Currently, molecular biology is generating information on the molecular properties of cells and organisms at an incredible pace. For example, we know the complete genome sequence of a rapidly increasing number of species. . Not only do these high-throughput experiments generate a complete view of the genetic information of cells, other techniques measure the level of expression of all genes at the same time or measure all the interactions between all the proteins present in a cell. Bioinformatics is obviously needed for the storage and primary analysis of these huge volumes of biomolecular data. More interestingly, the data uniquely allows bioinformatics to make biological discoveries that were not possible until now. This course introduces the concepts and approaches required to make evolutionary biological discoveries in this genome-scale data and presents examples of interesting pieces of biology that have been discovered using bioinformatics. Topics to be discussed include genome evolution (as opposed to single genes), and the origins of the eukaryotic cell. 

 The following subjects are discussed in the course:
1.     Sequence homology, Protein domains
2.     Gene trees and orthology
3.     Genome evolution: evolution of the presence of genes, evolution of gene order
4.     Formalizations of gene function (e.g. Gene Ontology)
5.     Introduction to high-throughput (HTP) techniques such as micro-array, ChIP-on-chip and yeast-2-hybrid
6.     Use of these HTP data to study evolution of function
7.     Origin of Eukaryotes, endo-symbiosis, explosion of gene duplicates
8.     Genome Evolution: Genome duplications

 After completion the course, the student should have a profound understanding of:
1. Genome Evolution, genome duplications, network evolution, gene evolution, comparative analysis of networks and complexes. The relationship amongst the major eukaryotic subgroups, the animals, the fungi and the plants.
At the end of the course, students should be able to:
Construct, root and interpret phylogenetic trees; for a given protein, find its homologs, annotate its protein domains, time its duplications, define its orthologs, pinpoint.