PLOS Computational Biology

2005 - 2022

From Public Library of Science
Bibliographic data for series maintained by ploscompbiol ().

Access Statistics for this journal.
Is something missing from the series or not right? See the RePEc data check for the archive and series.

Volume 14, issue 12, 2018

Regulation of harvester ant foraging as a closed-loop excitable system pp. 1-25

Renato Pagliara, Deborah M Gordon and Naomi Ehrich Leonard

Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics pp. 1-25

John M Jumper, Nabil F Faruk, Karl F Freed and Tobin R Sosnick

On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model pp. 1-20

Brian C Lee, Daniel J Tward, Partha P Mitra and Michael I Miller

Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading pp. 1-20

Kellen Chen, Xiao Hu, Silvia S Blemker and Jeffrey W Holmes

Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data pp. 1-17

Danesh Moradigaravand, Martin Palm, Anne Farewell, Ville Mustonen, Jonas Warringer and Leopold Parts

Identifying (un)controllable dynamical behavior in complex networks pp. 1-17

Jordan C Rozum and Réka Albert

Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy pp. 1-7

Wang Xi and Michael A Beer

A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome pp. 1-28

Jia Lu, Xiaoyi Cao and Sheng Zhong

Movement and conformity interact to establish local behavioural traditions in animal populations pp. 1-19

Marius Somveille, Josh A Firth, Lucy M Aplin, Damien R Farine, Ben C Sheldon and Robin N Thompson

Exploring chromatin hierarchical organization via Markov State Modelling pp. 1-35

Zhen Wah Tan, Enrico Guarnera and Igor N Berezovsky

Coherent chaos in a recurrent neural network with structured connectivity pp. 1-27

Itamar Daniel Landau and Haim Sompolinsky

PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development pp. 1-27

Jennifer L Wilson, Rebecca Racz, Tianyun Liu, Oluseyi Adeniyi, Jielin Sun, Anuradha Ramamoorthy, Michael Pacanowski and Russ Altman

Bayesian inference of protein conformational ensembles from limited structural data pp. 1-27

Wojciech Potrzebowski, Jill Trewhella and Ingemar Andre

Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study pp. 1-27

Anna Bochicchio, Miroslav Krepl, Fan Yang, Gabriele Varani, Jiri Sponer and Paolo Carloni

Bayesian adaptive dual control of deep brain stimulation in a computational model of Parkinson’s disease pp. 1-23

Logan L Grado, Matthew D Johnson and Theoden I Netoff

Coherency of circadian rhythms in the SCN is governed by the interplay of two coupling factors pp. 1-21

Isao T Tokuda, Daisuke Ono, Sato Honma, Ken-Ichi Honma and Hanspeter Herzel

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions pp. 1-21

Wen Zhang, Xiang Yue, Guifeng Tang, Wenjian Wu, Feng Huang and Xining Zhang

One thousand simple rules pp. 1-4

Philip E Bourne, Fran Lewitter, Scott Markel and Jason A Papin

Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours pp. 1-18

John M Jumper, Nabil F Faruk, Karl F Freed and Tobin R Sosnick

Hosts mobility and spatial spread of Rickettsia rickettsii pp. 1-18

Gina Polo, Carlos Mera Acosta, Marcelo B Labruna, Fernando Ferreira and Dirk Brockmann

Detection and analysis of spatiotemporal patterns in brain activity pp. 1-29

Rory G Townsend and Pulin Gong

The empirical characteristics of human pattern vision defy theoretically-driven expectations pp. 1-42

Peter Neri

Conventional analysis of trial-by-trial adaptation is biased: Empirical and theoretical support using a Bayesian estimator pp. 1-15

Daniel Blustein, Ahmed Shehata, Kevin Englehart and Jonathon Sensinger

TAMMiCol: Tool for analysis of the morphology of microbial colonies pp. 1-15

Hayden Tronnolone, Jennifer M Gardner, Joanna F Sundstrom, Vladimir Jiranek, Stephen G Oliver and Benjamin J Binder

Ten simple rules for documenting scientific software pp. 1-6

Benjamin D Lee

A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins pp. 1-22

Luhao Zhang, Maodong Li and Zhirong Liu

A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies pp. 1-22

Anne Cori, Pierre Nouvellet, Tini Garske, Hervé Bourhy, Emmanuel Nakouné and Thibaut Jombart

Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates pp. 1-22

Ashish B. George and Kirill S Korolev

Volume 14, issue 11, 2018

Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction pp. 1-25

Susann Vorberg, Stefan Seemayer and Johannes Söding

Ten simple rules for collaboratively writing a multi-authored paper pp. 1-8

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 and Núria Catalán

Moth olfactory receptor neurons adjust their encoding efficiency to temporal statistics of pheromone fluctuations pp. 1-17

Marie Levakova, Lubomir Kostal, Christelle Monsempès, Vincent Jacob and Philippe Lucas

Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes pp. 1-28

Weilong Zhao and Xinwei Sher

Mechanistic insight into spontaneous transition from cellular alternans to arrhythmia—A simulation study pp. 1-27

Wei Wang, Shanzhuo Zhang, Haibo Ni, Clifford J Garratt, Mark R Boyett, Jules C Hancox and Henggui Zhang

Binding of the general anesthetic sevoflurane to ion channels pp. 1-23

Letícia Stock, Juliana Hosoume, Leonardo Cirqueira and Werner Treptow

RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks pp. 1-18

Jun Li, Wei Zhu, Jun Wang, Wenfei Li, Sheng Gong, Jian Zhang and Wei Wang

powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire pp. 1-18

Hillary Koch, Dmytro Starenki, Sara J Cooper, Richard M Myers and Qunhua Li

Bayesian phylodynamic inference with complex models pp. 1-15

Erik M Volz and Igor Siveroni

Putting benchmarks in their rightful place: The heart of computational biology pp. 1-3

Bjoern Peters, Steven E Brenner, Edwin Wang, Donna Slonim and Maricel G Kann

Modulation of voltage-dependent K+ conductances in photoreceptors trades off investment in contrast gain for bandwidth pp. 1-33

Francisco J H Heras, Mikko Vähäsöyrinki and Jeremy E Niven

Rosetta FunFolDes – A general framework for the computational design of functional proteins pp. 1-30

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 and Bruno E Correia

A computational analysis of dynamic, multi-organ inflammatory crosstalk induced by endotoxin in mice pp. 1-16

Ruben Zamora, Sebastian Korff, Qi Mi, Derek Barclay, Lukas Schimunek, Riccardo Zucca, Xerxes D Arsiwalla, Richard L Simmons, Paul Verschure, Timothy R Billiar and Yoram Vodovotz

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks pp. 1-11

Ryan R Wick, Louise M Judd and Kathryn E Holt

Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers pp. 1-14

Andrej Berg, Oleksandra Kukharenko, Martin Scheffner and Christine Peter

Comparative structural dynamic analysis of GTPases pp. 1-19

Hongyang Li, Xin-Qiu Yao and Barry J Grant

Deterministic response strategies in a trial-and-error learning task pp. 1-19

Holger Mohr, Katharina Zwosta, Dimitrije Markovic, Sebastian Bitzer, Uta Wolfensteller and Hannes Ruge

Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter pp. 1-21

Yarden Golan, Raphael Alhadeff, Fabian Glaser, Assaf Ganoth, Arieh Warshel and Yehuda G Assaraf

Prediction and classification in equation-free collective motion dynamics pp. 1-21

Keisuke Fujii, Takeshi Kawasaki, Yuki Inaba and Yoshinobu Kawahara

Efficient pedigree recording for fast population genetics simulation pp. 1-21

Jerome Kelleher, Kevin R Thornton, Jaime Ashander and Peter L Ralph

Visual physiology of the layer 4 cortical circuit in silico pp. 1-47

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 and Christof Koch

A Bayesian mixture modelling approach for spatial proteomics pp. 1-29

Oliver M Crook, Claire M Mulvey, Paul D W Kirk, Kathryn S Lilley and Laurent Gatto

Determinants of early afterdepolarization properties in ventricular myocyte models pp. 1-24

Xiaodong Huang, Zhen Song and Zhilin Qu

Inferring interaction partners from protein sequences using mutual information pp. 1-24

Anne-Florence Bitbol

Comparing Bayesian and non-Bayesian accounts of human confidence reports pp. 1-34

William T Adler and Wei Ji Ma

Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch pp. 1-31

Lina Meinecke, Praveer P Sharma, Huijing Du, Lei Zhang, Qing Nie and Thomas F Schilling

A regularity index for dendrites - local statistics of a neuron's input space pp. 1-22

Laura Anton-Sanchez, Felix Effenberger, Concha Bielza, Pedro Larrañaga and Hermann Cuntz

Volume 14, issue 10, 2018

Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor pp. 1-8

Richard A Erickson, Michael N Fienen, S Grace McCalla, Emily L Weiser, Melvin L Bower, Jonathan M Knudson and Greg Thain

A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments pp. 1-30

Katharina Nöh, Sebastian Niedenführ, Martin Beyß and Wolfgang Wiechert

Self-organized traffic via priority rules in leaf-cutting ants pp. 1-13

Daniel Strömbom and Audrey Dussutour

A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria pp. 1-17

Erki Aun, Age Brauer, Veljo Kisand, Tanel Tenson and Maido Remm

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor pp. 1-17

Hao Wang, Simonas Marcišauskas, Benjamín J Sánchez, Iván Domenzain, Daniel Hermansson, Rasmus Agren, Jens Nielsen and Eduard J Kerkhoven

Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine pp. 1-16

Francisco Y Cai, Thomas Fussell, Sarah Cobey and Marc Lipsitch

meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays pp. 1-20

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 and Stephen J Eglen

Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells pp. 1-28

Ernest C Y Ho, Juan Nicolas Malagón, Abha Ahuja, Rama Singh and Ellen Larsen

State dependence of stimulus-induced variability tuning in macaque MT pp. 1-28

Joseph A Lombardo, Matthew V Macellaio, Bing Liu, Stephanie E Palmer and Leslie C Osborne

What to know before forecasting the flu pp. 1-7

Prithwish Chakraborty, Bryan Lewis, Stephen Eubank, John S Brownstein, Madhav Marathe and Naren Ramakrishnan

Virus and CTL dynamics in the extrafollicular and follicular tissue compartments in SIV-infected macaques pp. 1-19

Dominik Wodarz, Pamela J Skinner, David N Levy and Elizabeth Connick

Modeling and subtleties of K-Ras and Calmodulin interaction pp. 1-19

Eduardo Garrido, Juan Lázaro, Montserrat Jaumot, Neus Agell and Jaime Rubio-Martinez

Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data pp. 1-23

Misbah Razzaq, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon and Carito Guziolowski

Ten quick tips for getting the most scientific value out of numerical data pp. 1-21

Lars Ole Schwen and Sabrina Rueschenbaum

Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals pp. 1-21

Iksoo Huh, Isabel Mendizabal, Taesung Park and Soojin V Yi

Ten simple rules when considering retirement pp. 1-4

Philip E Bourne

Ten simple rules for developing good reading habits during graduate school and beyond pp. 1-4

Marcos Méndez

Predicting B cell receptor substitution profiles using public repertoire data pp. 1-24

Amrit Dhar, Kristian Davidsen, Frederick A Matsen Iv and Vladimir N Minin

Seizure pathways: A model-based investigation pp. 1-24

Philippa J Karoly, Levin Kuhlmann, Daniel Soudry, David B Grayden, Mark J Cook and Dean R Freestone

Modeling effects of voltage dependent properties of the cardiac muscarinic receptor on human sinus node function pp. 1-15

Robin Moss, Frank B Sachse, Eloy G Moreno-Galindo, Ricardo A Navarro-Polanco, Martin Tristani-Firouzi and Gunnar Seemann

Ten simple rules for scientists: Improving your writing productivity pp. 1-6

Todd C Peterson, Sofie R Kleppner and Crystal M Botham

Linking signal detection theory and encoding models to reveal independent neural representations from neuroimaging data pp. 1-42

Fabian A Soto, Lauren E Vucovich and F Gregory Ashby

Modeling sensory-motor decisions in natural behavior pp. 1-22

Ruohan Zhang, Shun Zhang, Matthew H Tong, Yuchen Cui, Constantin A Rothkopf, Dana H Ballard and Mary M Hayhoe

Volume 14, issue 9, 2018

Quantitative single cell analysis uncovers the life/death decision in CD95 network pp. 1-21

Jörn H Buchbinder, Dennis Pischel, Kai Sundmacher, Robert J Flassig and Inna N Lavrik

Comparison of fluctuations in global network topology of modeled and empirical brain functional connectivity pp. 1-27

Makoto Fukushima and Olaf Sporns

Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling pp. 1-23

Tatu Pantsar, Sami Rissanen, Daniel Dauch, Tuomo Laitinen, Ilpo Vattulainen and Antti Poso

Selective ion permeation involves complexation with carboxylates and lysine in a model human sodium channel pp. 1-32

Emelie Flood, Céline Boiteux and Toby W Allen

Co-evolution networks of HIV/HCV are modular with direct association to structure and function pp. 1-29

Ahmed Abdul Quadeer, David Morales-Jimenez and Matthew R McKay

Transition state characteristics during cell differentiation pp. 1-24

Rowan D Brackston, Eszter Lakatos and Michael P H Stumpf

An information theoretic treatment of sequence-to-expression modeling pp. 1-24

Farzaneh Khajouei and Saurabh Sinha

Multivariate classification of neuroimaging data with nested subclasses: Biased accuracy and implications for hypothesis testing pp. 1-18

Hamidreza Jamalabadi, Sarah Alizadeh, Monika Schönauer, Christian Leibold and Steffen Gais

Individualised aspiration dynamics: Calculation by proofs pp. 1-15

Bin Wu and Lei Zhou

Informational structures: A dynamical system approach for integrated information pp. 1-33

Francisco J Esteban, Javier A Galadí, José A Langa, José R Portillo and Fernando Soler-Toscano

Comparing two classes of biological distribution systems using network analysis pp. 1-31

Lia Papadopoulos, Pablo Blinder, Henrik Ronellenfitsch, Florian Klimm, Eleni Katifori, David Kleinfeld and Danielle S Bassett

Modeling and prediction of clinical symptom trajectories in Alzheimer’s disease using longitudinal data pp. 1-25

Nikhil Bhagwat, Joseph D Viviano, Aristotle N Voineskos, M Mallar Chakravarty and Alzheimer’s Disease Neuroimaging Initiative

The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow pp. 1-25

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 and Michele Migliore

Optimal multi-source forecasting of seasonal influenza pp. 1-16

Zeynep Ertem, Dorrie Raymond and Lauren Ancel Meyers

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets pp. 1-16

Davide Risso, Liam Purvis, Russell B Fletcher, Diya Das, John Ngai, Sandrine Dudoit and Elizabeth Purdom

Maintaining maximal metabolic flux by gene expression control pp. 1-20

Robert Planqué, Josephus Hulshof, Bas Teusink, Johannes C Hendriks and Frank J Bruggeman

Correction: A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling pp. 1-1

Vijay Vedula, Juhyun Lee, Hao Xu, Jay Kuo C-C, Tzung K Hsiai and Alison L Marsden

Inferring decoding strategies for multiple correlated neural populations pp. 1-40

Kaushik J Lakshminarasimhan, Alexandre Pouget, Gregory C DeAngelis, Dora E Angelaki and Xaq Pitkow

Implications of alternative routes to APC/C inhibition by the mitotic checkpoint complex pp. 1-19

Fridolin Gross, Paolo Bonaiuti, Silke Hauf and Andrea Ciliberto

Model-based spatial navigation in the hippocampus-ventral striatum circuit: A computational analysis pp. 1-28

Ivilin Peev Stoianov, Cyriel M A Pennartz, Carien S Lansink and Giovani Pezzulo

Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network pp. 1-28

Yafei Lyu, Lingzhou Xue, Feipeng Zhang, Hillary Koch, Laura Saba, Katerina Kechris and Qunhua Li

A Markov chain for numerical chromosomal instability in clonally expanding populations pp. 1-28

Sergi Elizalde, Ashley M Laughney and Samuel F Bakhoum

Volume 14, issue 8, 2018

New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images pp. 1-25

Ilya Patrushev, Christina James-Zorn, Aldo Ciau-Uitz, Roger Patient and Michael J Gilchrist

Identification of excitatory-inhibitory links and network topology in large-scale neuronal assemblies from multi-electrode recordings pp. 1-25

Vito Paolo Pastore, Paolo Massobrio, Aleksandar Godjoski and Sergio Martinoia

Inferring hidden structure in multilayered neural circuits pp. 1-30

Niru Maheswaranathan, David B Kastner, Stephen A Baccus and Surya Ganguli

Ten simple rules for measuring the impact of workshops pp. 1-12

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 and Vanessa Higgins

Rare-event sampling of epigenetic landscapes and phenotype transitions pp. 1-28

Margaret J Tse, Brian K Chu, Cameron P Gallivan and Elizabeth L Read

Regulation of Pom cluster dynamics in Myxococcus xanthus pp. 1-28

Silke Bergeler and Erwin Frey

Exploring of the feature space of de novo developed post-transcriptional riboregulators pp. 1-19

Gert Peters, Jo Maertens, Jeroen Lammertyn and Marjan De Mey

Interactive implementations of thermodynamics-based RNA structure and RNA–RNA interaction prediction approaches for example-driven teaching pp. 1-19

Martin Raden, Mostafa Mahmoud Mohamed, Syed Mohsin Ali and Rolf Backofen

SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks pp. 1-14

Rong Zhang, Zhao Ren and Wei Chen

Scaling up data curation using deep learning: An application to literature triage in genomic variation resources pp. 1-14

Kyubum Lee, Maria Livia Famiglietti, Aoife McMahon, Chih-Hsuan Wei, Jacqueline Ann Langdon MacArthur, Sylvain Poux, Lionel Breuza, Alan Bridge, Fiona Cunningham, Ioannis Xenarios and Zhiyong Lu

A simple computer vision pipeline reveals the effects of isolation on social interaction dynamics in Drosophila pp. 1-23

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 and Bassem A Hassan

Human Pavlovian fear conditioning conforms to probabilistic learning pp. 1-21

Athina Tzovara, Christoph W Korn and Dominik R Bach

Characterising seasonal influenza epidemiology using primary care surveillance data pp. 1-21

Robert C Cope, Joshua V Ross, Monique Chilver, Nigel P Stocks and Lewis Mitchell

Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models pp. 1-26

Bernard Cazelles, Clara Champagne and Joseph Dureau

Interplay of multiple pathways and activity-dependent rules in STDP pp. 1-32

Gaëtan Vignoud, Laurent Venance and Jonathan D Touboul

Dorsal anterior cingulate-brainstem ensemble as a reinforcement meta-learner pp. 1-32

Massimo Silvetti, Eliana Vassena, Elger Abrahamse and Tom Verguts

Lineage space and the propensity of bacterial cells to undergo growth transitions pp. 1-18

Arnab Bandyopadhyay, Huijing Wang and J Christian J Ray

Profiling cellular morphodynamics by spatiotemporal spectrum decomposition pp. 1-29

Xiao Ma, Onur Dagliyan, Klaus M Hahn and Gaudenz Danuser

An automated approach to the quantitation of vocalizations and vocal learning in the songbird pp. 1-29

David G Mets and Michael S Brainard

MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction pp. 1-24

Xing Chen, Jun Yin, Jia Qu and Li Huang

Irrelevance by inhibition: Learning, computation, and implications for schizophrenia pp. 1-37

Nathan Insel, Jordan Guerguiev and Blake A Richards

NFTsim: Theory and Simulation of Multiscale Neural Field Dynamics pp. 1-37

Paula Sanz-Leon, Peter A Robinson, Stuart A Knock, Peter M Drysdale, Romesh G Abeysuriya, Felix K Fung, Chris J Rennie and Xuelong Zhao

A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data pp. 1-22

Tianwei Yu

Volume 14, issue 7, 2018

Unsupervised clustering of temporal patterns in high-dimensional neuronal ensembles using a novel dissimilarity measure pp. 1-34

Lukas Grossberger, Francesco P Battaglia and Martin Vinck

Punishment and inspection for governing the commons in a feedback-evolving game pp. 1-15

Xiaojie Chen and Attila Szolnoki

Age-dependent Pavlovian biases influence motor decision-making pp. 1-22

Xiuli Chen, Robb B Rutledge, Harriet R Brown, Raymond J Dolan, Sven Bestmann and Joseph M Galea

Inter-trial effects in visual pop-out search: Factorial comparison of Bayesian updating models pp. 1-31

Fredrik Allenmark, Hermann J Müller and Zhuanghua Shi

miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts pp. 1-32

Albert Pla, Xiangfu Zhong and Simon Rayner

Post-Turing tissue pattern formation: Advent of mechanochemistry pp. 1-21

Felix Brinkmann, Moritz Mercker, Thomas Richter and Anna Marciniak-Czochra

PyPhi: A toolbox for integrated information theory pp. 1-21

William G P Mayner, William Marshall, Larissa Albantakis, Graham Findlay, Robert Marchman and Giulio Tononi

Gain control with A-type potassium current: IA as a switch between divisive and subtractive inhibition pp. 1-23

Joshua H Goldwyn, Bradley R Slabe, Joseph B Travers and David Terman

Real-time decision-making during emergency disease outbreaks pp. 1-18

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 and Michael J Tildesley

A minimally invasive neurostimulation method for controlling abnormal synchronisation in the neuronal activity pp. 1-18

Malbor Asllani, Paul Expert and Timoteo Carletti

OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement pp. 1-20

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 and Scott L Delp

A marginalized two-part Beta regression model for microbiome compositional data pp. 1-16

Haitao Chai, Hongmei Jiang, Lu Lin and Lei Liu

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning pp. 1-16

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 and Iddo Friedberg

Activation of the DNA-repair mechanism through NBS1 and MRE11 diffusion pp. 1-16

Ida Friis and Ilia A Solov’yov

Information-theoretic analysis of realistic odor plumes: What cues are useful for determining location? pp. 1-19

Sebastian D Boie, Erin G Connor, Margaret McHugh, Katherine I Nagel, G Bard Ermentrout, John P Crimaldi and Jonathan D Victor

Correction: A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens pp. 1-1

The PLOS Computational Biology Staff

Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception pp. 1-38

Luigi Acerbi, Kalpana Dokka, Dora E Angelaki and Wei Ji Ma

Phase-lags in large scale brain synchronization: Methodological considerations and in-silico analysis pp. 1-30

Spase Petkoski, J Matias Palva and Viktor K Jirsa

Excitable neuronal assemblies with adaptation as a building block of brain circuits for velocity-controlled signal propagation pp. 1-30

Hesam Setareh, Moritz Deger and Wulfram Gerstner

Volume 14, issue 6, 2018

Systems modelling of the EGFR-PYK2-c-Met interaction network predicts and prioritizes synergistic drug combinations for triple-negative breast cancer pp. 1-30

Sung-Young Shin, Anna-Katharina Müller, Nandini Verma, Sima Lev and Lan K Nguyen

The impact of temporal sampling resolution on parameter inference for biological transport models pp. 1-30

Jonathan U Harrison and Ruth E Baker

Mechanical positioning of multiple nuclei in muscle cells pp. 1-25

Angelika Manhart, Stefanie Windner, Mary Baylies and Alex Mogilner

Transmission of temporally correlated spike trains through synapses with short-term depression pp. 1-25

Alex D Bird and Magnus J E Richardson

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database pp. 1-14

Luke Zappia, Belinda Phipson and Alicia Oshlack

Stochastic shielding and edge importance for Markov chains with timescale separation pp. 1-35

Deena R Schmidt, Roberto F Galán and Peter J Thomas

Assessment of ab initio models of protein complexes by molecular dynamics pp. 1-13

Filip Radom, Andreas Plückthun and Emanuele Paci

Temporal precision of regulated gene expression pp. 1-16

Shivam Gupta, Julien Varennes, Hendrik C Korswagen and Andrew Mugler

Anticipating epidemic transitions with imperfect data pp. 1-18

Tobias S Brett, Eamon B O’Dea, Éric Marty, Paige B Miller, Andrew W Park, John M Drake and Pejman Rohani

Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions pp. 1-29

Logan C Brooks, David C Farrow, Sangwon Hyun, Ryan J Tibshirani and Roni Rosenfeld

Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology pp. 1-24

J Kyle Medley, Kiri Choi, Matthias König, Lucian Smith, Stanley Gu, Joseph Hellerstein, Stuart C Sealfon and Herbert M Sauro

Correction: A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems pp. 1-9

Robert C Wilson, Matthew R Nassar, Gaia Tavoni and Joshua I Gold

The role of intracellular signaling in the stripe formation in engineered Escherichia coli populations pp. 1-23

Xiaoru Xue, Chuan Xue and Min Tang

Instance-based generalization for human judgments about uncertainty pp. 1-27

Philipp Schustek and Rubén Moreno-Bote

Computation predicts rapidly adapting mechanotransduction currents cannot account for tactile encoding in Merkel cell-neurite complexes pp. 1-21

Gregory J Gerling, Lingtian Wan, Benjamin U Hoffman, Yuxiang Wang and Ellen A Lumpkin

3D morphology-based clustering and simulation of human pyramidal cell dendritic spines pp. 1-22

Sergio Luengo-Sanchez, Isabel Fernaud-Espinosa, Concha Bielza, Ruth Benavides-Piccione, Pedro Larrañaga and Javier DeFelipe

The effect of cell geometry on polarization in budding yeast pp. 1-22

Michael Trogdon, Brian Drawert, Carlos Gomez, Samhita P Banavar, Tau-Mu Yi, Otger Campàs and Linda R Petzold

2018 ISCB Innovator Award recognizes M. Madan Babu pp. 1-3

Christiana N Fogg, Diane E Kovats and Ron Shamir

Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria pp. 1-15

Nathaniel Mon Père, Tom Lenaerts, Jorge M Pacheco and David Dingli

Solving the RNA design problem with reinforcement learning pp. 1-15

Peter Eastman, Jade Shi, Bharath Ramsundar and Vijay S Pande

Classification of red blood cell shapes in flow using outlier tolerant machine learning pp. 1-15

Alexander Kihm, Lars Kaestner, Christian Wagner and Stephan Quint

Volume 14, issue 5, 2018

Minimal model of interictal and ictal discharges “Epileptor-2” pp. 1-25

Anton V Chizhov, Artyom V Zefirov, Dmitry V Amakhin, Elena Yu Smirnova and Aleksey V Zaitsev

Firing-rate based network modeling of the dLGN circuit: Effects of cortical feedback on spatiotemporal response properties of relay cells pp. 1-38

Milad Hobbi Mobarhan, Geir Halnes, Pablo Martínez-Cañada, Torkel Hafting, Marianne Fyhn and Gaute T Einevoll

Variability in pulmonary vein electrophysiology and fibrosis determines arrhythmia susceptibility and dynamics pp. 1-19

Caroline H Roney, Jason D Bayer, Hubert Cochet, Marianna Meo, Rémi Dubois, Pierre Jaïs and Edward J Vigmond

Assessing the public health impact of tolerance-based therapies with mathematical models pp. 1-14

Nathanaël Hozé, Sebastian Bonhoeffer and Roland Regoes

Predictive modelling of a novel anti-adhesion therapy to combat bacterial colonisation of burn wounds pp. 1-28

Paul A Roberts, Ryan M Huebinger, Emma Keen, Anne-Marie Krachler and Sara Jabbari

Community-based benchmarking improves spike rate inference from two-photon calcium imaging data pp. 1-13

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 and Matthias Bethge

Identification of animal behavioral strategies by inverse reinforcement learning pp. 1-20

Shoichiro Yamaguchi, Honda Naoki, Muneki Ikeda, Yuki Tsukada, Shunji Nakano, Ikue Mori and Shin Ishii

Logistical constraints lead to an intermediate optimum in outbreak response vaccination pp. 1-20

Yun Tao, Katriona Shea and Matthew Ferrari

Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme pp. 1-20

Jagannath Mondal, Navjeet Ahalawat, Subhendu Pandit, Lewis E Kay and Pramodh Vallurupalli

Design of optimal nonlinear network controllers for Alzheimer's disease pp. 1-24

Lazaro M Sanchez-Rodriguez, Yasser Iturria-Medina, Erica A Baines, Sabela C Mallo, Mehdy Dousty, Roberto C Sotero and on behalf of The Alzheimer’s Disease Neuroimaging Initiative

Detecting change in stochastic sound sequences pp. 1-24

Benjamin Skerritt-Davis and Mounya Elhilali

Can a time varying external drive give rise to apparent criticality in neural systems? pp. 1-29

Viola Priesemann and Oren Shriki

A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data pp. 1-29

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 and Bipolar Disorders Working Group of the Psychiatric Genomics Consortium

How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes pp. 1-26

Surya K Ghosh and Daniel Jost

Parameter uncertainty quantification using surrogate models applied to a spatial model of yeast mating polarization pp. 1-26

Marissa Renardy, Tau-Mu Yi, Dongbin Xiu and Ching-Shan Chou

Bi-stability in cooperative transport by ants in the presence of obstacles pp. 1-21

Jonathan E Ron, Itai Pinkoviezky, Ehud Fonio, Ofer Feinerman and Nir S Gov

The complex ecosystem in non small cell lung cancer invasion pp. 1-21

Seth Haney, Jessica Konen, Adam I Marcus and Maxim Bazhenov

Ten simple rules for writing a cover letter to accompany a job application for an academic position pp. 1-4

Lubomir Tomaska and Jozef Nosek

Submit a Topic Page to PLOS Computational Biology and Wikipedia pp. 1-4

Daniel Mietchen, Shoshana Wodak, Szymon Wasik, Natalia Szostak and Christophe Dessimoz

2018 ISCB accomplishments by a senior scientist award pp. 1-4

Christiana N Fogg, Diane E Kovats and Ron Shamir

Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago pp. 1-4

Milana Frenkel-Morgenstern, Lonnie Welch, Bruno Gaeta and Diane E Kovats

Enzyme sequestration by the substrate: An analysis in the deterministic and stochastic domains pp. 1-23

Andreas Petrides and Glenn Vinnicombe

Simulations to benchmark time-varying connectivity methods for fMRI pp. 1-23

William Hedley Thompson, Craig Geoffrey Richter, Pontus Plavén-Sigray and Peter Fransson

Porcupine: A visual pipeline tool for neuroimaging analysis pp. 1-10

Tim van Mourik, Lukas Snoek, Tomas Knapen and David G Norris

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types pp. 1-15

Aaron T L Lun, Hervé Pagès and Mike L Smith

Optimizing the learning rate for adaptive estimation of neural encoding models pp. 1-34

Han-Lin Hsieh and Maryam M Shanechi

Volume 14, issue 4, 2018

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer pp. 1-12

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 and Elana J Fertig

Compositional clustering in task structure learning pp. 1-25

Nicholas T Franklin and Michael J Frank

Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level pp. 1-25

Małgorzata Kardyńska, Anna Paszek, Jarosław Śmieja, David Spiller, Wiesława Widłak, Michael R H White, Pawel Paszek and Marek Kimmel

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design pp. 1-38

Jared Adolf-Bryfogle, Oleks Kalyuzhniy, Michael Kubitz, Brian D Weitzner, Xiaozhen Hu, Yumiko Adachi, William R Schief and Roland L Dunbrack

Interactions of spatial strategies producing generalization gradient and blocking: A computational approach pp. 1-35

Laurent Dollé, Ricardo Chavarriaga, Agnès Guillot and Mehdi Khamassi

Material and shape perception based on two types of intensity gradient information pp. 1-40

Masataka Sawayama and Shin'ya Nishida

Exploiting glycan topography for computational design of Env glycoprotein antigenicity pp. 1-28

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 and Galit Alter

Effects of spatiotemporal HSV-2 lesion dynamics and antiviral treatment on the risk of HIV-1 acquisition pp. 1-28

Catherine M Byrne, Soren Gantt and Daniel Coombs

Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy pp. 1-11

Martin Weigert, Kaushikaram Subramanian, Sebastian T Bundschuh, Eugene W Myers and Moritz Kreysing

Optimal dynamic control approach in a multi-objective therapeutic scenario: Application to drug delivery in the treatment of prostate cancer pp. 1-16

Itziar Irurzun-Arana, Alvaro Janda, Sergio Ardanza-Trevijano and Iñaki F Trocóniz

Correcting for batch effects in case-control microbiome studies pp. 1-17

Sean M Gibbons, Claire Duvallet and Eric J Alm

Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape pp. 1-24

David R J Pleydell, Samuel Soubeyrand, Sylvie Dallot, Gérard Labonne, Joël Chadœuf, Emmanuel Jacquot and Gaël Thébaud

Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data pp. 1-18

Travers Ching, Xun Zhu and Lana X Garmire

On the role of extrinsic noise in microRNA-mediated bimodal gene expression pp. 1-26

Marco Del Giudice, Stefano Bo, Silvia Grigolon and Carla Bosia

Spatial regularity control of phyllotaxis pattern generated by the mutual interaction between auxin and PIN1 pp. 1-23

Hironori Fujita and Masayoshi Kawaguchi

Personalizing physical exercise in a computational model of fuel homeostasis pp. 1-23

Maria Concetta Palumbo, Micaela Morettini, Paolo Tieri, Fasma Diele, Massimo Sacchetti and Filippo Castiglione

Principles that govern competition or co-existence in Rho-GTPase driven polarization pp. 1-23

Jian-Geng Chiou, Samuel A Ramirez, Timothy C Elston, Thomas P Witelski, David G Schaeffer and Daniel J Lew

Using pseudoalignment and base quality to accurately quantify microbial community composition pp. 1-23

Mark Reppell and John Novembre

Identifying robust hysteresis in networks pp. 1-23

Tomáš Gedeon, Bree Cummins, Shaun Harker and Konstantin Mischaikow

Rational metareasoning and the plasticity of cognitive control pp. 1-27

Falk Lieder, Amitai Shenhav, Sebastian Musslick and Thomas L Griffiths

Effect of Ca2+ on the promiscuous target-protein binding of calmodulin pp. 1-27

Annie M Westerlund and Lucie Delemotte

Need for speed: An optimized gridding approach for spatially explicit disease simulations pp. 1-27

Stefan Sellman, Kimberly Tsao, Michael J Tildesley, Peter Brommesson, Colleen T Webb, Uno Wennergren, Matt J Keeling and Tom Lindström

Computational mechanisms underlying cortical responses to the affordance properties of visual scenes pp. 1-31

Michael F Bonner and Russell A Epstein

Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly pp. 1-22

Juan Francisco Viso, Patricia Belelli, Matías Machado, Humberto González, Sergio Pantano, María Julia Amundarain, Fernando Zamarreño, Maria Marta Branda, Diego M A Guérin and Marcelo D Costabel

Ten simple rules for responsible referencing pp. 1-6

Bart Penders

RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning pp. 1-15

Ji-Sung Kim, Xin Gao and Andrey Rzhetsky

Whole-body iron transport and metabolism: Mechanistic, multi-scale model to improve treatment of anemia in chronic kidney disease pp. 1-34

Joydeep Sarkar, Alka A Potdar and Gerald M Saidel

Volume 14, issue 3, 2018

An evolutionary learning and network approach to identifying key metabolites for osteoarthritis pp. 1-18

Ting Hu, Karoliina Oksanen, Weidong Zhang, Ed Randell, Andrew Furey, Guang Sun and Guangju Zhai

Activation gating in HCN2 channels pp. 1-18

Sabine Hummert, Susanne Thon, Thomas Eick, Ralf Schmauder, Eckhard Schulz and Klaus Benndorf

From correlation to causation: Estimating effective connectivity from zero-lag covariances of brain signals pp. 1-18

Jonathan Schiefer, Alexander Niederbühl, Volker Pernice, Carolin Lennartz, Jürgen Hennig, Pierre LeVan and Stefan Rotter

Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units pp. 1-24

Timothy Kinyanjui, Jo Middleton, Stefan Güttel, Jackie Cassell, Joshua Ross and Thomas House

Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state pp. 1-24

Hao Ge, Pingping Wu, Hong Qian and Xiaoliang Sunney Xie

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules pp. 1-29

Albert Solernou, Benjamin S Hanson, Robin A Richardson, Robert Welch, Daniel J Read, Oliver G Harlen and Sarah A Harris

Classifying dynamic transitions in high dimensional neural mass models: A random forest approach pp. 1-27

Lauric A Ferrat, Marc Goodfellow and John R Terry

Deploying digital health data to optimize influenza surveillance at national and local scales pp. 1-23

Elizabeth C Lee, Ali Arab, Sandra M Goldlust, Cécile Viboud, Bryan T Grenfell and Shweta Bansal

Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA pp. 1-21

Hidetoshi Kono, Shun Sakuraba and Hisashi Ishida

Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells pp. 1-21

Yanting Luo, Jianlin He, Xiguang Xu, Ming-an Sun, Xiaowei Wu, Xuemei Lu and Hehuang Xie

Factors affecting basket catheter detection of real and phantom rotors in the atria: A computational study pp. 1-26

Laura Martinez-Mateu, Lucia Romero, Ana Ferrer-Albero, Rafael Sebastian, José F Rodríguez Matas, José Jalife, Omer Berenfeld and Javier Saiz

Dynamic combination of sensory and reward information under time pressure pp. 1-26

Shiva Farashahi, Chih-Chung Ting, Chang-Hao Kao, Shih-Wei Wu and Alireza Soltani

An open source tool for automatic spatiotemporal assessment of calcium transients and local ‘signal-close-to-noise’ activity in calcium imaging data pp. 1-34

Juan Prada, Manju Sasi, Corinna Martin, Sibylle Jablonka, Thomas Dandekar and Robert Blum

Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation pp. 1-25

Michael Pablo, Samuel A Ramirez and Timothy C Elston

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification pp. 1-25

Charlie Beirnaert, Pieter Meysman, Trung Nghia Vu, Nina Hermans, Sandra Apers, Luc Pieters, Adrian Covaci and Kris Laukens

Brain-state invariant thalamo-cortical coordination revealed by non-linear encoders pp. 1-25

Guillaume Viejo, Thomas Cortier and Adrien Peyrache

Use of temperature to improve West Nile virus forecasts pp. 1-25

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 and Jeffrey Shaman

SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data pp. 1-25

Ivan Dotu, Scott I Adamson, Benjamin Coleman, Cyril Fournier, Emma Ricart-Altimiras, Eduardo Eyras and Jeffrey H Chuang

Ten simple rules for collaborative lesson development pp. 1-8

Gabriel A Devenyi, Rémi Emonet, Rayna M Harris, Kate L Hertweck, Damien Irving, Ian Milligan and Greg Wilson

Correction: Correlated receptor transport processes buffer single-cell heterogeneity pp. 1-1

The PLOS Computational Biology Staff

Correction: Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue pp. 1-1

The PLOS Computational Biology Staff

Imbalanced amplification: A mechanism of amplification and suppression from local imbalance of excitation and inhibition in cortical circuits pp. 1-28

Christopher Ebsch and Robert Rosenbaum

Population dynamics of engineered underdominance and killer-rescue gene drives in the control of disease vectors pp. 1-28

Matthew P Edgington and Luke S Alphey

Astrocytic Kir4.1 channels and gap junctions account for spontaneous epileptic seizure pp. 1-19

Mengmeng Du, Jiajia Li, Liang Chen, Yuguo Yu and Ying Wu

Population-specific design of de-immunized protein biotherapeutics pp. 1-19

Benjamin Schubert, Charlotta Schärfe, Pierre Dönnes, Thomas Hopf, Debora Marks and Oliver Kohlbacher

Bat detective—Deep learning tools for bat acoustic signal detection pp. 1-19

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 and Kate E Jones

Across-subjects classification of stimulus modality from human MEG high frequency activity pp. 1-14

Britta U Westner, Sarang S Dalal, Simon Hanslmayr and Tobias Staudigl

An entropic barriers diffusion theory of decision-making in multiple alternative tasks pp. 1-14

Diego Fernandez Slezak, Mariano Sigman and Guillermo A Cecchi

Haptic communication between humans is tuned by the hard or soft mechanics of interaction pp. 1-17

Atsushi Takagi, Francesco Usai, Gowrishankar Ganesh, Vittorio Sanguineti and Etienne Burdet

Eleven quick tips for architecting biomedical informatics workflows with cloud computing pp. 1-11

Brian S Cole and Jason H Moore

The importance of geometry in the corneal micropocket angiogenesis assay pp. 1-20

James A Grogan, Anthony J Connor, Joe M Pitt-Francis, Philip K Maini and Helen M Byrne

Volume 14, issue 2, 2018

Heritable tumor cell division rate heterogeneity induces clonal dominance pp. 1-19

Margriet M Palm, Marjet Elemans and Joost B Beltman

The development and application of bioinformatics core competencies to improve bioinformatics training and education pp. 1-14

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 and Lonnie Welch

A maximum-entropy model for predicting chromatin contacts pp. 1-16

Pau Farré and Eldon Emberly

A model of risk and mental state shifts during social interaction pp. 1-20

Andreas Hula, Iris Vilares, Terry Lohrenz, Peter Dayan and P Read Montague

Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network pp. 1-20

Dorjsuren Battogtokh, Shihoko Kojima and John J Tyson

Spike and burst coding in thalamocortical relay cells pp. 1-36

Fleur Zeldenrust, Pascal Chameau and Wytse J Wadman

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems pp. 1-31

Ahmadreza Ghaffarizadeh, Randy Heiland, Samuel H Friedman, Shannon M Mumenthaler and Paul Macklin

A multiscale modelling approach to assess the impact of metabolic zonation and microperfusion on the hepatic carbohydrate metabolism pp. 1-22

Nikolaus Berndt, Marius Stefan Horger, Sascha Bulik and Hermann-Georg Holzhütter

Self-crowding of AMPA receptors in the excitatory postsynaptic density can effectuate anomalous receptor sub-diffusion pp. 1-34

Rahul Gupta

A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination pp. 1-21

Caitlin Collins and Xavier Didelot

Trade-off between synergy and efficacy in combinations of HIV-1 latency-reversing agents pp. 1-21

Vipul Gupta and Narendra M Dixit

Control fast or control smart: When should invading pathogens be controlled? pp. 1-21

Robin N Thompson, Christopher A Gilligan and Nik J Cunniffe

Interpretation of correlated neural variability from models of feed-forward and recurrent circuits pp. 1-26

Volker Pernice and Rava Azeredo da Silveira

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains pp. 1-26

Sneha Vishwanath, Alexandre G de Brevern and Narayanaswamy Srinivasan

Ten simple rules for writing a popular science book pp. 1-4

Adam J Kucharski

Simulation enabled search for explanatory mechanisms of the fracture healing process pp. 1-32

Ryan C Kennedy, Meir Marmor, Ralph Marcucio and C Anthony Hunt

Genetic programming based models in plant tissue culture: An addendum to traditional statistical approach pp. 1-13

Meenu R Mridula, Ashalatha S Nair and K Satheesh Kumar

Examining the controllability of sepsis using genetic algorithms on an agent-based model of systemic inflammation pp. 1-17

Robert Chase Cockrell and Gary An

Memory functions reveal structural properties of gene regulatory networks pp. 1-25

Edgar Herrera-Delgado, Ruben Perez-Carrasco, James Briscoe and Peter Sollich

Imaging of neural oscillations with embedded inferential and group prevalence statistics pp. 1-33

Peter W Donhauser, Esther Florin and Sylvain Baillet

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation pp. 1-6

Vasundra Touré, Nicolas Le Novère, Dagmar Waltemath and Olaf Wolkenhauer

Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub-classification pp. 1-15

Yishai Shimoni

The feasibility of equilibria in large ecosystems: A primary but neglected concept in the complexity-stability debate pp. 1-18

Michaël Dougoud, Laura Vinckenbosch, Rudolf P Rohr, Louis-Félix Bersier and Christian Mazza

Integrating linear optimization with structural modeling to increase HIV neutralization breadth pp. 1-18

Alexander M Sevy, Swetasudha Panda, James E Crowe, Jens Meiler and Yevgeniy Vorobeychik

Prediction of infectious disease epidemics via weighted density ensembles pp. 1-23

Evan L Ray and Nicholas G Reich

A biophysical model of dynamic balancing of excitation and inhibition in fast oscillatory large-scale networks pp. 1-27

Romesh G Abeysuriya, Jonathan Hadida, Stamatios N Sotiropoulos, Saad Jbabdi, Robert Becker, Benjamin A E Hunt, Matthew J Brookes and Mark W Woolrich

Volume 14, issue 1, 2018

Cardinal features of involuntary force variability can arise from the closed-loop control of viscoelastic afferented muscles pp. 1-29

Akira Nagamori, Christopher M Laine and Francisco J Valero-Cuevas

Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance pp. 1-29

Jacob C Kimmel, Amy Y Chang, Andrew S Brack and Wallace F Marshall

A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition pp. 1-24

Talia Zeppelin, Lucy Kate Ladefoged, Steffen Sinning, Xavier Periole and Birgit Schiøtt

A model for cooperative gating of L-type Ca2+ channels and its effects on cardiac alternans dynamics pp. 1-18

Daisuke Sato, Rose E Dixon, Luis F Santana and Manuel F Navedo

The E2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors pp. 1-18

Ravi Kumar Verma, Ara M Abramyan, Mayako Michino, R Benjamin Free, David R Sibley, Jonathan A Javitch, J Robert Lane and Lei Shi

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening pp. 1-44

Zixuan Cang, Lin Mu and Guo-Wei Wei

Bayesian inference of phylogenetic networks from bi-allelic genetic markers pp. 1-32

Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M Meudt and Luay Nakhleh

Modeling visual-based pitch, lift and speed control strategies in hoverflies pp. 1-21

Roman Goulard, Jean-Louis Vercher and Stéphane Viollet

Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission pp. 1-21

Wesley Wong, Edward A Wenger, Daniel L Hartl and Dyann F Wirth

The extent of ribosome queuing in budding yeast pp. 1-21

Alon Diament, Anna Feldman, Elisheva Schochet, Martin Kupiec, Yoav Arava and Tamir Tuller

A theory of how active behavior stabilises neural activity: Neural gain modulation by closed-loop environmental feedback pp. 1-26

Christopher L Buckley and Taro Toyoizumi

SozRank: A new approach for localizing the epileptic seizure onset zone pp. 1-26

Yonathan Murin, Jeremy Kim, Josef Parvizi and Andrea Goldsmith

Clustering gene expression time series data using an infinite Gaussian process mixture model pp. 1-27

Ian C McDowell, Dinesh Manandhar, Christopher M Vockley, Amy K Schmid, Timothy E Reddy and Barbara E Engelhardt

Improving pairwise comparison of protein sequences with domain co-occurrence pp. 1-23

Christophe Menichelli, Olivier Gascuel and Laurent Bréhélin

Sequence determinants of protein phase behavior from a coarse-grained model pp. 1-23

Gregory L Dignon, Wenwei Zheng, Young C Kim, Robert B Best and Jeetain Mittal

Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations pp. 1-15

Jagdish Suresh Patel, Celeste J Brown, F Marty Ytreberg and Deborah L Stenkamp

The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide pp. 1-12

Jigisha Anupama, Margherita Francescatto, Farzana Rahman, Nazeefa Fatima, Dan DeBlasio, Avinash Kumar Shanmugam, Venkata Satagopam, Alberto Santos, Pandurang Kolekar, Magali Michaut and Emre Guney

A systematic atlas of chaperome deregulation topologies across the human cancer landscape pp. 1-30

Ali Hadizadeh Esfahani, Angelina Sverchkova, Julio Saez-Rodriguez, Andreas A Schuppert and Marc Brehme

What drives the perceptual change resulting from speech motor adaptation? Evaluation of hypotheses in a Bayesian modeling framework pp. 1-38

Jean-François Patri, Pascal Perrier, Jean-Luc Schwartz and Julien Diard

GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies pp. 1-14

Runmin Wei, Jingye Wang, Erik Jia, Tianlu Chen, Yan Ni and Wei Jia

Mechanical feedback coordinates cell wall expansion and assembly in yeast mating morphogenesis pp. 1-19

Samhita P Banavar, Carlos Gomez, Michael Trogdon, Linda R Petzold, Tau-Mu Yi and Otger Campàs

Robust and efficient coding with grid cells pp. 1-28

Lajos Vágó and Balázs B Ujfalussy

A dynamical systems approach for estimating phase interactions between rhythms of different frequencies from experimental data pp. 1-20

Takayuki Onojima, Takahiro Goto, Hiroaki Mizuhara and Toshio Aoyagi

Interactions between species introduce spurious associations in microbiome studies pp. 1-20

Rajita Menon, Vivek Ramanan and Kirill S Korolev

The role of spatial heterogeneity in the evolution of local and global infections of viruses pp. 1-20

Koich Saeki and Akira Sasaki