Knowledge Discovery in Bioinformatics bringS 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
• biological database management

Contents

1. Current Methods for Protein Secondary-Structure Prediction Based on Support Vector Machines

• Support Vector Machine Method
• Performance Comparison of SVM Methods

2. Comparison of Seven Methods for Mining Hidden Links

• Analysis of the Literature on Raynaud’s Disease
• Related Work
• Methods
• Experiment Results and Analysis

3. Voting Scheme–Based Evolutionary Kernel Machines for Drug Activity Comparisons

• Granular Kernel and Kernel Tree Design
• GKTSESs
• Evolutionary Voting Kernel Machines
• Simulations

4. Bioinformatics Analyses of Arabidopsis thaliana Tiling Array Expression Data

• Tiling Array Design and Data Description
• Ontology Analyses
• Antisense Regulation Identification
• Correlated Expression Between Two DNA Strands
• Identification of Nonprotein Coding mRNA

5. Identification of Marker Genes from High-Dimensional Microarray Data for Cancer Classification

• Feature Selection
• Gene Selection
• Comparative Study of Gene Selection Methods

6. Patient Survival Prediction from Gene Expression Data

• General Methods
• Applications
• Incorporating Data Mining Techniques to Survival Prediction
• Selection of Extreme Patient Samples

7. RNA Interference and microRNA

• Mechanisms and Applications of RNA Interference
• Specificity of RNA Interference
• Computational Methods for microRNAs
• siRNA Silencing Efficacy

8. Protein Structure Prediction Using String Kernels

• Protein Structure: Granularities
• Learning from Data
• Structure Prediction: Capturing the Right Signals
• Secondary-Structure Prediction
• Remote Homology and Fold Prediction

9. Public Genomic Databases: Data Representation, Storage, and Access

• Data Representation
• Data Storage
• Data Access

10. Automatic Query Expansion with Keyphrases and POS Phrase Categorization for Effective Biomedical Text Mining

• Keyphrase Extraction-Based Pseudo-Relevance Feedback
• Query Expansion with WordNet
• Experiments on Medline Data Sets

11. Evolutionary Dynamics of Protein–Protein Interactions

• Class I Glutamine Amidotransferase–Like Superfamily
• Drifts in Interfaces of Close Homologs
• Drifts in Interfaces of Divergent Members
• Drifts in Interfaces at Extreme Divergence

12. On Comparing and Visualizing RNA Secondary Structures

• Background
• RSmatch
• RSview

13. Integrative Analysis of Yeast Protein Translation Networks

• Protein Biosynthesis and Translation
• Methods
• Results
• Conclusions

14. Identification of Transmembrane Proteins Using Variants of the Self-Organizing Feature Map Algorithm

• Physiochemical Analysis of Proteins
• Variants of the SOM Algorithm
• Results

15. TRICLUSTER: Mining Coherent Clusters in Three-Dimensional Microarray Data

• Preliminary Concepts
• Related Work
• The TRICLUSTER Algorithm
• Experiments

16. Clustering Methods in a Protein–Protein Interaction Network

• Protein–Protein Interaction
• Properties of PPI Networks
• Clustering Approaches
• Validation

Index

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