Systems Biology And Synthetic Biology

SYSTEMS BIOLOGY AND SYNTHETIC BIOLOGY Edited by Pengcheng Fu China University of Petroleum Beijing, China Sven Panke ETH Zurich, Institute of Process Engineering Zurich, Switzerland SYSTEMS BIOLOGY AND SYNTHETIC BIOLOGY SYSTEMS BIOLOGY AND SYNTHETIC BIOLOGY Edited by Pengcheng Fu China University of Petroleum Beijing, China Sven Panke ETH Zurich, Institute of Process Engineering Zurich, Switzerland Copyright  2009 by John Wiley & Sons, Inc. All rights reserved. Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400, fax 978-750-4470, or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, 201-748-6011, fax 201-748-6008, or online at http://www.wiley.com/go/permission. Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor author shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages. For general information on our other products and services or for technical support, please contact our Customer Care Department within the United States at 877-762-2974, outside the United States at 317-5723993 or fax 317- 572-4002. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic formats. For more information about Wiley products, visit our web site at www.wiley.com. Library of Congress Cataloging-in-Publication Data: Systems biology and synthetic biology / [edited by] Pengcheng Fu, Sven Panke. p. ; cm. Includes bibliographical references. ISBN 978-0-471-76778-7 (cloth) 1. Biotechnology. 2. Genetic engineering. 3. Biological systems. I. Fu, Pengcheng. II. Panke, Sven. [DNLM: 1. Genetic Engineering–methods. 2. Molecular Biology–methods. 3. Genes, Synthetic. 4. Genomics–methods. 5. Models, Genetic. 6. Systems Biology–methods. QU 450 S995 2009] TP248.2.S97 2009 660.6 –dc22 2008027981 Printed in the United States of America 10 9 8 7 6 5 4 3 2 1 To my wife Juan Huang and sons, Eugene and Edgar CONTENTS Foreword ix Contributors xi 1 Introduction 1 Pengcheng Fu 2 Basics of Molecular Biology, Genetic Engineering, and Metabolic Engineering 9 Michael X. Wang and Huidong Shi 3 High-Throughput Technologies and Functional Genomics 67 Xiu-Feng Wan and Dorothea K. Thompson 4 Genomic Signal Processing of DNA Microarray Data for the Enhanced Prediction of Axillary Lymph Node Status of Breast Cancer Tumors 115 Gordon S. Okimoto 5 Reco