SUBJECT

Title

Genomics

Type of instruction

lecture

Level

master

Faculty

Faculty of Science

Part of degree program

Biology MSc

Credits

Recommended in

Semester 3

Typically offered in

Autumn semester

Course description

1. Maps: gene, physical and cytology maps: Gene map and physical map correspondence based on genome sequences. Genome sequence databases.

2. Comparative genomics: Methods for the comparison of genomes. Genome similarities. Gene prediction traps. How many genes are there in a genome?

3. Genome sequences: Genome sequence determination. Determination of viral, prokaryotic and eukaryotic genomes.

4. Prokaryotic and bacteriophage genomes: Bacterial, bacteriophage genome. Phage genomes. Phage mosaicism. Phage evolutionary models.

5. Plant genomes: The arabidopsis genome programme. The sequence of rice. Structure of plant genomes.

6. Animal genomes: Mouse genome project. Vertebrate genome projects. Medical model organisms. Animal breeding programmes. Invertebrate model animals.

7. The human genome programme. The aims of the human genome programme. The content of the human genome.

8. Genome sequencing, annotation: Genome annotation. Functional annotation. Gene family clusters.

9. Genome sequencing: Automated sequencing. Contig assembly. Hierarchical sequencing. Shotgun sequencing. Sequence quality.

10. New techniques in sequencing: Resequencing. CHIP technology in sequencing, resequencing. SNP detection, genechip.

11. Variations in the population: HapMap project. Linkage disequilibrium (LD). Haplotype characters. Association studies in multigenic diseases. Possibilities for personalised drug therapy, medication.

12. Gene expression experiments, transcriptomics: Expression chip. Analysis of expression differences. The time and position of gene expression, tissue specific expression. Expression changes in cell transformation (malignant transformation).

13. Proteomics: Protein annotations. Hidden Markov Models in domain prediction. Analytical techniques of expressed proteins. 2D PAGE, tissue microarray (TMA). Protein microarray. Protein interaction map. Functional/structural genomics.

14. Integrative genomics: metabolomics, systems biology. Metabolic/biochemical pathway databases. Metabolic regulation analysis. System level modelling of gene/genetic networks.

Readings

M. Campbell, L. Heyer (2006): Genomics, proteomics, bioinformatics;
G. Gibson, S. Muse: A primer of genome science 3rd ed., Sinauer Associates, 2009ISBN 9780878932368