Regulatory genomics : proceedings of the 3rd annual RECOMB workshop : National University of Singapore, Singapore 17-18 July 2006 / editors, Leong Hon Wai, Sung Wing-Kin, Eleazar Eskin.

Includes bibliographical references and author index.

Keynote papers. Computational prediction of regulatory elements by comparative sequence analysis / M. Tompa. A tale of two topics -- motif significance and sensitivity of spaced seeds / M. Li. Computational challenges for top-down modeling and simulation of biological pathways / S. Miyano. An improved Gibbs sampling method for motif discovery via sequence weighting / T. Jiang. Discovering motifs with transcription factor domain knowledge / F. Chin. Applications of ILP in computational biology / A. Dress. On the evolution of transcription regulation networks / R. Shamir. Systems pharmacology in cancer therapeutics: iterative informatics-experimental interface / E. Liu. Computational structural proteomics and inhibitor discovery / R. Abagyan. Characterization of transcriptional responses to environmental stress by differential location analysis / H. Tang. A knowledge-based hybrid algorithm for protein secondary structure prediction / W.L. Hsu. Monotony and surprise (conservative approaches to pattern discovery) / A. Apostolico. Evolution of bacterial regulatory systems / M.S. Gelfand -- Contributed papers. TScan: a two-step De NoVo motif discovery method / O. Abul, G.K. Sandve, and F. Drabl²s. Redundancy elimination in motif discovery algorithms / H. Leung and F. Chin. GAMOT: an efficient genetic algorithm for finding challenging motifs in DNA sequences / N. Karaoglu, S. Maurer-Stroh, and B. Manderick. Identification of spaced regulatory sites via submotif modeling / E. Wijaya and R. Kanagasabai. Refining motif finders with E-value calculations / N. Nagarajan, P. Ng, and U. Keich. Multiple indexing sequence alignment for group feature identification / W.-Y. Chou [and others]. Improving the accuracy of signal transduction pathway construction using level-2 neighbours / T.K.F. Wong [and others]. Investigating roles of DNA flexibility in promoter recognition and regulation / J.D. Bashford. Regulatory networks of genes affected by MorA, a global regulator containing GGDEF and EAL domains in Pseudomonas Aeruginosa / W.-K. Choy [and others].

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.

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