöh & Sebastian Niedenführ & Martin Beyß & Wolfgang Wiechert
September 2018, Volume 14, Issue 9
- 1-15 Individualised aspiration dynamics: Calculation by proofs
by Bin Wu & Lei Zhou - 1-16 clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
by Davide Risso & Liam Purvis & Russell B Fletcher & Diya Das & John Ngai & Sandrine Dudoit & Elizabeth Purdom - 1-16 Optimal multi-source forecasting of seasonal influenza
by Zeynep Ertem & Dorrie Raymond & Lauren Ancel Meyers - 1-18 Multivariate classification of neuroimaging data with nested subclasses: Biased accuracy and implications for hypothesis testing
by Hamidreza Jamalabadi & Sarah Alizadeh & Monika Schönauer & Christian Leibold & Steffen Gais - 1-19 Implications of alternative routes to APC/C inhibition by the mitotic checkpoint complex
by Fridolin Gross & Paolo Bonaiuti & Silke Hauf & Andrea Ciliberto - 1-20 Maintaining maximal metabolic flux by gene expression control
by Robert Planqué & Josephus Hulshof & Bas Teusink & Johannes C Hendriks & Frank J Bruggeman - 1-23 Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling
by Tatu Pantsar & Sami Rissanen & Daniel Dauch & Tuomo Laitinen & Ilpo Vattulainen & Antti Poso - 1-24 An information theoretic treatment of sequence-to-expression modeling
by Farzaneh Khajouei & Saurabh Sinha - 1-24 Transition state characteristics during cell differentiation
by Rowan D Brackston & Eszter Lakatos & Michael P H Stumpf - 1-25 Modeling and prediction of clinical symptom trajectories in Alzheimer’s disease using longitudinal data
by Nikhil Bhagwat & Joseph D Viviano & Aristotle N Voineskos & M Mallar Chakravarty & Alzheimer’s Disease Neuroimaging Initiative - 1-25 The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow
by Rosanna Migliore & Carmen A Lupascu & Luca L Bologna & Armando Romani & Jean-Denis Courcol & Stefano Antonel & Werner A H Van Geit & Alex M Thomson & Audrey Mercer & Sigrun Lange & Joanne Falck & Christian A Rössert & Ying Shi & Olivier Hagens & Maurizio Pezzoli & Tamas F Freund & Szabolcs Kali & Eilif B Muller & Felix Schürmann & Henry Markram & Michele Migliore - 1-28 A Markov chain for numerical chromosomal instability in clonally expanding populations
by Sergi Elizalde & Ashley M Laughney & Samuel F Bakhoum - 1-29 Co-evolution networks of HIV/HCV are modular with direct association to structure and function
by Ahmed Abdul Quadeer & David Morales-Jimenez & Matthew R McKay - 1-31 Comparing two classes of biological distribution systems using network analysis
by Lia Papadopoulos & Pablo Blinder & Henrik Ronellenfitsch & Florian Klimm & Eleni Katifori & David Kleinfeld & Danielle S Bassett - 1-33 Informational structures: A dynamical system approach for integrated information
by Francisco J Esteban & Javier A Galadí & José A Langa & José R Portillo & Fernando Soler-Toscano - 1-40 Inferring decoding strategies for multiple correlated neural populations
by Kaushik J Lakshminarasimhan & Alexandre Pouget & Gregory C DeAngelis & Dora E Angelaki & Xaq Pitkow
August 2018, Volume 14, Issue 8
- 1-12 Ten simple rules for measuring the impact of workshops
by Shoaib Sufi & Aleksandra Nenadic & Raniere Silva & Beth Duckles & Iveta Simera & Jennifer A de Beyer & Caroline Struthers & Terhi Nurmikko-Fuller & Louisa Bellis & Wadud Miah & Adriana Wilde & Iain Emsley & Olivier Philippe & Melissa Balzano & Sara Coelho & Heather Ford & Catherine Jones & Vanessa Higgins - 1-14 Scaling up data curation using deep learning: An application to literature triage in genomic variation resources
by Kyubum Lee & Maria Livia Famiglietti & Aoife McMahon & Chih-Hsuan Wei & Jacqueline Ann Langdon MacArthur & Sylvain Poux & Lionel Breuza & Alan Bridge & Fiona Cunningham & Ioannis Xenarios & Zhiyong Lu - 1-14 SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks
by Rong Zhang & Zhao Ren & Wei Chen - 1-19 Interactive implementations of thermodynamics-based RNA structure and RNA–RNA interaction prediction approaches for example-driven teaching
by Martin Raden & Mostafa Mahmoud Mohamed & Syed Mohsin Ali & Rolf Backofen - 1-21 Human Pavlovian fear conditioning conforms to probabilistic learning
by Athina Tzovara & Christoph W Korn & Dominik R Bach - 1-22 A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data
by Tianwei Yu - 1-24 MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction
by Xing Chen & Jun Yin & Jia Qu & Li Huang - 1-25 New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images
by Ilya Patrushev & Christina James-Zorn & Aldo Ciau-Uitz & Roger Patient & Michael J Gilchrist - 1-25 Identification of excitatory-inhibitory links and network topology in large-scale neuronal assemblies from multi-electrode recordings
by Vito Paolo Pastore & Paolo Massobrio & Aleksandar Godjoski & Sergio Martinoia - 1-28 Rare-event sampling of epigenetic landscapes and phenotype transitions
by Margaret J Tse & Brian K Chu & Cameron P Gallivan & Elizabeth L Read - 1-29 An automated approach to the quantitation of vocalizations and vocal learning in the songbird
by David G Mets & Michael S Brainard - 1-29 Profiling cellular morphodynamics by spatiotemporal spectrum decomposition
by Xiao Ma & Onur Dagliyan & Klaus M Hahn & Gaudenz Danuser - 1-30 Inferring hidden structure in multilayered neural circuits
by Niru Maheswaranathan & David B Kastner & Stephen A Baccus & Surya Ganguli - 1-32 Interplay of multiple pathways and activity-dependent rules in STDP
by Gaëtan Vignoud & Laurent Venance & Jonathan D Touboul
July 2018, Volume 14, Issue 7
- 1-15 Punishment and inspection for governing the commons in a feedback-evolving game
by Xiaojie Chen & Attila Szolnoki - 1-16 Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning
by Naihui Zhou & Zachary D Siegel & Scott Zarecor & Nigel Lee & Darwin A Campbell & Carson M Andorf & Dan Nettleton & Carolyn J Lawrence-Dill & Baskar Ganapathysubramanian & Jonathan W Kelly & Iddo Friedberg - 1-16 Activation of the DNA-repair mechanism through NBS1 and MRE11 diffusion
by Ida Friis & Ilia A Solov’yov - 1-16 A marginalized two-part Beta regression model for microbiome compositional data
by Haitao Chai & Hongmei Jiang & Lu Lin & Lei Liu - 1-19 Information-theoretic analysis of realistic odor plumes: What cues are useful for determining location?
by Sebastian D Boie & Erin G Connor & Margaret McHugh & Katherine I Nagel & G Bard Ermentrout & John P Crimaldi & Jonathan D Victor - 1-21 PyPhi: A toolbox for integrated information theory
by William G P Mayner & William Marshall & Larissa Albantakis & Graham Findlay & Robert Marchman & Giulio Tononi - 1-21 Post-Turing tissue pattern formation: Advent of mechanochemistry
by Felix Brinkmann & Moritz Mercker & Thomas Richter & Anna Marciniak-Czochra - 1-22 Age-dependent Pavlovian biases influence motor decision-making
by Xiuli Chen & Robb B Rutledge & Harriet R Brown & Raymond J Dolan & Sven Bestmann & Joseph M Galea - 1-23 Gain control with A-type potassium current: IA as a switch between divisive and subtractive inhibition
by Joshua H Goldwyn & Bradley R Slabe & Joseph B Travers & David Terman - 1-31 Inter-trial effects in visual pop-out search: Factorial comparison of Bayesian updating models
by Fredrik Allenmark & Hermann J Müller & Zhuanghua Shi - 1-34 Unsupervised clustering of temporal patterns in high-dimensional neuronal ensembles using a novel dissimilarity measure
by Lukas Grossberger & Francesco P Battaglia & Martin Vinck - 1-38 Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception
by Luigi Acerbi & Kalpana Dokka & Dora E Angelaki & Wei Ji Ma
June 2018, Volume 14, Issue 6
- 1-15 Classification of red blood cell shapes in flow using outlier tolerant machine learning
by Alexander Kihm & Lars Kaestner & Christian Wagner & Stephan Quint - 1-15 Solving the RNA design problem with reinforcement learning
by Peter Eastman & Jade Shi & Bharath Ramsundar & Vijay S Pande - 1-15 Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria
by Nathaniel Mon Père & Tom Lenaerts & Jorge M Pacheco & David Dingli - 1-18 Anticipating epidemic transitions with imperfect data
by Tobias S Brett & Eamon B O’Dea & Éric Marty & Paige B Miller & Andrew W Park & John M Drake & Pejman Rohani - 1-21 Computation predicts rapidly adapting mechanotransduction currents cannot account for tactile encoding in Merkel cell-neurite complexes
by Gregory J Gerling & Lingtian Wan & Benjamin U Hoffman & Yuxiang Wang & Ellen A Lumpkin - 1-22 3D morphology-based clustering and simulation of human pyramidal cell dendritic spines
by Sergio Luengo-Sanchez & Isabel Fernaud-Espinosa & Concha Bielza & Ruth Benavides-Piccione & Pedro Larrañaga & Javier DeFelipe - 1-27 Instance-based generalization for human judgments about uncertainty
by Philipp Schustek & Rubén Moreno-Bote - 1-29 Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions
by Logan C Brooks & David C Farrow & Sangwon Hyun & Ryan J Tibshirani & Roni Rosenfeld - 1-30 The impact of temporal sampling resolution on parameter inference for biological transport models
by Jonathan U Harrison & Ruth E Baker - 1-35 Stochastic shielding and edge importance for Markov chains with timescale separation
by Deena R Schmidt & Roberto F Galán & Peter J Thomas
May 2018, Volume 14, Issue 5
- 1-4 2018 ISCB accomplishments by a senior scientist award
by Christiana N Fogg & Diane E Kovats & Ron Shamir - 1-4 Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago
by Milana Frenkel-Morgenstern & Lonnie Welch & Bruno Gaeta & Diane E Kovats - 1-4 Ten simple rules for writing a cover letter to accompany a job application for an academic position
by Lubomir Tomaska & Jozef Nosek - 1-13 Community-based benchmarking improves spike rate inference from two-photon calcium imaging data
by Philipp Berens & Jeremy Freeman & Thomas Deneux & Nikolay Chenkov & Thomas McColgan & Artur Speiser & Jakob H Macke & Srinivas C Turaga & Patrick Mineault & Peter Rupprecht & Stephan Gerhard & Rainer W Friedrich & Johannes Friedrich & Liam Paninski & Marius Pachitariu & Kenneth D Harris & Ben Bolte & Timothy A Machado & Dario Ringach & Jasmine Stone & Luke E Rogerson & Nicolas J Sofroniew & Jacob Reimer & Emmanouil Froudarakis & Thomas Euler & Miroslav Román Rosón & Lucas Theis & Andreas S Tolias & Matthias Bethge - 1-14 Assessing the public health impact of tolerance-based therapies with mathematical models
by Nathanaël Hozé & Sebastian Bonhoeffer & Roland Regoes - 1-15 beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types
by Aaron T L Lun & Hervé Pagès & Mike L Smith - 1-21 Bi-stability in cooperative transport by ants in the presence of obstacles
by Jonathan E Ron & Itai Pinkoviezky & Ehud Fonio & Ofer Feinerman & Nir S Gov - 1-23 Enzyme sequestration by the substrate: An analysis in the deterministic and stochastic domains
by Andreas Petrides & Glenn Vinnicombe - 1-23 Simulations to benchmark time-varying connectivity methods for fMRI
by William Hedley Thompson & Craig Geoffrey Richter & Pontus Plavén-Sigray & Peter Fransson - 1-24 Detecting change in stochastic sound sequences
by Benjamin Skerritt-Davis & Mounya Elhilali - 1-24 Design of optimal nonlinear network controllers for Alzheimer's disease
by Lazaro M Sanchez-Rodriguez & Yasser Iturria-Medina & Erica A Baines & Sabela C Mallo & Mehdy Dousty & Roberto C Sotero & on behalf of The Alzheimer’s Disease Neuroimaging Initiative - 1-26 How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes
by Surya K Ghosh & Daniel Jost - 1-26 Parameter uncertainty quantification using surrogate models applied to a spatial model of yeast mating polarization
by Marissa Renardy & Tau-Mu Yi & Dongbin Xiu & Ching-Shan Chou - 1-28 Predictive modelling of a novel anti-adhesion therapy to combat bacterial colonisation of burn wounds
by Paul A Roberts & Ryan M Huebinger & Emma Keen & Anne-Marie Krachler & Sara Jabbari - 1-29 A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data
by Aaditya V Rangan & Caroline C McGrouther & John Kelsoe & Nicholas Schork & Eli Stahl & Qian Zhu & Arjun Krishnan & Vicky Yao & Olga Troyanskaya & Seda Bilaloglu & Preeti Raghavan & Sarah Bergen & Anders Jureus & Mikael Landen & Bipolar Disorders Working Group of the Psychiatric Genomics Consortium - 1-34 Optimizing the learning rate for adaptive estimation of neural encoding models
by Han-Lin Hsieh & Maryam M Shanechi - 1-38 Firing-rate based network modeling of the dLGN circuit: Effects of cortical feedback on spatiotemporal response properties of relay cells
by Milad Hobbi Mobarhan & Geir Halnes & Pablo Martínez-Cañada & Torkel Hafting & Marianne Fyhn & Gaute T Einevoll
April 2018, Volume 14, Issue 4
- 1-15 RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning
by Ji-Sung Kim & Xin Gao & Andrey Rzhetsky - 1-16 Optimal dynamic control approach in a multi-objective therapeutic scenario: Application to drug delivery in the treatment of prostate cancer
by Itziar Irurzun-Arana & Alvaro Janda & Sergio Ardanza-Trevijano & Iñaki F Trocóniz - 1-17 Correcting for batch effects in case-control microbiome studies
by Sean M Gibbons & Claire Duvallet & Eric J Alm - 1-23 Using pseudoalignment and base quality to accurately quantify microbial community composition
by Mark Reppell & John Novembre - 1-24 Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape
by David R J Pleydell & Samuel Soubeyrand & Sylvie Dallot & Gérard Labonne & Joël Chadœuf & Emmanuel Jacquot & Gaël Thébaud - 1-25 Compositional clustering in task structure learning
by Nicholas T Franklin & Michael J Frank - 1-26 On the role of extrinsic noise in microRNA-mediated bimodal gene expression
by Marco Del Giudice & Stefano Bo & Silvia Grigolon & Carla Bosia - 1-27 Effect of Ca2+ on the promiscuous target-protein binding of calmodulin
by Annie M Westerlund & Lucie Delemotte - 1-27 Need for speed: An optimized gridding approach for spatially explicit disease simulations
by Stefan Sellman & Kimberly Tsao & Michael J Tildesley & Peter Brommesson & Colleen T Webb & Uno Wennergren & Matt J Keeling & Tom Lindström - 1-28 Exploiting glycan topography for computational design of Env glycoprotein antigenicity
by Wen-Han Yu & Peng Zhao & Monia Draghi & Claudia Arevalo & Christina B Karsten & Todd J Suscovich & Bronwyn Gunn & Hendrik Streeck & Abraham L Brass & Michael Tiemeyer & Michael Seaman & John R Mascola & Lance Wells & Douglas A Lauffenburger & Galit Alter - 1-31 Computational mechanisms underlying cortical responses to the affordance properties of visual scenes
by Michael F Bonner & Russell A Epstein - 1-38 RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
by Jared Adolf-Bryfogle & Oleks Kalyuzhniy & Michael Kubitz & Brian D Weitzner & Xiaozhen Hu & Yumiko Adachi & William R Schief & Roland L Dunbrack Jr. - 1-40 Material and shape perception based on two types of intensity gradient information
by Masataka Sawayama & Shin'ya Nishida
March 2018, Volume 14, Issue 3
- 1-14 Across-subjects classification of stimulus modality from human MEG high frequency activity
by Britta U Westner & Sarang S Dalal & Simon Hanslmayr & Tobias Staudigl - 1-14 An entropic barriers diffusion theory of decision-making in multiple alternative tasks
by Diego Fernandez Slezak & Mariano Sigman & Guillermo A Cecchi - 1-18 An evolutionary learning and network approach to identifying key metabolites for osteoarthritis
by Ting Hu & Karoliina Oksanen & Weidong Zhang & Ed Randell & Andrew Furey & Guang Sun & Guangju Zhai - 1-18 From correlation to causation: Estimating effective connectivity from zero-lag covariances of brain signals
by Jonathan Schiefer & Alexander Niederbühl & Volker Pernice & Carolin Lennartz & Jürgen Hennig & Pierre LeVan & Stefan Rotter - 1-18 Activation gating in HCN2 channels
by Sabine Hummert & Susanne Thon & Thomas Eick & Ralf Schmauder & Eckhard Schulz & Klaus Benndorf - 1-19 Astrocytic Kir4.1 channels and gap junctions account for spontaneous epileptic seizure
by Mengmeng Du & Jiajia Li & Liang Chen & Yuguo Yu & Ying Wu - 1-19 Bat detective—Deep learning tools for bat acoustic signal detection
by Oisin Mac Aodha & Rory Gibb & Kate E Barlow & Ella Browning & Michael Firman & Robin Freeman & Briana Harder & Libby Kinsey & Gary R Mead & Stuart E Newson & Ivan Pandourski & Stuart Parsons & Jon Russ & Abigel Szodoray-Paradi & Farkas Szodoray-Paradi & Elena Tilova & Mark Girolami & Gabriel Brostow & Kate E Jones - 1-19 Population-specific design of de-immunized protein biotherapeutics
by Benjamin Schubert & Charlotta Schärfe & Pierre Dönnes & Thomas Hopf & Debora Marks & Oliver Kohlbacher - 1-20 The importance of geometry in the corneal micropocket angiogenesis assay
by James A Grogan & Anthony J Connor & Joe M Pitt-Francis & Philip K Maini & Helen M Byrne - 1-21 Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells
by Yanting Luo & Jianlin He & Xiguang Xu & Ming-an Sun & Xiaowei Wu & Xuemei Lu & Hehuang Xie - 1-24 Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state
by Hao Ge & Pingping Wu & Hong Qian & Xiaoliang Sunney Xie - 1-24 Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units
by Timothy Kinyanjui & Jo Middleton & Stefan Güttel & Jackie Cassell & Joshua Ross & Thomas House - 1-25 SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data
by Ivan Dotu & Scott I Adamson & Benjamin Coleman & Cyril Fournier & Emma Ricart-Altimiras & Eduardo Eyras & Jeffrey H Chuang - 1-25 speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification
by Charlie Beirnaert & Pieter Meysman & Trung Nghia Vu & Nina Hermans & Sandra Apers & Luc Pieters & Adrian Covaci & Kris Laukens - 1-25 Brain-state invariant thalamo-cortical coordination revealed by non-linear encoders
by Guillaume Viejo & Thomas Cortier & Adrien Peyrache - 1-25 Use of temperature to improve West Nile virus forecasts
by Nicholas B DeFelice & Zachary D Schneider & Eliza Little & Christopher Barker & Kevin A Caillouet & Scott R Campbell & Dan Damian & Patrick Irwin & Herff M P Jones & John Townsend & Jeffrey Shaman - 1-26 Factors affecting basket catheter detection of real and phantom rotors in the atria: A computational study
by Laura Martinez-Mateu & Lucia Romero & Ana Ferrer-Albero & Rafael Sebastian & José F Rodríguez Matas & José Jalife & Omer Berenfeld & Javier Saiz - 1-26 Dynamic combination of sensory and reward information under time pressure
by Shiva Farashahi & Chih-Chung Ting & Chang-Hao Kao & Shih-Wei Wu & Alireza Soltani - 1-27 Classifying dynamic transitions in high dimensional neural mass models: A random forest approach
by Lauric A Ferrat & Marc Goodfellow & John R Terry - 1-28 Imbalanced amplification: A mechanism of amplification and suppression from local imbalance of excitation and inhibition in cortical circuits
by Christopher Ebsch & Robert Rosenbaum - 1-29 Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules
by Albert Solernou & Benjamin S Hanson & Robin A Richardson & Robert Welch & Daniel J Read & Oliver G Harlen & Sarah A Harris - 1-34 An open source tool for automatic spatiotemporal assessment of calcium transients and local ‘signal-close-to-noise’ activity in calcium imaging data
by Juan Prada & Manju Sasi & Corinna Martin & Sibylle Jablonka & Thomas Dandekar & Robert Blum
February 2018, Volume 14, Issue 2
- 1-4 Ten simple rules for writing a popular science book
by Adam J Kucharski - 1-13 Genetic programming based models in plant tissue culture: An addendum to traditional statistical approach
by Meenu R Mridula & Ashalatha S Nair & K Satheesh Kumar - 1-15 Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub-classification
by Yishai Shimoni - 1-16 A maximum-entropy model for predicting chromatin contacts
by Pau Farré & Eldon Emberly - 1-17 Examining the controllability of sepsis using genetic algorithms on an agent-based model of systemic inflammation
by Robert Chase Cockrell & Gary An - 1-18 Integrating linear optimization with structural modeling to increase HIV neutralization breadth
by Alexander M Sevy & Swetasudha Panda & James E Crowe Jr & Jens Meiler & Yevgeniy Vorobeychik - 1-20 A model of risk and mental state shifts during social interaction
by Andreas Hula & Iris Vilares & Terry Lohrenz & Peter Dayan & P Read Montague - 1-21 Control fast or control smart: When should invading pathogens be controlled?
by Robin N Thompson & Christopher A Gilligan & Nik J Cunniffe - 1-22 A multiscale modelling approach to assess the impact of metabolic zonation and microperfusion on the hepatic carbohydrate metabolism
by Nikolaus Berndt & Marius Stefan Horger & Sascha Bulik & Hermann-Georg Holzhütter - 1-23 Prediction of infectious disease epidemics via weighted density ensembles
by Evan L Ray & Nicholas G Reich - 1-26 Interpretation of correlated neural variability from models of feed-forward and recurrent circuits
by Volker Pernice & Rava Azeredo da Silveira - 1-26 Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains
by Sneha Vishwanath & Alexandre G de Brevern & Narayanaswamy Srinivasan - 1-32 Simulation enabled search for explanatory mechanisms of the fracture healing process
by Ryan C Kennedy & Meir Marmor & Ralph Marcucio & C Anthony Hunt - 1-33 Imaging of neural oscillations with embedded inferential and group prevalence statistics
by Peter W Donhauser & Esther Florin & Sylvain Baillet - 1-34 Self-crowding of AMPA receptors in the excitatory postsynaptic density can effectuate anomalous receptor sub-diffusion
by Rahul Gupta - 1-36 Spike and burst coding in thalamocortical relay cells
by Fleur Zeldenrust & Pascal Chameau & Wytse J Wadman
January 2018, Volume 14, Issue 1
- 1-12 The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide
by Jigisha Anupama & Margherita Francescatto & Farzana Rahman & Nazeefa Fatima & Dan DeBlasio & Avinash Kumar Shanmugam & Venkata Satagopam & Alberto Santos & Pandurang Kolekar & Magali Michaut & Emre Guney - 1-14 GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies
by Runmin Wei & Jingye Wang & Erik Jia & Tianlu Chen & Yan Ni & Wei Jia - 1-18 The E2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors
by Ravi Kumar Verma & Ara M Abramyan & Mayako Michino & R Benjamin Free & David R Sibley & Jonathan A Javitch & J Robert Lane & Lei Shi - 1-18 A model for cooperative gating of L-type Ca2+ channels and its effects on cardiac alternans dynamics
by Daisuke Sato & Rose E Dixon & Luis F Santana & Manuel F Navedo - 1-20 Interactions between species introduce spurious associations in microbiome studies
by Rajita Menon & Vivek Ramanan & Kirill S Korolev - 1-20 The role of spatial heterogeneity in the evolution of local and global infections of viruses
by Koich Saeki & Akira Sasaki - 1-23 Improving pairwise comparison of protein sequences with domain co-occurrence
by Christophe Menichelli & Olivier Gascuel & Laurent Bréhélin - 1-24 A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition
by Talia Zeppelin & Lucy Kate Ladefoged & Steffen Sinning & Xavier Periole & Birgit Schiøtt - 1-26 SozRank: A new approach for localizing the epileptic seizure onset zone
by Yonathan Murin & Jeremy Kim & Josef Parvizi & Andrea Goldsmith - 1-27 Clustering gene expression time series data using an infinite Gaussian process mixture model
by Ian C McDowell & Dinesh Manandhar & Christopher M Vockley & Amy K Schmid & Timothy E Reddy & Barbara E Engelhardt - 1-28 Robust and efficient coding with grid cells
by Lajos Vágó & Balázs B Ujfalussy - 1-29 Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance
by Jacob C Kimmel & Amy Y Chang & Andrew S Brack & Wallace F Marshall - 1-32 Bayesian inference of phylogenetic networks from bi-allelic genetic markers
by Jiafan Zhu & Dingqiao Wen & Yun Yu & Heidi M Meudt & Luay Nakhleh - 1-38 What drives the perceptual change resulting from speech motor adaptation? Evaluation of hypotheses in a Bayesian modeling framework
by Jean-François Patri & Pascal Perrier & Jean-Luc Schwartz & Julien Diard - 1-44 Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
by Zixuan Cang & Lin Mu & Guo-Wei Wei
December 2017, Volume 13, Issue 12
- 1-5 Ten simple rules for international short-term research stays
by Diego A Forero & Sandra Lopez-Leon & George P Patrinos - 1-6 Ten simple rules for writing a career development award proposal
by Crystal M Botham & Joshua A Arribere & Sky W Brubaker & Kevin T Beier - 1-8 Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP
by Sanjay Sonney & Jeremy Leipzig & Marie T Lott & Shiping Zhang & Vincent Procaccio & Douglas C Wallace & Neal Sondheimer - 1-11 MAGPIE: Simplifying access and execution of computational models in the life sciences
by Christoph Baldow & Sebastian Salentin & Michael Schroeder & Ingo Roeder & Ingmar Glauche - 1-13 A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design
by Rebecca F Alford & Andrew Leaver-Fay & Lynda Gonzales & Erin L Dolan & Jeffrey J Gray - 1-16 Stabilizing patterns in time: Neural network approach
by Nadav Ben-Shushan & Misha Tsodyks - 1-20 MPLasso: Inferring microbial association networks using prior microbial knowledge
by Chieh Lo & Radu Marculescu - 1-20 High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock
by Nawsad Alam & Oriel Goldstein & Bing Xia & Kathryn A Porter & Dima Kozakov & Ora Schueler-Furman - 1-21 Complete hazard ranking to analyze right-censored data: An ALS survival study
by Zhengnan Huang & Hongjiu Zhang & Jonathan Boss & Stephen A Goutman & Bhramar Mukherjee & Ivo D Dinov & Yuanfang Guan & for the Pooled Resource Open-Access ALS Clinical Trials Consortium - 1-28 LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction
by Xing Chen & Li Huang - 1-29 Costs of task allocation with local feedback: Effects of colony size and extra workers in social insects and other multi-agent systems
by Tsvetomira Radeva & Anna Dornhaus & Nancy Lynch & Radhika Nagpal & Hsin-Hao Su - 1-31 Genetic drift and selection in many-allele range expansions
by Bryan T Weinstein & Maxim O Lavrentovich & Wolfram Möbius & Andrew W Murray & David R Nelson - 1-37 Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks
by Ye Henry Li & Dangna Li & Nikolay Samusik & Xiaowei Wang & Leying Guan & Garry P Nolan & Wing Hung Wong
November 2017, Volume 13, Issue 11
- 1-12 fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks
by Edwin van Leeuwen & Petra Klepac & Dominic Thorrington & Richard Pebody & Marc Baguelin - 1-16 Tracking urban human activity from mobile phone calling patterns
by Daniel Monsivais & Asim Ghosh & Kunal Bhattacharya & Robin I M Dunbar & Kimmo Kaski - 1-16 The use of ambient humidity conditions to improve influenza forecast
by Jeffrey Shaman & Sasikiran Kandula & Wan Yang & Alicia Karspeck - 1-17 Individual versus superensemble forecasts of seasonal influenza outbreaks in the United States
by Teresa K Yamana & Sasikiran Kandula & Jeffrey Shaman - 1-18 Are there physicochemical differences between allosteric and competitive ligands?
by Richard D Smith & Jing Lu & Heather A Carlson - 1-18 Choose, rate or squeeze: Comparison of economic value functions elicited by different behavioral tasks
by Alizée Lopez-Persem & Lionel Rigoux & Sacha Bourgeois-Gironde & Jean Daunizeau & Mathias Pessiglione - 1-19 mixOmics: An R package for ‘omics feature selection and multiple data integration
by Florian Rohart & Benoît Gautier & Amrit Singh & Kim-Anh Lê Cao - 1-19 Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems
by Anthony Szedlak & Spencer Sims & Nicholas Smith & Giovanni Paternostro & Carlo Piermarocchi - 1-20 Multivariate pattern dependence
by Stefano Anzellotti & Alfonso Caramazza & Rebecca Saxe - 1-21 A Bayesian method for detecting pairwise associations in compositional data
by Emma Schwager & Himel Mallick & Steffen Ventz & Curtis Huttenhower - 1-22 The effect of spatial randomness on the average fixation time of mutants
by Suzan Farhang-Sardroodi & Amir H Darooneh & Moladad Nikbakht & Natalia L Komarova & Mohammad Kohandel - 1-23 Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs
by Michael F Sloma & David H Mathews - 1-25 Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq
by Ruolin Liu & Julie Dickerson - 1-26 Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil
by Shaima Hashem & Matteo Tiberti & Arianna Fornili - 1-27 An efficient moments-based inference method for within-host bacterial infection dynamics
by David J Price & Alexandre Breuzé & Richard Dybowski & Piero Mastroeni & Olivier Restif - 1-29 Initial-state-dependent, robust, transient neural dynamics encode conscious visual perception
by Alexis T Baria & Brian Maniscalco & Biyu J He - 1-32 Identifying influential neighbors in animal flocking
by Li Jiang & Luca Giuggioli & Andrea Perna & Ramón Escobedo & Valentin Lecheval & Clément Sire & Zhangang Han & Guy Theraulaz - 1-33 Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays
by Gonzalo E Mena & Lauren E Grosberg & Sasidhar Madugula & Paweł Hottowy & Alan Litke & John Cunningham & E J Chichilnisky & Liam Paninski - 1-38 A hierarchical stochastic model for bistable perception
by Stefan Albert & Katharina Schmack & Philipp Sterzer & Gaby Schneider
October 2017, Volume 13, Issue 10
- 1-5 Ten simple rules in considering a career in academia versus government
by Philip E Bourne - 1-9 Network propagation in the cytoscape cyberinfrastructure
by Daniel E Carlin & Barry Demchak & Dexter Pratt & Eric Sage & Trey Ideker - 1-14 Identification of immune signatures predictive of clinical protection from malaria
by John Joseph Valletta & Mario Recker - 1-15 Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing
by Yaron Orenstein & David Pellow & Guillaume Marçais & Ron Shamir & Carl Kingsford - 1-18 Vicus: Exploiting local structures to improve network-based analysis of biological data
by Bo Wang & Lin Huang & Yuke Zhu & Anshul Kundaje & Serafim Batzoglou & Anna Goldenberg - 1-18 A mechanistic spatio-temporal framework for modelling individual-to-individual transmission—With an application to the 2014-2015 West Africa Ebola outbreak
by Max S Y Lau & Gavin J Gibson & Hola Adrakey & Amanda McClelland & Steven Riley & Jon Zelner & George Streftaris & Sebastian Funk & Jessica Metcalf & Benjamin D Dalziel & Bryan T Grenfell - 1-21 Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization
by Claire N Bedbrook & Kevin K Yang & Austin J Rice & Viviana Gradinaru & Frances H Arnold - 1-21 Modeling the adenosine system as a modulator of cognitive performance and sleep patterns during sleep restriction and recovery
by Andrew J K Phillips & Elizabeth B Klerman & James P Butler - 1-22 Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster
by Cen Wan & Jonathan G Lees & Federico Minneci & Christine A Orengo & David T Jones - 1-23 Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time
by Anna Hake & Nico Pfeifer - 1-24 A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
by Shiran Abadi & Winston X Yan & David Amar & Itay Mayrose - 1-24 Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition
by Timothy N Rubin & Oluwasanmi Koyejo & Krzysztof J Gorgolewski & Michael N Jones & Russell A Poldrack & Tal Yarkoni