Next Generation Microarray Bioinformatics Methods and Protocols
Recent improvements in the efficiency, quality, and cost of genome-wide sequencing have prompted biologists and biomedical researchers to move away from microarray-based technology to ultra high-throughput, massively parallel genomic sequencing (Nex
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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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Next Generation Microarray Bioinformatics Methods and Protocols
Edited by
Junbai Wang Department of Pathology, Oslo University Hospital, Radium Hospital, Montebello, Oslo, Norway
Aik Choon Tan Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
Tianhai Tian School of Mathematical Sciences, Monash University, Melbourne, VIC, Australia
Editors Junbai Wang, Ph.D. Department of Pathology Oslo University Hospital Radium Hospital Montebello, Oslo, Norway [email protected]
Aik Choon Tan, Ph.D. Division of Medical Oncology Department of Medicine School of Medicine University of Colorado Anschutz Medical Campus Aurora, CO, USA [email protected]
Tianhai Tian, Ph.D. School of Mathematical Sciences Monash University Melbourne, VIC, Australia [email protected]
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-399-8 e-ISBN 978-1-61779-400-1 DOI 10.1007/978-1-61779-400-1 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2011943561 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 The twenty-first century is the time of excitement and optimism for biomedical research. Since the completion of the human genome project in 2001, we are entering into the postgenome era where the key research efforts are now interpreting and making sense of these massive genomic data, in order to translate into disease treatment and management. Over the past decade, DNA-based microarrays have been the assays of choice for highthroughput studies of gene expression. Microarray-based expression profiling was provided, for the first time, by means of monitoring genome-wide gene expression changes in a single experiment. Though microarray technology has been widely employed to reveal molecular portraits of gene expression in various cancers’ subtypes and correlations with disease progression as well as response to drug treatments, it is not limited to measure gene expre
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