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Table of Contents: December 2006

Closeup view of a region of the Protein Homology Network (PHN) that allows displaying either the homology relationships within a family or the genetic distance between the members. Protein families show a high density of connections. Different colors identify VirB1, AvhB1, VirB4, TraH, Slt, and TrbN bacterial families (See Covacci et al).

Image Credit: Illustration by Giorgio Corsi

Education Articles

Modularity and Dynamics of Cellular Networks

Yuan Qi, Hui Ge

Perspectives

The Genome: An Outsider's View

Carl Zimmer

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  1. Correction: The Genome: An Outsider's View

Research Articles

Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in α-Proteobacteria

Dmitry A Rodionov, Mikhail S Gelfand, Jonathan D Todd, Andrew R. J Curson, Andrew W. B Johnston

Transcriptional Regulation by Competing Transcription Factor Modules

Rutger Hermsen, Sander Tans, Pieter Rein ten Wolde

Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens

Jeroen de Ridder, Anthony Uren, Jaap Kool, Marcel Reinders, Lodewyk Wessels

Gene Expression of Caenorhabditis elegans Neurons Carries Information on Their Synaptic Connectivity

Alon Kaufman, Gideon Dror, Isaac Meilijson, Eytan Ruppin

On Side-Chain Conformational Entropy of Proteins

Jinfeng Zhang, Jun S Liu

Connectivity in the Yeast Cell Cycle Transcription Network: Inferences from Neural Networks

Christopher E Hart, Eric Mjolsness, Barbara J Wold

Insight into the Structure of Amyloid Fibrils from the Analysis of Globular Proteins

Antonio Trovato, Fabrizio Chiti, Amos Maritan, Flavio Seno

Protein Homology Network Families Reveal Step-Wise Diversification of Type III and Type IV Secretion Systems

Duccio Medini, Antonello Covacci, Claudio Donati

DARPP-32 Is a Robust Integrator of Dopamine and Glutamate Signals

Éric Fernandez, Renaud Schiappa, Jean-Antoine Girault, Nicolas Le Novère

Prediction of Amyloidogenic and Disordered Regions in Protein Chains

Oxana V Galzitskaya, Sergiy O Garbuzynskiy, Michail Yurievich Lobanov

Stern-Judging: A Simple, Successful Norm Which Promotes Cooperation under Indirect Reciprocity

Jorge M Pacheco, Francisco C Santos, Fabio A. C. C Chalub

Targeting Neuropilin-1 to Inhibit VEGF Signaling in Cancer: Comparison of Therapeutic Approaches

Feilim Mac Gabhann, Aleksander S Popel

Corrections