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Content
July 2018, Volume 14, Issue 7
- 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 - 1-25 Learning causal networks with latent variables from multivariate information in genomic data
by Louis Verny & Nadir Sella & Séverine Affeldt & Param Priya Singh & Hervé Isambert - 1-25 Point process analysis of noise in early invertebrate vision
by Kris V Parag & Glenn Vinnicombe - 1-25 A Bayesian approach to modelling heterogeneous calcium responses in cell populations
by Agne Tilūnaitė & Wayne Croft & Noah Russell & Tomas C Bellamy & Rüdiger Thul - 1-27 Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics
by Roman Shevchuk & Jochen S Hub - 1-27 A deep convolutional neural network for classification of red blood cells in sickle cell anemia
by Mengjia Xu & Dimitrios P Papageorgiou & Sabia Z Abidi & Ming Dao & Hong Zhao & George Em Karniadakis - 1-28 A unifying Bayesian account of contextual effects in value-based choice
by Francesco Rigoli & Christoph Mathys & Karl J Friston & Raymond J Dolan - 1-28 Object detection through search with a foveated visual system
by Emre Akbas & Miguel P Eckstein - 1-29 Clusternomics: Integrative context-dependent clustering for heterogeneous datasets
by Evelina Gabasova & John Reid & Lorenz Wernisch - 1-30 Neural field model to reconcile structure with function in primary visual cortex
by James Rankin & Frédéric Chavane - 1-31 The structured ‘low temperature’ phase of the retinal population code
by Mark L Ioffe & Michael J Berry II - 1-31 The evolutionary origins of Lévy walk foraging
by Marina E Wosniack & Marcos C Santos & Ernesto P Raposo & Gandhi M Viswanathan & Marcos G E da Luz - 1-31 Inferring oscillatory modulation in neural spike trains
by Kensuke Arai & Robert E Kass - 1-32 Distinct prediction errors in mesostriatal circuits of the human brain mediate learning about the values of both states and actions: evidence from high-resolution fMRI
by Jaron T Colas & Wolfgang M Pauli & Tobias Larsen & J Michael Tyszka & John P O’Doherty - 1-33 A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data
by Nan Lin & Yun Zhu & Ruzong Fan & Momiao Xiong - 1-37 A theoretical framework for analyzing coupled neuronal networks: Application to the olfactory system
by Andrea K Barreiro & Shree Hari Gautam & Woodrow L Shew & Cheng Ly - 1-41 A single-cell spiking model for the origin of grid-cell patterns
by Tiziano D’Albis & Richard Kempter - 1-44 Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models
by Vahid Rostami & PierGianLuca Porta Mana & Sonja Grün & Moritz Helias
September 2017, Volume 13, Issue 9
- 1-3 How can computation advance microbiome research?
by Ruth Nussinov & Jason A Papin - 1-4 Ten simple rules for developing a mentor–mentee expectations document
by Kristyn S Masters & Pamela K Kreeger - 1-8 Ten simple rules for successfully completing a graduate degree in Latin America
by Ernesto Ruelas Inzunza & Gabriela I Salazar-Rivera & Magdiel Láinez & María Guadalupe Ruiz-Gómez & Carlo A Domínguez-Eusebio & Griselda Cristóbal-Sánchez & Issaac A Teodosio Faustino & Edel Pérez-López & Meagan L Campbell & Marcus Vinicius Merfa & Ivonne Tatiana Latorre Beltrán & Fernanda Armas & Claudio Mota-Vargas - 1-9 Ten simple rules for structuring papers
by Brett Mensh & Konrad Kording - 1-13 Reconstructing promoter activity from Lux bioluminescent reporters
by Mudassar Iqbal & Neil Doherty & Anna M L Page & Saara N A Qazi & Ishan Ajmera & Peter A Lund & Theodore Kypraios & David J Scott & Philip J Hill & Dov J Stekel - 1-15 Flexibility to contingency changes distinguishes habitual and goal-directed strategies in humans
by Julie J Lee & Mehdi Keramati - 1-17 DeepPep: Deep proteome inference from peptide profiles
by Minseung Kim & Ameen Eetemadi & Ilias Tagkopoulos - 1-17 Exploiting ecology in drug pulse sequences in favour of population reduction
by Marianne Bauer & Isabella R Graf & Vudtiwat Ngampruetikorn & Greg J Stephens & Erwin Frey - 1-18 Cost-efficient vaccination protocols for network epidemiology
by Petter Holme & Nelly Litvak - 1-20 Stochastic principles governing alternative splicing of RNA
by Jianfei Hu & Eli Boritz & William Wylie & Daniel C Douek - 1-20 C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis
by Kaido Lepik & Tarmo Annilo & Viktorija Kukuškina & eQTLGen Consortium & Kai Kisand & Zoltán Kutalik & Pärt Peterson & Hedi Peterson - 1-22 Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies
by Burcu Tepekule & Hildegard Uecker & Isabel Derungs & Antoine Frenoy & Sebastian Bonhoeffer - 1-25 Relating dynamic brain states to dynamic machine states: Human and machine solutions to the speech recognition problem
by Cai Wingfield & Li Su & Xunying Liu & Chao Zhang & Phil Woodland & Andrew Thwaites & Elisabeth Fonteneau & William D Marslen-Wilson - 1-26 Probabilistic models for neural populations that naturally capture global coupling and criticality
by Jan Humplik & Gašper Tkačik - 1-29 A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms
by Pietro Balbi & Paolo Massobrio & Jeanette Hellgren Kotaleski - 1-35 Predictive representations can link model-based reinforcement learning to model-free mechanisms
by Evan M Russek & Ida Momennejad & Matthew M Botvinick & Samuel J Gershman & Nathaniel D Daw - 1-37 Features of spatial and functional segregation and integration of the primate connectome revealed by trade-off between wiring cost and efficiency
by Yuhan Chen & Shengjun Wang & Claus C Hilgetag & Changsong Zhou
August 2017, Volume 13, Issue 8
- 1-7 Ten simple rules for getting the most out of a summer laboratory internship
by Toby P Aicher & Dániel L Barabási & Benjamin D Harris & Ajay Nadig & Kaitlin L Williams - 1-7 Ten simple rules to initiate and run a postdoctoral association
by Chiara Bruckmann & Endre Sebestyén - 1-17 Mouth-clicks used by blind expert human echolocators – signal description and model based signal synthesis
by Lore Thaler & Galen M Reich & Xinyu Zhang & Dinghe Wang & Graeme E Smith & Zeng Tao & Raja Syamsul Azmir Bin Raja Abdullah & Mikhail Cherniakov & Christopher J Baker & Daniel Kish & Michail Antoniou - 1-18 Neuron’s eye view: Inferring features of complex stimuli from neural responses
by Xin Chen & Jeffrey M Beck & John M Pearson - 1-19 Robust averaging protects decisions from noise in neural computations
by Vickie Li & Santiago Herce Castañón & Joshua A Solomon & Hildward Vandormael & Christopher Summerfield - 1-19 Host population structure impedes reversion to drug sensitivity after discontinuation of treatment
by Jonas I Liechti & Gabriel E Leventhal & Sebastian Bonhoeffer - 1-21 Rearrangement moves on rooted phylogenetic networks
by Philippe Gambette & Leo van Iersel & Mark Jones & Manuel Lafond & Fabio Pardi & Celine Scornavacca - 1-22 Confirmation bias in human reinforcement learning: Evidence from counterfactual feedback processing
by Stefano Palminteri & Germain Lefebvre & Emma J Kilford & Sarah-Jayne Blakemore - 1-22 Polymodal allosteric regulation of Type 1 Serine/Threonine Kinase Receptors via a conserved electrostatic lock
by Wesley M Botello-Smith & Abdelaziz Alsamarah & Payal Chatterjee & Chen Xie & Jerome J Lacroix & Jijun Hao & Yun Luo - 1-22 Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate
by David Amar & Ron Shamir & Daniel Yekutieli - 1-23 Noise correlations in the human brain and their impact on pattern classification
by Vikranth R Bejjanki & Rava Azeredo da Silveira & Jonathan D Cohen & Nicholas B Turk-Browne - 1-24 Multi-scale approaches for high-speed imaging and analysis of large neural populations
by Johannes Friedrich & Weijian Yang & Daniel Soudry & Yu Mu & Misha B Ahrens & Rafael Yuste & Darcy S Peterka & Liam Paninski - 1-25 Stabilization of diastolic calcium signal via calcium pump regulation of complex local calcium releases and transient decay in a computational model of cardiac pacemaker cell with individual release channels
by Alexander V Maltsev & Victor A Maltsev & Michael D Stern - 1-26 Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data
by Lingfei Wang & Tom Michoel - 1-28 Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors
by Anna Cichonska & Balaguru Ravikumar & Elina Parri & Sanna Timonen & Tapio Pahikkala & Antti Airola & Krister Wennerberg & Juho Rousu & Tero Aittokallio - 1-34 A stochastic-field description of finite-size spiking neural networks
by Grégory Dumont & Alexandre Payeur & André Longtin - 1-34 A computational model of spatio-temporal cardiac intracellular calcium handling with realistic structure and spatial flux distribution from sarcoplasmic reticulum and t-tubule reconstructions
by Michael A Colman & Christian Pinali & Andrew W Trafford & Henggui Zhang & Ashraf Kitmitto - 1-36 The Stochastic Early Reaction, Inhibition, and late Action (SERIA) model for antisaccades
by Eduardo A Aponte & Dario Schöbi & Klaas E Stephan & Jakob Heinzle
July 2017, Volume 13, Issue 7
- 1-7 PCSF: An R-package for network-based interpretation of high-throughput data
by Murodzhon Akhmedov & Amanda Kedaigle & Renan Escalante Chong & Roberto Montemanni & Francesco Bertoni & Ernest Fraenkel & Ivo Kwee - 1-14 Combination therapeutics of Nilotinib and radiation in acute lymphoblastic leukemia as an effective method against drug-resistance
by Kamran Kaveh & Yutaka Takahashi & Michael A Farrar & Guy Storme & Marcucci Guido & Jamie Piepenburg & Jackson Penning & Jasmine Foo & Kevin Z Leder & Susanta K Hui - 1-15 Speciation trajectories in recombining bacterial species
by Pekka Marttinen & William P Hanage - 1-15 Inherent limitations of probabilistic models for protein-DNA binding specificity
by Shuxiang Ruan & Gary D Stormo - 1-16 mRNA/protein sequence complementarity and its determinants: The impact of affinity scales
by Lukas Bartonek & Bojan Zagrovic - 1-17 OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
by Peter Eastman & Jason Swails & John D Chodera & Robert T McGibbon & Yutong Zhao & Kyle A Beauchamp & Lee-Ping Wang & Andrew C Simmonett & Matthew P Harrigan & Chaya D Stern & Rafal P Wiewiora & Bernard R Brooks & Vijay S Pande - 1-18 Effect of depth information on multiple-object tracking in three dimensions: A probabilistic perspective
by James R H Cooke & Arjan C ter Horst & Robert J van Beers & W Pieter Medendorp