SubjectsSubjects(version: 850)
Course, academic year 2019/2020
  
Phylogenetics and Applied Genomics - M143009
Title in English: Fylogenetika a aplikovaná genomika
Guaranteed by: Department of Informatics and Chemistry (143)
Actual: from 2019
Semester: winter
Points: winter s.:3
E-Credits: winter s.:3
Examination process: winter s.:
Hours per week, examination: winter s.:2/0 Ex [hours/week]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type: Master's (post-Bachelor)
Note: course can be enrolled in outside the study plan
enabled for web enrollment
Guarantor: Pačes Jan Mgr. Ph.D.
Kolář Michal Mgr. Ph.D.
Annotation -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)
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.
Aim of the course -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

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

Literature -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

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

Learning resources -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

on-line courses

https://github.com/schatzlab/appliedgenomics

https://github.com/quinlan-lab/applied-computational-genomics

Requirements to the exam - Czech
Last update: Svozil Daniel doc. Mgr. Ph.D. (10.01.2018)

Zápočet: úlohy ze cvičení

Zkouška: písemný test, následná ústní zkouška 50/50

Syllabus -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

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

Registration requirements -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

Molecular biology/genetics, biochemistry, Linux and bash, foundations of bioinformatics

Course completion requirements -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

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.

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
Coursework assessment
Form Significance
Oral examination 100

 
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