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.

Message from ISCB

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

Lonnie R. Welch, Russell Schwartz, Fran Lewitter

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002570

Education

Visualization and Analysis of 3D Microscopic Images

Fuhui Long, Jianlong Zhou, Hanchuan Peng

PLOS Computational Biology: published June 14, 2012 | https://doi.org/10.1371/journal.pcbi.1002519

Perspective

What Can Systems Theory of Networks Offer to Biology?

Indika Rajapakse, Mark Groudine, Mehran Mesbahi

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002543

Review

Bringing Molecules Back into Molecular Evolution

Claus O. Wilke

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002572

Research Articles

Equation-Free Analysis of Two-Component System Signalling Model Reveals the Emergence of Co-Existing Phenotypes in the Absence of Multistationarity

Rebecca B. Hoyle, Daniele Avitabile, Andrzej M. Kierzek

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002396

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

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002531

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

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002546

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

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002552

Modeling Boundary Vector Cell Firing Given Optic Flow as a Cue

Florian Raudies, Michael E. Hasselmo

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002553

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

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

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002566

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

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

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002567

Fast Spatiotemporal Smoothing of Calcium Measurements in Dendritic Trees

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

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002569

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

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002571

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

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002573

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

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

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002576

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

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002586

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

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002588

Learning with Slight Forgetting Optimizes Sensorimotor Transformation in Redundant Motor Systems

Masaya Hirashima, Daichi Nozaki

PLOS Computational Biology: published June 28, 2012 | https://doi.org/10.1371/journal.pcbi.1002590

Modelling Cell Polarization Driven by Synthetic Spatially Graded Rac Activation

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

PLOS Computational Biology: published June 21, 2012 | https://doi.org/10.1371/journal.pcbi.1002366

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

PLOS Computational Biology: published June 21, 2012 | https://doi.org/10.1371/journal.pcbi.1002548

Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems

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

PLOS Computational Biology: published June 21, 2012 | https://doi.org/10.1371/journal.pcbi.1002551

Short Term Synaptic Depression Imposes a Frequency Dependent Filter on Synaptic Information Transfer

Robert Rosenbaum, Jonathan Rubin, Brent Doiron

PLOS Computational Biology: published June 21, 2012 | https://doi.org/10.1371/journal.pcbi.1002557

Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction

Magali Michaut, Gary D. Bader

PLOS Computational Biology: published June 21, 2012 | https://doi.org/10.1371/journal.pcbi.1002559

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

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

PLOS Computational Biology: published June 21, 2012 | https://doi.org/10.1371/journal.pcbi.1002560

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

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

PLOS Computational Biology: published June 21, 2012 | https://doi.org/10.1371/journal.pcbi.1002562

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

PLOS Computational Biology: published June 21, 2012 | https://doi.org/10.1371/journal.pcbi.1002568

Quantifying the Contribution of the Liver to Glucose Homeostasis: A Detailed Kinetic Model of Human Hepatic Glucose Metabolism

Matthias König, Sascha Bulik, Hermann-Georg Holzhütter

PLOS Computational Biology: published June 21, 2012 | https://doi.org/10.1371/journal.pcbi.1002577

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

Tatjana Škrbić, Cristian Micheletti, Pietro Faccioli

PLOS Computational Biology: published June 14, 2012 | https://doi.org/10.1371/journal.pcbi.1002504

Fast Coding of Orientation in Primary Visual Cortex

Oren Shriki, Adam Kohn, Maoz Shamir

PLOS Computational Biology: published June 14, 2012 | https://doi.org/10.1371/journal.pcbi.1002536

Spine Calcium Transients Induced by Synaptically-Evoked Action Potentials Can Predict Synapse Location and Establish Synaptic Democracy

David C. Sterratt, Martine R. Groen, Rhiannon M. Meredith, Arjen van Ooyen

PLOS Computational Biology: published June 14, 2012 | https://doi.org/10.1371/journal.pcbi.1002545

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

PLOS Computational Biology: published June 14, 2012 | https://doi.org/10.1371/journal.pcbi.1002547

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

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

PLOS Computational Biology: published June 14, 2012 | https://doi.org/10.1371/journal.pcbi.1002550

The Impact of Phenotypic Switching on Glioblastoma Growth and Invasion

Philip Gerlee, Sven Nelander

PLOS Computational Biology: published June 14, 2012 | https://doi.org/10.1371/journal.pcbi.1002556

Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach

Hector Garcia-Seisdedos, Beatriz Ibarra-Molero, Jose M. Sanchez-Ruiz

PLOS Computational Biology: published June 14, 2012 | https://doi.org/10.1371/journal.pcbi.1002558

Computing with Neural Synchrony

Romain Brette

PLOS Computational Biology: published June 14, 2012 | https://doi.org/10.1371/journal.pcbi.1002561

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

PLOS Computational Biology: published June 14, 2012 | https://doi.org/10.1371/journal.pcbi.1002565

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

PLOS Computational Biology: published June 13, 2012 | https://doi.org/10.1371/journal.pcbi.1002358

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