Computational Intelligence and Pattern Analysis in Biology Informatics / Edition 1

by Ujjwal Maulik, Sanghamitra Bandyopadhyay, Jason T. Wang, Yi Pan, Albert Y. Zomaya

Overview

An invaluable tool in Bioinformatics, this unique volume provides both theoretical and experimental results, and describes basic principles of computational intelligence and pattern analysis while deepening the reader's understanding of the ways in which these principles can be used for analyzing biological data in an efficient manner.

This book synthesizes current research in the integration of computational intelligence and pattern analysis techniques, either individually or in a hybridized manner. The purpose is to analyze biological data and enable extraction of more meaningful information and insight from it. Biological data for analysis include sequence data, secondary and tertiary structure data, and microarray data. These data types are complex and advanced methods are required, including the use of domain-specific knowledge for reducing search space, dealing with uncertainty, partial truth and imprecision, efficient linear and/or sub-linear scalability, incremental approaches to knowledge discovery, and increased level and intelligence of interactivity with human experts and decision makers

• Chapters authored by leading researchers in CI in biology informatics.
• Covers highly relevant topics: rational drug design; analysis of microRNAs and their involvement in human diseases.
• Supplementary material included: program code and relevant data sets correspond to chapters.

Product Details

ISBN-13:	9780470581599
Publisher:	Wiley
Publication date:	11/30/2010
Series:	Wiley Series in Bioinformatics , #13
Pages:	372
Product dimensions:	6.40(w) x 9.60(h) x 1.12(d)

About the Author

Dr. Ujjwal Maulik is Professor of Computer Science and Engineering at Jadavpur University (India). He is the editor or author of five books and coauthor of more than 150 articles. Dr. Maulik is a Senior Member of IEEE and also a Humboldt Fellow.

Dr. Sanghamitra Bandyopadhyay is Professor at the Indian Statistical Institute. She is the editor or author of six books and coauthor of more than 180 articles. Dr. Bandyopadhyay is a Senior Member of IEEE and also a Humboldt Fellow.

Dr. Jason T. L. Wang is a Professor and Director of the Data and Knowledge Engineering Lab at the New Jersey Institute of Technology. He is the editor or author of six books and Executive Editor of the World Scientific Book Series on Science, Engineering, and Biology Informatics.

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Table of Contents

Preface xi

Contributors xvii

Part I Introduction

1 Computational Intelligence: Foundations, Perspectives, and Recent Trends Swagatam Das Ajith Abraham B. K. Panigrahi 3

2 Fundamentals of Pattern Analysis: A Brief Overview Basabi Chakraborty 39

3 Biological Informatics: Data, Tools, and Applications Kevin Byron Miguel Cervantes-Cervantes Jason T. L. Wang 59

Part II Sequence Analysis

4 Promoter Recognition Using Neural Network Approaches T. Sobha Rani S. Durga Bhavani S. Bapi Raju 73

5 Predicting microRNA Prostate Cancer Target Genes Francesco Masulli Stefano Rovetta Giuseppe Russo 99

Part III Structure Analysis

6 Structural Search in RNA Motif Databases Dongrong Wen Jason T. L. Wang 119

7 Kernels on Protein Structures Sourangshu Bhattacharya Chiranjib Bhattacharyya Nagasuma R. Chandra 131

8 Characterization of Conformational Patterns in Active and Inactive Forms of Kinases using Protein Blocks Approach G. Agarwal D. C. Dinesh N. Srinivasan Alexandre G. de Brevern 169

9 Kernel Function Applications in Cheminformatics Aaron Smalter Jun Huan 189

10 In Silico Drug Design Using a Computational Intelligence Technique Soumi Sengupta Sanghamitra Bandyopadhyay 237

Part IV Microarray Data Analysis

11 Integrated Differential Fuzzy Clustering for Analysis of Microarray Data Indrajit Saha Ujjwal Maulik 259

12 Identifying Potential Gene Markers Using SVM Classifier Ensemble Anirban Mukhopadhyay Ujjwal Maulik Sanghamitra Bandyopadhyay 277

13 Gene Microarray Data Analysis Using Parallel Point Symmetry-Based Clustering Ujjwal Maulik Anasua Sarkar 293

Part V Systems Biology

14 Techniques for Prioritization of Candidate Disease Genes Jieun Jeong Jake Y. Chen 309

15 Prediction of Protein-Protein Interactions Angshuman Bagchi 325

16 Analyzing Topological Properties of Protein-Protein Interaction Networks: A Perspective Toward Systems Biology Malay Bhattacharyya Sanghamitra Bandyopadhyay 349

Index 369

What People are Saying About This

From the Publisher

"This collection of 16 papers, edited by Maulik (computer science and engineering, Jadavpur U., India), Bandyopadhyay (Indian Statistical Institute, India), and Wang (data and knowledge engineering, New Jersey Institute of Technology, US), brings together contributions from practitioners integrating computational intelligence and pattern analysis techniques for analyzing biological data, including sequence, structure, and microarray data. The material is organized into five sections that explore basic principles and methodologies of computational techniques, applications of computational intelligence and pattern analysis for biological sequence analysis, structural analysis; microarray data analysis, and systems biology." (Reference and Research Book News, February 2011)

Editorial Reviews

"This collection of 16 papers, edited by Maulik (computer science and engineering, Jadavpur U., India), Bandyopadhyay (Indian Statistical Institute, India), and Wang (data and knowledge engineering, New Jersey Institute of Technology, US), brings together contributions from practitioners integrating computational intelligence and pattern analysis techniques for analyzing biological data, including sequence, structure, and microarray data. The material is organized into five sections that explore basic principles and methodologies of computational techniques, applications of computational intelligence and pattern analysis for biological sequence analysis, structural analysis; microarray data analysis, and systems biology." (Reference and Research Book News, February 2011)

From the Publisher