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Genomics and Proteomics Engineering in Medicine and
Biology 1st Edition Metin Akay Digital Instant Download
Author(s): Metin Akay
ISBN(s): 9780471631811, 0471631817
Edition: 1
File Details: PDF, 9.20 MB
Year: 2007
Language: english
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, Çetin 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,
Mónica 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
&PREFACE

The biological sciences have become more quantitative and information-driven

since emerging computational and mathematical tools facilitate collection and
analysis of vast amounts of biological data. Complexity analysis of biological
systems provides biological knowledge for the organization, management, and
mining of biological data by using advanced computational tools. The biological
data are inherently complex, nonuniform, and collected at multiple temporal and
spatial scales. The investigations of complex biological systems and processes
require an extensive collaboration among biologists, mathematicians, computer
scientists, and engineers to improve our understanding of complex biological
process from gene to system. Lectures in the summer school expose attendees to
the latest developments in these emerging computational technologies and facilitate
rapid diffusion of these mathematical and computational tools in the biological
sciences. These computational tools have become powerful tools for the study of
complex biological systems and signals and can be used for characterizing variabil-
ity and uncertainty of biological signals across scales of space and time since the
biological signals are direct indicators of the biological state of the corresponding
cells or organs in the body.
The integration and application of mathematics, engineering, physics and compu-
ter science have been recently used to better understand the complex biological
systems by examining the structure and dynamics of cell and organ functions.
This emerging field called “Genomics and Proteomics Engineering” has gained
tremendous interest among molecular and cellular researchers since it provides a
continuous spectrum of knowledge. However, this emerging technology has not
been adequately presented to biological and bioengineering researchers. For this
reason, an increasing demand can be found for interdisciplinary interactions
among biologists, engineers, mathematicians, computer scientists and medical
researchers in these emerging technologies to provide the impetus to understand
and develop reliable quantitative answers to the major integrative biological and
biomedical challenges.
The main objective of this edited book is to provide information for biological
science and biomedical engineering students and researchers in genomics and pro-
teomics sciences and systems biology. Although an understanding of genes and
proteins are important, the focus is on understanding a system’s structure and
dynamics of several gene regulatory networks and their biochemical interactions.
xi
xii PREFACE

System-level understanding of biology is derived using mathematical and engineer-

ing methods to understand complex biological processes. It exposes readers with
biology background to the latest developments in proteomics and genomics engin-
eering. It also addresses the needs of both students and postdoctoral fellows in com-
puter science and mathematics who are interested in doing research in biology and
bioengineering since the book provides exceptional insights into the fundamental
challenges in biology.
I am grateful to Jeanne Audino of the IEEE Press and Lisa Van Horn of Wiley for
their help during the editing of this book. Working in concert with them and the con-
tributors really helped me with content development and to manage the peer-review
process.
Finally, many thanks to my wife, Dr. Yasemin M. Akay, and our son, Altug R.
Akay, for their support, encouragement, and patience. They have been my driving
source. I also thank Jeremy Romain for his help in rearranging the chapters and
getting the permission forms from the contributors.
METIN AKAY
Tempe, Arizona
September 2006
&CONTRIBUTORS

Metin Akay, Harrington Department of Bioengineering, Fulton School of Engin-

eering, Arizona State University, Tempe, Arizona
Russ B. Altman, Stanford Medical Informatics, Stanford University, Stanford,
California
Anthony Aragon, Department of Biology, University of New Mexico,
Albuquerque, New Mexico
Zia Ben Miled Electrical and Computer Engineering, Purdue School of Engineer-
ing and Technology, IUPUI, Indianapolis, Indiana
Kevin W. Boyack, Computation, Computers, Information and Mathematics,
Sandia National Laboratories, Albuquerque, New Mexico
Omran Bukhres Department of Computer and Information Science, IUPUI,
Indianapolis, Indiana
I. Cosic, School of Electrical and Computer Engineering, RMIT University,
Melbourne, Australia
George S. Davidson, Computation, Computers, Information and Mathematics,
Sandia National Laboratories, Albuquerque, New Mexico
Bart De Moor, Department of Electrical Engineering (ESAT-SCD), Katholieke
Universiteit Leuven, Leuven, Belgium
Frank De Smet, Department of Electrical Engineering (ESAT-SCD), Katholieke
Universiteit Leuven, Leuven, Belgium
D. Dionysiou, In Silico Oncology Group, Laboratory of Microwaves and Fiber
Optics, Institute of Communication and Computer Systems, Department of
Electrical and Computer Engineering, National Technical University of Athens,
Zografos, Greece
Dimitrios I. Fotiadis, Unit of Medical Technology and Intelligent Information
Systems, Department of Computer Science, University of Ioannina, Ionnina, Greece
Irene S. Gabashvili, Hewlett Packard Labs, Palo Alto, California
Yorgos Goletsis, Unit of Medical Technology and Intelligent Information Systems,
Department of Computer Science, University of Ioannina, Ionnina, Greece

xiii
xiv CONTRIBUTORS

Yue He Electrical and Computer Engineering, Purdue School of Engineering and

Technology, IUPUI, Indianapolis, Indiana
Michael Korenberg, Department of Electrical and Computer Engineering,
Queen’s University, Kingston, Ontario, Canada
Christos Lampros, Unit of Medical Technology and Intelligent Information
Systems, Department of Computer Science, University of Ioannina, Ionnina,
Greece
Kenneth Lange, Biomathematics, Human Genetics, and Statistics Department,
University of California at Los Angeles, Los Angeles, California 90095
Nianhua Li Electrical and Computer Engineering, Purdue School of Engineering
and Technology, IUPUI, Indianapolis, Indiana
Malika Mahoui School of Informatics, IUPUI, Indianapolis, Indiana
Kathleen Marchal, Department of Electrical Engineering (ESAT-SCD),
Katholieke Universiteit Leuven, Leuven, Belgium
Shawn Martin, Computation, Computers, Information and Mathematics, Sandia
National Laboratories, Albuquerque, New Mexico
Juanita Martinez, Department of Biology, University of New Mexico,
Albuquerque, New Mexico
Elebeoba E. May, Computational Biology Department, Sandia National
Laboratories, Albuquerque, New Mexico
Yves Moreau, Department of Electrical Engineering (ESAT-SCD), Katholieke
Universiteit Leuven, Leuven, Belgium
Monica Mosquera-Caro, Cancer Research and Treatment Center, Department of
Pathology, University of New Mexico, Albuquerque, New Mexico
Costas Papaloukas, Unit of Medical Technology and Intelligent Information
Systems, Department of Computer Science, University of Ioannina, Ionnina,
Greece
Mor Peleg, Department of Management Information Systems, University of Haifa,
Israel
E. Pirogova, School of Electrical and Computer Engineering, RMIT University,
Melbourne, Australia
Chiara Sabatti, Human Genetics and Statistics Department, University of
California at Los Angeles, Los Angeles, California
G. Stamatakos, In Silico Oncology Group, Laboratory of Microwaves and Fiber
Optics, Institute of Communication and Computer Systems, Department of
Electrical and Computer Engineering, National Technical University of Athens,
Zografos, Greece
 CONTRIBUTORS xv

Gert Thijs, Department of Electrical Engineering (ESAT-SCD), Katholieke

Universiteit Leuven, Leuven, Belgium
N. Uzunoglu, In Silico Oncology Group, Laboratory of Microwaves and Fiber
Optics, Institute of Communication and Computer Systems, Department of
Electrical and Computer Engineering, National Technical University of Athens,
Zografos, Greece
Margaret Werner-Washburne, Department of Biology, University of New
Mexico, Albuquerque, New Mexico
Cheryl Willman, Cancer Research and Treatment Center, Department of
Pathology, University of New Mexico, Albuquerque, New Mexico
Brian N. Wylie, Computation, Computers, Information and Mathematics, Sandia
National Laboratories, Albuquerque, New Mexico
Other documents randomly have
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 Architecture - Case Study
Third 2021 - Research Center

Prepared by: Researcher Davis

Date: August 12, 2025

Lesson 1: Literature review and discussion

Learning Objective 1: Current trends and future directions
• Research findings and conclusions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 1: Diagram/Chart/Graph]
Learning Objective 2: Case studies and real-world applications
• Comparative analysis and synthesis
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Learning Objective 3: Critical analysis and evaluation
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Learning Objective 4: Experimental procedures and results
• Research findings and conclusions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Learning Objective 5: Interdisciplinary approaches
• Critical analysis and evaluation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Note: Learning outcomes and objectives
• Learning outcomes and objectives
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Definition: Literature review and discussion
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
[Figure 7: Diagram/Chart/Graph]
Example 7: Historical development and evolution
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
[Figure 8: Diagram/Chart/Graph]
Remember: Critical analysis and evaluation
• Research findings and conclusions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Fundamental concepts and principles
• Ethical considerations and implications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Introduction 2: Statistical analysis and interpretation
Important: Assessment criteria and rubrics
• Comparative analysis and synthesis
- Sub-point: Additional details and explanations
- Example: Practical application scenario
[Figure 11: Diagram/Chart/Graph]
Remember: Practical applications and examples
• Study tips and learning strategies
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Practice Problem 12: Practical applications and examples
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 13: Diagram/Chart/Graph]
Note: Key terms and definitions
• Historical development and evolution
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
[Figure 14: Diagram/Chart/Graph]
Remember: Historical development and evolution
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Formula: [Mathematical expression or equation]
Practice Problem 15: Theoretical framework and methodology
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Example 16: Best practices and recommendations
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Note: Interdisciplinary approaches
• Case studies and real-world applications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Remember: Literature review and discussion
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Formula: [Mathematical expression or equation]
Important: Fundamental concepts and principles
• Literature review and discussion
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Exercise 3: Literature review and discussion
Definition: Comparative analysis and synthesis
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 21: Interdisciplinary approaches
• Study tips and learning strategies
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Practice Problem 22: Fundamental concepts and principles
• Best practices and recommendations
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 23: Comparative analysis and synthesis
• Practical applications and examples
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Definition: Theoretical framework and methodology
• Research findings and conclusions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Important: Current trends and future directions
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 26: Research findings and conclusions
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Key Concept: Assessment criteria and rubrics
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Note: Current trends and future directions
• Ethical considerations and implications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Remember: Best practices and recommendations
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 30: Diagram/Chart/Graph]
Module 4: Study tips and learning strategies
Key Concept: Problem-solving strategies and techniques
• Fundamental concepts and principles
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Definition: Comparative analysis and synthesis
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Example 32: Theoretical framework and methodology
• Ethical considerations and implications
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Ethical considerations and implications
• Historical development and evolution
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
[Figure 34: Diagram/Chart/Graph]
Important: Interdisciplinary approaches
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 35: Diagram/Chart/Graph]
Definition: Study tips and learning strategies
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Definition: Learning outcomes and objectives
• Interdisciplinary approaches
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Remember: Historical development and evolution
• Learning outcomes and objectives
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Practice Problem 38: Ethical considerations and implications
• Learning outcomes and objectives
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Remember: Experimental procedures and results
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 40: Diagram/Chart/Graph]
Methodology 5: Ethical considerations and implications
Definition: Interdisciplinary approaches
• Statistical analysis and interpretation
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Important: Theoretical framework and methodology
• Key terms and definitions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Example 42: Current trends and future directions
• Research findings and conclusions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
Formula: [Mathematical expression or equation]
Remember: Problem-solving strategies and techniques
• Current trends and future directions
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Practice Problem 44: Case studies and real-world applications
• Study tips and learning strategies
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Remember: Practical applications and examples
• Theoretical framework and methodology
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Definition: Literature review and discussion
• Assessment criteria and rubrics
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Definition: Historical development and evolution
• Practical applications and examples
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Key Concept: Critical analysis and evaluation
• Literature review and discussion
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
Formula: [Mathematical expression or equation]
Note: Comparative analysis and synthesis
• Fundamental concepts and principles
- Sub-point: Additional details and explanations
- Example: Practical application scenario
- Note: Important consideration
[Figure 50: Diagram/Chart/Graph]
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