Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications

The purpose of this edited book is to bring together the ideas and findings of data mining researchers and bioinformaticians by discussing cutting-edge research topics such as, gene expressions, protein/RNA structure prediction, phylogenetics, sequence and structural motifs, genomics and proteomics, gene findings, drug design, RNAi and microRNA analysis, text mining in bioinformatics, modelling of biochemical pathways, biomedical ontologies, system biology and pathways, and biological database management.Content: Chapter 1 Current Methods for Protein Secondary?Structure Prediction Based on Support Vector Machines (pages 1–26): Hae?Jin Hu, Robert W. Harrison, Phang C. Tai and Yi PanChapter 2 Comparison of Seven Methods for Mining Hidden Links (pages 27–44): Xiaohua Hu, Xiaodan Zhang and Xiaohua ZhouChapter 3 Voting Scheme–Based Evolutionary Kernel Machines for Drug Activity Comparisons (pages 45–56): Bo Jin and Yan?Qing ZhangChapter 4 Bioinformatics Analyses of Arabidopsis thaliana Tiling Array Expression Data (pages 57–70): Trupti Joshi, Jinrong Wan, Curtis J. Palm, Kara Juneau, Ron Davis, Audrey Southwick, Katrina M. Ramonell, Gary Stacey and Dong XuChapter 5 Identification of Marker Genes from High?Dimensional Microarray Data for Cancer Classification (pages 71–87): Jiexun Li, Hua Su and Hsinchun ChenChapter 6 Patient Survival Prediction from Gene Expression Data (pages 89–111): Huiqing Liu, Limsoon Wong and Ying XuChapter 7 RNA Interference and microRNA (pages 113–144): Shibin Qiu and Terran LaneChapter 8 Protein Structure Prediction using String Kernels (pages 145–168): Huzefa Rangwala, Kevin DeRonne and George KarypisChapter 9 Public Genomic Databases: Data Representation, Storage, and Access (pages 169–195): Andrew Robinson, Wenny Rahayu and David TaniarChapter 10 Automatic Query Expansion with Keyphrases and POS Phrase Categorization for Effective Biomedical Text Mining (pages 197–207): Min Song and Il?Yeol SongChapter 11 Evolutionary Dynamics of Protein–Protein Interactions (pages 209–231): L. S. Swapna, B. Offmann and N. SrinivasanChapter 12 On Comparing and Visualizing RNA Secondary Structures (pages 233–249): Jason T. L. Wang, Dongrong Wen and Jianghui LiuChapter 13 Integrative Analysis of Yeast Protein Translation Networks (pages 251–266): Daniel D. Wu and Xiaohua HuChapter 14 Identification of Transmembrane Proteins Using Variants of the Self?Organizing Feature Map Algorithm (pages 267–293): Mary Qu Yang, Jack Y. Yang and Craig W. CodringtonChapter 15 TriCluster: Mining Coherent Clusters in Three?Dimensional Microarray Data (pages 295–317): Lizhuang Zhao and Mohammed J. ZakiChapter 16 Clustering Methods in a Protein–Protein Interaction Network (pages 319–355): Chuan Lin, Young?Rae Cho, Woo?Chang Hwang, Pengjun Pei and Aidong Zhang