Bioinformatics and Evolutionary Genomics A course for Master-students and PhD-students

April 14-18, 2008

Organizer: Dr. B. Snel, Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University

Venue: Kruyt building, Padualaan 8, Utrecht University

Registration: Please register by sending an e-mail message to the organizer of this course (b.snel@uu.nl)

Required knowledge and abilities for entrance:

This course requires basic knowledge and skills such as taught in the new first year biology course Bioinformatic Pattern Analysis, which is an introductory course into bioinformatics. Participants are thus expected to have some hands on experience with basic bioinformatics tools such as e.g. blast, as well as knowledge of basic concepts such as alignments and trees.

Description of content

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 large number of species. These naturally include human, fruit fly and yeast, but extent to over 500 bacteria, more than 20 fungi as well as a number of protists with weird and often pathogenic lifestyles. And the number of these genome sequences is increasing. Not only do these so called high-throughput experiments generate complete pictures of the genetic information of cells, but 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, these data uniquely allow bioinformatics to make biological discoveries that hitherto were not possible. This course will try to teach the concepts and approaches that are necessary to make biological discoveries in these genome scale data and will present many examples of interesting pieces of biology that have been discovered using bioinformatics. Topics that will be discussed include: how does the genome evolve (as opposed to single genes), how did the eukaryotic cell originate, and how can I predict the function of an uncharacterized gene using only bioinformatics.

The course takes one week (1.5 ECTS) and consist of lectures, computer excercises and literature discussion. For last year's (=2007) program, click here.

The following subjects are discussed in the course:

• Sequence homology, Protein domains
• Gene trees and orthology
• Genome evolution: evolution of the presence of genes, evolution of gene order
• Formalizations of gene function (e.g. Gene Ontology)
• Using Genomic context to predict pathways and processes
• Introduction to high-throughput (HTP) techniques such as micro-array, ChIP-on-chip and yeast-2-hybrid
• Exploiting these HTP data for function prediction
• How bioinformatics can improve the usefulness of these HTP data
• Use of these HTP data to study evolution of function
• Horizontal Gene Transfer
• Origin of Eukaryotes, endo-symbiosis, explosion of gene duplicates
• Genome Evolution: Genome duplications

Minimum number of participants: 8

If less than 8 participants will have registered for this course 3 weeks prior to the starting date, it will be cancelled.