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Table of Contents: June 2012

COVER

Mode-hopping Markov Chain Monte Carlo.

Image Credit: Theresa Niederberger, Gene Center, Ludwig-Maximilians-Universität München.
Issue Image

This mountain view of the Stubai Alps illustrates a search and optimization strategy for rugged score landscapes. Each green circle represents a graphical model describing the interactions of four components. The height of the circle corresponds to its likelihood score. Mode-hopping constructs a representative chain of models where the decision upon acceptance or rejection of a new proposal is based on the score of the respective nearest local maximum (red circles at the mountain top). This reduces the cost of walking through deep valleys, and increases the search efficiency. See Niederberger et al., doi:10.1371/journal.pcbi.1002568.

Message from ISCB

A Report of the Curriculum Task Force of the ISCB Education Committee

Lonnie R. Welch, Russell Schwartz, Fran Lewitter

Education

Visualization and Analysis of 3D Microscopic Images

Fuhui Long, Jianlong Zhou, Hanchuan Peng

Perspective

What Can Systems Theory of Networks Offer to Biology?

Indika Rajapakse, Mark Groudine, Mehran Mesbahi

Review

Research Articles

Viral Perturbations of Host Networks Reflect Disease Etiology

Natali Gulbahce, Han Yan, Amélie Dricot, Megha Padi, Danielle Byrdsong, Rachel Franchi, Deok-Sun Lee, Orit Rozenblatt-Rosen, Jessica C. Mar, Michael A. Calderwood, Amy Baldwin, Bo Zhao, Balaji Santhanam, Pascal Braun, Nicolas Simonis, Kyung-Won Huh, Karin Hellner, Miranda Grace, Alyce Chen, Renee Rubio, Jarrod A. Marto, Nicholas A. Christakis, Elliott Kieff, Frederick P. Roth, Jennifer Roecklein-Canfield, James A. DeCaprio, Michael E. Cusick, John Quackenbush, David E. Hill, Karl Münger, Marc Vidal, Albert-László Barabási

Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection

Erik M. Volz, James S. Koopman, Melissa J. Ward, Andrew Leigh Brown, Simon D. W. Frost

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

John A. Capra, Alexander G. Williams, Katherine S. Pollard

Fast Spatiotemporal Smoothing of Calcium Measurements in Dendritic Trees

Eftychios A. Pnevmatikakis, Keith Kelleher, Rebecca Chen, Petter Saggau, Krešimir Josić, Liam Paninski

Virtual Patients and Sensitivity Analysis of the Guyton Model of Blood Pressure Regulation: Towards Individualized Models of Whole-Body Physiology

Robert Moss, Thibault Grosse, Ivanny Marchant, Nathalie Lassau, François Gueyffier, S. Randall Thomas

A Model-Based Bayesian Estimation of the Rate of Evolution of VNTR Loci in Mycobacterium tuberculosis

R. Zachariah Aandahl, Josephine F. Reyes, Scott A. Sisson, Mark M. Tanaka

Deceleration of Fusion–Fission Cycles Improves Mitochondrial Quality Control during Aging

Marc Thilo Figge, Andreas S. Reichert, Michael Meyer-Hermann, Heinz D. Osiewacz

From Dynamic Expression Patterns to Boundary Formation in the Presomitic Mesoderm

Hendrik B. Tiedemann, Elida Schneltzer, Stefan Zeiser, Bastian Hoesel, Johannes Beckers, Gerhard K. H. Przemeck, Martin Hrabě de Angelis

Modeling Within-Host Dynamics of Influenza Virus Infection Including Immune Responses

Kasia A. Pawelek, Giao T. Huynh, Michelle Quinlivan, Ann Cullinane, Libin Rong, Alan S. Perelson

Modelling Cell Polarization Driven by Synthetic Spatially Graded Rac Activation

William R. Holmes, Benjamin Lin, Andre Levchenko, Leah Edelstein-Keshet

Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling

Matthias Kahm, Clara Navarrete, Vicent Llopis-Torregrosa, Rito Herrera, Lina Barreto, Lynne Yenush, Joaquin Ariño, Jose Ramos, Maik Kschischo

Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems

Carlo Chan, Xinfeng Liu, Liming Wang, Lee Bardwell, Qing Nie, Germán Enciso

Complementarity of Spike- and Rate-Based Dynamics of Neural Systems

M. T. Wilson, P. A. Robinson, B. O'Neill, D. A. Steyn-Ross

A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks

Daniele De Martino, Matteo Figliuzzi, Andrea De Martino, Enzo Marinari

MC EMiNEM Maps the Interaction Landscape of the Mediator

Theresa Niederberger, Stefanie Etzold, Michael Lidschreiber, Kerstin C. Maier, Dietmar E. Martin, Holger Fröhlich, Patrick Cramer, Achim Tresch

The Role of Non-Native Interactions in the Folding of Knotted Proteins

Tatjana Škrbić, Cristian Micheletti, Pietro Faccioli

Fast Coding of Orientation in Primary Visual Cortex

Oren Shriki, Adam Kohn, Maoz Shamir

Complex Spatial Dynamics of Oncolytic Viruses In Vitro: Mathematical and Experimental Approaches

Dominik Wodarz, Andrew Hofacre, John W. Lau, Zhiying Sun, Hung Fan, Natalia L. Komarova

Location-Dependent Effects of Inhibition on Local Spiking in Pyramidal Neuron Dendrites

Monika Jadi, Alon Polsky, Jackie Schiller, Bartlett W. Mel

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation

Crina-Maria Ionescu, Radka Svobodová Vařeková, Jochen H. M. Prehn, Heinrich J. Huber, Jaroslav Koča

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Sahar Abubucker, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Mitreva, Curtis Huttenhower

Fine-Tuning Tomato Agronomic Properties by Computational Genome Redesign

Javier Carrera, Asun Fernández del Carmen, Rafael Fernández-Muñoz, Jose Luis Rambla, Clara Pons, Alfonso Jaramillo, Santiago F. Elena, Antonio Granell

Structural and Dynamic Requirements for Optimal Activity of the Essential Bacterial Enzyme Dihydrodipicolinate Synthase

C. F. Reboul, B. T. Porebski, M. D. W. Griffin, R. C. J. Dobson, M. A. Perugini, J. A. Gerrard, A. M. Buckle

Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases

David Ruau, Joel T. Dudley, Rong Chen, Nicholas G. Phillips, Gary E. Swan, Laura C. Lazzeroni, J. David Clark, Atul J. Butte, Martin S. Angst

A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE

Kevin P. Keegan, William L. Trimble, Jared Wilkening, Andreas Wilke, Travis Harrison, Mark D'Souza, Folker Meyer

Sarcomeric Pattern Formation by Actin Cluster Coalescence

Benjamin M. Friedrich, Elisabeth Fischer-Friedrich, Nir S. Gov, Samuel A. Safran

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

Yasuhiro Matsunaga, Hiroshi Fujisaki, Tohru Terada, Tadaomi Furuta, Kei Moritsugu, Akinori Kidera