Computational Biology of Transcription Factor Binding
Through great experimental difficulty, we’ve witnessed rapid, crucial developments at the intersection of computational biology, experimental technology, and statistics through which the vital process of transcriptional regulation can be further examined.
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MO L E C U L A R BI O L O G Y
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
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Computational Biology of Transcription Factor Binding
Edited by
Istvan Ladunga Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE, USA
Editor Istvan Ladunga Department of Statistics University of Nebraska-Lincoln 1901 Vine St., E145 Beadle Center Lincoln, NE 68588-0665, USA [email protected]
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-60761-853-9 e-ISBN 978-1-60761-854-6 DOI 10.1007/978-1-60761-854-6 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2010934132 © Springer Science+Business Media, LLC 2010 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: Crystal structure of Fis bound to 27 bp optimal binding sequence F2 from Stella, S., Cascio, D., Johnson, R.C. (2010) The shape of the DNA minor groove directs binding by the DNA-bending protein Fis. Genes Dev. 24: 814–826. Printed on acid-free paper Humana Press is part of Springer Science+Business Media (www.springer.com)
Preface Transcriptional regulation controls the basic processes of life. Its complex, dynamic, and hierarchical networks control the momentary availability of messenger RNAs for protein synthesis. Transcriptional regulation is key to cell division, development, tissue differentiation, and cancer as discussed in Chapters 1 and 2. We have witnessed rapid, major developments at the intersection of computational biology, experimental technology, and statistics. A decade ago, researches were struggling with notoriously challenging predictions of isolated binding sites from low-throughput experiments. Now we can accurately predict cis-regulatory modules, conserved clusters of binding sites (Chapters 13 and 15), partly based on high-throughput chromatin immunoprecipitation experiments in which tens of millions of DNA segments are sequenced by massively parallel, next-generation sequencers (ChIP-seq, Chapters 9, 10, and 11). These spectacular developments have allowed for the genome-wide mappings of tens of thousands of transcription factor binding sites in yeast, bacteria, mammals, insects, worms, and plants. Please also note the no less spectacular failures in
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