Table of Contents

June 2012

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.

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

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Visualization and Analysis of 3D Microscopic Images

Fuhui Long, Jianlong Zhou, Hanchuan Peng


What Can Systems Theory of Networks Offer to Biology?

Indika Rajapakse, Mark Groudine, Mehran Mesbahi


Bringing Molecules Back into Molecular Evolution

Claus O. Wilke

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Prosthetic Avian Vocal Organ Controlled by a Freely Behaving Bird Based on a Low Dimensional Model of the Biomechanical Periphery

Ezequiel M. Arneodo, Yonatan Sanz Perl, Franz Goller, Gabriel B. Mindlin

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

Modeling Boundary Vector Cell Firing Given Optic Flow as a Cue

Florian Raudies, Michael E. Hasselmo

Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations

Xin Wang, Mauro A. Castro, Klaas W. Mulder, Florian Markowetz

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

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