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Genomics and proteomics engineering in medicine and biology PDF

316 Pages·2007·10.54 MB·English
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GENOMICS AND PROTEOMICS ENGINEERING IN MEDICINE AND BIOLOGY IEEE Press 445 Hoes Lane Piscataway, NJ 08854 IEEE Press Editorial Board Mohamed E. El-Hawary, Editor in Chief J. B. Anderson S. V. Kartalopoulos N. Schulz R. J. Baker M. Montrose C. Singh T. G. Croda M. S. Newman G. Zobrist R. J. Herrick F. M. B. Periera Kenneth Moore, Director of IEEE Book and Information Services (BIS) Catherine Faduska, Senior Acquisitions Editor Steve Welch, Acquisitions Editor Jeanne Audino, Project Editor IEEE Engineering in Medicine and Biology Society, Sponsor EMB-S Liaison to IEEE Press, Metin Akay GENOMICS AND PROTEOMICS ENGINEERING IN MEDICINE AND BIOLOGY Edited by Metin Akay IEEE Engineering in Medicine and Biology Society, Sponsor Copyright # 2007 by the Institute of Electrical and Electronics Engineers, Inc. All rights reserved. Published by John Wiley & Sons, Inc. 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 com- pleteness 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 (800) 762-2974, outside the United States at (317) 572-3993 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 is available ISBN-13 978-0-471-63181-1 ISBN-10 0-471-63181-7 Printed in the United States of America 10 9 8 7 6 5 4 3 2 1 To the memory of my late brother, C¸ etin Akay, who dedicated his short but meaningful life to the well-being and happiness of others as well as a democratic and secular Turkey. May God bless his soul. &CONTENTS Preface xi Contributors xiii 1. Qualitative Knowledge Models in Functional Genomics and Proteomics 1 Mor Peleg, Irene S. Gabashvili, and Russ B. Altman 1.1. Introduction 1 1.2. Methods and Tools 3 1.3. Modeling Approach and Results 6 1.4. Discussion 19 1.5. Conclusion 20 References 21 2. Interpreting Microarray Data and Related Applications Using Nonlinear System Identification 25 Michael Korenberg 2.1. Introduction 25 2.2. Background 25 2.3. Parallel Cascade Identification 30 2.4. Constructing Class Predictors 34 2.5. Prediction Based on Gene Expression Profiling 35 2.6. Comparing Different Predictors Over the Same Data Set 46 2.7. Concluding Remarks 48 References 49 3. Gene Regulation Bioinformatics of Microarray Data 55 Gert Thijs, Frank De Smet, Yves Moreau, Kathleen Marchal, and Bart De Moor 3.1. Introduction 55 3.2. Introduction to Transcriptional Regulation 57 3.3. Measuring Gene Expression Profiles 59 3.4. Preprocessing of Data 61 3.5. Clustering of Gene Expression Profiles 63 vii viii CONTENTS 3.6. Cluster Validation 70 3.7. Searching for Common Binding Sites of Coregulated Genes 76 3.8. Inclusive: Online Integrated Analysis of Microarray Data 87 3.9. Further Integrative Steps 89 3.10. Conclusion 90 References 91 4. Robust Methods for Microarray Analysis 99 George S. Davidson, Shawn Martin, Kevin W. Boyack, Brian N. Wylie, Juanita Martinez, Anthony Aragon, Margaret Werner-Washburne, Mo´nica Mosquera-Caro, and Cheryl Willman 4.1. Introduction 99 4.2. Microarray Experiments and Analysis Methods 100 4.3. Unsupervised Methods 103 4.4. Supervised Methods 117 4.5. Conclusion 127 References 128 5. In Silico Radiation Oncology: A Platform for Understanding Cancer Behavior and Optimizing Radiation Therapy Treatment 131 G. Stamatakos, D. Dionysiou, and N. Uzunoglu 5.1. Philosophiae Tumoralis Principia Algorithmica: Algorithmic Principles of Simulating Cancer on Computer 131 5.2. Brief Literature Review 133 5.3. Paradigm of Four-Dimensional Simulation of Tumor Growth and Response to Radiation Therapy In Vivo 135 5.4. Discussion 148 5.5. Future Trends 150 References 150 6. Genomewide Motif Identification Using a Dictionary Model 157 Chiara Sabatti and Kenneth Lange 6.1. Introduction 157 6.2. Unified Model 160 6.3. Algorithms for Likelihood Evaluation 164 6.4. Parameter Estimation via Minorization–Maximization Algorithm 167 6.5. Examples 170 6.6. Discussion and Conclusion 171 References 172 7. Error Control Codes and the Genome 173 Elebeoba E. May 7.1. Error Control and Communication: A Review 173 CONTENTS ix 7.2. Central Dogma as Communication System 180 7.3. Reverse Engineering the Genetic Error Control System 184 7.4. Applications of Biological Coding Theory 203 References 205 8. Complex Life Science Multidatabase Queries 209 Zina Ben Miled, Nianhua Li, Yue He, Malika Mahoui, and Omran Bukhres 8.1. Introduction 209 8.2. Architecture 212 8.3. Query Execution Plans 214 8.4. Related Work 219 8.5. Future Trends 222 References 223 9. Computational Analysis of Proteins 227 Dimitrios I. Fotiadis, Yorgos Goletsis, Christos Lampros, and Costas Papaloukas 9.1. Introduction: Definitions 227 9.2. Databases 229 9.3. Sequence Motifs and Domains 232 9.4. Sequence Alignment 235 9.5. Modeling 241 9.6. Classification and Prediction 242 9.7. Natural Language Processing 248 9.8. Future Trends 252 References 252 10. Computational Analysis of Interactions Between Tumor and Tumor Suppressor Proteins 257 E. Pirogova, M. Akay, and I. Cosic 10.1. Introduction 257 10.2. Methodology: Resonant Recognition Model 261 10.3. Results and Discussions 265 10.4. Conclusion 284 References 285 Index 289 About the Editor 299

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