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Table of Contents

December 2014

A model for transcription of NNS RNA viruses, which include Ebola, measles and VSV, is presented by Tang et al. The yellow strand represents the RNA genome fully encapsidated with proteins. The orange, ball-shaped objects are polymerases that transcribe the genome. Transcription initiates at the end of the genome as shown by polymerases on the left. The other polymerases (shown on the right) are attached to the template but slide randomly until they collide with the transcribing polymerases. These collisions kick sliding polymerases loose (top center) allowing them to diffuse to the end of the genome and start transcription.

Image Credit: Dave Meikle

Editorial

Ten Simple Rules for Finishing Your PhD

Jacopo Marino, Melanie I. Stefan, Sarah Blackford

Education

“Bioinformatics: Introduction and Methods,” a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education

Yang Ding, Meng Wang, Yao He, Adam Yongxin Ye, Xiaoxu Yang, Fenglin Liu, Yuqi Meng, Ge Gao, Liping Wei

Research Articles

ECOD: An Evolutionary Classification of Protein Domains

Hua Cheng, R. Dustin Schaeffer, Yuxing Liao, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Bong-Hyun Kim, Nick V. Grishin

The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data

Norman E. Davey, Venkata P. Satagopam, Salvador Santiago-Mozos, Carlos Villacorta-Martin, Tanmay A. M. Bharat, Reinhard Schneider, John A. G. Briggs

Live Imaging-Based Model Selection Reveals Periodic Regulation of the Stochastic G1/S Phase Transition in Vertebrate Axial Development

Mayu Sugiyama, Takashi Saitou, Hiroshi Kurokawa, Asako Sakaue-Sawano, Takeshi Imamura, Atsushi Miyawaki, Tadahiro Iimura

Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I

Bill R. Miller III, Carol A. Parish, Eugene Y. Wu

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

Alexandra Gavryushkina, David Welch, Tanja Stadler, Alexei J. Drummond

Some Work and Some Play: Microscopic and Macroscopic Approaches to Labor and Leisure

Ritwik K. Niyogi, Peter Shizgal, Peter Dayan

Yielding Elastic Tethers Stabilize Robust Cell Adhesion

Matt J. Whitfield, Jonathon P. Luo, Wendy E. Thomas

Contradictory Behavioral Biases Result from the Influence of Past Stimuli on Perception

Ofri Raviv, Itay Lieder, Yonatan Loewenstein, Merav Ahissar

Evolution of the Division of Labor between Genes and Enzymes in the RNA World

Gergely Boza, András Szilágyi, Ádám Kun, Mauro Santos, Eörs Szathmáry

Intrinsic Neuronal Properties Switch the Mode of Information Transmission in Networks

Julijana Gjorgjieva, Rebecca A. Mease, William J. Moody, Adrienne L. Fairhall

A Network Convergence Zone in the Hippocampus

Bratislav Mišić, Joaquín Goñi, Richard F. Betzel, Olaf Sporns, Anthony R. McIntosh

Lattice-Based Model of Ductal Carcinoma In Situ Suggests Rules for Breast Cancer Progression to an Invasive State

Eline Boghaert, Derek C. Radisky, Celeste M. Nelson

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

James F. Denton, Jose Lugo-Martinez, Abraham E. Tucker, Daniel R. Schrider, Wesley C. Warren, Matthew W. Hahn

Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel

Yana Gofman, Charlotta Schärfe, Debora S. Marks, Turkan Haliloglu, Nir Ben-Tal

Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences

Alex N. Nguyen Ba, Bob Strome, Jun Jie Hua, Jonathan Desmond, Isabelle Gagnon-Arsenault, Eric L. Weiss, Christian R. Landry, Alan M. Moses

Heterogeneity and Convergence of Olfactory First-Order Neurons Account for the High Speed and Sensitivity of Second-Order Neurons

Jean-Pierre Rospars, Alexandre Grémiaux, David Jarriault, Antoine Chaffiol, Christelle Monsempes, Nina Deisig, Sylvia Anton, Philippe Lucas, Dominique Martinez

A Reaction-Diffusion Model of Cholinergic Retinal Waves

Benjamin Lansdell, Kevin Ford, J. Nathan Kutz

Hippocampal Remapping Is Constrained by Sparseness rather than Capacity

Axel Kammerer, Christian Leibold

The Social Bayesian Brain: Does Mentalizing Make a Difference When We Learn?

Marie Devaine, Guillaume Hollard, Jean Daunizeau

Developmental Self-Construction and -Configuration of Functional Neocortical Neuronal Networks

Roman Bauer, Frédéric Zubler, Sabina Pfister, Andreas Hauri, Michael Pfeiffer, Dylan R. Muir, Rodney J. Douglas

Exploring O2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site

A. Sofia F. Oliveira, João M. Damas, António M. Baptista, Cláudio M. Soares

Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments

Christoph Zechner, Heinz Koeppl

Dissecting Dynamic Genetic Variation That Controls Temporal Gene Response in Yeast

Avital Brodt, Maya Botzman, Eyal David, Irit Gat-Viks

Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation

Michael M. H. Graf, Lin Zhixiong, Urban Bren, Dietmar Haltrich, Wilfred F. van Gunsteren, Chris Oostenbrink

Thermodynamic Costs of Information Processing in Sensory Adaptation

Pablo Sartori, Léo Granger, Chiu Fan Lee, Jordan M. Horowitz

Molecular Insights into the Dynamics of Pharmacogenetically Important N-Terminal Variants of the Human β2-Adrenergic Receptor

Ganesh Shahane, Chirag Parsania, Durba Sengupta, Manali Joshi

The Role of Membrane-Mediated Interactions in the Assembly and Architecture of Chemoreceptor Lattices

Christoph A. Haselwandter, Ned S. Wingreen

Oscillation-Induced Signal Transmission and Gating in Neural Circuits

Sven Jahnke, Raoul-Martin Memmesheimer, Marc Timme

Protein-Protein Docking with Dynamic Residue Protonation States

Krishna Praneeth Kilambi, Kavan Reddy, Jeffrey J. Gray

Related Articles

Competing ParA Structures Space Bacterial Plasmids Equally over the Nucleoid

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Vesicular Stomatitis Virus Polymerase's Strong Affinity to Its Template Suggests Exotic Transcription Models

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Disrupted Calcium Release as a Mechanism for Atrial Alternans Associated with Human Atrial Fibrillation

Kelly C. Chang, Jason D. Bayer, Natalia A. Trayanova

Symmetry Restoring Bifurcation in Collective Decision-Making

Natalia Zabzina, Audrey Dussutour, Richard P. Mann, David J. T. Sumpter, Stamatios C. Nicolis

Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation

Lin Chen, Javad Noorbakhsh, Rhys M. Adams, Joseph Samaniego-Evans, Germaine Agollah, Dmitry Nevozhay, Jennie Kuzdzal-Fick, Pankaj Mehta, Gábor Balázsi

An Extra Dimension to Decision-Making in Animals: The Three-way Trade-off between Speed, Effort per-Unit-Time and Accuracy

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Deep Neural Networks Rival the Representation of Primate IT Cortex for Core Visual Object Recognition

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Segregating Complex Sound Sources through Temporal Coherence

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Bilinearity in Spatiotemporal Integration of Synaptic Inputs

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Metadynamics Simulations Reveal a Na+ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT

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Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu

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Glutamate Mediated Astrocytic Filtering of Neuronal Activity

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