Bioinformatics Book from C.H.I.P.S.

Knowledge Discovery in Bioinformatics
Techniques, Methods, and Applications
edited by Xiaohua Hu

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


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
  • 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


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Knowledge Discovery in Bioinformatics
Techniques, Methods, and Applications
edited by Xiaohua Hu

2007 • 363 pages • $98.95 + shipping
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