ComparativeGenomics

Class 1. Genome organisation

Intended Learning Objectives:

• Introduction to genomes
• Genome properties in different species
• Gene content of genomes
• Regulatory sequences
• Non-coding sequences
• Metagenomics

Class 2. Gene prediction

Intended Learning Objectives:

• Gene structure in different species
• Gene prediction in different species
• Promoter prediction in different species

Class 3. Phylogenetics

Intended Learning Objectives:

• Understand principles of phylogenetic trees
• Understand methods of phylogenetic tree building
• Understand methods to assess the quality of phylogenetic trees

Class 4. Phylogenomics

Intended Learning Objectives:

• Understand principles of phylogenomics
• Understand applications of phylogenomics
• Understand phylogenetic profiles, metaphylogeny, and tree of life
• Understand reasons for phylogenetic disagreement

Class 5. Gene order

Intended Learning Objectives:

• Introduction to gene order conservation (synteny)
• Analysing synteny with dotplots
• Using synteny for inferring phylogeny

Class 6. Orthology

Intended Learning Objectives:

• Definitions & assumptions
• Applications
• How to identify orthologs
• Tree reconciliation
• Graph-based methods; Tree-based methods; Other methods
• Comparison of ortholog databases

Class 7. Interaction networks

Intended Learning Objectives:

• Introduction to network biology
• Discovering protein interactions
• Network properties
• Network databases (STRING, FunCoup)

Class 8. Applications of network analysis

Intended Learning Objectives:

• Network analysis for gene identification
• Pathway analysis
• Gene regulatory networks