This second edition integrates the more technical and mathematical aspects of bioinformatics with concrete examples of their application to current research problems in molecular, cellular and evolutionary biology. This broad, unified approach is made possible, in large part, by the very wide scope of Dr. Xia’s own research experience. The integration of genomics, proteomics and transcriptomics into a single volume makes this book required reading for anyone entering the new and emerging fields of Systems Biology and Evolutionary Bioinformatics.

Table of Contents

Chapter 1: String Mathematics, BLAST, and FASTA

Chapter 2: Sequence Alignment

Chapter 3: Position weight matrix and Perceptron

Chapter 4: Gibbs sampler

Chapter 5: Transcriptomics and RNA-Seq Data Analysis

Chapter 6: Self-Organizing Map and Other Clustering Methods in Transcriptomics

Chapter 7: Hidden Markov Models and Protein Secondary Structure Prediction

Chapter 8: Bioinformatics and Translation Initiation

Chapter 9: Bioinformatics and Translation Elongation

Chapter 10: Bioinformatics and Translation Termination in Bacteria

Chapter 11: Genomic Features: Content Sensors, Nucleotide Skew Plot, Strand Asymmetry, and DNA Methylation

Chapter 12: Nucleotide Substitution Models and Evolutionary Distances

Chapter 13: Protein Substitution Model and Evolutionary Distance

Chapter 14: Maximum Parsimony Method in Phylogenetics

Chapter 15: Distance-Based Phylogenetic Methods

Chapter 16: Maximum Likelihood in Molecular Phylogenetics

Chapter 17: Protein lsoelectric Point and Helicobacter pylori

Chapter 18: Bioinformatics and In Silico 2D Gel Electrophoresis

Chapter 19: Fundamentals of Proteomics

About the Author

Xuhua Xia is full professor in bioinformatics and molecular evolution at University of Ottawa where I teach population genetics, molecular evolution and bioinformatics. He serves as associate editor for Molecular Biology and Evolution.