Evolutionary Genomics

Introduction to Genome Biology and Diversity.- Probability, Statistics, and Computational Science.- A Not-So-Long Introduction to Computational Molecular Evolution.- Whole-Genome Alignment.- Inferring Orthology and Paralogy.- Transposable Elements and Their Identification.- Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model.- Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life.- The Methodology Behind Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution.- Bayesian Molecular Clock Dating Using Genome-Scale Datasets.- Genome Evolution in Outcrossing vs. Selfing vs. Asexual Species.- Selection Acting on Genomes.- Looking for Darwin in Genomic Sequences: Validity and Success Depends on the Relationship between Model and Data.- Evolution of Viral Genomes: Interplay between Selection, Recombination, and Other Forces.- Evolution of Protein Domain Architectures.- New Insights on the Evolution of GenomeContent: Population Dynamics of Transposable Elements in Flies and Humans.- Association Mapping and Disease: Evolutionary Perspectives.- Ancestral Population Genomics.- Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN.- Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials.- Systems Genetics for Evolutionary Studies.- Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases.- Semantic Integration and Enrichment of Heterogeneous Biological Databases.- High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE.- Scalable Workflows and Reproducible Data Analysis for Genomics.- Sharing Programming Resources between Bio* Projects.