Table of Contents: April 2006

A dipeptide nanotube, composed of 2,000 diphenylalanine molecules, is optimized under a two-dimensional lattice wrapping system (see Tsai et al) with an all-atom force field. The constructed tube can be used as a foundation for building an atomic model with the tube geometry observed experimentally.

Image Credit: Image created by Chung-Jung Tsai with graphics software, BioChem.


Practical Strategies for Discovering Regulatory DNA Sequence Motifs

Kenzie D MacIsaac, Ernest Fraenkel

Research Articles

A Model for Integrating Elementary Neural Functions into Delayed-Response Behavior

Thomas Gisiger, Michel Kerszberg

Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation

Eli S Groban, Arjun Narayanan, Matthew P Jacobson

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

Jakob Skou Pedersen, Gill Bejerano, Adam Siepel, Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S Lander, Jim Kent, Webb Miller, David Haussler

SAGE2Splice: Unmapped SAGE Tags Reveal Novel Splice Junctions

Byron Yu-Lin Kuo, Ying Chen, Slavita Bohacec, Öjvind Johansson, Wyeth W Wasserman, Elizabeth M Simpson

Codon Usage Domains over Bacterial Chromosomes

Marc Bailly-Bechet, Antoine Danchin, Mudassar Iqbal, Matteo Marsili, Massimo Vergassola

Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome

Leonardo Arbiza, Joaquín Dopazo, Hernán Dopazo

Designing a Nanotube Using Naturally Occurring Protein Building Blocks

Chung-Jung Tsai, Jie Zheng, Ruth Nussinov


The Signal in the Genomes

David Sankoff