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Content
June 2018, Volume 14, Issue 6
- 1-23 The role of intracellular signaling in the stripe formation in engineered Escherichia coli populations
by Xiaoru Xue & Chuan Xue & Min Tang - 1-24 Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology
by J Kyle Medley & Kiri Choi & Matthias König & Lucian Smith & Stanley Gu & Joseph Hellerstein & Stuart C Sealfon & Herbert M Sauro - 1-25 Transmission of temporally correlated spike trains through synapses with short-term depression
by Alex D Bird & Magnus J E Richardson - 1-25 Mechanical positioning of multiple nuclei in muscle cells
by Angelika Manhart & Stefanie Windner & Mary Baylies & Alex Mogilner - 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 Systems modelling of the EGFR-PYK2-c-Met interaction network predicts and prioritizes synergistic drug combinations for triple-negative breast cancer
by Sung-Young Shin & Anna-Katharina Müller & Nandini Verma & Sima Lev & Lan K Nguyen - 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 Submit a Topic Page to PLOS Computational Biology and Wikipedia
by Daniel Mietchen & Shoshana Wodak & Szymon Wasik & Natalia Szostak & Christophe Dessimoz - 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 - 1-10 Porcupine: A visual pipeline tool for neuroimaging analysis
by Tim van Mourik & Lukas Snoek & Tomas Knapen & David G Norris - 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 - 1-19 Variability in pulmonary vein electrophysiology and fibrosis determines arrhythmia susceptibility and dynamics
by Caroline H Roney & Jason D Bayer & Hubert Cochet & Marianna Meo & Rémi Dubois & Pierre Jaïs & Edward J Vigmond - 1-20 Logistical constraints lead to an intermediate optimum in outbreak response vaccination
by Yun Tao & Katriona Shea & Matthew Ferrari - 1-20 Identification of animal behavioral strategies by inverse reinforcement learning
by Shoichiro Yamaguchi & Honda Naoki & Muneki Ikeda & Yuki Tsukada & Shunji Nakano & Ikue Mori & Shin Ishii - 1-20 Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme
by Jagannath Mondal & Navjeet Ahalawat & Subhendu Pandit & Lewis E Kay & Pramodh Vallurupalli - 1-21 The complex ecosystem in non small cell lung cancer invasion
by Seth Haney & Jessica Konen & Adam I Marcus & Maxim Bazhenov - 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 - 1-25 Minimal model of interictal and ictal discharges “Epileptor-2”
by Anton V Chizhov & Artyom V Zefirov & Dmitry V Amakhin & Elena Yu Smirnova & Aleksey V Zaitsev - 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 - 1-29 Can a time varying external drive give rise to apparent criticality in neural systems?
by Viola Priesemann & Oren Shriki - 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
- 1-6 Ten simple rules for responsible referencing
by Bart Penders - 1-11 Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy
by Martin Weigert & Kaushikaram Subramanian & Sebastian T Bundschuh & Eugene W Myers & Moritz Kreysing - 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 - 1-18 Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data
by Travers Ching & Xun Zhu & Lana X Garmire - 1-22 Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly
by Juan Francisco Viso & Patricia Belelli & Matías Machado & Humberto González & Sergio Pantano & María Julia Amundarain & Fernando Zamarreño & Maria Marta Branda & Diego M A Guérin & Marcelo D Costabel - 1-23 Identifying robust hysteresis in networks
by Tomáš Gedeon & Bree Cummins & Shaun Harker & Konstantin Mischaikow - 1-23 Using pseudoalignment and base quality to accurately quantify microbial community composition
by Mark Reppell & John Novembre - 1-23 Personalizing physical exercise in a computational model of fuel homeostasis
by Maria Concetta Palumbo & Micaela Morettini & Paolo Tieri & Fasma Diele & Massimo Sacchetti & Filippo Castiglione - 1-23 Spatial regularity control of phyllotaxis pattern generated by the mutual interaction between auxin and PIN1
by Hironori Fujita & Masayoshi Kawaguchi - 1-23 Principles that govern competition or co-existence in Rho-GTPase driven polarization
by Jian-Geng Chiou & Samuel A Ramirez & Timothy C Elston & Thomas P Witelski & David G Schaeffer & Daniel J Lew - 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 - 1-25 Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level
by Małgorzata Kardyńska & Anna Paszek & Jarosław Śmieja & David Spiller & Wiesława Widłak & Michael R H White & Pawel Paszek & Marek Kimmel - 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 Rational metareasoning and the plasticity of cognitive control
by Falk Lieder & Amitai Shenhav & Sebastian Musslick & Thomas L Griffiths - 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 - 1-28 Effects of spatiotemporal HSV-2 lesion dynamics and antiviral treatment on the risk of HIV-1 acquisition
by Catherine M Byrne & Soren Gantt & Daniel Coombs - 1-31 Computational mechanisms underlying cortical responses to the affordance properties of visual scenes
by Michael F Bonner & Russell A Epstein - 1-34 Whole-body iron transport and metabolism: Mechanistic, multi-scale model to improve treatment of anemia in chronic kidney disease
by Joydeep Sarkar & Alka A Potdar & Gerald M Saidel - 1-35 Interactions of spatial strategies producing generalization gradient and blocking: A computational approach
by Laurent Dollé & Ricardo Chavarriaga & Agnès Guillot & Mehdi Khamassi - 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
- 1-1 Correction: Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue
by The PLOS Computational Biology Staff - 1-1 Correction: Correlated receptor transport processes buffer single-cell heterogeneity
by The PLOS Computational Biology Staff - 1-8 Ten simple rules for collaborative lesson development
by Gabriel A Devenyi & Rémi Emonet & Rayna M Harris & Kate L Hertweck & Damien Irving & Ian Milligan & Greg Wilson - 1-11 Eleven quick tips for architecting biomedical informatics workflows with cloud computing
by Brian S Cole & Jason H Moore - 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 - 1-17 Haptic communication between humans is tuned by the hard or soft mechanics of interaction
by Atsushi Takagi & Francesco Usai & Gowrishankar Ganesh & Vittorio Sanguineti & Etienne Burdet - 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 - 1-21 Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA
by Hidetoshi Kono & Shun Sakuraba & Hisashi Ishida - 1-23 Deploying digital health data to optimize influenza surveillance at national and local scales
by Elizabeth C Lee & Ali Arab & Sandra M Goldlust & Cécile Viboud & Bryan T Grenfell & Shweta Bansal - 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 Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation
by Michael Pablo & Samuel A Ramirez & Timothy C Elston - 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 Population dynamics of engineered underdominance and killer-rescue gene drives in the control of disease vectors
by Matthew P Edgington & Luke S Alphey - 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 - 1-6 Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation
by Vasundra Touré & Nicolas Le Novère & Dagmar Waltemath & Olaf Wolkenhauer - 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 - 1-14 The development and application of bioinformatics core competencies to improve bioinformatics training and education
by Nicola Mulder & Russell Schwartz & Michelle D Brazas & Cath Brooksbank & Bruno Gaeta & Sarah L Morgan & Mark A Pauley & Anne Rosenwald & Gabriella Rustici & Michael Sierk & Tandy Warnow & Lonnie Welch - 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 The feasibility of equilibria in large ecosystems: A primary but neglected concept in the complexity-stability debate
by Michaël Dougoud & Laura Vinckenbosch & Rudolf P Rohr & Louis-Félix Bersier & Christian Mazza - 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 - 1-19 Heritable tumor cell division rate heterogeneity induces clonal dominance
by Margriet M Palm & Marjet Elemans & Joost B Beltman - 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 - 1-20 Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network
by Dorjsuren Battogtokh & Shihoko Kojima & John J Tyson - 1-21 Trade-off between synergy and efficacy in combinations of HIV-1 latency-reversing agents
by Vipul Gupta & Narendra M Dixit - 1-21 Control fast or control smart: When should invading pathogens be controlled?
by Robin N Thompson & Christopher A Gilligan & Nik J Cunniffe - 1-21 A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination
by Caitlin Collins & Xavier Didelot - 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 - 1-25 Memory functions reveal structural properties of gene regulatory networks
by Edgar Herrera-Delgado & Ruben Perez-Carrasco & James Briscoe & Peter Sollich - 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 - 1-27 A biophysical model of dynamic balancing of excitation and inhibition in fast oscillatory large-scale networks
by Romesh G Abeysuriya & Jonathan Hadida & Stamatios N Sotiropoulos & Saad Jbabdi & Robert Becker & Benjamin A E Hunt & Matthew J Brookes & Mark W Woolrich - 1-31 PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
by Ahmadreza Ghaffarizadeh & Randy Heiland & Samuel H Friedman & Shannon M Mumenthaler & Paul Macklin - 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 - 1-15 Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations
by Jagdish Suresh Patel & Celeste J Brown & F Marty Ytreberg & Deborah L Stenkamp - 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 - 1-19 Mechanical feedback coordinates cell wall expansion and assembly in yeast mating morphogenesis
by Samhita P Banavar & Carlos Gomez & Michael Trogdon & Linda R Petzold & Tau-Mu Yi & Otger Campàs - 1-20 Interactions between species introduce spurious associations in microbiome studies
by Rajita Menon & Vivek Ramanan & Kirill S Korolev - 1-20 A dynamical systems approach for estimating phase interactions between rhythms of different frequencies from experimental data
by Takayuki Onojima & Takahiro Goto & Hiroaki Mizuhara & Toshio Aoyagi - 1-20 The role of spatial heterogeneity in the evolution of local and global infections of viruses
by Koich Saeki & Akira Sasaki - 1-21 Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission
by Wesley Wong & Edward A Wenger & Daniel L Hartl & Dyann F Wirth - 1-21 The extent of ribosome queuing in budding yeast
by Alon Diament & Anna Feldman & Elisheva Schochet & Martin Kupiec & Yoav Arava & Tamir Tuller - 1-21 Modeling visual-based pitch, lift and speed control strategies in hoverflies
by Roman Goulard & Jean-Louis Vercher & Stéphane Viollet - 1-23 Improving pairwise comparison of protein sequences with domain co-occurrence
by Christophe Menichelli & Olivier Gascuel & Laurent Bréhélin - 1-23 Sequence determinants of protein phase behavior from a coarse-grained model
by Gregory L Dignon & Wenwei Zheng & Young C Kim & Robert B Best & Jeetain Mittal - 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 A theory of how active behavior stabilises neural activity: Neural gain modulation by closed-loop environmental feedback
by Christopher L Buckley & Taro Toyoizumi - 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 - 1-29 Cardinal features of involuntary force variability can arise from the closed-loop control of viscoelastic afferented muscles
by Akira Nagamori & Christopher M Laine & Francisco J Valero-Cuevas - 1-30 A systematic atlas of chaperome deregulation topologies across the human cancer landscape
by Ali Hadizadeh Esfahani & Angelina Sverchkova & Julio Saez-Rodriguez & Andreas A Schuppert & Marc Brehme - 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
- 1-1 Correction: Signatures of criticality arise from random subsampling in simple population models
by The PLOS Computational Biology Staff - 1-3 Correction: Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions
by The PLOS Computational Biology Staff - 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 - 1-15 pSSAlib: The partial-propensity stochastic chemical network simulator
by Oleksandr Ostrenko & Pietro Incardona & Rajesh Ramaswamy & Lutz Brusch & Ivo F Sbalzarini - 1-16 Stabilizing patterns in time: Neural network approach
by Nadav Ben-Shushan & Misha Tsodyks - 1-18 Feature reliability determines specificity and transfer of perceptual learning in orientation search
by Amit Yashar & Rachel N Denison - 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 System identification of signaling dependent gene expression with different time-scale data
by Takaho Tsuchiya & Masashi Fujii & Naoki Matsuda & Katsuyuki Kunida & Shinsuke Uda & Hiroyuki Kubota & Katsumi Konishi & Shinya Kuroda - 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 - 1-32 Non-linear auto-regressive models for cross-frequency coupling in neural time series
by Tom Dupré la Tour & Lucille Tallot & Laetitia Grabot & Valérie Doyère & Virginie van Wassenhove & Yves Grenier & Alexandre Gramfort - 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 - 1-50 Physiological models of the lateral superior olive
by Go Ashida & Daniel J Tollin & Jutta Kretzberg
November 2017, Volume 13, Issue 11
- 1-1 Correction: A Unifying Probabilistic View of Associative Learning
by The PLOS Computational Biology Staff - 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 Metabolic dynamics restricted by conserved carriers: Jamming and feedback
by Tetsuhiro S Hatakeyama & Chikara Furusawa - 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 - 1-17 A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation
by Rosemary M McCloskey & Art F Y Poon - 1-18 Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation
by Alejandro F Villaverde & Julio R Banga - 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 - 1-22 A free-boundary model of a motile cell explains turning behavior
by Masoud Nickaeen & Igor L Novak & Stephanie Pulford & Aaron Rumack & Jamie Brandon & Boris M Slepchenko & Alex Mogilner - 1-23 A modeling study of budding yeast colony formation and its relationship to budding pattern and aging
by Yanli Wang & Wing-Cheong Lo & Ching-Shan Chou - 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 Competitive tuning: Competition's role in setting the frequency-dependence of Ca2+-dependent proteins
by Daniel R Romano & Matthew C Pharris & Neal M Patel & Tamara L Kinzer-Ursem - 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 - 1-30 Estimating the probabilities of rare arrhythmic events in multiscale computational models of cardiac cells and tissue
by Mark A Walker & Viatcheslav Gurev & John J Rice & Joseph L Greenstein & Raimond L Winslow - 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 - 1-40 Improving virtual screening of G protein-coupled receptors via ligand-directed modeling
by Thomas Coudrat & John Simms & Arthur Christopoulos & Denise Wootten & Patrick M Sexton - 1-50 A Rescorla-Wagner drift-diffusion model of conditioning and timing
by André Luzardo & Eduardo Alonso & Esther Mondragón
October 2017, Volume 13, Issue 10
- 1-1 Correction: Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model
by The PLOS Computational Biology Staff - 1-4 Ten simple rules for writing a response to reviewers
by William Stafford Noble - 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 - 1-11 Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience
by Kim T Gurwitz & Shaun Aron & Sumir Panji & Suresh Maslamoney & Pedro L Fernandes & David P Judge & Amel Ghouila & Jean-Baka Domelevo Entfellner & Fatma Z Guerfali & Colleen Saunders & Ahmed Mansour Alzohairy & Samson P Salifu & Rehab Ahmed & Ruben Cloete & Jonathan Kayondo & Deogratius Ssemwanga & Nicola Mulder & H3ABioNet Consortium's Education Training and Working Group as members of the H3Africa Consortium - 1-11 Learning infectious disease epidemiology in a modern framework
by Andreas Handel