Regulatory Genomics RECOMB 2004 International Workshop, RRG 2004, Sa
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Edited by S. Istrail, P. Pevzner, and M. Waterman Editorial Board: A. Apostolico S. Brunak M. Gelfand T. Lengauer S. Miyano G. Myers M.-F. Sagot D. Sankoff R. Shamir T. Speed M. Vingron W. Wong
Subseries of Lecture Notes in Computer Science
Eleazar Eskin Chris Workman (Eds.)
Regulatory Genomics RECOMB 2004 International Workshop, RRG 2004 San Diego, CA, USA, March 26-27, 2004 Revised Selected Papers
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Series Editors Sorin Istrail, Celera Genomics, Applied Biosystems, Rockville, MD, USA Pavel Pevzner, University of California, San Diego, CA, USA Michael Waterman, University of Southern California, Los Angeles, CA, USA Volume Editors Eleazar Eskin University of California, Department of Computer Science and Engineering San Diego, USA E-mail: [email protected] Chris Workman University of California, Department of Bioengineering San Diego, USA E-mail: [email protected]
Library of Congress Control Number: 2004118137
CR Subject Classification (1998): F.2, G.2, E.1, H.2.8, J.3 ISSN 0302-9743 ISBN 3-540-24456-5 Springer Berlin Heidelberg New York This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, re-use of illustrations, recitation, broadcasting, reproduction on microfilms or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. Springer is a part of Springer Science+Business Media springeronline.com © Springer-Verlag Berlin Heidelberg 2005 Printed in Germany Typesetting: Camera-ready by author, data conversion by Olgun Computergrafik Printed on acid-free paper SPIN: 11380795 06/3142 543210
Preface
Research in the field of gene regulation is evolving rapidly in an ever-changing scientific environment. Microarray techniques and comparative genomics have enabled more comprehensive studies of regulatory genomics and are proving to be powerful tools of discovery. The application of chromatin immunoprecipitation and microarrays (chIP-on-chip) to directly study the genomic binding locations of transcription factors has enabled more comprehensive modeling of regulatory networks. In addition, complete genome sequences and the comparison of numerous related species has demonstrated that conservation in non-coding DNA sequences often provides evidence for cis-regulatory binding sites. That said, much is still to be learned about the regulatory networks of these sequenced genomes. Systematic methods to decipher the regulatory mechanism are also crucial for corroborating these regulatory networks. The core of these methods are the 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 comparati
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