Yeast Systems Biology Methods and Protocols
Systems Biology aims at deciphering the genotype-phenotype relationships at the levels of genes, transcripts (RNAs), peptides, proteins, metabolites, and environmental factors participating in complex cellular networks in order to reveal the mechanisms an
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IN
M OLECULAR B IOLOGY TM
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For other titles published in this series, go to www.springer.com/series/7651
Yeast Systems Biology Methods and Protocols
Edited by
Juan I. Castrillo Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
Stephen G. Oliver Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
Editors Juan I. Castrillo Department of Biochemistry Cambridge Systems Biology Centre University of Cambridge Cambridge, CB2 1GA, UK [email protected]
Stephen G. Oliver Department of Biochemistry Cambridge Systems Biology Centre University of Cambridge Cambridge, CB2 1GA, UK [email protected]
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-172-7 e-ISBN 978-1-61779-173-4 DOI 10.1007/978-1-61779-173-4 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2011933223 © Springer Science+Business Media, LLC 2011 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Cover illustration: Scanning electron micrograph of the budding yeast Saccharomyces cerevisiae (Photo courtesy of Dr. Alan E. Wheals. Department of Biology and Biochemistry. University of Bath, UK). Printed on acid-free paper Humana Press is part of Springer Science+Business Media (www.springer.com)
Preface The explosion of new technologies in the post-genomic era is allowing the study of biological systems on a genome-wide scale, at the main functional genomic levels: (epi)-genome, transcriptome, proteome, endo- and exometabolome, and their interactions. At the same time that these techniques are being applied and refined, the complexity of biological systems is being rediscovered (1) with thousands of components (e.g., genes, transcripts, proteins, metabolites) participating in finely tuned metabolic and regulatory networks. “Molecular pathways, rather than being linear, independent from or parallel to each other, are instead incredibly intertwined and form very complex biological networks. Phenotypes are probably more directly related to systems properties than they are to DNA and ‘genes’” (Marc Vidal in (2)). The idea that multi-scale dynamic complex systems formed by interacting macromolecules and metabolites, cell
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