Preface -- Pairwise Sequence Alignment -- Sequence and Sequence Alignment Statistics -- Practical Multiple Sequence Alignment -- Phylogenetic Trees from Sequences -- Phylogenetic Networks -- Modern BLAST Programs -- Stochastic Calculus and Stochastic Simulation -- Genomic Sequence Comparison -- Genome Rearrangements -- Population Genetics Data Analysis -- Genome Wide Association Studies -- Practical Implications of Coalescent Theory -- Networks in Computational Systems Biology -- Practical Use of the Gene Ontology -- Techniques for Protein Structure -- Microarray Experiment Statistics -- Reasoning with Protein Contact Maps -- Identifying Modules in Protein-Protein Interaction Networks -- Motifs for Transcriptional Regulation -- Time Course Analysis -- Computational Simulation of Biochemical Networks -- Biomedical Data Integration -- Functional Annotation and Discovery -- Matrix and Tensor Decompositions -- Text Processing and Mining -- Formal Logics -- Index.