August 2006

Graphic depiction of a prototypic transcriptional regulatory system (TRS), representative of the Escherichia coli TRS, circumscribing a matrix that would capture the associated regulatory rules. Such a matrix formalism (see Gianchandani et al) enables the calculation of system properties of a TRS.

Image Credit: Image designed by Erwin Gianchandani

Editorial

One Year of PLoS Computational Biology

Philip E Bourne

PLOS Computational Biology: published August 25, 2006 | https://doi.org/10.1371/journal.pcbi.0020111

Message from ISCB

ISCB Honors Michael S. Waterman and Mathieu Blanchette

Merry Maisel

PLOS Computational Biology: published August 4, 2006 | https://doi.org/10.1371/journal.pcbi.0020105

Review

The Ion Channel Inverse Problem: Neuroinformatics Meets Biophysics

Robert C Cannon, Giampaolo D'Alessandro

PLOS Computational Biology: published August 25, 2006 | https://doi.org/10.1371/journal.pcbi.0020091

Research Articles

An Integrative Method for Accurate Comparative Genome Mapping

Firas Swidan, Eduardo P. C Rocha, Michael Shmoish, Ron Y Pinter

PLOS Computational Biology: published August 4, 2006 | https://doi.org/10.1371/journal.pcbi.0020075

Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes

Chad Haynes, Christopher J Oldfield, Fei Ji, Niels Klitgord, Michael E Cusick, Predrag Radivojac, Vladimir N Uversky, Marc Vidal, Lilia M Iakoucheva

PLOS Computational Biology: published August 4, 2006 | https://doi.org/10.1371/journal.pcbi.0020100

Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems

Erwin P Gianchandani, Jason A Papin, Nathan D Price, Andrew R Joyce, Bernhard O Palsson

PLOS Computational Biology: published August 11, 2006 | https://doi.org/10.1371/journal.pcbi.0020101

Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families

Guohui Ding, Jiuhong Kang, Qi Liu, Tieliu Shi, Gang Pei, Yixue Li

PLOS Computational Biology: published August 11, 2006 | https://doi.org/10.1371/journal.pcbi.0020102

Transient Resetting: A Novel Mechanism for Synchrony and Its Biological Examples

Chunguang Li, Luonan Chen, Kazuyuki Aihara

PLOS Computational Biology: published August 4, 2006 | https://doi.org/10.1371/journal.pcbi.0020103

Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States

Yonatan Bilu, Tomer Shlomi, Naama Barkai, Eytan Ruppin

PLOS Computational Biology: published August 18, 2006 | https://doi.org/10.1371/journal.pcbi.0020106

Modeling Somatic Evolution in Tumorigenesis

Sabrina L Spencer, Ryan A Gerety, Kenneth J Pienta, Stephanie Forrest

PLOS Computational Biology: published August 18, 2006 | https://doi.org/10.1371/journal.pcbi.0020108

High Epitope Expression Levels Increase Competition between T Cells

Almut Scherer, Marcel Salathé, Sebastian Bonhoeffer

PLOS Computational Biology: published August 18, 2006 | https://doi.org/10.1371/journal.pcbi.0020109

Expansion of Protein Domain Repeats

Åsa K Björklund, Diana Ekman, Arne Elofsson

PLOS Computational Biology: published August 25, 2006 | https://doi.org/10.1371/journal.pcbi.0020114

Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice

Carene Rizzon, Loic Ponger, Brandon S Gaut

PLOS Computational Biology: published September 1, 2006 | https://doi.org/10.1371/journal.pcbi.0020115

Correction

Correction: Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance

Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li

PLOS Computational Biology: published August 25, 2006 | https://doi.org/10.1371/journal.pcbi.0020112

Cover

Depiction of a prototypic transcriptional regulatory system