Table of Contents

April 2008

Image of a Miconia sp. leaf, from Ilha Grande, Brazil. Some features shared by all angiosperm leaves can be observed. One is the hierarchy of the veins, signed by their radii and originating in the successive formation of veins during the growth. Another feature is the abundance of closed loops: the leaf blade is divided by the venation array into small polygonal surfaces. A model based on the existence of mechanical instabilities leads very naturally to this kind of pattern (see Laguna et al., doi:10.1371/journal.pcbi.1000055).

Image Credit: Image by M. F. Laguna


A Quick Guide for Computer-Assisted Instruction in Computational Biology and Bioinformatics

Manuel João Costa, Eduardo Galembeck, Guilherme A. Marson, Bayardo B. Torres


Bioinformatics in China: A Personal Perspective

Liping Wei, Jun Yu


Translational Systems Biology of Inflammation

Yoram Vodovotz, Marie Csete, John Bartels, Steven Chang, Gary An

Research Articles

Dimensionality and Dynamics in the Behavior of C. elegans

Greg J. Stephens, Bethany Johnson-Kerner, William Bialek, William S. Ryu

A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach

Peng Wang, John Sidney, Courtney Dow, Bianca Mothé, Alessandro Sette, Bjoern Peters

Biosynthetic Potentials of Metabolites and Their Hierarchical Organization

Franziska Matthäus, Carlos Salazar, Oliver Ebenhöh

The Statistical Neuroanatomy of Frontal Networks in the Macaque

Bruno B. Averbeck, Moonsang Seo

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer

Ali Bashir, Stanislav Volik, Colin Collins, Vineet Bafna, Benjamin J. Raphael

Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm

Ignacio E. Sánchez, Pedro Beltrao, Francois Stricher, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Frederic Rousseau, Luis Serrano

Efficient Olfactory Coding in the Pheromone Receptor Neuron of a Moth

Lubomir Kostal, Petr Lansky, Jean-Pierre Rospars

Predicting Co-Complexed Protein Pairs from Heterogeneous Data

Jian Qiu, William Stafford Noble

The Role of Elastic Stresses on Leaf Venation Morphogenesis

Maria F. Laguna, Steffen Bohn, Eduardo A. Jagla

The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli

Mark W. J. van Passel, Pradeep Reddy Marri, Howard Ochman

Binding-Induced Folding of a Natively Unstructured Transcription Factor

Adrian Gustavo Turjanski, J. Silvio Gutkind, Robert B. Best, Gerhard Hummer

Distinct Timing Mechanisms Produce Discrete and Continuous Movements

Raoul Huys, Breanna E. Studenka, Nicole L. Rheaume, Howard N. Zelaznik, Viktor K. Jirsa

Synaptic Learning Rules and Sparse Coding in a Model Sensory System

Luca A. Finelli, Seth Haney, Maxim Bazhenov, Mark Stopfer, Terrence J. Sejnowski

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data

Sourav Bandyopadhyay, Ryan Kelley, Nevan J. Krogan, Trey Ideker

An AP Endonuclease 1–DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces

Alexej Abyzov, Alper Uzun, Phyllis R. Strauss, Valentin A. Ilyin

Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes

Michael F. Lin, Ameya N. Deoras, Matthew D. Rasmussen, Manolis Kellis