Table of Contents: April 2013

Linear models of volumetric changes in healthy aging (right diagonal) and Alzheimer's disease (left diagonal). The healthy aging model shows voxel-wise changes in grey matter volume from age 50 to 80 y, with the 50-y-old brain as baseline. The Alzheimer's disease model shows voxel-wise grey matter volume changes with increased symptom severity as measured by the Mini Mental State Examination score (range 30 to 20) and controlled for changes observed in healthy aging. The 3D plot at the bottom left displays both models for a single voxel. See Dukart et al.

Image Credit: Juergen Dukart

Education Articles

Chapter 15: Disease Gene Prioritization

Yana Bromberg

Chapter 16: Text Mining for Translational Bioinformatics

K. Bretonnel Cohen, Lawrence E. Hunter

Chapter 17: Bioimage Informatics for Systems Pharmacology

Fuhai Li, Zheng Yin, Guangxu Jin, Hong Zhao, Stephen T. C. Wong

Research Articles

The Interaction of Vinculin with Actin

Javad Golji, Mohammad R. K. Mofrad

Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing

Recep Colak, TaeHyung Kim, Magali Michaut, Mark Sun, Manuel Irimia, Jeremy Bellay, Chad L. Myers, Benjamin J. Blencowe, Philip M. Kim

Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect

Anne-Sophie Coquel, Jean-Pascal Jacob, Mael Primet, Alice Demarez, Mariella Dimiccoli, Thomas Julou, Lionel Moisan, Ariel B. Lindner, Hugues Berry

Human Germline Antibody Gene Segments Encode Polyspecific Antibodies

Jordan R. Willis, Bryan S. Briney, Samuel L. DeLuca, James E. Crowe Jr, Jens Meiler

Lifespan Differences in Hematopoietic Stem Cells are Due to Imperfect Repair and Unstable Mean-Reversion

Hans B Sieburg, Giulio Cattarossi, Christa E. Muller-Sieburg

Cleavage Entropy as Quantitative Measure of Protease Specificity

Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Michael A. Margreiter, Gudrun M. Spitzer, Hannes G. Wallnoefer, Klaus R. Liedl

Phosphorylation of the Retinoic Acid Receptor Alpha Induces a Mechanical Allosteric Regulation and Changes in Internal Dynamics

Yassmine Chebaro, Ismail Amal, Natacha Rochel, Cécile Rochette-Egly, Roland H. Stote, Annick Dejaegere

Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria

Juho Rousu, Daniel D. Agranoff, Olugbemiro Sodeinde, John Shawe-Taylor, Delmiro Fernandez-Reyes

Semi-automated 3D Leaf Reconstruction and Analysis of Trichome Patterning from Light Microscopic Images

Henrik Failmezger, Benjamin Jaegle, Andrea Schrader, Martin Hülskamp, Achim Tresch

Learning Multisensory Integration and Coordinate Transformation via Density Estimation

Joseph G. Makin, Matthew R. Fellows, Philip N. Sabes

The Evolution of Collective Restraint: Policing and Obedience among Non-conjugative Plasmids

Kyriakos Kentzoglanakis, Diana García López, Sam P. Brown, Richard A. Goldstein

Optimal Balance of the Striatal Medium Spiny Neuron Network

Adam Ponzi, Jeffery R. Wickens

Reinforcement Learning Using a Continuous Time Actor-Critic Framework with Spiking Neurons

Nicolas Frémaux, Henning Sprekeler, Wulfram Gerstner

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data

Lauren M. Bragg, Glenn Stone, Margaret K. Butler, Philip Hugenholtz, Gene W. Tyson

Reduced Lateral Mobility of Lipids and Proteins in Crowded Membranes

Joseph E. Goose, Mark S. P. Sansom

Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations

Daniel L. Parton, Alex Tek, Marc Baaden, Mark S. P. Sansom

Noise Suppression and Surplus Synchrony by Coincidence Detection

Matthias Schultze-Kraft, Markus Diesmann, Sonja Grün, Moritz Helias

Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation

Gabriela V. Cohen Freue, Anna Meredith, Derek Smith, Axel Bergman, Mayu Sasaki, Karen K. Y. Lam, Zsuzsanna Hollander, Nina Opushneva, Mandeep Takhar, David Lin, Janet Wilson-McManus, Robert Balshaw, Paul A. Keown, Christoph H. Borchers, Bruce McManus, Raymond T. Ng, W. Robert McMaster, for the Biomarkers in Transplantation and the NCE CECR Prevention of Organ Failure Centre of Excellence Teams

Analysis of Accuracy in Pointing with Redundant Hand-held Tools: A Geometric Approach to the Uncontrolled Manifold Method

Domenico Campolo, Ferdinan Widjaja, Hong Xu, Wei Tech Ang, Etienne Burdet

Generative FDG-PET and MRI Model of Aging and Disease Progression in Alzheimer's Disease

Juergen Dukart, Ferath Kherif, Karsten Mueller, Stanislaw Adaszewski, Matthias L. Schroeter, Richard S. J. Frackowiak, Bogdan Draganski, for the Alzheimer's Disease Neuroimaging Initiative

A Computational Model Predicting Disruption of Blood Vessel Development

Nicole Kleinstreuer, David Dix, Michael Rountree, Nancy Baker, Nisha Sipes, David Reif, Richard Spencer, Thomas Knudsen

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

Stefano Lonardi, Denisa Duma, Matthew Alpert, Francesca Cordero, Marco Beccuti, Prasanna R. Bhat, Yonghui Wu, Gianfranco Ciardo, Burair Alsaihati, Yaqin Ma, Steve Wanamaker, Josh Resnik, Serdar Bozdag, Ming-Cheng Luo, Timothy J. Close

Data-Driven Modeling of Src Control on the Mitochondrial Pathway of Apoptosis: Implication for Anticancer Therapy Optimization

Annabelle Ballesta, Jonathan Lopez, Nikolay Popgeorgiev, Philippe Gonzalo, Marie Doumic, Germain Gillet

Dual Process for Intentional and Reactive Decisions

Marie Devaine, Florian Waszak, Pascal Mamassian

Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps

Andrei Zinovyev, Inna Kuperstein, Emmanuel Barillot, Wolf-Dietrich Heyer

Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

Emily V. Chambers, Wendy A. Bickmore, Colin A. Semple

A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase

Lin-Tai Da, Fátima Pardo Avila, Dong Wang, Xuhui Huang

Trading Speed and Accuracy by Coding Time: A Coupled-circuit Cortical Model

Dominic Standage, Hongzhi You, Da-Hui Wang, Michael C. Dorris

Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure

Xiaobo Wan, Yue Ma, Christopher L. McClendon, Lily Jun-shen Huang, Niu Huang

Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity

Adria Carbo, Raquel Hontecillas, Barbara Kronsteiner, Monica Viladomiu, Mireia Pedragosa, Pinyi Lu, Casandra W. Philipson, Stefan Hoops, Madhav Marathe, Stephen Eubank, Keith Bisset, Katherine Wendelsdorf, Abdul Jarrah, Yongguo Mei, Josep Bassaganya-Riera