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Bioinformatics:
Concepts, Methodologies, Tools,
and Applications
Information Resources Management Association
USA
Managing Director: Lindsay Johnston
Editorial Director: Joel Gamon
Assistant Acquisitions Editor: Kayla Wolfe
Book Production Manager: Jennifer Yoder
Publishing Systems Analyst: Adrienne Freeland
Development Editor: Chris Wozniak
Assistnt Book Production Editor: Deanna Jo Zombro
Cover Design: Jason Mull

Published in the United States of America by

Medical Information Science Reference (an imprint of IGI Global)
701 E. Chocolate Avenue
Hershey PA 17033
Tel: 717-533-8845
Fax: 717-533-8661
E-mail: [email protected]
Web site: http://www.igi-global.com

Copyright © 2013 by IGI Global. All rights reserved. No part of this publication may be reproduced, stored or distributed in
any form or by any means, electronic or mechanical, including photocopying, without written permission from the publisher.
Product or company names used in this set are for identification purposes only. Inclusion of the names of the products or
companies does not indicate a claim of ownership by IGI Global of the trademark or registered trademark.

Library of Congress Cataloging-in-Publication Data

Bioinformatics : concepts, methodologies, tools, and applications / Information Resources Management Association, editors.
volumes cm
Includes bibliographical references and index.
ISBN 978-1-4666-3604-0 (hardcover) -- ISBN 978-1-4666-3606-4 (print & perpetual access) -- ISBN 978-1-4666-3605-7
(ebook) 1. Bioinformatics. I. Information Resources Management Association.
QH324.2.B54734 2013
572.80285--dc23
2012049182

British Cataloguing in Publication Data

A Cataloguing in Publication record for this book is available from the British Library.

The views expressed in this book are those of the authors, but not necessarily of the publisher.
Editor-in-Chief
Mehdi Khosrow-Pour, DBA
Contemporary Research in Information Science and Technology, Book Series

Associate Editors
Steve Clarke, University of Hull, UK
Murray E. Jennex, San Diego State University, USA
Annie Becker, Florida Institute of Technology, USA
Ari-Veikko Anttiroiko, University of Tampere, Finland

Editorial Advisory Board

Sherif Kamel, American University in Cairo, Egypt
In Lee, Western Illinois University, USA
Jerzy Kisielnicki, Warsaw University, Poland
Keng Siau, University of Nebraska-Lincoln, USA
Amar Gupta, Arizona University, USA
Craig van Slyke, University of Central Florida, USA
John Wang, Montclair State University, USA
Vishanth Weerakkody, Brunel University, UK
List of Contributors

Abdullah, Azween / University Technology PATRONAS, Malaysia................................................ 1745

Adamaki, Maria / University of Athens, Greece ............................................................................. 1025
Ahmad, Muneer / King Faisal University, Saudi Arabia................................................................ 1745
Ahsan, Syed / University of Engineering and Technology, Pakistan ................................................. 345
Aidinis, Vasilis / Biomedical Sciences Research Center “Alexander Fleming,” Greece ................ 1196
Ali, Hesham / University of Nebraska at Omaha, USA & University of Nebraska Medical
Center, USA ................................................................................................................................. 1536
Al-Naymat, Ghazi / University of Tabuk, Saudi Arabia .................................................................... 222
Alvarez, Marco A. / Utah State University, United States .................................................................. 93
Alves de Melo, Alba Cristina Magalhaes / University of Brasilia, Brazil....................................... 605
Anand, Swadha / National Institute of Immunology, India ............................................................. 1642
Ane, Bernadetta Kwintiana / Universität Stuttgart, Germany....................................................... 1570
Angelopoulos, Nicos / Edinburgh University, UK ............................................................................. 364
Apparao, Allam / Jawaharlal Nehru Technological University, India ............................................. 948
Appel, Ana Paula / Federal University of Espirito Santo at São Mateus, Brazil ............................. 446
Arai, Hiroyuki / Tohoku University, Japan ....................................................................................... 438
Archer, John A. C. / King Abdullah University of Science and Technology, Kingdom of
Saudi Arabia ............................................................................................................................... 1522
Asraf, S. Sheik / Madurai Kamaraj University, India ..................................................................... 1354
Azar, Ahmad Taher / Modern Science and Arts University, Egypt....................................................... 1
Bae, Seung-Hee / Indiana University - Bloomington, USA ............................................................... 287
Bajic, Vladimir B. / King Abdullah University of Science and Technology, Kingdom of
Saudi Arabia ............................................................................................................................... 1522
Bapi, Raju S. / University of Hyderabad, India................................................................................. 937
Batmaz, Inci / Middle East Technical University, Turkey ................................................................... 42
Beason, Scott / Computer Sciences Corporation, USA...................................................................... 287
Beever, Jonathan / Purdue University, USA.................................................................................... 1405
Beligiannis, Grigorios / University of Western Greece, Greece ........................................................ 805
Benos, Panayiotis V. / University of Pittsburgh, USA ....................................................................... 513
Bernstein, Richard / Cornell University, USA .................................................................................. 273
Bertucci, François / Inserm, Paoli Calmettes Institute, France ........................................................ 151
Bhardwaj, Minakshi / Cardiff University, UK ................................................................................ 1334
Bhattacharya, Arnab / Indian Institute of Technology Kanpur, India ............................................ 1599
Bhavani, S.Durga / University of Hyderabad, India. ........................................................................ 937
Bidaut, Ghislain / Inserm, Paoli Calmettes Institute, France ........................................................... 151
Birnbaum, Daniel / Inserm, Paoli Calmettes Institute, France ........................................................ 151
Borboudakis, G. / ICS-FORTH, Greece & University of Crete, Greece ........................................... 586
Buabin, Emmanuel / Methodist University College Ghana, Ghana ................................................ 761
Cai, Meihong / Nanjing University, China ...................................................................................... 1184
Cárdenas, Martha-Ivón / Universitat Politècnica de Catalunya, Spain .......................................... 817
Chatziioannou, Aristotle / National Hellenic Research Foundation, Greece ................................ 1283
Chen, Jake Y. / Indiana Center for Systems Biology and Personalized Medicine, USA; Indiana
University, USA & Purdue University, USA ............................................................................... 1378
Chen, Xin / Zhejiang University, China........................................................................................... 1174
Chen, Zheng / Beijing Geriatric Hospital, China ............................................................................. 268
Choi, Jong Youl / Indiana University - Bloomington, USA ............................................................... 287
Chowdhary, Rajesh / Biomedical Informatics Research Center, USA............................................ 1522
Christodoulou, E. G. / BIOTEC Technische Universität Dresden, Germany ................................... 586
Chui, Dehua / Peking University, China & Third Hospital of Peking University, China ................. 268
Corbit, Margaret / Cornell University, USA ..................................................................................... 273
Cui, Jun / Nanjing University, China............................................................................................... 1184
Culbertson, Adam / Indiana University, USA ................................................................................. 1378
Currall, Benjamin / Creighton University, USA ............................................................................. 1536
Dang, Loan Thi-Tung / Vietnam National University, Vietnam ........................................................ 920
Daniel, Varghese M / Monash University, Australia ......................................................................... 249
Degenkolbe, Elisa / Charité-Universitätsmedizin Berlin, Berlin-Brandenburg Center for
Regenerative Therapies, Germany.............................................................................................. 1252
Dempsey, Kathryn / University of Nebraska at Omaha, USA & University of Nebraska Medical
Center, USA ................................................................................................................................. 1536
Deng, Si / South China University of Technology, China ................................................................... 798
Deris, Safaai / Universiti Teknologi Malaysia, Malaysia ................................................................ 1727
deVersterre, Lori Watrous / New Jersey Institute of Technology, USA ......................................... 1306
Dileep, A. D. / Indian Institute of Technology Madras, India .............................................................. 72
Dimitrakopoulos, Christos M. / University of Patras, Greece ...................................................... 1237
Ding, Wei / Merck & Co., Inc., USA .................................................................................................. 465
Döring, Ole / HGI-Charité Berlin, Germany ................................................................................... 1344
Doukas, Charalampos / University of the Aegean, Greece ............................................................ 1283
Dunham, Margaret H. / Southern Methodist University, USA ....................................................... 1705
Dutta, Sourav / IBM Research Lab, India ....................................................................................... 1599
Ekanayake, Jaliya / Indiana University - Bloomington, USA........................................................... 287
Ekanayake, Saliya / Indiana University - Bloomington, USA .......................................................... 287
Emili, Andrew / University of Toronto, Canada ................................................................................ 831
Facelli, Julio Cesar / The University of Utah, USA........................................................................... 195
Faloutsos, Christos / Carnegie Mellon University, USA ................................................................... 446
Famili, Fazel / National Research Council, Canada ......................................................................... 513
Fan, Dongsheng / Third Hospital of Peking University, China ......................................................... 268
Feng, Wenqing / Accela Sciences, LLC, USA.................................................................................... 465
Finetti, Pascal / Inserm, Paoli Calmettes Institute, France ............................................................... 151
Fliss, Ismail / Université Laval, Canada.......................................................................................... 1755
Fox, Geoffrey / Indiana University - Bloomington, USA................................................................... 287
Fukuyama, Hidenao / Kyoto University Graduate School of Medicine, Japan ............................... 427
Furukawa, Katsutoshi / Tohoku University, Japan .......................................................................... 438
Furumoto, Shozo / Tohoku University, Japan ................................................................................... 438
Gao, Xieping / Xiangtan University, China ....................................................................................... 786
Garcia-Manteiga, Jose M. / Protein Transport and Secretion Unit, San Raffaele – DIBIT,
Italy ............................................................................................................................................. 1494
Garcia, Maxime / Inserm, Paoli Calmettes Institute, France ........................................................... 151
Gardiner, Eleanor Joyce / University of Shefield, UK................................................................... 1126
Georgopoulos, Efstratios F. / Technological Educational Institute of Kalamata, Greece ............. 1237
Ghiggi, Athos / University of Lugano, Switzerland ........................................................................... 884
Giraldo, Jesús / Universitat Autònoma de Barcelona, Spain ............................................................ 817
Gondro, Cedric / The Centre for Genetic Analysis and Applications, University of New England,
Australia ........................................................................................................................................ 105
Grover, Abhinav / Indian Institute of Technology, India ................................................................... 330
Gunarathne, Thilina / Indiana University - Bloomington, USA ....................................................... 287
Gunasekaran, P. / Madurai Kamaraj University, India .................................................................. 1354
Hadjiprocopis, Andreas / Higher Technical Institute, Cyprus ......................................................... 364
Hallworth, Richard / Creighton University, USA ........................................................................... 1536
Hammami, Riadh / Université Laval, Canada ............................................................................... 1755
Hattori, Masahiro / Tokyo University of Technology, Japan ............................................................ 986
Herwig, Ralf / Max Planck Institute for Molecular Genetics, Germany ......................................... 1072
Hu, Pingzhao / York University, Canada & University of Toronto, Canada ..................................... 831
Hurdle, John F. / The University of Utah, USA................................................................................. 195
Hussain, Pz Tasaduq / University of Kashmir, India ...................................................................... 1424
Iqbal, Mir Javid / University of Kashmir, India .............................................................................. 1424
Ishaq, Geer Mohammad / University of Kashmir, India ................................................................ 1424
Jankovic, Boris R. / King Abdullah University of Science and Technology, Kingdom of
Saudi Arabia ............................................................................................................................... 1522
Jiang, Hui / York University, Canada ................................................................................................ 831
Jose, Jimmy / University of Nizwa, Oman ....................................................................................... 1453
Junior, Caetano Traina / University of São Paulo at São Carlos, Brazil ......................................... 446
Jyothi, Koona Saradha / Andhra University, India .......................................................................... 948
Kafetzopoulos, Dimitris / ICS-Forth, Greece ................................................................................. 1676
Kaforou, Soia / IMBB-Forth, Greece ............................................................................................. 1676
Kalia, Awdhesh / University of Louisville, USA ................................................................................ 745
Kalina, Jan / Institute of Computer Science of the Academy of Sciences of the Czech Republic,
Czech Republic............................................................................................................................ 1113
Kandpal, K. N. / Indian Veterinary Research Institute, India ......................................................... 1564
Kane, Michael D. / Purdue University, USA ................................................................................... 1405
Khan, Mohammad Faheem / Indian Veterinary Research Institute, India .................................... 1564
Khoon, Chan Chee / Universiti Sains Malaysia, Malaysia .............................................................. 240
Koksal, Guser / Middle East Technical University, Turkey ................................................................. 42
Kossida, Sophia / Biomedical Research Foundation of the Academy of Athens, Greece.................. 805
Kotamarti, Rao M. / Southern Methodist University, USA............................................................. 1705
Kotera, Masaaki / Kyoto University, Japan ...................................................................................... 986
Koultouki, Eleftheria / University of Athens, Greece ..................................................................... 1025
Krishnaveni, Marimuthu / Avinashilingam Deemed University for Women, Thadagam Post,
India ............................................................................................................................................ 1570
Küçükural, Alper / University of Kansas, USA & Sabanci University, Turkey ................................ 386
Kudo, Yukitsuka / Tohoku University, Japan .................................................................................... 438
Kumar, Sonu / Indian Institute of Technology, India ........................................................................ 330
Kwan, Paul / University of New England, Australia ......................................................................... 105
Lambrou, George I. / University of Athens, Greece ....................................................................... 1025
Lian, Yongsheng / University of Louisville, USA .............................................................................. 745
Liberati, Diego / Italian National Research Council, Italy, Italian National Nuclear Physics
Institute, Italy & Politecnico di Milano University, Italy ............................................................. 664
Li, Bin / Merrimack Pharmaceuticals, USA ...................................................................................... 690
Lidbury, Brett A. / Australian National University, Australia .................................................. 29, 1474
Likothanassis, Spiridon D. / University of Patras, Greece .................................................... 805, 1237
Li, Miaoxin / Shanghai Center for Bioinformation Technology, China ............................................ 570
Liu, Jing / China Agricultural University, China ............................................................................ 1667
Liu, Jun-Qian / Kagawa University, Japan....................................................................................... 432
Liu, Tingting / Peking University, China........................................................................................... 268
Liu, Wei / Agios Pharmaceuticals Inc, USA ...................................................................................... 173
Liu, Xinying / Peking University, China............................................................................................ 268
Liu, Yan-Hui / Merck & Co., Inc., USA ............................................................................................. 465
Lu, Jiangyang / First Afiliated Hospital of General Hospital of PLA, China .................................. 268
Luo, Lixin / South China University of Technology, China ............................................................... 798
Maglogiannis, Ilias / University of Central Greece, Greece ........................................................... 1283
Martín-Merino, Manuel / University Pontiicia of Salamanca, Spain ........................................... 1609
Martin, Victoria / George Mason University, USA ........................................................................... 130
Masso, Majid / George Mason University, USA.............................................................................. 1010
Matsumoto, Yoshiki / Kagawa University, Japan ............................................................................. 432
Maulik, Ujjwal / Jadavpur University, India .................................................................................. 1626
Mavroudi, Seferina P. / University of Patras, Greece .................................................................... 1237
Meslin, Eric M. / Indiana University Center for Bioethics, USA & Indiana University, USA........ 1378
Miki, Takanori / Kagawa University, Japan ..................................................................................... 432
Mitchell, Joyce A. / The University of Utah, USA ............................................................................. 195
Mohanty, Debasisa / National Institute of Immunology, India........................................................ 1642
Montemanni, Roberto / Istituto Dalle Molle di Studi sull’Intelligenza Artiiciale, Switzerland ...... 884
Moore, Jason H. / Dartmouth Medical School, USA ........................................................................ 725
Morar, Nicolae / Purdue University, USA ....................................................................................... 1405
Moreano, Nahri / Federal University of Mato Grosso do Sul, Brazil ............................................... 605
Mori, Hiroshi / Osaka City University Medical School, Japan....................................................... 1557
Moschopoulos, Charalampos / Biomedical Research Foundation of the Academy of Athens,
Greece & University of Patras, Greece ........................................................................................ 805
Moschovi, Maria / University of Athens, Greece ............................................................................ 1025
Murray, Stuart / Agios Pharmaceuticals Inc, USA........................................................................... 173
Mushtaq, Mohsin Bin / Sindh Medical College, Pakistan & Dow University of Health Sciences,
Pakistan....................................................................................................................................... 1424
Natarajan, Madhusudan / Pizer, USA ............................................................................................. 552
Nikolaidou-Katsaridou, Maria Nefeli / Biomedical Sciences Research Center “Alexander
Fleming,” Greece........................................................................................................................ 1196
Nikolova, Elena V. / Bulgarian Academy of Sciences, Bulgaria ..................................................... 1072
Nikolov, S. / Institute of Mechanics and Biomechanics, Bulgaria ..................................................... 851
Nikolov, Svetoslav G. / Bulgarian Academy of Sciences, Bulgaria ................................................ 1072
Norton-Barker, Catherine / Cornell University,USA ....................................................................... 273
Nyeki, Catherine / Plurimedia Artist,“plasticienne”, France ........................................................ 1441
Okamura, Nobuyuki / Tohoku University, Japan ............................................................................. 438
Olier, Iván / The University of Manchester, UK ................................................................................ 817
Palshikar, Girish Keshav / Tata Research Development and Design Centre, India ........................ 400
Pan, Youlian / National Research Council, Canada .......................................................................... 513
Paparountas, Triantafyllos / Biomedical Sciences Research Center “Alexander Fleming,”
Greece ......................................................................................................................................... 1196
Pattin, Kristine A. / Dartmouth Medical School, USA...................................................................... 725
Penchovsky, Robert / Soia University “St. Kliment Ohridski”, Bulgaria ....................................... 860
Petrov, Valko G. / Bulgarian Academy of Sciences, Bulgaria......................................................... 1072
Phan, Ngoc Kim / Vietnam National University, Vietnam ................................................................. 920
Popescu, George V. / University Politehnica Bucharest, Romania ................................................... 676
Popescu, Sorina C. / Boyce Thompson Institute for Plant Research, USA ....................................... 676
Potamias, George / ICS-Forth, Greece ........................................................................................... 1676
Prasanthi, S. / University of Hyderabad, India. ................................................................................ 937
Punetha, Ankita / Indian Institute of Technology, India ................................................................... 330
Putty, Kalyani / University of Louisville, USA .................................................................................. 745
Qiu, Judy / Indiana University - Bloomington, USA ......................................................................... 287
Qiu, Ping / Merck & Co., Inc., USA ................................................................................................... 465
Qi, Xiaojun / Utah State University, United States.............................................................................. 93
Rajnish, K.N. / Madurai Kamaraj University, India ....................................................................... 1354
Rani, T. Sobha / University of Hyderabad, India. ............................................................................. 937
Rao, B. Subba / Andhra University, India ......................................................................................... 948
Rawat, S. S. / Indian Veterinary Research Institute, India .............................................................. 1564
Reddy, Padmalatha S. / Pizer, USA ................................................................................................. 173
Remli, Muhammad Akmal / Universiti Teknologi Malaysia, Malaysia ........................................ 1727
Reyes, Vicente M. / Rochester Institute of Technology, Rochester, USA ......................................... 1158
Rho, Mina / Indiana University - Bloomington, USA ........................................................................ 287
Røe, O. D. / Levanger Hospital—Nord-Trøndelag Health Trust, Norway, & Norwegian
University of Science and Technology, Norway ............................................................................ 586
Roller, Dieter / Universität Stuttgart, Germany............................................................................... 1570
Rovira, Xavier / Universitat Autònoma de Barcelona, Spain ........................................................... 817
Ruan, Yang / Indiana University - Bloomington, USA ...................................................................... 287
Rustici, Gabriella / European Molecular Biology Laboratory-European Bioinformatics
Institute, UK ................................................................................................................................ 1196
Sakr, Sherif / University of New South Wales, Australia ................................................................... 222
Sarkar, Anasua / Government College of Engineering and Leather Technology, India ................. 1626
Sarkar, Anita / Indian Institute of Technology, India ........................................................................ 330
Satoh, Jun-Ichi / Meiji Pharmaceutical University, Japan ............................................................... 964
Schaefer, Ulf / King Abdullah University of Science and Technology, Kingdom of Saudi
Arabia ......................................................................................................................................... 1522
Seemann, Petra / Charité-Universitätsmedizin Berlin, Berlin-Brandenburg Center for
Regenerative Therapies, Germany.............................................................................................. 1252
Sekhar, C. Chandra / Indian Institute of Technology Madras, India ................................................. 72
Serenko, Natalia / Lakehead University, Canada ........................................................................... 1317
Sethu, Palaniappan / University of Louisville, USA ......................................................................... 745
Sezerman, O. Uğur / Sabanci University, Turkey ............................................................................. 386
Shah, Abad / University of Engineering and Technology, Pakistan .................................................. 345
Shen, Pingping / Nanjing University, China.................................................................................... 1184
Shen, Yong / Center for Advanced Therapeutic Strategies for Brain Disorders, Raskamp
Institute, USA ................................................................................................................................ 322
Sheth, Vrunda / Rochester Institute of Technology, Rochester, USA............................................... 1158
Shi, Pan / The Pennsylvania State University, USA ......................................................................... 1378
Shi, Zhiao / Vanderbilt University, USA ............................................................................................ 637
Shyr, Yu / Vanderbilt University, USA Yixue Li Shanghai Center for Bioinformation Technology,
China ............................................................................................................................................. 570
Singh, Amardeep / Punjabi University, India ................................................................................. 1769
Singh, Shailendra / PEC University of Technology, India .............................................................. 1769
Singhera, Zafar / Oracle Corporation, USA ..................................................................................... 345
Song, Min / New Jersey Institute of Technology, USA ..................................................................... 1306
Sotoca, Ana M. / Radboud University, The Netherlands ................................................................. 1688
Sprague, Jon E. / Ohio Northern University, USA .......................................................................... 1405
Springer, John A. / Purdue University, USA ................................................................................... 1405
Sridhar, G. R. / Endocrine and Diabetes Centre, India .................................................................... 948
Srinivas, Kudipudi / V R Siddhartha Engineering College, India .................................................... 948
Stahl, Olivier / Inserm, Paoli Calmettes Institute, France ................................................................ 151
Subhasini, Parthasarathy / Avinashilingam Deemed University for Women, Thadagam Post,
India ............................................................................................................................................ 1570
Sundar, Durai / Indian Institute of Technology, India ....................................................................... 330
Sun, Miao / Peking University, China................................................................................................ 268
Sun, Tingzhe / Nanjing University, China ....................................................................................... 1184
Szilagyi, Andras / University of Kansas, USA ................................................................................... 386
Takeuchi, Yoshiki / Kagawa University, Japan ................................................................................. 432
Tang, Haixu / Indiana University - Bloomington, USA ..................................................................... 287
Tao, Yi-Min / China Agricultural University, China ....................................................................... 1667
Tashiro, Manabu / Tohoku University, Japan ................................................................................... 438
Tchagang, Alain B. / National Research Council, Canada ............................................................... 513
Tewik, Ahmed H. / University of Minnesota, USA ........................................................................... 513
Theoilatos, Konstantinos A. / University of Patras, Greece ......................................................... 1237
Thornton, Mitchell A. / Southern Methodist University, USA ........................................................ 1705
Truong, Nhung Hai / Vietnam National University, Vietnam............................................................ 920
Tsakalidis, Athanasios K. / University of Patras, Greece............................................................... 1237
Tsamardinos, I. / ICS-FORTH, Greece & University of Crete, Greece ............................................ 586
Tulpan, Dan / National Research Council of Canada, Canada ........................................................ 884
Van Pham, Phuc / Vietnam National University, Vietnam................................................................. 920
van Zoelen, Everardus J. J. / Radboud University, The Netherlands ............................................ 1688
Veena, T. / Indian Institute of Technology Madras, India .................................................................... 72
Vellido, Alfredo / Universitat Politècnica de Catalunya, Spain ........................................................ 817
Vera, J. / University of Rostock, Germany ......................................................................................... 851
Walkinshaw, Malcolm D. / Edinburgh University, UK..................................................................... 364
Wang, Ruofei / Xiangtan University, China ...................................................................................... 786
Wang, Zhi-Yu / Kagawa University, Japan ....................................................................................... 432
Warita, Katsuhiko / Kagawa University, Japan ............................................................................... 432
Weber, Michael / Hans Knöll Institute, Germany ........................................................................... 1688
Wildemann, Britt / Charité-Universitätsmedizin Berlin, Berlin-Brandenburg Center for
Regenerative Therapies, Germany.............................................................................................. 1252
Wolkenhauer, O. / University of Rostock, Germany ......................................................................... 851
Wu, Jun / Shanghai Center for Bioinformation Technology, China .................................................. 570
Wu, Stephen / Indiana University - Bloomington, USA .................................................................... 287
Xiao, Weizhong / Third Hospital of Peking University, China.......................................................... 268
Xie, Lu / Shanghai Center for Bioinformation Technology, China .................................................... 570
Xiong, Wei / New Jersey Institute of Technology, USA.................................................................... 1306
Xu, Hangyang / Zhejiang University, China ................................................................................... 1174
Xu, Heng / The Pennsylvania State University, USA ....................................................................... 1378
Yakura, Tomiko / Kagawa University, Japan ................................................................................... 432
Yanai, Kazuhiko / Tohoku University, Japan .................................................................................... 438
Yan, Changhui / North Dakota State University, United States .......................................................... 93
Yan, Ren-Xiang / China Agricultural University, China................................................................. 1667
Yi, Yajun / Vanderbilt University, USA .............................................................................................. 570
Yuan, Guo-Cheng / Harvard School of Public Health, USA & Dana-Farber Cancer Institute,
USA ............................................................................................................................................... 498
Yu, Jian / Tongji University, China .................................................................................................... 570
Yu, Jia / Peking University, China & Beijing Geriatric Hospital, China .......................................... 268
Zaman, Noor / King Faisal University, Saudi Arabia ..................................................................... 1745
Zhang, Bing / Vanderbilt University School of Medicine, USA ......................................................... 637
Zhang, Felicia / University of Canberra, Australia ............................................................................. 29
Zhang, Yang / University of Kansas, USA ......................................................................................... 386
Zhou, Liang / Peking University, China ............................................................................................ 268
Zhu, Fang / South China Universityof Technology, China ................................................................ 798
Zimmer, Julia / Charité-Universitätsmedizin Berlin, Berlin-Brandenburg Center for
Regenerative Therapies, Germany.............................................................................................. 1252
Zvárová, Jana / Institute of Computer Science of the Academy of Sciences of the Czech Republic,
Czech Republic............................................................................................................................ 1113
Table of Contents

Preface .............................................................................................................................................. xxvii

Volume I

Section 1
Fundamental Concepts and Theories
This section serves as a foundation for this exhaustive reference tool by addressing underlying principles
essential to the understanding of Bioinformatics. Chapters found within these pages provide an excellent
framework in which to position Bioinformatics within the ield of information science and technology.
Insight regarding the critical incorporation of global measures into Bioinformatics is addressed, while
crucial stumbling blocks of this ield are explored. With 17 chapters comprising this foundational sec-
tion, the reader can learn and chose from a compendium of expert research on the elemental theories
underscoring the Bioinformatics discipline.

Chapter 1
Overview of Biomedical Engineering ................................................................................................... 1
Ahmad Taher Azar, Modern Science and Arts University, Egypt

Chapter 2
Evaluating a Genetics Concept Inventory ............................................................................................ 29
Felicia Zhang, University of Canberra, Australia
Brett A. Lidbury, Australian National University, Australia

Chapter 3
Overview of Knowledge Discovery in Databases Process and Data Mining for Surveillance
Technologies and EWS ........................................................................................................................ 42
Inci Batmaz, Middle East Technical University, Turkey
Guser Koksal, Middle East Technical University, Turkey

Chapter 4
A Review of Kernel Methods Based Approaches to Classiication and Clustering of Sequential
Patterns: Sequences of Discrete Symbols ............................................................................................. 72
T. Veena, Indian Institute of Technology Madras, India
A. D. Dileep, Indian Institute of Technology Madras, India
C. Chandra Sekhar, Indian Institute of Technology Madras, India
Chapter 5
GO-Based Term Semantic Similarity .................................................................................................. 93
Marco A. Alvarez, Utah State University, United States
Xiaojun Qi, Utah State University, United States
Changhui Yan, North Dakota State University, United States

Chapter 6
Parallel Evolutionary Computation in R ............................................................................................ 105
Cedric Gondro, The Centre for Genetic Analysis and Applications, University of New
England, Australia
Paul Kwan, University of New England, Australia

Chapter 7
Developing a Library Collection in Bioinformatics: Support for an Evolving Profession................. 130
Victoria Martin, George Mason University, USA

Chapter 8
Linking Interactome to Disease: A Network-Based Analysis of Metastatic Relapse in Breast
Cancer ................................................................................................................................................. 151
Maxime Garcia, Inserm, Paoli Calmettes Institute, France
Olivier Stahl, Inserm, Paoli Calmettes Institute, France
Pascal Finetti, Inserm, Paoli Calmettes Institute, France
Daniel Birnbaum, Inserm, Paoli Calmettes Institute, France
François Bertucci, Inserm, Paoli Calmettes Institute, France
Ghislain Bidaut, Inserm, Paoli Calmettes Institute, France

Chapter 9
Knowledge-Driven, Data-Assisted Integrative Pathway Analytics ................................................... 173
Padmalatha S. Reddy, Pizer, USA
Stuart Murray, Agios Pharmaceuticals Inc, USA
Wei Liu, Agios Pharmaceuticals Inc, USA

Chapter 10
Medical Informatics and Bioinformatics ........................................................................................... 195
Julio Cesar Facelli, The University of Utah, USA
John F. Hurdle, The University of Utah, USA
Joyce A. Mitchell, The University of Utah, USA

Chapter 11
An Overview of Graph Indexing and Querying Techniques ............................................................. 222
Sherif Sakr, University of New South Wales, Australia
Ghazi Al-Naymat, University of Tabuk, Saudi Arabia
Chapter 12
Genomics and Population Health: A Social Epidemiology Perspective ............................................. 240
Chan Chee Khoon, Universiti Sains Malaysia, Malaysia

Chapter 13
Genomics and Genetic Engineering: Playing God?............................................................................ 249
Varghese M Daniel, Monash University, Australia

Chapter 14
The Important Role of Lipids in Cognitive Impairment .................................................................... 268
Jia Yu, Peking University, China & Beijing Geriatric Hospital, China
Zheng Chen, Beijing Geriatric Hospital, China
Jiangyang Lu, First Afiliated Hospital of General Hospital of PLA, China
Tingting Liu, Peking University, China
Liang Zhou, Peking University, China
Xinying Liu, Peking University, China
Miao Sun, Peking University, China
Weizhong Xiao, Third Hospital of Peking University, China
Dongsheng Fan, Third Hospital of Peking University, China
Dehua Chui, Peking University, China & Third Hospital of Peking University, China

Chapter 15
Virtual Worlds for Teaching: A Comparison of Traditional Methods and Virtual Worlds for
Science Instruction .............................................................................................................................. 273
Catherine Norton-Barker, Cornell University,USA
Margaret Corbit, Cornell University, USA
Richard Bernstein, Cornell University, USA

Chapter 16
Data Intensive Computing for Bioinformatics ................................................................................... 287
Judy Qiu, Indiana University - Bloomington, USA
Jaliya Ekanayake, Indiana University - Bloomington, USA
Thilina Gunarathne, Indiana University - Bloomington, USA
Jong Youl Choi, Indiana University - Bloomington, USA
Seung-Hee Bae, Indiana University - Bloomington, USA
Yang Ruan, Indiana University - Bloomington, USA
Saliya Ekanayake, Indiana University - Bloomington, USA
Stephen Wu, Indiana University - Bloomington, USA
Scott Beason, Computer Sciences Corporation, USA
Geoffrey Fox, Indiana University - Bloomington, USA
Mina Rho, Indiana University - Bloomington, USA
Haixu Tang, Indiana University - Bloomington, USA
Chapter 17
From Bench to Bedside: BACE1, Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1, From
Basic Science to Clinical Investigation............................................................................................... 322
Yong Shen, Center for Advanced Therapeutic Strategies for Brain Disorders, Raskamp Institute, USA

Section 2
Tools and Technologies
This section presents an extensive coverage of various tools and technologies available in the ield of
Bioinformatics that practitioners and academicians alike can utilize to develop different techniques.
These chapters enlighten readers about fundamental research on the many tools facilitating the bur-
geoning ield of Bioinformatics. It is through these rigorously researched chapters that the reader is
provided with countless examples of the up-and-coming tools and technologies emerging from the ield
of Bioinformatics. With 16 chapters, this section offers a broad treatment of some of the many tools and
technologies within the Bioinformatics ield.

Chapter 18
Analysis and Prediction of DNA-Recognition by Zinc Finger Proteins: Applications in Genome
Modiication ........................................................................................................................................ 330
Anita Sarkar, Indian Institute of Technology, India
Sonu Kumar, Indian Institute of Technology, India
Ankita Punetha, Indian Institute of Technology, India
Abhinav Grover, Indian Institute of Technology, India
Durai Sundar, Indian Institute of Technology, India

Chapter 19
Web Services for Bioinformatics ....................................................................................................... 345
Abad Shah, University of Engineering and Technology, Pakistan
Zafar Singhera, Oracle Corporation, USA
Syed Ahsan, University of Engineering and Technology, Pakistan

Chapter 20
Learning Binding Afinity from Augmented High Throughput Screening Data ............................... 364
Nicos Angelopoulos, Edinburgh University, UK
Andreas Hadjiprocopis, Higher Technical Institute, Cyprus
Malcolm D. Walkinshaw, Edinburgh University, UK

Chapter 21
Protein Homology Analysis for Function Prediction with Parallel Sub-Graph Isomorphism ........... 386
Alper Küçükural, University of Kansas, USA & Sabanci University, Turkey
Andras Szilagyi, University of Kansas, USA
O. Uğur Sezerman, Sabanci University, Turkey
Yang Zhang, University of Kansas, USA
Chapter 22
Techniques for Named Entity Recognition: A Survey ........................................................................ 400
Girish Keshav Palshikar, Tata Research Development and Design Centre, India

Chapter 23
Neuroimaging in Alzheimer’s Disease .............................................................................................. 427
Hidenao Fukuyama, Kyoto University Graduate School of Medicine, Japan

Chapter 24
Neuronal Transcytosis of WGA Conjugated Protein: A New Approach to Amyloid-β In Vivo.......... 432
Yoshiki Takeuchi, Kagawa University, Japan
Yoshiki Matsumoto, Kagawa University, Japan
Takanori Miki, Kagawa University, Japan
Katsuhiko Warita, Kagawa University, Japan
Zhi-Yu Wang, Kagawa University, Japan
Tomiko Yakura, Kagawa University, Japan
Jun-Qian Liu, Kagawa University, Japan

Chapter 25
Noninvasive Detection of Misfolded Proteins in the Brain Using [11C]BF-227 PET ...................... 438
Nobuyuki Okamura, Tohoku University, Japan
Shozo Furumoto, Tohoku University, Japan
Manabu Tashiro, Tohoku University, Japan
Katsutoshi Furukawa, Tohoku University, Japan
Hiroyuki Arai, Tohoku University, Japan
Yukitsuka Kudo, Tohoku University, Japan
Kazuhiko Yanai, Tohoku University, Japan

Chapter 26
Graph Mining Techniques: Focusing on Discriminating between Real and Synthetic Graphs .......... 446
Ana Paula Appel, Federal University of Espirito Santo at São Mateus, Brazil
Christos Faloutsos, Carnegie Mellon University, USA
Caetano Traina Junior, University of São Paulo at São Carlos, Brazil

Chapter 27
Current Omics Technologies in Biomarker Discovery ...................................................................... 465
Wei Ding, Merck & Co., Inc., USA
Ping Qiu, Merck & Co., Inc., USA
Yan-Hui Liu, Merck & Co., Inc., USA
Wenqing Feng, Accela Sciences, LLC, USA

Chapter 28
Prediction of Epigenetic Target Sites by Using Genomic DNA Sequence ........................................ 498
Guo-Cheng Yuan, Harvard School of Public Health, USA & Dana-Farber Cancer Institute, USA
Chapter 29
Biclustering of DNA Microarray Data: Theory, Evaluation, and Applications .................................. 513
Alain B. Tchagang, National Research Council, Canada
Youlian Pan, National Research Council, Canada
Fazel Famili, National Research Council, Canada
Ahmed H. Tewik, University of Minnesota, USA
Panayiotis V. Benos, University of Pittsburgh, USA

Chapter 30
Unsupervised Methods to Identify Cellular Signaling Networks from Perturbation Data ................ 552
Madhusudan Natarajan, Pizer, USA

Chapter 31
Cross-Platform Microarray Data Integration Combining Meta-Analysis and Gene Set Enrichment
Analysis .............................................................................................................................................. 570
Jian Yu, Tongji University, China
Jun Wu, Shanghai Center for Bioinformation Technology, China
Miaoxin Li, Shanghai Center for Bioinformation Technology, China
Yajun Yi, Vanderbilt University, USA
Yu Shyr, Vanderbilt University, USA Yixue Li Shanghai Center for Bioinformation Technology, China
Lu Xie, Shanghai Center for Bioinformation Technology, China

Chapter 32
Chemosensitivity Prediction of Tumours based on Expression, miRNA, and Proteomics Data ....... 586
I. Tsamardinos, ICS-FORTH, Greece & University of Crete, Greece
G. Borboudakis, ICS-FORTH, Greece & University of Crete, Greece
E. G. Christodoulou, BIOTEC Technische Universität Dresden, Germany
O. D. Røe, Levanger Hospital—Nord-Trøndelag Health Trust, Norway, & Norwegian
University of Science and Technology, Norway

Volume II
Chapter 33
FPGA-Based Accelerators for Bioinformatics Applications ............................................................. 605
Alba Cristina Magalhaes Alves de Melo, University of Brasilia, Brazil
Nahri Moreano, Federal University of Mato Grosso do Sul, Brazil

Section 3
Frameworks and Methodologies
This section provides in-depth coverage of conceptual architecture frameworks to provide the reader
with a comprehensive understanding of the emerging developments within the ield of Bioinformatics.
Research fundamentals imperative to the understanding of developmental processes within Bioinformat-
ics are offered. From broad examinations to speciic discussions on methodology, the research found
within this section spans the discipline while offering detailed, speciic discussions. From basic designs
to abstract development, these chapters serve to expand the reaches of development and design tech-
nologies within the Bioinformatics community. This section includes 15 contributions from researchers
throughout the world on the topic of Bioinformatics.

Chapter 34
Modules in Biological Networks: Identiication and Application ...................................................... 637
Bing Zhang, Vanderbilt University School of Medicine, USA
Zhiao Shi, Vanderbilt University, USA

Chapter 35
A Framework for Networked Experiments in Global E-Science: Perspectives for E-Learning in
Global Contexts .................................................................................................................................. 664
Diego Liberati, Italian National Research Council, Italy, Italian National Nuclear Physics
Institute, Italy & Politecnico di Milano University, Italy

Chapter 36
Complexity and Modularity of MAPK Signaling Networks ............................................................. 676
George V. Popescu, University Politehnica Bucharest, Romania
Sorina C. Popescu, Boyce Thompson Institute for Plant Research, USA

Chapter 37
Using Systems Biology Approaches to Predict New Players in the Innate Immune System ............ 690
Bin Li, Merrimack Pharmaceuticals, USA

Chapter 38
Addressing the Challenges of Detecting Epistasis in Genome-Wide Association Studies of
Common Human Diseases Using Biological Expert Knowledge ...................................................... 725
Kristine A. Pattin, Dartmouth Medical School, USA
Jason H. Moore, Dartmouth Medical School, USA

Chapter 39
Connecting Microbial Population Genetics with Microbial Pathogenesis: Engineering
Microluidic Cell Arrays for High-throughput Interrogation of Host-Pathogen Interaction ............. 745
Palaniappan Sethu, University of Louisville, USA
Kalyani Putty, University of Louisville, USA
Yongsheng Lian, University of Louisville, USA
Awdhesh Kalia, University of Louisville, USA

Chapter 40
Hybrid Neural Genetic Architecture: New Directions for Intelligent Recommender System
Design ................................................................................................................................................. 761
Emmanuel Buabin, Methodist University College Ghana, Ghana
Chapter 41
A Two-Layer Learning Architecture for Multi-Class Protein Folds Classiication ........................... 786
Ruofei Wang, Xiangtan University, China
Xieping Gao, Xiangtan University, China

Chapter 42
The Mathematical Modeling and Computational Simulation for Error-Prone PCR ......................... 798
Lixin Luo, South China University of Technology, China
Fang Zhu, South China Universityof Technology, China
Si Deng, South China University of Technology, China

Chapter 43
Using a Genetic Algorithm and Markov Clustering on Protein–Protein Interaction Graphs ............ 805
Charalampos Moschopoulos, Biomedical Research Foundation of the Academy of Athens,
Greece & University of Patras, Greece
Grigorios Beligiannis, University of Western Greece, Greece
Spiridon D. Likothanassis, University of Patras, Greece
Sophia Kossida, Biomedical Research Foundation of the Academy of Athens, Greece

Chapter 44
Kernel Generative Topographic Mapping of Protein Sequences ....................................................... 817
Martha-Ivón Cárdenas, Universitat Politècnica de Catalunya, Spain
Alfredo Vellido, Universitat Politècnica de Catalunya, Spain
Iván Olier, The University of Manchester, UK
Xavier Rovira, Universitat Autònoma de Barcelona, Spain
Jesús Giraldo, Universitat Autònoma de Barcelona, Spain

Chapter 45
Incorporating Correlations among Gene Ontology Terms into Predicting Protein Functions ........... 831
Pingzhao Hu, York University, Canada & University of Toronto, Canada
Hui Jiang, York University, Canada
Andrew Emili, University of Toronto, Canada

Chapter 46
Bifurcation Analysis of a Model Accounting for the 14-3-3σ Signalling Compartmentalisation ..... 851
S. Nikolov, Institute of Mechanics and Biomechanics, Bulgaria
J. Vera, University of Rostock, Germany
O. Wolkenhauer, University of Rostock, Germany

Chapter 47
Engineering Gene Control Circuits with Allosteric Ribozymes in Human Cells as a Medicine
of the Future ....................................................................................................................................... 860
Robert Penchovsky, Soia University “St. Kliment Ohridski”, Bulgaria
Chapter 48
Computational Sequence Design Techniques for DNA Microarray Technologies ............................ 884
Dan Tulpan, National Research Council of Canada, Canada
Athos Ghiggi, University of Lugano, Switzerland
Roberto Montemanni, Istituto Dalle Molle di Studi sull’Intelligenza Artiiciale, Switzerland

Section 4
Cases and Applications
This section discusses a variety of applications and opportunities available that can be considered by
practitioners in developing viable and effective Bioinformatics programs and processes. This section
includes 16 chapters that review topics from case studies in the EU to best practices in Africa and ongoing
research in the United States. Further chapters discuss Bioinformatics in a variety of settings. Contribu-
tions included in this section provide excellent coverage of today’s IT community and how research into
Bioinformatics is impacting the social fabric of our present-day global village.

Chapter 49
Can Activated Platelet Rich Plasma Combined with Adipose-Derived Stem Cells Be Used to
Treat Skin Wrinkles? A Mechanism Study ......................................................................................... 920
Phuc Van Pham, Vietnam National University, Vietnam
Loan Thi-Tung Dang, Vietnam National University, Vietnam
Nhung Hai Truong, Vietnam National University, Vietnam
Ngoc Kim Phan, Vietnam National University, Vietnam

Chapter 50
Analysis of Kinase Inhibitors and Druggability of Kinase-Targets Using Machine Learning
Techniques ......................................................................................................................................... 937
S. Prasanthi, University of Hyderabad, India.
S.Durga Bhavani, University of Hyderabad, India.
T. Sobha Rani, University of Hyderabad, India.
Raju S. Bapi, University of Hyderabad, India.

Chapter 51
In Silico Pharmaco-Gene-Informatic Identiication of Insulin-Like Proteins in Plants ..................... 948
Koona Saradha Jyothi, Andhra University, India
G. R. Sridhar, Endocrine and Diabetes Centre, India
Kudipudi Srinivas, V R Siddhartha Engineering College, India
B. Subba Rao, Andhra University, India
Allam Apparao, Jawaharlal Nehru Technological University, India

Chapter 52
Molecular Network Analysis of Target RNAs and Interacting Proteins of TDP-43, a Causative
Gene for the Neurodegenerative Diseases ALS/FTLD ...................................................................... 964
Jun-Ichi Satoh, Meiji Pharmaceutical University, Japan
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