PLOS Computational Biology

2005 - 2025

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Volume 12, issue 12, 2016

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

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

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

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

Simeon Carstens, Michael Nilges and Michael Habeck

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

Andrew F Neuwald and Stephen F Altschul

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

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

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

Florent Meyniel, Maxime Maheu and Stanislas Dehaene

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

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

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

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

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

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

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

Nadezda Kryuchkova-Mostacci and Marc Robinson-Rechavi

Volume 12, issue 11, 2016

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

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

Kieran R Campbell and Christopher Yau

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

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

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

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

Improved Measures of Integrated Information pp. 1-34

Max Tegmark

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

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

Volume 12, issue 10, 2016

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

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

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

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

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

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

David T Manallack and Elizabeth Yuriev

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

Duncan K Ralph and Frederick A Matsen Iv

Volume 12, issue 9, 2016

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

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

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

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

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

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

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

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

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

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 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

Volume 12, issue 8, 2016

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

Boxue Tian, C Dale Poulter and Matthew P Jacobson

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

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

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

Wouter Kool, Fiery A Cushman and Samuel J Gershman

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

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

Bradley Voytek

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

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

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

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

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

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

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

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

Volume 12, issue 7, 2016

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

Yuheng Lu and Christina S Leslie

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

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

Greg J McInerny

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

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

Takahiro Ezaki, Yutaka Horita, Masanori Takezawa and Naoki Masuda

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

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

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

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

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

Dynamic Reweighting of Auditory Modulation Filters pp. 1-23

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

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 Writing a Postdoctoral Fellowship pp. 1-6

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

Volume 12, issue 6, 2016

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

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

Stojan Jovanović and Stefan Rotter

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

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

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

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

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

Berk Ekmekci, Charles E McAnany and Cameron Mura

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

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

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

Michelle D Brazas and B F Francis Ouellette

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

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

Margaritis Voliotis, Philipp Thomas, Simon Grima and Clive Bowsher

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

Tobias Sikosek, Heinrich Krobath and Hue Sun Chan

Volume 12, issue 5, 2016

Neuroprosthetic Decoder Training as Imitation Learning pp. 1-24

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

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

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

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

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

Optimal Current Transfer in Dendrites pp. 1-12

Alex D Bird and Hermann Cuntz

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

Jerome Kelleher, Alison M Etheridge and Gilean McVean

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

Arthur Bernard, Jean-Baptiste André and Nicolas Bredeche

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

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

John Wiedenhoeft, Eric Brugel and Alexander Schliep

The Maximum Entropy Fallacy Redux? pp. 1-7

Erik Aurell

Volume 12, issue 4, 2016

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

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

Lorenzo Asti, Guido Uguzzoni, Paolo Marcatili and Andrea Pagnani

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

Wendy J Adams

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

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

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

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

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

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

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

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

André Schultz and Amina A Qutub

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

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

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

Christine Vogel

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

Volume 12, issue 2, 2016

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

Ensemble Tractography pp. 1-22

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

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

Zohar Z Bronfman, Noam Brezis and Marius Usher

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

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

Volume 12, issue 1, 2016

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

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

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

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

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

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

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

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

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

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