生物信息学知识新发现：技术，方法与应用 Knowledge Discovery in Bioinformatics
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作者： Xiaohua Hu 著
出 版 社： 吉林长白山
出版时间： 2006-12-1字数：版次： 1页数： 363印刷时间： 2007/02/01开本：印次：纸张： 胶版纸I S B N ： 9780471777960包装： 精装内容简介
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.
作者简介
Xiaohua Hu, PhD, is Assistant Professor of Computer Science in the College of Information Science and Technology at Drexel University. His research has been published in such journals as IEEE Computer, Knowledge and Information Systems, Journal of Intelligent Systems, and the International Journal of Applied Intelligence.
目录
Contributors
Preface
1 Current Methods for Protein Secondary-Structure Prediction Based on Support Vector Machines (Hae-Jin Hu, Robert WHarrison, Phang CTai, and Yi Pan)
1.2 Support Vector Machine Method
1.3 Performance Comparison of SVM Methods
1.4 Discussion and Conclusions
2 Comparison of Seven Methods for Mining Hidden Links (Xiaohua Hu, Xiaodan Zhang, and Xiaohua Zhou)
2.1 Analysis of the Literature on Raynaud’s Disease
2.2 Related Work
2.3 Methods
2.4 Experiment Results and Analysis
2.5 Discussion and Conclusions
3 Voting Scheme–Based Evolutionary Kernel Machines for Drug Activity Comparisons (Bo Jin and Yan-Qing Zhang)
3.1 Granular Kernel and Kernel Tree Design
3.2 GKTSESs
3.3 Evolutionary Voting Kernel Machines
3.4 Simulations
3.5 Conclusions and Future Work
4 Bioinformatics Analyses of Arabidopsis thaliana Tiling Array Expression Data (Trupti Joshi, Jinrong Wan, Curtis JPalm, Kara Juneau, Ron Davis, Audrey Southwick, Katrina MRamonell, Gary Stacey, and Dong Xu)
4.1 Tiling Array Design and Data Description
4.2 Ontology Analyses
4.3 Antisense Regulation Identification
4.4 Correlated Expression Between Two DNA Strands.
4.5 Identification of Nonprotein Coding mRNA
4.6 Summary
5 Identification of Marker Genes from High-Dimensional Microarray Data for Cancer Classification (Jiexun Li, Hua Su, and Hsinchun Chen)
5.1 Feature Selection
5.2 Gene Selection
5.3 Comparative Study of Gene Selection Methods
5.4 Conclusions and Discussion
6 Patient Survival Prediction from Gene Expression Data (Huiqing Liu, Limsoon Wong, and Ying Xu)
6.1 General Methods
6.2 Applications
6.3 Incorporating Data Mining Techniques to Survival Prediction
6.4 Selection of Extreme Patient Samples
6.5 Summary and Concluding Remarks
7 RNA Interference and microRNA (Shibin Qiu and Terran Lane)
7.1 Mechanisms and Applications of RNA Interference
7.2 Specificity of RNA Interference
7.3 Computational Methods for microRNAs
7.4 siRNA Silencing Efficacy
7.5 Summary and Open Questions.
8 Protein Structure Prediction Using String Kernels (Huzefa Rangwala, Kevin DeRonne, and George Karypis)
8.1 Protein Structure: Granularities
8.2 Learning from Data
8.3 Structure Prediction: Capturing the Right Signals
8.4 Secondary-Structure Prediction
8.5 Remote Homology and Fold Prediction
8.6 Concluding Remarks
9 Public Genomic Databases: Data Representation, Storage, and Access (Andrew Robinson, Wenny Rahayu, and David Taniar)
9.1 Data Representation
9.2 Data Storage
9.3 Data Access
9.4 Discussion
9.5 Conclusions
10 Automatic Query Expansion with Keyphrases and POS Phrase Categorization for Effective Biomedical Text Mining (Min Song and Il-Yeol Song)
10.1 Keyphrase Extraction-Based Pseudo-Relevance Feedback
10.2 Query Expansion with WordNet
10.3 Experiments on Medline Data Sets
10.4 Conclusions
11 Evolutionary Dynamics of Protein–Protein Interactions (LSSwapna, BOffmann, and NSrinivasan)
11.1 Class I Glutamine Amidotransferase–Like Superfamily
11.2 Drifts in Interfaces of Close Homologs
11.3 Drifts in Interfaces of Divergent Members
11.4 Drifts in Interfaces at Extreme Divergence
11.5 Conclusions
12 On Comparing and Visualizing RNA Secondary Structures (Jason TLWang, Dongrong Wen, and Jianghui Liu)
12.1 Background
12.2 RSmatch
12.3 RSview
12.4 Conclusions
13 Integrative Analysis of Yeast Protein Translation Networks (Daniel DWu and Xiaohua Hu)
13.1 Protein Biosynthesis and Translation
13.2 Methods
13.3 Results
13.4 Conclusions
14 Identification of Transmembrane Proteins Using Variants of the Self-Organizing Feature Map Algorithm (Mary Qu Yang, Jack YYang, and Craig WCodrington)
14.1 Physiochemical Analysis of Proteins
14.2 Variants of the SOM Algorithm
14.3 Results
14.4 Discussion and Conclusions
15 TRICLUSTER: Mining Coherent Clusters in Three-Dimensional Microarray Data (Lizhuang Zhao and Mohammed JZaki)
15.1 Preliminary Concepts
15.2 Related Work
15.3 The TRICLUSTER Algorithm
15.4 Experiments
15.5 Conclusions
16 Clustering Methods in a Protein–Protein Interaction Network (Chuan Lin, Young-Rae Cho, Woo-Chang Hwang, Pengjun Pei, and Aidong Zhang)
16.1 Protein–Protein Interaction
16.2 Properties of PPI Networks
16.3 Clustering Approaches
16.4 Validation
16.5 Conclusions
References
Index
