Discovering Biomolecular Mechanisms with Computational Biology (eBook)

CONTENTS 5
INTRODUCTION Bloinformatics: Mystery, Astrology or Service Technology? 12
SECTION I Deriving Biological Function of Genome Information with Biomolecular Sequence and Structure Analysis 22
CHAPTER 1 Reliable and Specific Protein Function Prediction by Combining Homology with Genomic(s) G)ntext 23
CHAPTER 2 Clues from Three-Dimensional Structure Analysis and Molecular Modelling: New Insights into Cytochrome P450 Mechanisms and Functions 40
CHAPTER 3 Prediction of Protein Function: Two Basic Concepts and One Practical Recipe 49
SECTION II Complementing Biomolecular Sequence Analysis with Text Mining in Scientific Articles 65
CHAPTER 4 Extracting Information for Meaningful Function Inference through Text-Mining 66
CHAPTER 5 Literature and Genome Data Mining for Prioritizing Disease-Associated Genes 83
SECTION III Mechanistic Predictions from the Analysis of Biomolecular Networks 91
CHAPTER 6 Model-Based Inference of Transcriptional Regulatory Mechanisms from DNA Microarray Data 92
CHAPTER 7 The Predictive Power of Molecular Network Modelling: Case Studies of Predictions widi Subsequent Experimental Verification 102
SECTION IV Mechanistic Predictions from the Analysis of Biomolecular Sequence Populations: G) nsidering Evolution for Function Prediction 111
CHAPTER 8 Theory of Early Molecular Evolution: Predictions and Confirmations 112
CHAPTER 9 Hitchhiking Mapping: Limitations and Potential for the Identification of Ecologically Important Genes 122
CHAPTER 10 Understanding the Functional Importance of Human Single Nucleotide Polymorphisms 131
CHAPTER 11 Correlations between Quantitative Measures of Genome Evolution, Expression and Function 138
Index 150