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Table of Contents

April 2008

Cover

A leaf's venation pattern

Issue Image

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

Education

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

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

PLOS Computational Biology: published April 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000035

Perspective

Bioinformatics in China: A Personal Perspective

Liping Wei, Jun Yu

PLOS Computational Biology: published April 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000020

Review

Translational Systems Biology of Inflammation

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

PLOS Computational Biology: published April 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000014

Research Articles

Dimensionality and Dynamics in the Behavior of C. elegans

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

PLOS Computational Biology: published April 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000028

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

PLOS Computational Biology: published April 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000048

Biosynthetic Potentials of Metabolites and Their Hierarchical Organization

Franziska Matthäus, Carlos Salazar, Oliver Ebenhöh

PLOS Computational Biology: published April 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000049

The Statistical Neuroanatomy of Frontal Networks in the Macaque

Bruno B. Averbeck, Moonsang Seo

PLOS Computational Biology: published April 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000050

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

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

PLOS Computational Biology: published April 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000051

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

PLOS Computational Biology: published April 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000052

Efficient Olfactory Coding in the Pheromone Receptor Neuron of a Moth

Lubomir Kostal, Petr Lansky, Jean-Pierre Rospars

PLOS Computational Biology: published April 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000053

Predicting Co-Complexed Protein Pairs from Heterogeneous Data

Jian Qiu, William Stafford Noble

PLOS Computational Biology: published April 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000054

The Role of Elastic Stresses on Leaf Venation Morphogenesis

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

PLOS Computational Biology: published April 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000055

A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains

Alexandr P. Kornev, Susan S. Taylor, Lynn F. Ten Eyck

PLOS Computational Biology: published April 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000056

Related Articles

  1. Correction: A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains

Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes

Jon Bohlin, Eystein Skjerve, David W. Ussery

PLOS Computational Biology: published April 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000057

Related Articles

  1. Correction: Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
  2. Correction: Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
  3. Correction: Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
  4. Correction: Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
  5. Correction: Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes

The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli

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

PLOS Computational Biology: published April 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000059

Binding-Induced Folding of a Natively Unstructured Transcription Factor

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

PLOS Computational Biology: published April 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000060

Distinct Timing Mechanisms Produce Discrete and Continuous Movements

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

PLOS Computational Biology: published April 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000061

Synaptic Learning Rules and Sparse Coding in a Model Sensory System

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

PLOS Computational Biology: published April 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000062

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data

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

PLOS Computational Biology: published April 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000065

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

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

PLOS Computational Biology: published April 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000066

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

PLOS Computational Biology: published April 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000067