Biomedical Informatics for Cancer Research
In the past two decades, the large investment in cancer research led to identification of the complementary roles of genetic mutation and epigenetic change as the fundamental drivers of cancer. With these discoveries, we now recognize the deep heterogenei
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Michael F. Ochs John T. Casagrande Ramana V. Davuluri ●
Editors
Biomedical Informatics for Cancer Research
Editors Michael F. Ochs Division of Oncology Biostatistics and Bioinformatics Sidney Kimmel Comprehensive Cancer Center John Hopkins University Baltimore, MD 21205-2011 USA [email protected]
John T. Casagrande Cancer Research Informatics Core University of Southern California Kenneth Norris Jr. Comprehensive Cancer Center Los Angeles, CA 90089 USA [email protected]
Ramana V. Davuluri The Wistar Institute Philadelphia, PA 19104 USA [email protected]
ISBN 978-1-4419-5712-2 e-ISBN 978-1-4419-5714-6 DOI 10.1007/978-1-4419-5714-6 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2010924049 © 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 (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: An image of matrix production by fibroblasts, showing the extracellular matrix and cell adhesion structures that play a key role in cancer cell behavior and metastasis. Indirect immunofluorescent images, of NIH-3T3 cells (murine fibroblasts), were acquired during the cellular process of extracellular matrix deposition. Nuclei are shown in blue while extracellular fibronectin matrix fibers (red) and cellular adhesion structures (integrin in green) can be seen co-localizing in yellow. Image was acquired after 4 days of matrix production. Image kindly provided by Dr. Edna Cukierman of the Fox Chase Cancer Center in Philadelphia. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)
Michael F. Ochs dedicates this volume to Erica Golemis Over half of our lives together so far, forget the asymptotic limit, let’s go for all of our lives together. John T. Casagrande dedicates this volume to Yolee Casagrande Her continuous support and encouragement in all aspects of my life are greatly appreciated. I would like to especially thank her for encouraging me to pursue my “creative” side, which has resulted in this volume. Ramana V. Davuluri dedicates this volume to Adinarayana Davuluri I owe a lot to my father, whose commitment encouraged me to go to school. His loss to cancer inspired me to pursue medical research in cancer.
Acknowledgments
Many people dedicated significant effort to making this volume possible. I would like to thank Alisa Moore, who keeps my endle
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