Computational Methods with Applications in Bioinformatics Analysis

233 Pages·2017·3.494 MB·English

by  Jeffrey J. P. Tsai, Jeffrey J. P. Tsai, Ka-log Ng

COMPUTATIONAL METHODS
WITH APPLICATIONS IN
BIOINFORMATICS ANALYSIS
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Vol. 20: Computational Methods with Applications in Bioinformatics Analysis
edited by Jeffrey J. P. Tsai and Ka-Lok Ng
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Advanced Series in Electrical and Computer Engineering – Vol. 20
COMPUTATIONAL METHODS
WITH APPLICATIONS IN
BIOINFORMATICS ANALYSIS
Editors
Jeffrey J. P. Tsai
Ka-Lok Ng
Asia University, Taiwan
World Scientific
NEW JERSEY • LONDON • SINGAPORE • BEIJING • SHANGHAI • HONG KONG • TAIPEI • CHENNAI
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Library of Congress Cataloging-in-Publication Data
Names: Tsai, Jeffrey J.-P., editor. | Ng, Ka-Lok, editor.
Title: Computational methods with applications in bioinformatics analysis /
edited by: Jeffrey J.P. Tsai (Asia University, Taiwan), Ka-Lok Ng (Asia University, Taiwan).
Description: New Jersey : World Scientific, 2017. | Series: Advanced series in
electrical and computer engineering ; volume 20
Identifiers: LCCN 2016059286 | ISBN 9789813207974 (hc : alk. paper)
Subjects: LCSH: Bioinformatics--Mathematics. | Computational biology.
Classification: LCC QH324.2 .C6359 2017 | DDC 570.285--dc23
LC record available at https://lccn.loc.gov/2016059286
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Copyright © 2017 by World Scientific Publishing Co. Pte. Ltd.
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Preface
In the past decade, we have seen mounting evidence of the usefulness
of computational approaches to bioinformatics and biomedical research.
Semanticcomputing,machinelearningclassifiers,clusteringalgorithmsand
mathematical methods have been particularly influential in contributing
insights in the era of post-genomics research. In the post-genomics era,
computational biology will certainly play an increasingly important role in
elucidating the underlying features and mechanisms in biological systems.
The use of advanced computational approaches is an effective mean
to address difficult problems in bioinformatics and biomedical research.
An advantage of applying computational methods is to reduce the cost
and time compared to doing real experiments; hence, there are needs for
developing and advancing such area of research. As the volume of biomed-
ical data increases, so does demand for establishing and building up more
computational methods for solving a wide range of applications.
This book is a collection of 10 chapters written by international
researchers with expertise in microarray data analysis, semantic comput-
ing,dynamicsmodellingofbiomolecularinteractions,fuzzyintegral,molec-
ular simulation and machine learning algorithms. In particular, a variety
of computational methods are presented to different areas of studies in
biomedicine andbioinformatics analysis; suchas, time series data analysis,
ensemble clustering, protein and nucleic acid interaction, host–pathogen
interaction system, RNA network in autoimmune diseases, multiple omics
data integration, T-cell epitope and cytometry.
v
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vi Preface
Inshort,thisbookpresentstheuseofadvancedcomputationalmethods
for a range of biomedical applications. Instead of focusing on problems in
molecular biology, sequence analysis or cancer-related research, the book
payattentiontoarangeofbiomedicalissuesratherthanthefundamentals.
Jeffrey J.P. Tsai
Ka-Lok Ng
Taichung, 2017
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Acknowledgment
We are gratefulfor all the authors for their efforts and involvementin pro-
ducing this book. This book would not have been possible without the
financial support by the Ministry of Science and Technology of Taiwan
(MOST) under contractnumber MOST 105-2632-E-468-002, andthe sup-
portfromAsiaUniversity. Finally,wewouldliketothanktheeditorialand
production staffs at World Scientific Publishing, in particular Steven Patt,
Herbert Moses and Rajesh Babu, for making this book possible.
vii
b2530 International Strategic Relations and China’s National Security: World at the Crossroads
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About the Authors
Jeffrey J. P. Tsai received a PhD degree in Computer Science from the
Northwestern University, Evanston, Illinois. He is currently the President
and Chair Professor of Asia University, Taiwan. Dr. Tsai was a Profes-
sor of Computer Science and the Director of the Distributed Real-Time
Intelligent Systems Laboratory at the University of Illinois, Chicago. He
was also an Adjunct Professor at Tulane University, a Visiting Professor
at Stanford University, a Visiting Scholar at the University of Califor-
nia at Berkeley, and a Senior Research Fellow of IC2 at the University
of Texas at Austin. His research interests include bioinformatics, intru-
sion detection, knowledge-based software engineering, formal modelling
and verification, distributed real-time systems, sensor networks, ubiqui-
tous computing, services computing, and intelligent agents. His research
hasbeensupportedbyUSNSF,DARPA,USAFRomeLaboratory,Depart-
mentofDefense,ArmyResearchLaboratory,Motorola,Fujitsu,andGtech.
Thetechnologyonknowledge-basedsoftwareengineeringdevelopedbyhim
and his research team resulted the world’s first complete transformation
of an embedded software product in 1993 and is now used to produce
communication software systems worldwide. Tsai coauthored Knowledge-
Based Software Development for Real-Time Distributed Systems (World
Scientific, 1993), Distributed Real-Time Systems (Wiley, 1996), Composi-
tionalVerificationofConcurrentandReal-TimeSystems(Springer/Kluwer,
2002), Security Modeling and Analysis of Mobile Agent Systems (Imperial
College Press, 2006), Intrusion Detection: A Machine Learning Approach
(Imperial College Press, 2010), and coedited Monitoring and Debugging
of Distributed Real-Time Systems (IEEE Computer Society Press, 1995),
Machine Learning Applications in Software Engineering (WSP, 2005),
ix