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The course focuses on comparative genomics both in the vertical direction, between species, with an emphasis on biological evolution, and in the horizontal direction, interspecies, with emphasis on diversity of populations. It describes the main evolutionary principles and their application to genomic and proteomic data with a focus on second and third generation high-throughput sequencing methods. It describes methods and algorithms of construction of phylogenetic trees from genic, genomic and protein sequences. It shows the differences between genome and species trees. It also describes known mutation processes, genome evolution, the molecular clock concept, selection and genetic drift on the molecular level, nucleotide composition, polymorphisms. One lecture is devoted to evaluating the quality and reliability of genetic trees. Furthermore, the course describes genetic variability within populations, ways of measuring this variability, and various models of population genetics. Special attention is paid to the main evolutionary forces that shape this population variability (genetic drift, isolation, migration, selection). Clinical applications include the detection of mutations in both germline and somatic lineage and their link to human diseases.
Last update: Svozil Daniel (26.01.2018)
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Students will know: How to prepare data for phylogenetic and comparative analysis Create phylogenetic trees from DNA or protein sequences Test quality of phylogenetic tree Understand phylogenetic algorithms such as UPGMA, WPGMA, Maximum parsimony, and Maximum likelihood Identify mutations in the cells of germinal and somatic lineage Identify small and large structure variants Annotate mutations and variants Last update: Svozil Daniel (26.01.2018)
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A credit will be given based on exercises assigned during the seminars. The final exam consists of a written test followed by an oral exam. Last update: Svozil Daniel (26.01.2018)
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R: Miloš Macholán: Základy fylogenetické analýzy, 978-80-210-6363-1, Masarykova univerzita Brno, 2014 R: Relichová Jiřina: Genetika populací, ISBN 978-80-210-4795-2, Masarykova univerzita Brno, 2009 A: Flegr: Evoluční biologie. Academia, 2009 A: Mark Jobling, Edward Hollox, Toomas Kivisild, Chris Tyler-Smith: Human Evolutionary Genetics, Garland Science, 2014 A: Baum, D. A., & S. D. Smith. 2013. Tree-Thinking: An Introduction to Phylogenetic Biology. A: Philip W. Hedrick: Genetics of populations, ISBN 978-0763757373, Jones and Bartlett Publishers Sudbury, USA, 2009 Last update: Svozil Daniel (26.01.2018)
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Zápočet: úlohy ze cvičení Zkouška: písemný test, následná ústní zkouška 50/50 Last update: Svozil Daniel (10.01.2018)
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1. Molecular phylogenetics analysis 2. Molecular evolution, evolution of genomes 3. Molecular clocks, UPGMA, WPGMA, neighbour joining 4. Phylogenetic tree, evolution models 5. Methods for phylogenetic tree reconstruction 6. Tree quality assessment 7. Human genome, population and genetic variability 8. Levels of genetic variability, Hardy-Weinberg equilibrium 9. Genetic drift, migration, isolation 10. Computational methods for detection of selection 11. Short genetic variation and their detection 12. Genetic diseases, mutations in germinal and somatic cells 13. Large structural variants 14. Annotation and interpretation of genetic variants Last update: Svozil Daniel (26.01.2018)
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on-line courses https://github.com/schatzlab/appliedgenomics https://github.com/quinlan-lab/applied-computational-genomics Last update: Svozil Daniel (26.01.2018)
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Molecular biology/genetics, biochemistry, Linux and bash, foundations of bioinformatics Last update: Svozil Daniel (26.01.2018)
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| Teaching methods | ||||
| Activity | Credits | Hours | ||
| Účast na přednáškách | 1 | 28 | ||
| Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi | 1 | 28 | ||
| Příprava na zkoušku a její absolvování | 1 | 28 | ||
| 3 / 3 | 84 / 84 | |||