Table of Contents: December 2014

Issue Image

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.


Ten Simple Rules for Finishing Your PhD

Jacopo Marino, Melanie I. Stefan, Sarah Blackford


“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

Symmetry Restoring Bifurcation in Collective Decision-Making

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

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

Charles F. Cadieu, Ha Hong, Daniel L. K. Yamins, Nicolas Pinto, Diego Ardila, Ethan A. Solomon, Najib J. Majaj, James J. DiCarlo

Glutamate Mediated Astrocytic Filtering of Neuronal Activity

Gilad Wallach, Jules Lallouette, Nitzan Herzog, Maurizio De Pittà, Eshel Ben Jacob, Hugues Berry, Yael Hanein

Evolution of Integrated Causal Structures in Animats Exposed to Environments of Increasing Complexity

Larissa Albantakis, Arend Hintze, Christof Koch, Christoph Adami, Giulio Tononi

Segregating Complex Sound Sources through Temporal Coherence

Lakshmi Krishnan, Mounya Elhilali, Shihab Shamma

Competing ParA Structures Space Bacterial Plasmids Equally over the Nucleoid

Robert Ietswaart, Florian Szardenings, Kenn Gerdes, Martin Howard

Bilinearity in Spatiotemporal Integration of Synaptic Inputs

Songting Li, Nan Liu, Xiao-hui Zhang, Douglas Zhou, David Cai

Oscillation-Induced Signal Transmission and Gating in Neural Circuits

Sven Jahnke, Raoul-Martin Memmesheimer, Marc Timme

Thermodynamic Costs of Information Processing in Sensory Adaptation

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

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

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

Protein-Protein Docking with Dynamic Residue Protonation States

Krishna Praneeth Kilambi, Kavan Reddy, Jeffrey J. Gray

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

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

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

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

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

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

Ofri Raviv, Itay Lieder, Yonatan Loewenstein, Merav Ahissar

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

A Reaction-Diffusion Model of Cholinergic Retinal Waves

Benjamin Lansdell, Kevin Ford, J. Nathan Kutz

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

Intrinsic Neuronal Properties Switch the Mode of Information Transmission in Networks

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

Yielding Elastic Tethers Stabilize Robust Cell Adhesion

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

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

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

A Network Convergence Zone in the Hippocampus

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

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

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

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis

Marnix H. Medema, Peter Cimermancic, Andrej Sali, Eriko Takano, Michael A. Fischbach