Table of Contents: November 2014

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Activation of Parkin by PINK1-dependent phosphorylation of Serine-65 initiates a cleft widening between the UBL domain and the adjacent linker region that propagates through release of the E2 binding region and further conformational adjustments of the active site region. The UBL domain begins its dynamic movement on the left side. Phospho-Ser65 is indicated by the 'black hole' in the UBL domain positioned on top right near the active site after its movement. See Caulfield et al.


Education Articles

Teaching Bioinformatics in Concert

Anya L. Goodman, Alex Dekhtyar

Research Articles

BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities

Mahdi Shafiei, Katherine A. Dunn, Hugh Chipman, Hong Gu, Joseph P. Bielawski

Epidemic Spreading Model to Characterize Misfolded Proteins Propagation in Aging and Associated Neurodegenerative Disorders

Yasser Iturria-Medina, Roberto C. Sotero, Paule J. Toussaint, Alan C. Evans , and the Alzheimer's Disease Neuroimaging Initiative

Estimating Relative Changes of Metabolic Fluxes

Lei Huang, Dongsung Kim, Xiaojing Liu, Christopher R. Myers, Jason W. Locasale

High-Fidelity Coding with Correlated Neurons

Rava Azeredo da Silveira, Michael J. Berry II

How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations

Tarja Äijänen, Artturi Koivuniemi, Matti Javanainen, Sami Rissanen, Tomasz Rog, Ilpo Vattulainen

Global Disease Monitoring and Forecasting with Wikipedia

Nicholas Generous, Geoffrey Fairchild, Alina Deshpande, Sara Y. Del Valle, Reid Priedhorsky

Characterization of K-Complexes and Slow Wave Activity in a Neural Mass Model

Arne Weigenand, Michael Schellenberger Costa, Hong-Viet Victor Ngo, Jens Christian Claussen, Thomas Martinetz

Pattern of Tick Aggregation on Mice: Larger Than Expected Distribution Tail Enhances the Spread of Tick-Borne Pathogens

Luca Ferreri, Mario Giacobini, Paolo Bajardi, Luigi Bertolotti, Luca Bolzoni, Valentina Tagliapietra, Annapaola Rizzoli, Roberto Rosà

Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes

Frederik Graw, Ashwin Balagopal, Abraham J. Kandathil, Stuart C. Ray, David L. Thomas, Ruy M. Ribeiro, Alan S. Perelson

Evolution of All-or-None Strategies in Repeated Public Goods Dilemmas

Flávio L. Pinheiro, Vítor V. Vasconcelos, Francisco C. Santos, Jorge M. Pacheco

A Statistical Method of Identifying Interactions in Neuron–Glia Systems Based on Functional Multicell Ca2+ Imaging

Ken Nakae, Yuji Ikegaya, Tomoe Ishikawa, Shigeyuki Oba, Hidetoshi Urakubo, Masanori Koyama, Shin Ishii

Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data

Sathej Gopalakrishnan, Hesam Montazeri, Stephan Menz, Niko Beerenwinkel, Wilhelm Huisinga

Size Does Matter: An Integrative In Vivo-In Silico Approach for the Treatment of Critical Size Bone Defects

Aurélie Carlier, Nick van Gastel, Liesbet Geris, Geert Carmeliet, Hans Van Oosterwyck

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

Marcin J. Skwark, Daniele Raimondi, Mirco Michel, Arne Elofsson

Effect of Global Cardiac Ischemia on Human Ventricular Fibrillation: Insights from a Multi-scale Mechanistic Model of the Human Heart

Ivan V. Kazbanov, Richard H. Clayton, Martyn P. Nash, Chris P. Bradley, David J. Paterson, Martin P. Hayward, Peter Taggart, Alexander V. Panfilov

Mouse Hair Cycle Expression Dynamics Modeled as Coupled Mesenchymal and Epithelial Oscillators

Ryan Tasseff, Anjali Bheda-Malge, Teresa DiColandrea, Charles C. Bascom, Robert J. Isfort, Richard Gelinas

Stability Depends on Positive Autoregulation in Boolean Gene Regulatory Networks

Ricardo Pinho, Victor Garcia, Manuel Irimia, Marcus W. Feldman

Phosphorylation by PINK1 Releases the UBL Domain and Initializes the Conformational Opening of the E3 Ubiquitin Ligase Parkin

Thomas R. Caulfield, Fabienne C. Fiesel, Elisabeth L. Moussaud-Lamodière, Daniel F. A. R. Dourado, Samuel C. Flores, Wolfdieter Springer

Statistical Computations Underlying the Dynamics of Memory Updating

Samuel J. Gershman, Angela Radulescu, Kenneth A. Norman, Yael Niv