E-Book Overview
This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2005 satellite events: the First Annual Workshop on Systems Biology, RSB 2005 and the Second Annual Workshop on Regulatory Genomics, RRG 2005, held in San Diego, CA, USA in December 2005.
The 21 revised full papers presented were carefully reviewed and selected for inclusion in the book. The papers address a broad variety of topics in systems biology and regulatory genomics including inference of gene regulatory and protein signaling networks, model prediction of drug mechanism, pathway mapping and evolution in protein interaction networks, multi-scale methods which bridge abstract and detailed models, systematic design of genome-scale experiments, modeling and recognition of regulatory elements, identification and modeling of cis-regulatory regions, modeling the structure and function of the regulatory region, and comparative genomics of regulation.
E-Book Content
Lecture Notes in Bioinformatics
4023
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 Trey Ideker Ben Raphael Christopher Workman (Eds.)
Systems Biology and Regulatory Genomics Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics San Diego, CA, USA, December 2-4, 2005 Revised Selected Papers
13
Series Editors Sorin Istrail, Brown University, Providence, RI, USA Pavel Pevzner, University of California, San Diego, CA, USA Michael Waterman, University of Southern California, Los Angeles, CA, USA Volume Editors Eleazar Eskin Ben Raphael University of California Department of Computer Science San Diego, CA, USA E-mail: {eeskin,braphael}@cs.ucsd.edu Trey Ideker Christopher Workman University of California Department of Bioengineering San Diego, CA, USA E-mail: {trey,cworkman}@bioeng.ucsd.edu
Library of Congress Control Number: 2006940071
CR Subject Classification (1998): F.2, G.3, E.1, H.2.8, J.3 LNCS Sublibrary: SL 8 – Bioinformatics ISSN ISBN-10 ISBN-13
0302-9743 3-540-48293-8 Springer Berlin Heidelberg New York 978-3-540-48293-2 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 springer.com © Springer-Verlag Berlin Heidelberg 2007 Printed in Germany Typesetting: Camera-ready by author, data conversion by Scientific Publishing Services, Chennai, India Printed on acid-free paper SPIN: 11916338 06/3142 543210
Preface
It has become increasingly evident that the use of large-scale experimental data and the application of principles from systems biology are gaining widespread acceptance in mainstream biology. Systems biology involves the use of global cellular measurements, i.e., genomic, proteomic, and metabolomic, to construct computational models of cellular processes and disease. These approaches involve an integration of experimental and computational techniques and may include: 1) developing models of cellular processes, 2) measuring the response to perturbations of model components, and 3) iteratively formula