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February 2019, Volume 15, Issue 2
- 1-21 Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components
by Nicholas Rogers & John Hermiz & Mehran Ganji & Erik Kaestner & Kıvılcım Kılıç & Lorraine Hossain & Martin Thunemann & Daniel R Cleary & Bob S Carter & David Barba & Anna Devor & Eric Halgren & Shadi A Dayeh & Vikash Gilja - 1-21 A local measure of symmetry and orientation for individual spikes of grid cells
by Simon N Weber & Henning Sprekeler - 1-21 A data-driven interactome of synergistic genes improves network-based cancer outcome prediction
by Amin Allahyar & Joske Ubels & Jeroen de Ridder - 1-21 Phylogenies from dynamic networks
by Cornelia Metzig & Oliver Ratmann & Daniela Bezemer & Caroline Colijn - 1-22 Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions
by Daniel Rüdiger & Sascha Young Kupke & Tanja Laske & Pawel Zmora & Udo Reichl - 1-22 Efficient neural decoding of self-location with a deep recurrent network
by Ardi Tampuu & Tambet Matiisen & H Freyja Ólafsdóttir & Caswell Barry & Raul Vicente - 1-24 Identifying individual risk rare variants using protein structure guided local tests (POINT)
by Rachel Marceau West & Wenbin Lu & Daniel M Rotroff & Melaine A Kuenemann & Sheng-Mao Chang & Michael C Wu & Michael J Wagner & John B Buse & Alison A Motsinger-Reif & Denis Fourches & Jung-Ying Tzeng - 1-24 A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks
by Koichiro Uriu & Hajime Tei - 1-25 Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling
by Nitzan Shahar & Tobias U Hauser & Michael Moutoussis & Rani Moran & Mehdi Keramati & NSPN consortium & Raymond J Dolan - 1-25 Changes in morphogen kinetics and pollen grain size are potential mechanisms of aberrant pollen aperture patterning in previously observed and novel mutants of Arabidopsis thaliana
by Shayne M Plourde & Prativa Amom & Michelle Tan & Adriana T Dawes & Anna A Dobritsa - 1-25 16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses
by Stephen Woloszynek & Zhengqiao Zhao & Jian Chen & Gail L Rosen - 1-26 Information integration in large brain networks
by Daniel Toker & Friedrich T Sommer - 1-26 ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics
by Moritz Hoffmann & Christoph Fröhner & Frank Noé - 1-27 Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos
by Julien Moukhtar & Alain Trubuil & Katia Belcram & David Legland & Zhor Khadir & Aurélie Urbain & Jean-Christophe Palauqui & Philippe Andrey - 1-28 Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis
by Hongyu Zhou & Zheng Dong & Gennady Verkhivker & Brian D Zoltowski & Peng Tao - 1-29 Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors
by Lior Tiroshi & Joshua A Goldberg - 1-32 Maps of variability in cell lineage trees
by Damien G Hicks & Terence P Speed & Mohammed Yassin & Sarah M Russell - 1-32 Learning the payoffs and costs of actions
by Moritz Möller & Rafal Bogacz - 1-36 Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion
by Nico M Franz & Lukas J Musher & Joseph W Brown & Shizhuo Yu & Bertram Ludäscher
January 2019, Volume 15, Issue 1
- 1-1 Notice of Republication: Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects
by The PLOS Computational Biology Staff - 1-4 Ten simple rules on how to create open access and reproducible molecular simulations of biological systems
by Arne Elofsson & Berk Hess & Erik Lindahl & Alexey Onufriev & David van der Spoel & Anders Wallqvist - 1-13 Context-explorer: Analysis of spatially organized protein expression in high-throughput screens
by Joel Ostblom & Emanuel J P Nazareth & Mukul Tewary & Peter W Zandstra - 1-13 Designing and running an advanced Bioinformatics and genome analyses course in Tunisia
by Fatma Z Guerfali & Dhafer Laouini & Abdellatif Boudabous & Fredj Tekaia - 1-15 Prediction of ultra-high-order antibiotic combinations based on pairwise interactions
by Itay Katzir & Murat Cokol & Bree B Aldridge & Uri Alon - 1-17 Protein—protein binding supersites
by Raji Viswanathan & Eduardo Fajardo & Gabriel Steinberg & Matthew Haller & Andras Fiser - 1-18 On identifying collective displacements in apo-proteins that reveal eventual binding pathways
by Dheeraj Dube & Navjeet Ahalawat & Himanshu Khandelia & Jagannath Mondal & Surajit Sengupta - 1-18 OpenCASA: A new open-source and scalable tool for sperm quality analysis
by Carlos Alquézar-Baeta & Silvia Gimeno-Martos & Sara Miguel-Jiménez & Pilar Santolaria & Jesús Yániz & Inmaculada Palacín & Adriana Casao & José Álvaro Cebrián-Pérez & Teresa Muiño-Blanco & Rosaura Pérez-Pé - 1-19 Calcium phosphate precipitation inhibits mitochondrial energy metabolism
by Sathyavani Malyala & Yizhu Zhang & Jasiel O Strubbe & Jason N Bazil - 1-19 Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis
by Xiaohu Hu & Yibo Wang & Amanda Hunkele & Davide Provasi & Gavril W Pasternak & Marta Filizola - 1-19 Computational translation of genomic responses from experimental model systems to humans
by Douglas K Brubaker & Elizabeth A Proctor & Kevin M Haigis & Douglas A Lauffenburger - 1-20 Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization
by Timothy D Majarian & Robert F Murphy & Seema S Lakdawala - 1-20 A low-threshold potassium current enhances sparseness and reliability in a model of avian auditory cortex
by Margot C Bjoring & C Daniel Meliza - 1-21 Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures
by Jordan J Clark & Mark L Benson & Richard D Smith & Heather A Carlson - 1-23 The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments
by Zachary R Fox & Brian Munsky - 1-23 STRFs in primary auditory cortex emerge from masking-based statistics of natural sounds
by Abdul-Saboor Sheikh & Nicol S Harper & Jakob Drefs & Yosef Singer & Zhenwen Dai & Richard E Turner & Jörg Lücke - 1-23 Deep image reconstruction from human brain activity
by Guohua Shen & Tomoyasu Horikawa & Kei Majima & Yukiyasu Kamitani - 1-24 Locus Coeruleus tracking of prediction errors optimises cognitive flexibility: An Active Inference model
by Anna C Sales & Karl J Friston & Matthew W Jones & Anthony E Pickering & Rosalyn J Moran - 1-24 Sour grapes and sweet victories: How actions shape preferences
by Fabien Vinckier & Lionel Rigoux & Irma T Kurniawan & Chen Hu & Sacha Bourgeois-Gironde & Jean Daunizeau & Mathias Pessiglione - 1-26 Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli
by David Hodgson & Andrew D Rowan & Francesco Falciani & Carole J Proctor - 1-26 PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data
by Yu-Han H Hsu & Claire Churchhouse & Tune H Pers & Josep M Mercader & Andres Metspalu & Krista Fischer & Kristen Fortney & Eric K Morgen & Clicerio Gonzalez & Maria E Gonzalez & Tonu Esko & Joel N Hirschhorn - 1-29 Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor
by Keesha E Erickson & Oleksii S Rukhlenko & Md Shahinuzzaman & Kalina P Slavkova & Yen Ting Lin & Ryan Suderman & Edward C Stites & Marian Anghel & Richard G Posner & Dipak Barua & Boris N Kholodenko & William S Hlavacek - 1-31 Predicting change: Approximate inference under explicit representation of temporal structure in changing environments
by Dimitrije Marković & Andrea M F Reiter & Stefan J Kiebel - 1-42 Spatial synchronization codes from coupled rate-phase neurons
by Joseph D Monaco & Rose M De Guzman & Hugh T Blair & Kechen Zhang
April 2019, Volume 14, Issue 4
- 1-12 CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer
by Thomas D Sherman & Luciane T Kagohara & Raymon Cao & Raymond Cheng & Matthew Satriano & Michael Considine & Gabriel Krigsfeld & Ruchira Ranaweera & Yong Tang & Sandra A Jablonski & Genevieve Stein-O'Brien & Daria A Gaykalova & Louis M Weiner & Christine H Chung & Elana J Fertig
December 2018, Volume 14, Issue 12
- 1-4 One thousand simple rules
by Philip E Bourne & Fran Lewitter & Scott Markel & Jason A Papin - 1-6 Ten simple rules for documenting scientific software
by Benjamin D Lee - 1-7 Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy
by Wang Xi & Michael A Beer - 1-15 TAMMiCol: Tool for analysis of the morphology of microbial colonies
by Hayden Tronnolone & Jennifer M Gardner & Joanna F Sundstrom & Vladimir Jiranek & Stephen G Oliver & Benjamin J Binder - 1-15 Conventional analysis of trial-by-trial adaptation is biased: Empirical and theoretical support using a Bayesian estimator
by Daniel Blustein & Ahmed Shehata & Kevin Englehart & Jonathon Sensinger - 1-17 Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data
by Danesh Moradigaravand & Martin Palm & Anne Farewell & Ville Mustonen & Jonas Warringer & Leopold Parts - 1-17 Identifying (un)controllable dynamical behavior in complex networks
by Jordan C Rozum & Réka Albert - 1-18 Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours
by John M Jumper & Nabil F Faruk & Karl F Freed & Tobin R Sosnick - 1-18 Hosts mobility and spatial spread of Rickettsia rickettsii
by Gina Polo & Carlos Mera Acosta & Marcelo B Labruna & Fernando Ferreira & Dirk Brockmann - 1-19 Movement and conformity interact to establish local behavioural traditions in animal populations
by Marius Somveille & Josh A Firth & Lucy M Aplin & Damien R Farine & Ben C Sheldon & Robin N Thompson - 1-20 Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading
by Kellen Chen & Xiao Hu & Silvia S Blemker & Jeffrey W Holmes - 1-20 On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model
by Brian C Lee & Daniel J Tward & Partha P Mitra & Michael I Miller - 1-21 Coherency of circadian rhythms in the SCN is governed by the interplay of two coupling factors
by Isao T Tokuda & Daisuke Ono & Sato Honma & Ken-Ichi Honma & Hanspeter Herzel - 1-21 SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions
by Wen Zhang & Xiang Yue & Guifeng Tang & Wenjian Wu & Feng Huang & Xining Zhang - 1-22 A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies
by Anne Cori & Pierre Nouvellet & Tini Garske & Hervé Bourhy & Emmanuel Nakouné & Thibaut Jombart - 1-22 A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins
by Luhao Zhang & Maodong Li & Zhirong Liu - 1-22 Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates
by Ashish B. George & Kirill S Korolev - 1-23 Bayesian adaptive dual control of deep brain stimulation in a computational model of Parkinson’s disease
by Logan L Grado & Matthew D Johnson & Theoden I Netoff - 1-25 Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics
by John M Jumper & Nabil F Faruk & Karl F Freed & Tobin R Sosnick - 1-25 Regulation of harvester ant foraging as a closed-loop excitable system
by Renato Pagliara & Deborah M Gordon & Naomi Ehrich Leonard - 1-27 Bayesian inference of protein conformational ensembles from limited structural data
by Wojciech Potrzebowski & Jill Trewhella & Ingemar Andre - 1-27 PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development
by Jennifer L Wilson & Rebecca Racz & Tianyun Liu & Oluseyi Adeniyi & Jielin Sun & Anuradha Ramamoorthy & Michael Pacanowski & Russ Altman - 1-27 Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study
by Anna Bochicchio & Miroslav Krepl & Fan Yang & Gabriele Varani & Jiri Sponer & Paolo Carloni - 1-27 Coherent chaos in a recurrent neural network with structured connectivity
by Itamar Daniel Landau & Haim Sompolinsky - 1-28 A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome
by Jia Lu & Xiaoyi Cao & Sheng Zhong - 1-29 Detection and analysis of spatiotemporal patterns in brain activity
by Rory G Townsend & Pulin Gong - 1-35 Exploring chromatin hierarchical organization via Markov State Modelling
by Zhen Wah Tan & Enrico Guarnera & Igor N Berezovsky - 1-42 The empirical characteristics of human pattern vision defy theoretically-driven expectations
by Peter Neri
November 2018, Volume 14, Issue 11
- 1-3 Putting benchmarks in their rightful place: The heart of computational biology
by Bjoern Peters & Steven E Brenner & Edwin Wang & Donna Slonim & Maricel G Kann - 1-8 Ten simple rules for collaboratively writing a multi-authored paper
by Marieke A Frassl & David P Hamilton & Blaize A Denfeld & Elvira de Eyto & Stephanie E Hampton & Philipp S Keller & Sapna Sharma & Abigail S L Lewis & Gesa A Weyhenmeyer & Catherine M O’Reilly & Mary E Lofton & Núria Catalán - 1-11 Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks
by Ryan R Wick & Louise M Judd & Kathryn E Holt - 1-14 Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers
by Andrej Berg & Oleksandra Kukharenko & Martin Scheffner & Christine Peter - 1-15 Bayesian phylodynamic inference with complex models
by Erik M Volz & Igor Siveroni - 1-16 A computational analysis of dynamic, multi-organ inflammatory crosstalk induced by endotoxin in mice
by Ruben Zamora & Sebastian Korff & Qi Mi & Derek Barclay & Lukas Schimunek & Riccardo Zucca & Xerxes D Arsiwalla & Richard L Simmons & Paul Verschure & Timothy R Billiar & Yoram Vodovotz - 1-17 Moth olfactory receptor neurons adjust their encoding efficiency to temporal statistics of pheromone fluctuations
by Marie Levakova & Lubomir Kostal & Christelle Monsempès & Vincent Jacob & Philippe Lucas - 1-18 RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks
by Jun Li & Wei Zhu & Jun Wang & Wenfei Li & Sheng Gong & Jian Zhang & Wei Wang - 1-18 powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire
by Hillary Koch & Dmytro Starenki & Sara J Cooper & Richard M Myers & Qunhua Li - 1-19 Deterministic response strategies in a trial-and-error learning task
by Holger Mohr & Katharina Zwosta & Dimitrije Markovic & Sebastian Bitzer & Uta Wolfensteller & Hannes Ruge - 1-19 Comparative structural dynamic analysis of GTPases
by Hongyang Li & Xin-Qiu Yao & Barry J Grant - 1-21 Prediction and classification in equation-free collective motion dynamics
by Keisuke Fujii & Takeshi Kawasaki & Yuki Inaba & Yoshinobu Kawahara - 1-21 Efficient pedigree recording for fast population genetics simulation
by Jerome Kelleher & Kevin R Thornton & Jaime Ashander & Peter L Ralph - 1-21 Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter
by Yarden Golan & Raphael Alhadeff & Fabian Glaser & Assaf Ganoth & Arieh Warshel & Yehuda G Assaraf - 1-22 A regularity index for dendrites - local statistics of a neuron's input space
by Laura Anton-Sanchez & Felix Effenberger & Concha Bielza & Pedro Larrañaga & Hermann Cuntz - 1-23 Binding of the general anesthetic sevoflurane to ion channels
by Letícia Stock & Juliana Hosoume & Leonardo Cirqueira & Werner Treptow - 1-24 Determinants of early afterdepolarization properties in ventricular myocyte models
by Xiaodong Huang & Zhen Song & Zhilin Qu - 1-24 Inferring interaction partners from protein sequences using mutual information
by Anne-Florence Bitbol - 1-25 Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction
by Susann Vorberg & Stefan Seemayer & Johannes Söding - 1-27 Mechanistic insight into spontaneous transition from cellular alternans to arrhythmia—A simulation study
by Wei Wang & Shanzhuo Zhang & Haibo Ni & Clifford J Garratt & Mark R Boyett & Jules C Hancox & Henggui Zhang - 1-28 Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes
by Weilong Zhao & Xinwei Sher - 1-29 A Bayesian mixture modelling approach for spatial proteomics
by Oliver M Crook & Claire M Mulvey & Paul D W Kirk & Kathryn S Lilley & Laurent Gatto - 1-30 Rosetta FunFolDes – A general framework for the computational design of functional proteins
by Jaume Bonet & Sarah Wehrle & Karen Schriever & Che Yang & Anne Billet & Fabian Sesterhenn & Andreas Scheck & Freyr Sverrisson & Barbora Veselkova & Sabrina Vollers & Roxanne Lourman & Mélanie Villard & Stéphane Rosset & Thomas Krey & Bruno E Correia - 1-31 Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch
by Lina Meinecke & Praveer P Sharma & Huijing Du & Lei Zhang & Qing Nie & Thomas F Schilling - 1-33 Modulation of voltage-dependent K+ conductances in photoreceptors trades off investment in contrast gain for bandwidth
by Francisco J H Heras & Mikko Vähäsöyrinki & Jeremy E Niven - 1-34 Comparing Bayesian and non-Bayesian accounts of human confidence reports
by William T Adler & Wei Ji Ma - 1-47 Visual physiology of the layer 4 cortical circuit in silico
by Anton Arkhipov & Nathan W Gouwens & Yazan N Billeh & Sergey Gratiy & Ramakrishnan Iyer & Ziqiang Wei & Zihao Xu & Reza Abbasi-Asl & Jim Berg & Michael Buice & Nicholas Cain & Nuno da Costa & Saskia de Vries & Daniel Denman & Severine Durand & David Feng & Tim Jarsky & Jérôme Lecoq & Brian Lee & Lu Li & Stefan Mihalas & Gabriel K Ocker & Shawn R Olsen & R Clay Reid & Gilberto Soler-Llavina & Staci A Sorensen & Quanxin Wang & Jack Waters & Massimo Scanziani & Christof Koch
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 - 1-6 Ten simple rules for scientists: Improving your writing productivity
by Todd C Peterson & Sofie R Kleppner & Crystal M Botham - 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 - 1-13 Self-organized traffic via priority rules in leaf-cutting ants
by Daniel Strömbom & Audrey Dussutour - 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 - 1-16 Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine
by Francisco Y Cai & Thomas Fussell & Sarah Cobey & Marc Lipsitch - 1-17 RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
by Hao Wang & Simonas Marcišauskas & Benjamín J Sánchez & Iván Domenzain & Daniel Hermansson & Rasmus Agren & Jens Nielsen & Eduard J Kerkhoven - 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 Modeling and subtleties of K-Ras and Calmodulin interaction
by Eduardo Garrido & Juan Lázaro & Montserrat Jaumot & Neus Agell & Jaime Rubio-Martinez - 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 - 1-42 Linking signal detection theory and encoding models to reveal independent neural representations from neuroimaging data
by Fabian A Soto & Lauren E Vucovich & F Gregory Ashby
September 2018, Volume 14, Issue 9
- 1-1 Correction: A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling
by Vijay Vedula & Juhyun Lee & Hao Xu & C-C Jay Kuo & Tzung K Hsiai & Alison L Marsden - 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 - 1-21 Quantitative single cell analysis uncovers the life/death decision in CD95 network
by Jörn H Buchbinder & Dennis Pischel & Kai Sundmacher & Robert J Flassig & Inna N Lavrik - 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 - 1-27 Comparison of fluctuations in global network topology of modeled and empirical brain functional connectivity
by Makoto Fukushima & Olaf Sporns - 1-28 Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network
by Yafei Lyu & Lingzhou Xue & Feipeng Zhang & Hillary Koch & Laura Saba & Katerina Kechris & Qunhua Li - 1-28 A Markov chain for numerical chromosomal instability in clonally expanding populations
by Sergi Elizalde & Ashley M Laughney & Samuel F Bakhoum - 1-28 Model-based spatial navigation in the hippocampus-ventral striatum circuit: A computational analysis
by Ivilin Peev Stoianov & Cyriel M A Pennartz & Carien S Lansink & Giovani Pezzulo - 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 - 1-32 Selective ion permeation involves complexation with carboxylates and lysine in a model human sodium channel
by Emelie Flood & Céline Boiteux & Toby W Allen - 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 - 1-18 Lineage space and the propensity of bacterial cells to undergo growth transitions
by Arnab Bandyopadhyay & Huijing Wang & J Christian J Ray - 1-19 Exploring of the feature space of de novo developed post-transcriptional riboregulators
by Gert Peters & Jo Maertens & Jeroen Lammertyn & Marjan De Mey - 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 - 1-21 Characterising seasonal influenza epidemiology using primary care surveillance data
by Robert C Cope & Joshua V Ross & Monique Chilver & Nigel P Stocks & Lewis Mitchell - 1-22 A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data
by Tianwei Yu - 1-23 A simple computer vision pipeline reveals the effects of isolation on social interaction dynamics in Drosophila
by Guangda Liu & Tanmay Nath & Gerit A Linneweber & Annelies Claeys & Zhengyu Guo & Jin Li & Mercedes Bengochea & Steve De Backer & Barbara Weyn & Manu Sneyders & Hans Nicasy & Peng Yu & Paul Scheunders & Bassem A Hassan - 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 - 1-26 Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models
by Bernard Cazelles & Clara Champagne & Joseph Dureau - 1-28 Regulation of Pom cluster dynamics in Myxococcus xanthus
by Silke Bergeler & Erwin Frey - 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 - 1-32 Dorsal anterior cingulate-brainstem ensemble as a reinforcement meta-learner
by Massimo Silvetti & Eliana Vassena & Elger Abrahamse & Tom Verguts - 1-37 NFTsim: Theory and Simulation of Multiscale Neural Field Dynamics
by Paula Sanz-Leon & Peter A Robinson & Stuart A Knock & Peter M Drysdale & Romesh G Abeysuriya & Felix K Fung & Chris J Rennie & Xuelong Zhao - 1-37 Irrelevance by inhibition: Learning, computation, and implications for schizophrenia
by Nathan Insel & Jordan Guerguiev & Blake A Richards
July 2018, Volume 14, Issue 7
- 1-1 Correction: A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens
by The PLOS Computational Biology Staff - 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 - 1-18 A minimally invasive neurostimulation method for controlling abnormal synchronisation in the neuronal activity
by Malbor Asllani & Paul Expert & Timoteo Carletti - 1-18 Real-time decision-making during emergency disease outbreaks
by William J M Probert & Chris P Jewell & Marleen Werkman & Christopher J Fonnesbeck & Yoshitaka Goto & Michael C Runge & Satoshi Sekiguchi & Katriona Shea & Matt J Keeling & Matthew J Ferrari & Michael J Tildesley - 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 - 1-20 OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement
by Ajay Seth & Jennifer L Hicks & Thomas K Uchida & Ayman Habib & Christopher L Dembia & James J Dunne & Carmichael F Ong & Matthew S DeMers & Apoorva Rajagopal & Matthew Millard & Samuel R Hamner & Edith M Arnold & Jennifer R Yong & Shrinidhi K Lakshmikanth & Michael A Sherman & Joy P Ku & Scott L Delp - 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 - 1-30 Excitable neuronal assemblies with adaptation as a building block of brain circuits for velocity-controlled signal propagation
by Hesam Setareh & Moritz Deger & Wulfram Gerstner - 1-30 Phase-lags in large scale brain synchronization: Methodological considerations and in-silico analysis
by Spase Petkoski & J Matias Palva & Viktor K Jirsa - 1-31 Inter-trial effects in visual pop-out search: Factorial comparison of Bayesian updating models
by Fredrik Allenmark & Hermann J Müller & Zhuanghua Shi - 1-32 miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts
by Albert Pla & Xiangfu Zhong & Simon Rayner - 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
- 1-3 2018 ISCB Innovator Award recognizes M. Madan Babu
by Christiana N Fogg & Diane E Kovats & Ron Shamir - 1-9 Correction: A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems
by Robert C Wilson & Matthew R Nassar & Gaia Tavoni & Joshua I Gold - 1-13 Assessment of ab initio models of protein complexes by molecular dynamics
by Filip Radom & Andreas Plückthun & Emanuele Paci - 1-14 Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
by Luke Zappia & Belinda Phipson & Alicia Oshlack - 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 - 1-16 Temporal precision of regulated gene expression
by Shivam Gupta & Julien Varennes & Hendrik C Korswagen & Andrew Mugler - 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 - 1-22 The effect of cell geometry on polarization in budding yeast
by Michael Trogdon & Brian Drawert & Carlos Gomez & Samhita P Banavar & Tau-Mu Yi & Otger Campàs & Linda R Petzold