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E-raamat: Regulatory Genomics - Proceedings Of The 3rd Annual Recomb Workshop

Edited by (Nus, S'pore), Edited by (Nus, S'pore), Edited by (Univ Of California, San Diego, Usa)
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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.
Foreword v
RECOMB Regulatory Genomics 2006 Organization vii
Keynote Papers
Computational Prediction of Regulatory Elements by Comparative Sequence Analysis
3(1)
M. Tompa
A Tale of Two Topics---Motif Significance and Sensitivity of Spaced Seeds
4(1)
M. Li
Computational Challenges for Top-Down Modeling and Simulation of Biological Pathways
5(1)
S. Miyano
An Improved Gibbs Sampling Method for Motif Discovery via Sequence Weighting
6(1)
T. Jiang
Discovering Motifs with Transcription Factor Domain Knowledge
7(1)
F. Chin
Applications of ILP in Computational Biology
8(1)
A. Dress
On the Evolution of Transcription Regulation Networks
9(1)
R. Shamir
Systems Pharmacology in Cancer Therapeutics: Iterative Informatics-Experimental Interface
10(1)
E. Liu
Computational Structural Proteomics and Inhibitor Discovery
11(1)
R. Abagyan
Characterization of Transcriptional Responses to Environmental Stress by Differential Location Analysis
12(1)
H. Tang
A Knowledge-based Hybrid Algorithm for Protein Secondary Structure Prediction
13(1)
W. L. Hsu
Monotony and Surprise (Conservative Approaches to Pattern Discovery)
14(1)
A. Apostolico
Evolution of Bacterial Regulatory Systems
15(4)
M. S. Gelfand
Contributed Papers
TScan: A Two-step De Novo Motif Discovery Method
19(12)
O. Abul
G. K. Sandve
F. Drabløs
Redundancy Elimination in Motif Discovery Algorithms
31(12)
H. Leung
F. Chin
GAMOT: An Efficient Genetic Algorithm for Finding Challenging Motifs in DNA Sequences
43(14)
N. Karaoglu
S. Maurer-Stroh
B. Manderick
Identification of Spaced Regulatory Sites via Submotif Modeling
57(16)
E. Wijaya
R. Kanagasabai
Refining Motif Finders with E-value Calculations
73(12)
N. Nagarajan
P. Ng
U. Keich
Multiple Indexing Sequence Alignment for Group Feature Identification
85(14)
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
Improving the Accuracy of Signal Transduction Pathway Construction Using Level-2 Neighbours
99(10)
T. K. F. Wong
S. M. Yiu
T. W. Lam
S. C. K. Wong
Investigating Roles of DNA Flexibility in Promoter Recognition and Regulation
109(14)
J. D. Bashford
Regulatory Networks of Genes Affected By MorA, A Global Regulator Containing GGDEF and EAL Domains in Pseudomonas Aeruginosa
123(8)
W.-K. Choy
V. B. Bajic
M.-W. Heng
M. Veronika
S. Swarup
Author Index 131