Regulatory Genomics - Proceedings Of The 3rd Annual Recomb Workshop

by Hon Wai Leong (Editor), Ken Wing-kin Sung (Editor), Eleazar Eskin (Editor)

Overview

Research in the field of gene regulation is evolving rapidly in the ever-changing scientific environment. Advances in microarray techniques and comparative genomics have enabled more comprehensive studies of regulatory genomics. The study of genomic binding locations of transcription factors has enabled a more comprehensive modeling of regulatory networks. In addition, complete genomic sequences and comparison of numerous related species have demonstrated the conservation of non-coding DNA sequences, which often provide evidence for cis-regulatory binding sites. Systematic methods to decipher the regulatory mechanism are also crucial for corroborating these regulatory networks; key to these methods are motif discovery algorithms that can help predict cis-regulatory elements. These DNA-motif discovery programs are becoming more sophisticated and are beginning to leverage evidence from comparative genomics. These topics and more were discussed at the 3rd Annual RECOMB Workshop on Regulatory Genomics, which brought together more than 90 attendees and included about 22 excellent talks from leading researchers in the field. This proceedings volume contains ten selected, original manuscripts that were presented during the workshop.

Product Details

ISBN-13:	9781848162518
Publisher:	Imperial College Press
Publication date:	07/09/2008
Series:	Series On Advances In Bioinformatics And Computational Biology , #8
Pages:	144
Product dimensions:	6.70(w) x 9.80(h) x 0.60(d)

Table of Contents

Foreword v

Recomb Regulatory Genomics 2006 Organization vii

Keynote Papers

Computational Prediction of Regulatory Elements by Comparative Sequence Analysis M. Tompa 3

A Tale of Two Topics - Motif Significance and Sensitivity of Spaced Seeds M. Li 4

Computational Challenges for Top-Down Modeling and Simulation of Biological Pathways S. Miyano 5

An Improved Gibbs Sampling Method for Motif Discovery via Sequence Weighting T. Jiang 6

Discovering Motifs with Transcription Factor Domain Knowledge F. Chin 7

Applications of ILP in Computational Biology A. Dress 8

On the Evolution of Transcription Regulation Networks R. Shamir 9

Systems Pharmacology in Cancer Therapeutics: Iterative Informatics-Experimental Interface E. Liu 10

Computational Structural Proteomics and Inhibitor Discovery R. Abagyan 11

Characterization of Transcriptional Responses to Environmental Stress by Differential Location Analysis H. Tang 12

A Knowledge-based Hybrid Algorithm for Protein Secondary Structure Prediction W. L. Hsu 13

Monotony and Surprise (Conservative Approaches to Pattern Discovery) A. Apostolico 14

Evolution of Bacterial Regulatory Systems M. S. Gelfand 15

Contributed Papers

TScan: A Two-step De Novo Motif Discovery Method O. Abul G. K. Sandve F. Drablos 19

Redundancy Elimination in Motif Discovery Algorithms H. Leung F. Chin 31

GAMOT: An Efficient Genetic Algorithm for Finding Challenging Motifs in DNA Sequences N. Karaoglu S. Maurer-Stroh B. Manderick 43

Identification of Spaced Regulatory Sites via Submotif Modeling E. Wijaya R. Kanagasabai 57

Refining Motif Finders with E-value Calculations N. Nagarajan P. Ng U. Keich 73

Multiple Indexing SequenceAlignment for Group Feature Identification W.-Y. Chou T.-W. Pai J. Z.-C. Lai W.-S. Tzou M. D.-T. Chang H.-T. Chang W.-Y. Chou T.-C. Fan 85

Improving the Accuracy of Signal Transduction Pathway Construction Using Level-2 Neighbours T. K. F. Wong S. M. Yiu T. W. Lam S. C. K. Wong 99

Investigating Roles of DNA Flexibility in Promoter Recognition and Regulation J. D. Bashford 109

Regulatory Networks of Genes Affected By MorA, A Global Regulator Containing GGDEF and EAL Domains in Pseudomonas Aeruginosa W.-K. Choy V. B. Bajic M.-W. Heng M. Veronika S. Swarup 123

Author Index 131