MPŠ
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Jožef Stefan
International
Postgraduate School

Jamova 39
SI-1000 Ljubljana
Slovenia

Phone: +386 1 477 31 00
Fax: +386 1 477 31 10
Email: info@mps.si

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Course Description

Evolutionary Genomics

Program

Nanosciences and Nanotechnologies, third-level study programme

Lecturers:

prof. dr. Dušan Kordiš

Goals:

Students will acquire a thorough understanding of genome organization and activity, of complete genome analysis (prokaryotic and eukaryotic), and mechanisms and patterns of genome evolution. Students will be able to extract and understand the enormous amount of information that is hidden in genome sequences. Students will learn how to use the specialized genome and proteome databases, and diverse approaches that are necessary for the evolutionary analyses of different genome components.

Content:

What is a genome?
Understanding a genome sequence
Genome anatomies (eukaryotes vs prokaryotes)
Regulation of genome activity
Molecular basis of genome evolution
Paterns of genome evolution
Molecular phylogenetics and phylogenomics
Protein evolution

Laboratory work (computational):
Genome databases
Protein and proteome databases
Evolutionary analyses of genome sequences
Evolutionary analyses of proteomes

Course literature:

1. Lynch, M. (2007) The Origins of Genome Architecture. Sinauer.

2. Brown, T.A. (2006) Genomes. 3rd Edition, Garland Science.

3. Patthy, L. (2007). Protein Evolution. 2nd ed. Blackwell, Oxford.

4. Nei, M. & Kumar, S. (2000) Molecular Evolution and Phylogenetics. Oxford Univ. Press.

5. Graur, D. & Li, W. H. (1999) Fundamentals of Molecular Evolution. 2nd edition. Sinauer.

Significant publications and references:

1. Kordiš, D.and Gubenšek, F. (2000) Adaptive evolution of animal toxin multigene families. Gene 261:43-52.

2. Župunski, V. Gubenšek, F.and Kordiš, D. (2001) Evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons. Mol. Biol. Evol. 18:1849-1863.

3. Lovšin, N. Gubenšek, F. and Kordiš, D. (2001) Evolutionary dynamics in a novel L2 clade of non-LTR retrotransposons in Deuterostomia. Mol. Biol. Evol. 18:2213-2224.

4. Kordiš, D. Križaj, I. and Gubenšek, F. (2002) Functional diversification of animal toxins by adaptive evolution. V knjigi Perspectives in Molecular Toxinology (ed. by Menez, A.). pp. 401-419, John Wiley & Sons, Ltd.

5. Gorinšek, B. Gubenšek, F. and Kordiš, D. (2004) Evolutionary genomics of chromoviruses in Eukaryotes. Mol. Biol. Evol. 21:781-798.

6. Novinec, M. Kordiš, D. Turk, V. and Lenarčič, B. (2006). Diversity and evolution of the thyroglobulin type-1 domain superfamily. Mol. Biol. Evol. 23:744-755.

7. Kordiš, D. Lovšin, N. and Gubenšek, F. (2006). Phylogenomic analysis of the L1 retrotransposons in Deuterostomia. Syst. Biol. 55:886-901.

Examination:

Oral exam and presentation of seminar.

Students obligations:

Oral exam and presentation of seminar.

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