Bacterial Molecular Networks Methods and Protocols
Network-based representations have become pervasive in most fields in biology. Bacterial Molecular Networks: Methods and Protocols provides authoritative descriptions of various experimental and computational methods enabling the characterization and anal
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MOLECULAR BIOLOGY
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes: http://www.springer.com/series/7651
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Bacterial Molecular Networks Methods and Protocols
Edited by
Jacques van Helden and Ariane Toussaint Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bruxelles, Belgium
Denis Thieffry Institut de Biologie de l'Ecole Normale Supérieure (IBENS), UMR ENS, CNRS 8197, INSERM 1024, Paris, France
Editors Jacques van Helden Laboratoire de Bioinformatique des Ge´nomes et des Re´seaux (BiGRe) Universite´ Libre de Bruxelles Bruxelles, Belgium [email protected]
Ariane Toussaint Laboratoire de Bioinformatique des Ge´nomes et des Re´seaux (BiGRe) Universite´ Libre de Bruxelles Bruxelles, Belgium [email protected]
Denis Thieffry Institut de Biologie de l’Ecole Normale Supe´rieure (IBENS) UMR ENS CNRS 8197 INSERM 1024 Paris, France [email protected]
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-360-8 e-ISBN 978-1-61779-361-5 DOI 10.1007/978-1-61779-361-5 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2011938202 ª Springer Science+Business Media, LLC 2012 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. Printed on acid-free paper Humana Press is part of Springer Science+Business Media (www.springer.com)
Preface Network-based representations have become pervasive in most fields in biology. Focusing on networks applied to bacteria, this volume provides authoritative descriptions of various experimental and computational methods enabling the characterization and analysis of molecular interaction networks. Intended primarily for postgraduate students and researchers working in the field of experimental and computational microbiology, this volume combines up-to-date reviews along with detailed protocols written by the developers of bioinformatics resources (databases and software tools). Each protocol emphasizes the crucial steps and the way to set up the parameters in order to obtain the best results. The first section provides an extensive coverage of various experimental and in silico approaches aiming at the characterization of network components. The second section is devoted to the presentation of computational approaches to analyze the topo
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