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New Articles in PLOS Computational Biology

Published December 01, 2016 to December 30, 2016

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PLOS Computational Biology
Volume 12(12) December 2016

View Table of Contents on web site

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The 5th ISCB Wikipedia Competition: Coming to a Classroom Near You?
Alastair M. Kilpatrick

Research Articles

In Silico Knockout Studies of Xenophagic Capturing of Salmonella
Jennifer Scheidel, Leonie Amstein, Jörg Ackermann, Ivan Dikic, Ina Koch

Detecting Mild Traumatic Brain Injury Using Resting State Magnetoencephalographic Connectivity
Vasily A. Vakorin, Sam M. Doesburg, Leodante da Costa, Rakesh Jetly, Elizabeth W. Pang, Margot J. Taylor

A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics
Haixu Tang, Sujun Li, Yuzhen Ye

Fused Regression for Multi-source Gene Regulatory Network Inference
Kari Y. Lam, Zachary M. Westrick, Christian L. Müller, Lionel Christiaen, Richard Bonneau

Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites
Angela Re, Levi Waldron, Alessandro Quattrone

The Kinematics of Plant Nutation Reveals a Simple Relation between Curvature and the Orientation of Differential Growth
Renaud Bastien, Yasmine Meroz

The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems
Andrew White, Malachi Tolman, Howard D. Thames, Hubert Rodney Withers, Kathy A. Mason, Mark K. Transtrum

Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series
Anna Klimovskaia, Stefan Ganscha, Manfred Claassen

Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms
Thomas LaBar, Christoph Adami

Scaling Properties of Dimensionality Reduction for Neural Populations and Network Models
Ryan C. Williamson, Benjamin R. Cowley, Ashok Litwin-Kumar, Brent Doiron, Adam Kohn, Matthew A. Smith, Byron M. Yu

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist
Brian Drawert, Andreas Hellander, Ben Bales, Debjani Banerjee, Giovanni Bellesia, Bernie J. Daigle Jr., Geoffrey Douglas, Mengyuan Gu, Anand Gupta, Stefan Hellander, Chris Horuk, Dibyendu Nath, Aviral Takkar, Sheng Wu, Per Lötstedt, Chandra Krintz, Linda R. Petzold

Dopamine Neurons Change the Type of Excitability in Response to Stimuli
Ekaterina O. Morozova, Denis Zakharov, Boris S. Gutkin, Christopher C. Lapish, Alexey Kuznetsov

Spatiotemporal Analysis of the 2014 Ebola Epidemic in West Africa
Jantien A. Backer, Jacco Wallinga

Stimulus-Driven Population Activity Patterns in Macaque Primary Visual Cortex
Benjamin R. Cowley, Matthew A. Smith, Adam Kohn, Byron M. Yu

Alpha Helices Are More Robust to Mutations than Beta Strands
György Abrusán, Joseph A. Marsh

Utility and Limitations of Using Gene Expression Data to Identify Functional Associations
Sahra Uygun, Cheng Peng, Melissa D. Lehti-Shiu, Robert L. Last, Shin-Han Shiu

Beyond the Hypercube: Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks
Marcin Zagorski, Zdzislaw Burda, Bartlomiej Waclaw

Synchronization and Random Triggering of Lymphatic Vessel Contractions
James W. Baish, Christian Kunert, Timothy P. Padera, Lance L. Munn

A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability
Debashis Barik, David A. Ball, Jean Peccoud, John J. Tyson

Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos
Jonathan Desponds, Huy Tran, Teresa Ferraro, Tanguy Lucas, Carmina Perez Romero, Aurelien Guillou, Cecile Fradin, Mathieu Coppey, Nathalie Dostatni, Aleksandra M. Walczak

Feedback Loops of the Mammalian Circadian Clock Constitute Repressilator
J. Patrick Pett, Anja Korenčič, Felix Wesener, Achim Kramer, Hanspeter Herzel

Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model
Kristen A. Marino, Diego Prada-Gracia, Davide Provasi, Marta Filizola

Temporal Dynamics and Developmental Maturation of Salience, Default and Central-Executive Network Interactions Revealed by Variational Bayes Hidden Markov Modeling
Srikanth Ryali, Kaustubh Supekar, Tianwen Chen, John Kochalka, Weidong Cai, Jonathan Nicholas, Aarthi Padmanabhan, Vinod Menon

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology
James C. Schaff, Fei Gao, Ye Li, Igor L. Novak, Boris M. Slepchenko

Evolution at ‘Sutures’ and ‘Centers’: Recombination Can Aid Adaptation of Spatially Structured Populations on Rugged Fitness Landscapes
Jacob D. Cooper, Benjamin Kerr

Encoding in Balanced Networks: Revisiting Spike Patterns and Chaos in Stimulus-Driven Systems
Guillaume Lajoie, Kevin K. Lin, Jean-Philippe Thivierge, Eric Shea-Brown

When Optimal Feedback Control Is Not Enough: Feedforward Strategies Are Required for Optimal Control with Active Sensing
Sang-Hoon Yeo, David W. Franklin, Daniel M. Wolpert

Lack of Ecological and Life History Context Can Create the Illusion of Social Interactions in Dictyostelium discoideum
Ricardo Martínez-García, Corina E. Tarnita

Role of Autoregulation and Relative Synthesis of Operon Partners in Alternative Sigma Factor Networks
Jatin Narula, Abhinav Tiwari, Oleg A. Igoshin

Universal or Specific? A Modeling-Based Comparison of Broad-Spectrum Influenza Vaccines against Conventional, Strain-Matched Vaccines
Rahul Subramanian, Andrea L. Graham, Bryan T. Grenfell, Nimalan Arinaminpathy

Hierarchical Post-transcriptional Regulation of Colicin E2 Expression in Escherichia coli
Matthias Lechner, Mathias Schwarz, Madeleine Opitz, Erwin Frey

An Extended Normalization Model of Attention Accounts for Feature-Based Attentional Enhancement of Both Response and Coherence Gain
Philipp Schwedhelm, B. Suresh Krishna, Stefan Treue

The Multilayer Connectome of Caenorhabditis elegans
Barry Bentley, Robyn Branicky, Christopher L. Barnes, Yee Lian Chew, Eviatar Yemini, Edward T. Bullmore, Petra E. Vértes, William R. Schafer

Modeling Contact Inhibition of Locomotion of Colliding Cells Migrating on Micropatterned Substrates
Dirk Alexander Kulawiak, Brian A. Camley, Wouter-Jan Rappel

Atrial Heterogeneity Generates Re-entrant Substrate during Atrial Fibrillation and Anti-arrhythmic Drug Action: Mechanistic Insights from Canine Atrial Models
Marta Varela, Michael A. Colman, Jules C. Hancox, Oleg V. Aslanidi

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns
Matthew Huska, Martin Vingron

Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota
Sébastien Raguideau, Sandra Plancade, Nicolas Pons, Marion Leclerc, Béatrice Laroche

Competing Mechanistic Hypotheses of Acetaminophen-Induced Hepatotoxicity Challenged by Virtual Experiments
Andrew K. Smith, Brenden K. Petersen, Glen E. P. Ropella, Ryan C. Kennedy, Neil Kaplowitz, Murad Ookhtens, C. Anthony Hunt

Glycoside Hydrolases across Environmental Microbial Communities
Renaud Berlemont, Adam C. Martiny

Systematic Approximations to Susceptible-Infectious-Susceptible Dynamics on Networks
Matt J. Keeling, Thomas House, Alison J. Cooper, Lorenzo Pellis

Zipf’s Law Arises Naturally When There Are Underlying, Unobserved Variables
Laurence Aitchison, Nicola Corradi, Peter E. Latham

Normal Modes Expose Active Sites in Enzymes
Yitav Glantz-Gashai, Tomer Meirson, Abraham O. Samson

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations
Andrew F. Neuwald, Stephen F. Altschul

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks
Songyao Zhang, Shaowu Zhang, Lian Liu, Jia Meng, Yufei Huang

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data
Simeon Carstens, Michael Nilges, Michael Habeck

The Effect of Gap Junctional Coupling on the Spatiotemporal Patterns of Ca2+ Signals and the Harmonization of Ca2+-Related Cellular Responses
Michaël Dougoud, Laura Vinckenbosch, Christian Mazza, Beat Schwaller, Laszlo Pecze

Feedback, Mass Conservation and Reaction Kinetics Impact the Robustness of Cellular Oscillations
Katharina Baum, Antonio Z. Politi, Bente Kofahl, Ralf Steuer, Jana Wolf

The Hamiltonian Brain: Efficient Probabilistic Inference with Excitatory-Inhibitory Neural Circuit Dynamics
Laurence Aitchison, Máté Lengyel

Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level
Kawai Leung, Aylia Mohammadi, William S. Ryu, Ilya Nemenman

Decoding Single Molecule Time Traces with Dynamic Disorder
Wonseok Hwang, Il-Buem Lee, Seok-Cheol Hong, Changbong Hyeon

Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1
Russell Gould, David M. Bassen, Anirikh Chakrabarti, Jeffrey D. Varner, Jonathan Butcher

Novel Models of Visual Topographic Map Alignment in the Superior Colliculus
Ruben A. Tikidji-Hamburyan, Tarek A. El-Ghazawi, Jason W. Triplett

Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs
Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi

Human Inferences about Sequences: A Minimal Transition Probability Model
Florent Meyniel, Maxime Maheu, Stanislas Dehaene

Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets
Aitor Blanco-Míguez, Jan P. Meier-Kolthoff, Alberto Gutiérrez-Jácome, Markus Göker, Florentino Fdez-Riverola, Borja Sánchez, Anália Lourenço

Stability of Cross-Feeding Polymorphisms in Microbial Communities
Ivana Gudelj, Margie Kinnersley, Peter Rashkov, Karen Schmidt, Frank Rosenzweig

Game-Changing Innovations: How Culture Can Change the Parameters of Its Own Evolution and Induce Abrupt Cultural Shifts
Oren Kolodny, Nicole Creanza, Marcus W. Feldman



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