PLOS Computational Biology

2005 - 2025

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Volume 14, issue 12, 2018

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

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

Jia Lu, Xiaoyi Cao and Sheng Zhong

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

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

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

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

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

Wojciech Potrzebowski, Jill Trewhella and Ingemar Andre

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

Rory G Townsend and Pulin Gong

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

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

Luhao Zhang, Maodong Li and Zhirong Liu

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

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

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

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

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

Ryan R Wick, Louise M Judd and Kathryn E Holt

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

Anne-Florence Bitbol

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

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

Weilong Zhao and Xinwei Sher

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

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

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

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

William T Adler and Wei Ji Ma

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

Letícia Stock, Juliana Hosoume, Leonardo Cirqueira and Werner Treptow

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

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

Volume 14, issue 10, 2018

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

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

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

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

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

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

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

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

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

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

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

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

Volume 14, issue 9, 2018

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

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

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

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

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

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

Sergi Elizalde, Ashley M Laughney and Samuel F Bakhoum

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

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

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

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

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

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

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

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

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

Athina Tzovara, Christoph W Korn and Dominik R Bach

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

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

Xing Chen, Jun Yin, Jia Qu and Li Huang

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

Gaëtan Vignoud, Laurent Venance and Jonathan D Touboul

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

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

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

Tianwei Yu

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

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

Volume 14, issue 7, 2018

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

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

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

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

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

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

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

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

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

Xiaojie Chen and Attila Szolnoki

Volume 14, issue 6, 2018

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

Philipp Schustek and Rubén Moreno-Bote

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

Deena R Schmidt, Roberto F Galán and Peter J Thomas

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

Jonathan U Harrison and Ruth E Baker

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

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

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

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

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

Volume 14, issue 5, 2018

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

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

Han-Lin Hsieh and Maryam M Shanechi

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

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

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

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

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

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

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

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

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

Nathanaël Hozé, Sebastian Bonhoeffer and Roland Regoes

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

Volume 14, issue 4, 2018

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

Michael F Bonner and Russell A Epstein

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

Mark Reppell and John Novembre

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

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

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

Masataka Sawayama and Shin'ya Nishida

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

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

Sean M Gibbons, Claire Duvallet and Eric J Alm

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

Ji-Sung Kim, Xin Gao and Andrey Rzhetsky

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

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

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

Compositional clustering in task structure learning pp. 1-25

Nicholas T Franklin and Michael J Frank

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

Volume 14, issue 3, 2018

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

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

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

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

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

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

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

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

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

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

Volume 14, issue 2, 2018

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

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

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

Evan L Ray and Nicholas G Reich

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

Fleur Zeldenrust, Pascal Chameau and Wytse J Wadman

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

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

Robin N Thompson, Christopher A Gilligan and Nik J Cunniffe

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

Peter W Donhauser, Esther Florin and Sylvain Baillet

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

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

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

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

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

Pau Farré and Eldon Emberly

Volume 14, issue 1, 2018

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

Christophe Menichelli, Olivier Gascuel and Laurent Bréhélin

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

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

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

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

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

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

Lajos Vágó and Balázs B Ujfalussy

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

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

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

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

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

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

Yonathan Murin, Jeremy Kim, Josef Parvizi and Andrea Goldsmith