PLOS Computational Biology

2005 - 2022

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Volume 12, issue 12, 2016

Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites pp. 1-25

Angela Re, Levi Waldron and Alessandro Quattrone

Encoding in Balanced Networks: Revisiting Spike Patterns and Chaos in Stimulus-Driven Systems pp. 1-30

Guillaume Lajoie, Kevin K Lin, Jean-Philippe Thivierge and Eric Shea-Brown

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations pp. 1-30

Andrew F Neuwald and Stephen F Altschul

Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs pp. 1-13

Nadezda Kryuchkova-Mostacci and Marc Robinson-Rechavi

Stability of Cross-Feeding Polymorphisms in Microbial Communities pp. 1-17

Ivana Gudelj, Margie Kinnersley, Peter Rashkov, Karen Schmidt and Frank Rosenzweig

Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series pp. 1-20

Anna Klimovskaia, Stefan Ganscha and Manfred Claassen

Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level pp. 1-20

Kawai Leung, Aylia Mohammadi, William S Ryu and Ilya Nemenman

Novel Models of Visual Topographic Map Alignment in the Superior Colliculus pp. 1-20

Ruben A Tikidji-Hamburyan, Tarek A El-Ghazawi and Jason W Triplett

Correction: Separating Timing, Movement Conditions and Individual Differences in the Analysis of Human Movement pp. 1-1

The PLOS Computational Biology Staff

Correction: Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets pp. 1-1

The PLOS Computational Biology Staff

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology pp. 1-23

James C Schaff, Fei Gao, Ye Li, Igor L Novak and Boris M Slepchenko

Scaling Properties of Dimensionality Reduction for Neural Populations and Network Models pp. 1-27

Ryan C Williamson, Benjamin R Cowley, Ashok Litwin-Kumar, Brent Doiron, Adam Kohn, Matthew A Smith and Byron M Yu

Utility and Limitations of Using Gene Expression Data to Identify Functional Associations pp. 1-27

Sahra Uygun, Cheng Peng, Melissa D Lehti-Shiu, Robert L Last and Shin-Han Shiu

The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems pp. 1-26

Andrew White, Malachi Tolman, Howard D Thames, Hubert Rodney Withers, Kathy A Mason and Mark K Transtrum

Human Inferences about Sequences: A Minimal Transition Probability Model pp. 1-26

Florent Meyniel, Maxime Maheu and Stanislas Dehaene

Zipf’s Law Arises Naturally When There Are Underlying, Unobserved Variables pp. 1-32

Laurence Aitchison, Nicola Corradi and Peter E Latham

Systematic Approximations to Susceptible-Infectious-Susceptible Dynamics on Networks pp. 1-18

Matt J Keeling, Thomas House, Alison J Cooper and Lorenzo Pellis

The Hamiltonian Brain: Efficient Probabilistic Inference with Excitatory-Inhibitory Neural Circuit Dynamics pp. 1-24

Laurence Aitchison and Máté Lengyel

Competing Mechanistic Hypotheses of Acetaminophen-Induced Hepatotoxicity Challenged by Virtual Experiments pp. 1-24

Andrew K Smith, Brenden K Petersen, Glen E P Ropella, Ryan C Kennedy, Neil Kaplowitz, Murad Ookhtens and C Anthony Hunt

Temporal Dynamics and Developmental Maturation of Salience, Default and Central-Executive Network Interactions Revealed by Variational Bayes Hidden Markov Modeling pp. 1-29

Srikanth Ryali, Kaustubh Supekar, Tianwen Chen, John Kochalka, Weidong Cai, Jonathan Nicholas, Aarthi Padmanabhan and Vinod Menon

Decoding Single Molecule Time Traces with Dynamic Disorder pp. 1-29

Wonseok Hwang, Il-Buem Lee, Seok-Cheol Hong and Changbong Hyeon

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist pp. 1-15

Brian Drawert, Andreas Hellander, Ben Bales, Debjani Banerjee, Giovanni Bellesia, Bernie J Daigle, Geoffrey Douglas, Mengyuan Gu, Anand Gupta, Stefan Hellander, Chris Horuk, Dibyendu Nath, Aviral Takkar, Sheng Wu, Per Lötstedt, Chandra Krintz and Linda R Petzold

Stimulus-Driven Population Activity Patterns in Macaque Primary Visual Cortex pp. 1-31

Benjamin R Cowley, Matthew A Smith, Adam Kohn and Byron M Yu

Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos pp. 1-31

Jonathan Desponds, Huy Tran, Teresa Ferraro, Tanguy Lucas, Carmina Perez Romero, Aurelien Guillou, Cecile Fradin, Mathieu Coppey, Nathalie Dostatni and Aleksandra M Walczak

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks pp. 1-31

Song-Yao Zhang, Shao-Wu Zhang, Lian Liu, Jia Meng and Yufei Huang

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data pp. 1-33

Simeon Carstens, Michael Nilges and Michael Habeck

When Optimal Feedback Control Is Not Enough: Feedforward Strategies Are Required for Optimal Control with Active Sensing pp. 1-22

Sang-Hoon Yeo, David W Franklin and Daniel M Wolpert

Volume 12, issue 11, 2016

Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning pp. 1-22

Jonathan A Michaels, Benjamin Dann and Hansjörg Scherberger

As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy pp. 1-31

Mona Habibi, Jörg Rottler and Steven S Plotkin

Improved Measures of Integrated Information pp. 1-34

Max Tegmark

Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1 pp. 1-34

Jeffrey S Seely, Matthew T Kaufman, Stephen I Ryu, Krishna V Shenoy, John P Cunningham and Mark M Churchland

A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging pp. 1-15

Sagi Snir, Bridgett M vonHoldt and Matteo Pellegrini

Kinase Inhibition Leads to Hormesis in a Dual Phosphorylation-Dephosphorylation Cycle pp. 1-15

Peter Rashkov, Ian P Barrett, Robert E Beardmore, Claus Bendtsen and Ivana Gudelj

Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway pp. 1-18

Kazunari Iwamoto, Yuki Shindo and Koichi Takahashi

Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan pp. 1-29

Elizabeth N Davison, Benjamin O Turner, Kimberly J Schlesinger, Michael B Miller, Scott T Grafton, Danielle S Bassett and Jean M Carlson

Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains pp. 1-46

Arno Onken, Jian K Liu, P P Chamanthi R Karunasekara, Ioannis Delis, Tim Gollisch and Stefano Panzeri

Error-Robust Modes of the Retinal Population Code pp. 1-32

Jason S Prentice, Olivier Marre, Mark L Ioffe, Adrianna R Loback, Gašper Tkačik and Michael J Berry

High-Frequency Resonance in the Gerbil Medial Superior Olive pp. 1-23

Jason Mikiel-Hunter, Vibhakar Kotak and John Rinzel

Drivers of Inter-individual Variation in Dengue Viral Load Dynamics pp. 1-26

Rotem Ben-Shachar, Scott Schmidler and Katia Koelle

Do Vascular Networks Branch Optimally or Randomly across Spatial Scales? pp. 1-28

Elif Tekin, David Hunt, Mitchell G Newberry and Savage Van M

Machine Learning for Characterization of Insect Vector Feeding pp. 1-14

Denis S Willett, Justin George, Nora S Willett, Lukasz L Stelinski and Stephen L Lapointe

Correction: Multi-level Modeling of Light-Induced Stomatal Opening Offers New Insights into Its Regulation by Drought pp. 1-1

The PLOS Computational Biology Staff

WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning pp. 1-35

George L Sutphin, J Matthew Mahoney, Keith Sheppard, David O Walton and Ron Korstanje

Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay pp. 1-35

Adam F Prasanphanich, Douglas E White, Margaret A Gran and Melissa L Kemp

Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference pp. 1-20

Kieran R Campbell and Christopher Yau

Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion pp. 1-16

Mahdi Golkaram, Stefan Hellander, Brian Drawert and Linda R Petzold

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks pp. 1-30

Hulda S Haraldsdóttir and Ronan M T Fleming

Interrogating Emergent Transport Properties for Molecular Motor Ensembles: A Semi-analytical Approach pp. 1-30

Shreyas Bhaban, Donatello Materassi, Mingang Li, Thomas Hays and Murti Salapaka

NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents pp. 1-12

Sophia S Liu, Adam J Hockenberry, Andrea Lancichinetti, Michael C Jewett and Luís A N Amaral

Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue pp. 1-38

Geir Halnes, Tuomo Mäki-Marttunen, Daniel Keller, Klas H Pettersen, Ole A Andreassen and Gaute T Einevoll

Volume 12, issue 10, 2016

Forgetting in Reinforcement Learning Links Sustained Dopamine Signals to Motivation pp. 1-41

Ayaka Kato and Kenji Morita

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison pp. 1-18

Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi and Burkhard Morgenstern

Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements pp. 1-18

Samuel M D Oliveira, Antti Häkkinen, Jason Lloyd-Price, Huy Tran, Vinodh Kandavalli and Andre S Ribeiro

Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction pp. 1-24

Daniel Machado, Markus J Herrgård and Isabel Rocha

Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches pp. 1-23

Ruben Perez-Carrasco, Pilar Guerrero, James Briscoe and Karen M Page

Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing pp. 1-26

Hansaim Lim, Aleksandar Poleksic, Yuan Yao, Hanghang Tong, Di He, Luke Zhuang, Patrick Meng and Lei Xie

Ten Simple Rules for Developing a MOOC pp. 1-4

David T Manallack and Elizabeth Yuriev

A Parsimonious Model of the Rabbit Action Potential Elucidates the Minimal Physiological Requirements for Alternans and Spiral Wave Breakup pp. 1-21

Richard A Gray and Pras Pathmanathan

Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections pp. 1-21

Jason Karslake, Jeff Maltas, Peter Brumm and Kevin B Wood

Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair pp. 1-21

Mae L Woods and Chris P Barnes

The Spatial Dynamics of Predators and the Benefits and Costs of Sharing Information pp. 1-22

Matthieu Barbier and James R Watson

Structural Identifiability of Dynamic Systems Biology Models pp. 1-22

Alejandro F Villaverde, Antonio Barreiro and Antonis Papachristodoulou

PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse pp. 1-22

Kerstin Reuter, Alexander Biehl, Laurena Koch and Volkhard Helms

Retrospective Parameter Estimation and Forecast of Respiratory Syncytial Virus in the United States pp. 1-15

Julia Reis and Jeffrey Shaman

Identifying Anatomical Origins of Coexisting Oscillations in the Cortical Microcircuit pp. 1-34

Hannah Bos, Markus Diesmann and Moritz Helias

How Do Efficient Coding Strategies Depend on Origins of Noise in Neural Circuits? pp. 1-34

Braden A W Brinkman, Alison I Weber, Fred Rieke and Eric Shea-Brown

Functional Connectivity’s Degenerate View of Brain Computation pp. 1-25

Guillaume Marrelec, Arnaud Messé, Alain Giron and David Rudrauf

Likelihood-Based Inference of B Cell Clonal Families pp. 1-28

Duncan K Ralph and Frederick A Matsen Iv

Glucose Oscillations Can Activate an Endogenous Oscillator in Pancreatic Islets pp. 1-19

Joseph P McKenna, Raghuram Dhumpa, Nikita Mukhitov, Michael G Roper and Richard Bertram

SARAH Domain-Mediated MST2-RASSF Dimeric Interactions pp. 1-20

Goar Sánchez-Sanz, Bartłomiej Tywoniuk, David Matallanas, David Romano, Lan K Nguyen, Boris N Kholodenko, Edina Rosta, Walter Kolch and Nicolae-Viorel Buchete

Mechano-chemical Interactions in Cardiac Sarcomere Contraction: A Computational Modeling Study pp. 1-20

Lauren J Dupuis, Joost Lumens, Theo Arts and Tammo Delhaas

Volume 12, issue 9, 2016

Statistical Analysis of Tract-Tracing Experiments Demonstrates a Dense, Complex Cortical Network in the Mouse pp. 1-22

Rolf J F Ypma and Edward T Bullmore

The Edge of Stability: Response Times and Delta Oscillations in Balanced Networks pp. 1-22

Grant Gillary and Ernst Niebur

Leukocyte Motility Models Assessed through Simulation and Multi-objective Optimization-Based Model Selection pp. 1-34

Mark N Read, Jacqueline Bailey, Jon Timmis and Tatyana Chtanova

The Computational Properties of a Simplified Cortical Column Model pp. 1-18

Nicholas Cain, Ramakrishnan Iyer, Christof Koch and Stefan Mihalas

Nonlinear Hebbian Learning as a Unifying Principle in Receptive Field Formation pp. 1-24

Carlos S N Brito and Wulfram Gerstner

Separating Timing, Movement Conditions and Individual Differences in the Analysis of Human Movement pp. 1-27

Lars Lau Raket, Britta Grimme, Gregor Schöner, Christian Igel and Bo Markussen

Stimulation-Based Control of Dynamic Brain Networks pp. 1-23

Sarah Feldt Muldoon, Fabio Pasqualetti, Shi Gu, Matthew Cieslak, Scott T Grafton, Jean M Vettel and Danielle S Bassett

Forecasting Human African Trypanosomiasis Prevalences from Population Screening Data Using Continuous Time Models pp. 1-23

Harwin de Vries, Albert P M Wagelmans, Epco Hasker, Crispin Lumbala, Pascal Lutumba, Sake J de Vlas and Joris van de Klundert

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent pp. 1-23

Nicola De Maio, Chieh-Hsi Wu and Daniel J Wilson

Learning Reward Uncertainty in the Basal Ganglia pp. 1-28

John G Mikhael and Rafal Bogacz

SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis pp. 1-19

Maria Kogadeeva and Nicola Zamboni

M-Track: A New Software for Automated Detection of Grooming Trajectories in Mice pp. 1-19

Sheldon L Reeves, Kelsey E Fleming, Lin Zhang and Annalisa Scimemi

Novel Covariance-Based Neutrality Test of Time-Series Data Reveals Asymmetries in Ecological and Economic Systems pp. 1-14

Alex D Washburne, Joshua W Burby and Daniel Lacker

Bipartite Community Structure of eQTLs pp. 1-17

John Platig, Peter J Castaldi, Dawn DeMeo and John Quackenbush

How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates pp. 1-17

Fabian Paul and Thomas R Weikl

Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes pp. 1-17

Abibatou Mbodj, E Hilary Gustafson, Lucia Ciglar, Guillaume Junion, Aitor Gonzalez, Charles Girardot, Laurent Perrin, Eileen E M Furlong and Denis Thieffry

Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline pp. 1-17

Hao Chen, Jorge Chan-Lau, Michael Thomas Wong, Evan W Newell, Michael Poidinger and Jinmiao Chen

The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community pp. 1-13

Xiaokan Guo and James Q Boedicker

A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains pp. 1-11

Florian C Rieger and Peter Virnau

The Statistical Determinants of the Speed of Motor Learning pp. 1-20

Kang He, You Liang, Farnaz Abdollahi, Moria Fisher Bittmann, Konrad Kording and Kunlin Wei

Including Thermal Fluctuations in Actomyosin Stable States Increases the Predicted Force per Motor and Macroscopic Efficiency in Muscle Modelling pp. 1-20

Lorenzo Marcucci, Takumi Washio and Toshio Yanagida

A Computational Model of Hepatic Energy Metabolism: Understanding Zonated Damage and Steatosis in NAFLD pp. 1-30

William B Ashworth, Nathan A Davies and I David L Bogle

Error Correction and the Structure of Inter-Trial Fluctuations in a Redundant Movement Task pp. 1-30

Joby John, Jonathan B Dingwell and Joseph P Cusumano

Direct Correlation between Motile Behavior and Protein Abundance in Single Cells pp. 1-25

Yann S Dufour, Sébastien Gillet, Nicholas W Frankel, Douglas B Weibel and Thierry Emonet

Volume 12, issue 8, 2016

Impact of Heterogeneity in Sexual Behavior on Effectiveness in Reducing HIV Transmission with Test-and-Treat Strategy pp. 1-20

Ganna Rozhnova, Maarten F Schim van der Loeff, Janneke C M Heijne and Mirjam E Kretzschmar

Inference of Gene Regulatory Network Based on Local Bayesian Networks pp. 1-17

Fei Liu, Shao-Wu Zhang, Wei-Feng Guo, Ze-Gang Wei and Luonan Chen

Structure Prediction of RNA Loops with a Probabilistic Approach pp. 1-17

Jun Li, Jian Zhang, Jun Wang, Wenfei Li and Wei Wang

Defining the Product Chemical Space of Monoterpenoid Synthases pp. 1-13

Boxue Tian, C Dale Poulter and Matthew P Jacobson

Predicted Molecular Effects of Sequence Variants Link to System Level of Disease pp. 1-14

Jonas Reeb, Maximilian Hecht, Yannick Mahlich, Yana Bromberg and Burkhard Rost

Modeling of Large-Scale Functional Brain Networks Based on Structural Connectivity from DTI: Comparison with EEG Derived Phase Coupling Networks and Evaluation of Alternative Methods along the Modeling Path pp. 1-28

Holger Finger, Marlene Bönstrup, Bastian Cheng, Arnaud Messé, Claus Hilgetag, Götz Thomalla, Christian Gerloff and Peter König

Neuromotor Noise Is Malleable by Amplifying Perceived Errors pp. 1-28

Christopher J Hasson, Zhaoran Zhang, Masaki O Abe and Dagmar Sternad

The Representation of Prediction Error in Auditory Cortex pp. 1-28

Jonathan Rubin, Nachum Ulanovsky, Israel Nelken and Naftali Tishby

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data pp. 1-28

Daphne Ezer, Victoria Moignard, Berthold Göttgens and Boris Adryan

The Complexity of Dynamics in Small Neural Circuits pp. 1-35

Diego Fasoli, Anna Cattani and Stefano Panzeri

A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases pp. 1-38

Tamra Heberling, Lisa Davis, Jakub Gedeon, Charles Morgan and Tomáš Gedeon

metagene Profiles Analyses Reveal Regulatory Element’s Factor-Specific Recruitment Patterns pp. 1-12

Charles Joly Beauparlant, Fabien C Lamaze, Astrid Deschênes, Rawane Samb, Audrey Lemaçon, Pascal Belleau, Steve Bilodeau and Arnaud Droit

Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells pp. 1-34

Ruth Merkle, Bernhard Steiert, Florian Salopiata, Sofia Depner, Andreas Raue, Nao Iwamoto, Max Schelker, Helge Hass, Marvin Wäsch, Martin E Böhm, Oliver Mücke, Daniel B Lipka, Christoph Plass, Wolf D Lehmann, Clemens Kreutz, Jens Timmer, Marcel Schilling and Ursula Klingmüller

When Does Model-Based Control Pay Off? pp. 1-34

Wouter Kool, Fiery A Cushman and Samuel J Gershman

The Virtuous Cycle of a Data Ecosystem pp. 1-6

Bradley Voytek

Evolutionary Games of Multiplayer Cooperation on Graphs pp. 1-15

Jorge Peña, Bin Wu, Jordi Arranz and Arne Traulsen

Comparison of Detailed and Simplified Models of Human Atrial Myocytes to Recapitulate Patient Specific Properties pp. 1-15

Daniel M Lombardo, Flavio H Fenton, Sanjiv M Narayan and Wouter-Jan Rappel

Autonomous Optimization of Targeted Stimulation of Neuronal Networks pp. 1-22

Sreedhar S Kumar, Jan Wülfing, Samora Okujeni, Joschka Boedecker, Martin Riedmiller and Ulrich Egert

Inverse Stochastic Resonance in Cerebellar Purkinje Cells pp. 1-31

Anatoly Buchin, Sarah Rieubland, Michael Häusser, Boris S Gutkin and Arnd Roth

Malaria Incidence Rates from Time Series of 2-Wave Panel Surveys pp. 1-26

Marcia C Castro, Mathieu Maheu-Giroux, Christinah Chiyaka and Burton H Singer

Flow-Based Network Analysis of the Caenorhabditis elegans Connectome pp. 1-27

Karol A Bacik, Michael T Schaub, Mariano Beguerisse-Díaz, Yazan N Billeh and Mauricio Barahona

Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes pp. 1-23

Mohammad Soltani, Cesar A Vargas-Garcia, Duarte Antunes and Abhyudai Singh

Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks pp. 1-23

Brendan Chambers and Jason N MacLean

Volume 12, issue 7, 2016

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles pp. 1-22

Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S McLean and Shibu Yooseph

Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling pp. 1-33

Manikandan Narayanan, Andrew J Martins and John S Tsang

Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering pp. 1-39

Chuan Gao, Ian C McDowell, Shiwen Zhao, Christopher D Brown and Barbara E Engelhardt

ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains pp. 1-34

Emiliano Torre, Carlos Canova, Michael Denker, George Gerstein, Moritz Helias and Sonja Grün

Ten Simple Rules for Writing a Postdoctoral Fellowship pp. 1-6

Ke Yuan, Lei Cai, Siu Ping Ngok, Li Ma and Crystal M Botham

Computing Biology pp. 1-3

Ruth Nussinov and Jason A Papin

Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling pp. 1-29

Javier Estrada, Natalie Andrew, Daniel Gibson, Frederick Chang, Florian Gnad and Jeremy Gunawardena

Modeling Electrophysiological Coupling and Fusion between Human Mesenchymal Stem Cells and Cardiomyocytes pp. 1-29

Joshua Mayourian, Ruben M Savizky, Eric A Sobie and Kevin D Costa

A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism pp. 1-24

Nathan Mih, Elizabeth Brunk, Aarash Bordbar and Bernhard O Palsson

Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data pp. 1-18

Yuheng Lu and Christina S Leslie

Near Equilibrium Calculus of Stem Cells in Application to the Airway Epithelium Lineage pp. 1-21

Zheng Sun, Maksim V Plikus and Natalia L Komarova

Intrinsic Valuation of Information in Decision Making under Uncertainty pp. 1-21

Daniel Bennett, Stefan Bode, Maja Brydevall, Hayley Warren and Carsten Murawski

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights pp. 1-26

Edoardo Pasolli, Duy Tin Truong, Faizan Malik, Levi Waldron and Nicola Segata

A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation pp. 1-23

Pei-Chi Yang, Britton W Boras, Mao-Tsuen Jeng, Steffen S Docken, Timothy J Lewis, Andrew D McCulloch, Robert D Harvey and Colleen E Clancy

Dynamic Reweighting of Auditory Modulation Filters pp. 1-23

Eva R M Joosten, Shihab A Shamma, Christian Lorenzi and Peter Neri

Properties of Neurons in External Globus Pallidus Can Support Optimal Action Selection pp. 1-28

Rafal Bogacz, Eduardo Martin Moraud, Azzedine Abdi, Peter J Magill and Jérôme Baufreton

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion pp. 1-28

Fabian Fröhlich, Philipp Thomas, Atefeh Kazeroonian, Fabian J Theis, Simon Grima and Jan Hasenauer

Ancestral Reconstruction pp. 1-20

Jeffrey B Joy, Richard H Liang, Rosemary M McCloskey, T Nguyen and Art F Y Poon

Disease Surveillance on Complex Social Networks pp. 1-16

Jose L Herrera, Ravi Srinivasan, John S Brownstein, Alison P Galvani and Lauren Ancel Meyers

Ten Simple Rules for Taking Advantage of Git and GitHub pp. 1-11

Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J Eglen, Daniel S Katz, Tom J Pollard, Alexander Konovalov, Robert M Flight, Kai Blin and Juan Antonio Vizcaíno

How People Use Social Information to Find out What to Want in the Paradigmatic Case of Inter-temporal Preferences pp. 1-17

Michael Moutoussis, Raymond J Dolan and Peter Dayan

The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube Formation pp. 1-13

Julian Weichsel and Phillip L Geissler

Reinforcement Learning Explains Conditional Cooperation and Its Moody Cousin pp. 1-13

Takahiro Ezaki, Yutaka Horita, Masanori Takezawa and Naoki Masuda

Ten Simple Rules for Curating and Facilitating Small Workshops pp. 1-8

Greg J McInerny

Volume 12, issue 6, 2016

Ten Simple Rules for Effective Statistical Practice pp. 1-8

Robert E Kass, Brian S Caffo, Marie Davidian, Xiao-Li Meng, Bin Yu and Nancy Reid

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale pp. 1-25

Daniel L Parton, Patrick B Grinaway, Sonya M Hanson, Kyle A Beauchamp and John D Chodera

The Computational Development of Reinforcement Learning during Adolescence pp. 1-25

Stefano Palminteri, Emma J Kilford, Giorgio Coricelli and Sarah-Jayne Blakemore

Electrophysiology of Heart Failure Using a Rabbit Model: From the Failing Myocyte to Ventricular Fibrillation pp. 1-25

Aditya V S Ponnaluri, Luigi E Perotti, Michael Liu, Zhilin Qu, James N Weiss, Daniel B Ennis, William S Klug and Alan Garfinkel

Adaptive Spike Threshold Enables Robust and Temporally Precise Neuronal Encoding pp. 1-25

Chao Huang, Andrey Resnik, Tansu Celikel and Bernhard Englitz

Graded, Dynamically Routable Information Processing with Synfire-Gated Synfire Chains pp. 1-17

Zhuo Wang, Andrew T Sornborger and Louis Tao

Interplay between Graph Topology and Correlations of Third Order in Spiking Neuronal Networks pp. 1-28

Stojan Jovanović and Stefan Rotter

Mechanistic Mathematical Modeling Tests Hypotheses of the Neurovascular Coupling in fMRI pp. 1-28

Karin Lundengård, Gunnar Cedersund, Sebastian Sten, Felix Leong, Alexander Smedberg, Fredrik Elinder and Maria Engström

Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches pp. 1-27

Tobias Sikosek, Heinrich Krobath and Hue Sun Chan

Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level pp. 1-23

Xinge Jessie Jeng, Zhongyin John Daye, Wenbin Lu and Jung-Ying Tzeng

Stochastic Simulation of Biomolecular Networks in Dynamic Environments pp. 1-18

Margaritis Voliotis, Philipp Thomas, Simon Grima and Clive Bowsher

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis pp. 1-41

Rebeca Campos-Sánchez, Marzia A Cremona, Alessia Pini, Francesca Chiaromonte and Kateryna D Makova

Program Bytes: Satellite Meetings, SIGs, and AKEs at ISMB 2016 pp. 1-2

Christiana N Fogg and Diane E Kovats

Competitive Dynamics in MSTd: A Mechanism for Robust Heading Perception Based on Optic Flow pp. 1-37

Oliver W Layton and Brett R Fajen

Modeling Inter-trial Variability of Saccade Trajectories: Effects of Lesions of the Oculomotor Part of the Fastigial Nucleus pp. 1-33

Thomas Eggert, Farrel R Robinson and Andreas Straube

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases pp. 1-33

David Lee, Sayoni Das, Natalie L Dawson, Dragana Dobrijevic, John Ward and Christine Orengo

Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers pp. 1-12

Michelle D Brazas and B F Francis Ouellette

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data pp. 1-12

Daniel H Huson, Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh and Rewati Tappu

Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data pp. 1-20

John D O’Brien, Zamin Iqbal, Jason Wendler and Lucas Amenga-Etego

Filopodial-Tension Model of Convergent-Extension of Tissues pp. 1-20

Julio M Belmonte, Maciej H Swat and James A Glazier

Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations pp. 1-16

Samuel Hertig, Naomi R Latorraca and Ron O Dror

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis pp. 1-16

David P Noren, Byron L Long, Raquel Norel, Kahn Rrhissorrakrai, Kenneth Hess, Chenyue Wendy Hu, Alex J Bisberg, Andre Schultz, Erik Engquist, Li Liu, Xihui Lin, Gregory M Chen, Honglei Xie, Geoffrey A M Hunter, Paul C Boutros, Oleg Stepanov, 9 AML-OPC Consortium Dream, Thea Norman, Stephen H Friend, Gustavo Stolovitzky, Steven Kornblau and Amina A Qutub

Implementation Considerations, Not Topological Differences, Are the Main Determinants of Noise Suppression Properties in Feedback and Incoherent Feedforward Circuits pp. 1-16

Gentian Buzi and Mustafa Khammash

Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks pp. 1-16

Anthony Szedlak, Nicholas Smith, Li Liu, Giovanni Paternostro and Carlo Piermarocchi

Computing Average Passive Forces in Sarcomeres in Length-Ramp Simulations pp. 1-14

Gudrun Schappacher-Tilp, Timothy Leonard, Gertrud Desch and Walter Herzog

Computationally Efficient Implementation of a Novel Algorithm for the General Unified Threshold Model of Survival (GUTS) pp. 1-19

Carlo Albert, Sören Vogel and Roman Ashauer

How to Estimate Epidemic Risk from Incomplete Contact Diaries Data? pp. 1-19

Rossana Mastrandrea and Alain Barrat

Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering pp. 1-32

Elisa Boari de Lima, Wagner Meira Júnior and Raquel Cardoso de Melo-Minardi

Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability pp. 1-10

Bastian Schiffthaler, Myrto Kostadima, Trainer Consortium Ngs, Nicolas Delhomme and Gabriella Rustici

Learning Universal Computations with Spikes pp. 1-29

Dominik Thalmeier, Marvin Uhlmann, Hilbert J Kappen and Raoul-Martin Memmesheimer

An Introduction to Programming for Bioscientists: A Python-Based Primer pp. 1-43

Berk Ekmekci, Charles E McAnany and Cameron Mura

Model Constrained by Visual Hierarchy Improves Prediction of Neural Responses to Natural Scenes pp. 1-22

Ján Antolík, Sonja B Hofer, James A Bednar and Thomas D Mrsic-Flogel

Formal Models of the Network Co-occurrence Underlying Mental Operations pp. 1-31

Danilo Bzdok, Gaël Varoquaux, Olivier Grisel, Michael Eickenberg, Cyril Poupon and Bertrand Thirion

Volume 12, issue 5, 2016

Optimal Current Transfer in Dendrites pp. 1-12

Alex D Bird and Hermann Cuntz

The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach pp. 1-16

Pascal Giehr, Charalampos Kyriakopoulos, Gabriella Ficz, Verena Wolf and Jörn Walter

Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks pp. 1-20

Song Feng, Julien F Ollivier and Orkun S Soyer

A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett’s Esophagus pp. 1-20

Kit Curtius, Chao-Jen Wong, William D Hazelton, Andrew M Kaz, Amitabh Chak, Joseph E Willis, William M Grady and E Georg Luebeck

The Maximum Entropy Fallacy Redux? pp. 1-7

Erik Aurell

Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression pp. 1-28

John Wiedenhoeft, Eric Brugel and Alexander Schliep

Structural Determinants of Misfolding in Multidomain Proteins pp. 1-28

Pengfei Tian and Robert B Best

To Cooperate or Not to Cooperate: Why Behavioural Mechanisms Matter pp. 1-14

Arthur Bernard, Jean-Baptiste André and Nicolas Bredeche

Tuning Curves for Arm Posture Control in Motor Cortex Are Consistent with Random Connectivity pp. 1-27

Hagai Lalazar, L F Abbott and Eilon Vaadia

Evaluation of the Phase-Dependent Rhythm Control of Human Walking Using Phase Response Curves pp. 1-23

Tetsuro Funato, Yuki Yamamoto, Shinya Aoi, Takashi Imai, Toshio Aoyagi, Nozomi Tomita and Kazuo Tsuchiya

A Single Mechanism Can Account for Human Perception of Depth in Mixed Correlation Random Dot Stereograms pp. 1-21

Sid Henriksen, Bruce G Cumming and Jenny C A Read

Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties pp. 1-21

Andrew F Neuwald and Stephen F Altschul

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee) pp. 1-4

Lonnie Welch, Cath Brooksbank, Russell Schwartz, Sarah L Morgan, Bruno Gaeta, Alastair M Kilpatrick, Daniel Mietchen, Benjamin L Moore, Nicola Mulder, Mark Pauley, William Pearson, Predrag Radivojac, Naomi Rosenberg, Anne Rosenwald, Gabriella Rustici and Tandy Warnow

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics pp. 1-26

Lisa M Breckels, Sean B Holden, David Wojnar, Claire M Mulvey, Andy Christoforou, Arnoud Groen, Matthew W B Trotter, Oliver Kohlbacher, Kathryn S Lilley and Laurent Gatto

Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? pp. 1-10

Erik van Nimwegen

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models pp. 1-18

Hugo Jacquin, Amy Gilson, Eugene Shakhnovich, Simona Cocco and Rémi Monasson

Neuroprosthetic Decoder Training as Imitation Learning pp. 1-24

Josh Merel, David Carlson, Liam Paninski and John P Cunningham

Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions pp. 1-29

Natalie S Scholes and Robert O J Weinzierl

Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance pp. 1-15

Hannah E Clapham, Than Ha Quyen, Duong Thi Hue Kien, Ilaria Dorigatti, Cameron P Simmons and Neil M Ferguson

Bridging Mechanistic and Phenomenological Models of Complex Biological Systems pp. 1-34

Mark K Transtrum and Peng Qiu

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes pp. 1-22

Jerome Kelleher, Alison M Etheridge and Gilean McVean

Volume 12, issue 4, 2016

Problem Solving as Probabilistic Inference with Subgoaling: Explaining Human Successes and Pitfalls in the Tower of Hanoi pp. 1-30

Francesco Donnarumma, Domenico Maisto and Giovanni Pezzulo

MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks pp. 1-35

Konstantin Popov, James Komianos and Garegin A Papoian

Quorum Sensing Desynchronization Leads to Bimodality and Patterned Behaviors pp. 1-19

David N Quan, Chen-Yu Tsao, Hsuan-Chen Wu and William E Bentley

Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System pp. 1-14

Maulik K Nariya, Johnny Israeli, Jack J Shi and Eric J Deeds

Fast and Accurate Learning When Making Discrete Numerical Estimates pp. 1-28

Adam N Sanborn and Ulrik R Beierholm

AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression pp. 1-28

Sara Ballouz and Jesse Gillis

The Development of Audio-Visual Integration for Temporal Judgements pp. 1-17

Wendy J Adams

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity pp. 1-20

Lorenzo Asti, Guido Uguzzoni, Paolo Marcatili and Andrea Pagnani

Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees pp. 1-29

Eben Kenah, Tom Britton, M Elizabeth Halloran and Ira M Longini

Detecting Presymptomatic Infection Is Necessary to Forecast Major Epidemics in the Earliest Stages of Infectious Disease Outbreaks pp. 1-18

Robin N Thompson, Christopher A Gilligan and Nik J Cunniffe

The Evolution of Quorum Sensing as a Mechanism to Infer Kinship pp. 1-18

Jonas Schluter, Armin P Schoech, Kevin R Foster and Sara Mitri

Mechanical Stress Induces Remodeling of Vascular Networks in Growing Leaves pp. 1-21

Yohai Bar-Sinai, Jean-Daniel Julien, Eran Sharon, Shahaf Armon, Naomi Nakayama, Mokhtar Adda-Bedia and Arezki Boudaoud

Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes pp. 1-21

Amit A Upadhyay, Aaron D Fleetwood, Ogun Adebali, Robert D Finn and Igor B Zhulin

Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery pp. 1-21

Robert Kalescky, Hongyu Zhou, Jin Liu and Peng Tao

An Electrostatic Funnel in the GABA-Binding Pathway pp. 1-23

Timothy S Carpenter and Felice C Lightstone

A Geometrically-Constrained Mathematical Model of Mammary Gland Ductal Elongation Reveals Novel Cellular Dynamics within the Terminal End Bud pp. 1-23

Ingrid Paine, Arnaud Chauviere, John Landua, Amulya Sreekumar, Vittorio Cristini, Jeffrey Rosen and Michael T Lewis

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics pp. 1-70

Tatiana Maximova, Ryan Moffatt, Buyong Ma, Ruth Nussinov and Amarda Shehu

Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory pp. 1-33

Evgeni V Nikolaev and Eduardo D Sontag

Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming pp. 1-22

Stephen Gang Wu, Yuxuan Wang, Wu Jiang, Tolutola Oyetunde, Ruilian Yao, Xuehong Zhang, Kazuyuki Shimizu, Yinjie J Tang and Forrest Sheng Bao

Traveling Pulses for a Two-Species Chemotaxis Model pp. 1-22

Casimir Emako, Charlène Gayrard, Axel Buguin, Luís Neves de Almeida and Nicolas Vauchelet

Exploiting Gene-Expression Deconvolution to Probe the Genetics of the Immune System pp. 1-22

Yael Steuerman and Irit Gat-Viks

A Robust Feedforward Model of the Olfactory System pp. 1-15

Yilun Zhang and Tatyana O Sharpee

Volume 12, issue 3, 2016

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments pp. 1-23

Ramya Raviram, Pedro P Rocha, Christian L Müller, Emily R Miraldi, Sana Badri, Yi Fu, Emily Swanzey, Charlotte Proudhon, Valentina Snetkova, Richard Bonneau and Jane A Skok

Pathway-Based Genomics Prediction using Generalized Elastic Net pp. 1-23

Artem Sokolov, Daniel E Carlin, Evan O Paull, Robert Baertsch and Joshua M Stuart

Persistence and Adaptation in Immunity: T Cells Balance the Extent and Thoroughness of Search pp. 1-23

G Matthew Fricke, Kenneth A Letendre, Melanie E Moses and Judy L Cannon

A Sensorimotor Model for Computing Intended Reach Trajectories pp. 1-27

Cevat Üstün

Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability pp. 1-27

Sam F Greenbury, Steffen Schaper, Sebastian E Ahnert and Ard A Louis

Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection pp. 1-27

Andreas Milias-Argeitis, Ana Paula Oliveira, Luca Gerosa, Laura Falter, Uwe Sauer and John Lygeros

Noise Expands the Response Range of the Bacillus subtilis Competence Circuit pp. 1-21

Andrew Mugler, Mark Kittisopikul, Luke Hayden, Jintao Liu, Chris H Wiggins, Gürol M Süel and Aleksandra M Walczak

Stability and Competition in Multi-spike Models of Spike-Timing Dependent Plasticity pp. 1-26

Baktash Babadi and L F Abbott

Stability of Ensemble Models Predicts Productivity of Enzymatic Systems pp. 1-18

Matthew K Theisen, Jimmy G Lafontaine Rivera and James C Liao

ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing pp. 1-2

Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine Orengo, Bruno Gaeta, Scott Markel and Alfonso Valencia

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA pp. 1-33

André Schultz and Amina A Qutub

Annealed Importance Sampling for Neural Mass Models pp. 1-25

Will Penny and Biswa Sengupta

Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb pp. 1-25

Anat Kahan and Yoram Ben-Shaul

Quantitative Analysis of Axonal Branch Dynamics in the Developing Nervous System pp. 1-25

Kelsey Chalmers, Elizabeth M Kita, Ethan K Scott and Geoffrey J Goodhill

A New Fiji-Based Algorithm That Systematically Quantifies Nine Synaptic Parameters Provides Insights into Drosophila NMJ Morphometry pp. 1-25

Bonnie Nijhof, Anna Castells-Nobau, Louis Wolf, Jolanda M Scheffer- de Gooyert, Ignacio Monedero, Laura Torroja, Lluis Coromina, Jeroen A W M van der Laak and Annette Schenck

Systems Approaches to the Eukaryotic Stress Response pp. 1-8

Christine Vogel

Estimation of Directed Effective Connectivity from fMRI Functional Connectivity Hints at Asymmetries of Cortical Connectome pp. 1-30

Matthieu Gilson, Ruben Moreno-Bote, Adrián Ponce-Alvarez, Petra Ritter and Gustavo Deco

Causal Inference for Spatial Constancy across Saccades pp. 1-20

Jeroen Atsma, Femke Maij, Mathieu Koppen, David E Irwin and W Pieter Medendorp

Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data pp. 1-20

Andrej Kuritzin, Tabea Kischka, Jürgen Schmitz and Gennady Churakov

H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation pp. 1-13

Jinzen Ikebe, Shun Sakuraba and Hidetoshi Kono

Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces pp. 1-17

Cristiano De Michele, Paolo De Los Rios, Giuseppe Foffi and Francesco Piazza

Early Transcriptome Signatures from Immunized Mouse Dendritic Cells Predict Late Vaccine-Induced T-Cell Responses pp. 1-17

Nicolas Dérian, Bertrand Bellier, Hang Phuong Pham, Eliza Tsitoura, Dorothea Kazazi, Christophe Huret, Penelope Mavromara, David Klatzmann and Adrien Six

Dynamic Modelling Reveals ‘Hotspots’ on the Pathway to Enzyme-Substrate Complex Formation pp. 1-17

Shane E Gordon, Daniel K Weber, Matthew T Downton, John Wagner and Matthew A Perugini

Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies pp. 1-28

Nils Giordano, Francis Mairet, Jean-Luc Gouzé, Johannes Geiselmann and Hidde de Jong

SMOG 2: A Versatile Software Package for Generating Structure-Based Models pp. 1-14

Jeffrey K Noel, Mariana Levi, Mohit Raghunathan, Heiko Lammert, Ryan L Hayes, José N Onuchic and Paul C Whitford

Distinguishing Antimicrobial Models with Different Resistance Mechanisms via Population Pharmacodynamic Modeling pp. 1-19

Matthieu Jacobs, Nicolas Grégoire, William Couet and Jurgen B Bulitta

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference pp. 1-19

Michael D Karcher, Julia A Palacios, Trevor Bedford, Marc A Suchard and Vladimir N Minin

Volume 12, issue 2, 2016

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt pp. 1-15

Nicola J Mulder, Alan Christoffels, Tulio de Oliveira, Junaid Gamieldien, Scott Hazelhurst, Fourie Joubert, Judit Kumuthini, Ché S Pillay, Jacky L Snoep, Özlem Tastan Bishop and Nicki Tiffin

The 2015 Bioinformatics Open Source Conference (BOSC 2015) pp. 1-6

Nomi L Harris, Peter J A Cock, Hilmar Lapp, Brad Chapman, Rob Davey, Christopher Fields, Karsten Hokamp and Monica Munoz-Torres

Ten Simple Rules for Selecting a Bio-ontology pp. 1-6

James Malone, Robert Stevens, Simon Jupp, Tom Hancocks, Helen Parkinson and Cath Brooksbank

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers pp. 1-31

Yasin Şenbabaoğlu, Selçuk Onur Sümer, Francisco Sánchez-Vega, Debra Bemis, Giovanni Ciriello, Nikolaus Schultz and Chris Sander

Ensemble Tractography pp. 1-22

Hiromasa Takemura, Cesar F Caiafa, Brian A Wandell and Franco Pestilli

Non-monotonic Response to Monotonic Stimulus: Regulation of Glyoxylate Shunt Gene-Expression Dynamics in Mycobacterium tuberculosis pp. 1-22

Joao A Ascensao, Pratik Datta, Baris Hancioglu, Eduardo Sontag, Maria L Gennaro and Oleg A Igoshin

Recovery of Dynamics and Function in Spiking Neural Networks with Closed-Loop Control pp. 1-27

Ioannis Vlachos, Taşkin Deniz, Ad Aertsen and Arvind Kumar

Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin pp. 1-23

Tiziano Dallavilla, Laurence Abrami, Patrick A Sandoz, Georgios Savoglidis, Vassily Hatzimanikatis and F Gisou van der Goot

Non-monotonic Temporal-Weighting Indicates a Dynamically Modulated Evidence-Integration Mechanism pp. 1-21

Zohar Z Bronfman, Noam Brezis and Marius Usher

On the Origins and Control of Community Types in the Human Microbiome pp. 1-21

Travis E Gibson, Amir Bashan, Hong-Tai Cao, Scott T Weiss and Yang-Yu Liu

Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction pp. 1-26

Yong Liu, Min Wu, Chunyan Miao, Peilin Zhao and Xiao-Li Li

Control of βAR- and N-methyl-D-aspartate (NMDA) Receptor-Dependent cAMP Dynamics in Hippocampal Neurons pp. 1-32

Andrew Chay, Ilaria Zamparo, Andreas Koschinski, Manuela Zaccolo and Kim T Blackwell

What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast pp. 1-18

Artémis Llamosi, Andres M Gonzalez-Vargas, Cristian Versari, Eugenio Cinquemani, Giancarlo Ferrari-Trecate, Pascal Hersen and Gregory Batt

A Feedback Model of Attention Explains the Diverse Effects of Attention on Neural Firing Rates and Receptive Field Structure pp. 1-18

Thomas Miconi and Rufin VanRullen

Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia pp. 1-24

Javier Macia, Romilde Manzoni, Núria Conde, Arturo Urrios, Eulàlia de Nadal, Ricard Solé and Francesc Posas

PSAMM: A Portable System for the Analysis of Metabolic Models pp. 1-29

Jon Lund Steffensen, Keith Dufault-Thompson and Ying Zhang

Quantifying Transmission Investment in Malaria Parasites pp. 1-16

Megan A Greischar, Nicole Mideo, Andrew F Read and Ottar N Bjørnstad

FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks pp. 1-16

Ting Wang, Zhao Ren, Ying Ding, Zhou Fang, Zhe Sun, Matthew L MacDonald, Robert A Sweet, Jieru Wang and Wei Chen

Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies pp. 1-28

Benedikt Frieg, Boris Görg, Nadine Homeyer, Verena Keitel, Dieter Häussinger and Holger Gohlke

Oligomers of Heat-Shock Proteins: Structures That Don’t Imply Function pp. 1-14

William M Jacobs, Tuomas P J Knowles and Daan Frenkel

Cortical Resonance Frequencies Emerge from Network Size and Connectivity pp. 1-19

Caroline A Lea-Carnall, Marcelo A Montemurro, Nelson J Trujillo-Barreto, Laura M Parkes and Wael El-Deredy

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories pp. 1-25

Rory M Donovan, Jose-Juan Tapia, Devin P Sullivan, James R Faeder, Robert F Murphy, Markus Dittrich and Daniel M Zuckerman

Evolution of Cooperation in Social Dilemmas on Complex Networks pp. 1-25

Swami Iyer and Timothy Killingback

Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons pp. 1-38

Skander Mensi, Olivier Hagens, Wulfram Gerstner and Christian Pozzorini

Persistent Chaos of Measles Epidemics in the Prevaccination United States Caused by a Small Change in Seasonal Transmission Patterns pp. 1-12

Benjamin D Dalziel, Ottar N Bjørnstad, Willem G van Panhuis, Donald S Burke, C Jessica E Metcalf and Bryan T Grenfell

Volume 12, issue 1, 2016

Measuring Integrated Information from the Decoding Perspective pp. 1-18

Masafumi Oizumi, Shun-ichi Amari, Toru Yanagawa, Naotaka Fujii and Naotsugu Tsuchiya

A Quick Introduction to Version Control with Git and GitHub pp. 1-18

John D Blischak, Emily R Davenport and Greg Wilson

Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes pp. 1-24

Junaid Hassan, Zhi Qu, Linda L Bergaust and Lars R Bakken

Discovery of Influenza A Virus Sequence Pairs and Their Combinations for Simultaneous Heterosubtypic Targeting that Hedge against Antiviral Resistance pp. 1-24

Keng Boon Wee, Raphael Tze Chuen Lee, Jing Lin, Zacharias Aloysius Dwi Pramono and Sebastian Maurer-Stroh

Long-Lasting Sparks: Multi-Metastability and Release Competition in the Calcium Release Unit Network pp. 1-24

Zhen Song, Alain Karma, James N Weiss and Zhilin Qu

Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines pp. 1-24

Andrea N Kravats, Sam Tonddast-Navaei and George Stan

Ten Simple Rules for a Bioinformatics Journal Club pp. 1-9

Andrew Lonsdale, Jocelyn Sietsma Penington, Timothy Rice, Michael Walker and Harriet Dashnow

Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles pp. 1-23

Olga Kononova, Joost Snijder, Yaroslav Kholodov, Kenneth A Marx, Gijs J L Wuite, Wouter H Roos and Valeri Barsegov

A Network Model to Describe the Terminal Differentiation of B Cells pp. 1-26

Akram Méndez and Luis Mendoza

Computational Modeling, Formal Analysis, and Tools for Systems Biology pp. 1-22

Ezio Bartocci and Pietro Lió

Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities pp. 1-22

Maria E Tomasso, Micheal J Tarver, Deepa Devarajan and Steven T Whitten

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation pp. 1-25

Duncan K Ralph and Frederick A Matsen Iv

Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates pp. 1-14

Marco A Deriu, Gianvito Grasso, Jack A Tuszynski, Diego Gallo, Umberto Morbiducci and Andrea Danani

Social Norms of Cooperation in Small-Scale Societies pp. 1-13

Fernando P Santos, Francisco C Santos and Jorge M Pacheco

Neurally Encoding Time for Olfactory Navigation pp. 1-16

In Jun Park, Andrew M Hein, Yuriy V Bobkov, Matthew A Reidenbach, Barry W Ache and Jose C Principe

Spontaneous Decoding of the Timing and Content of Human Object Perception from Cortical Surface Recordings Reveals Complementary Information in the Event-Related Potential and Broadband Spectral Change pp. 1-20

Kai J Miller, Gerwin Schalk, Dora Hermes, Jeffrey G Ojemann and Rajesh P N Rao

Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance? pp. 1-20

Troy Day and Andrew F Read

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics pp. 1-20

David Lamparter, Daniel Marbach, Rico Rueedi, Zoltán Kutalik and Sven Bergmann