460-6028/02 – Computational Genomics (VG)

Gurantor departmentDepartment of Computer ScienceCredits10
Subject guarantordoc. MUDr. František Mrázek, Ph.D.Subject version guarantordoc. MUDr. František Mrázek, Ph.D.
Study levelpostgraduateRequirementChoice-compulsory type B
YearSemesterwinter + summer
Study languageEnglish
Year of introduction2019/2020Year of cancellation
Intended for the facultiesFEIIntended for study typesDoctoral
Instruction secured by
LoginNameTuitorTeacher giving lectures
DYS0006 Mgr. Tereza Dýšková, Ph.D.
FIL0152 Ing. Regina Fillerová, Ph.D.
KRI0203 doc. Dr. Ing. Eva Kriegová
MIK0424 Mgr. Zuzana Mikulková, Ph.D.
MRA0096 doc. MUDr. František Mrázek, Ph.D.
SCH0341 Mgr. Petra Schneiderová
Extent of instruction for forms of study
Form of studyWay of compl.Extent
Full-time Examination 28+0
Part-time Examination 28+0

Subject aims expressed by acquired skills and competences

The aim of the course is to deepen students' knowledge in the field of genomics and genetics, new methods for genome analysis, data analysis and interpretation. In addition, this knowledge and skills will be further enhanced in a direction that is in line with the specific focus of its Ph.D. studies and dissertation work.

Teaching methods

Seminars
Individual consultations
Project work
Other activities

Summary

The subject focuses on the current quantitative understanding of human genetics and computational interdisciplinary research in genetics. Students will learn how to design, perform and analyze experiments to evaluate complex genome changes, gene expression and transcription factors activity. They will learn how to work with DNA sequences (contig assemblage, polymorphism identification, sequence annotation). Annotated sequences in public databases will then be used to analyze unknown sequences, identify them, or determine their function based on similarity to known sequences. Mutual sequence comparisons will allow identification of mutations and their impact in the form of genetically-mediated diseases. Particular emphasis will be placed on the analysis of "big" data and the acquisition of knowledge for the design and analysis of sequencing genomic assays.

Compulsory literature:

• Pevsner J. Bioinformatics and Functional Genomics, 3rd Edition (2015), Wiley-Blackwell, Hoboken, New Jersey • Pierce B.A. Genetics: A Conceptual Approach, 5th Edition (2013) W. H. Freeman and Co., New York • Cristianini N. Introduction to computational genomics (2012), Cambridge University Press • Mount D. W. Bioinformatics - Genome and Sequence Analysis, 2nd Edition (2004), Cold Spring Harbor Laboratory Press, New York

Recommended literature:

• Deonier R.C. et al. Computational Genome Analysis: An Introduction (2010), Springer, New York

Way of continuous check of knowledge in the course of semester

Continuous monitoring of study activities and assigned tasks during regular consultations. If some publication activity will be a part of the student's tasks, the relevant article would be presented in the course.

E-learning

Other requirements

The student prepares and presents the work on a given topic.

Prerequisities

Subject has no prerequisities.

Co-requisities

Subject has no co-requisities.

Subject syllabus:

• introduction to genetics, history of the human population • bond analysis, association analysis • proposals for association studies • isolated / mixed populations, population substructure, human structural variations • statistical techniques for measuring gene expression and evaluating the activity of transcription factors / regulatory molecules • model organisms and genotypic technologies • DNA sequence - annotation, identification of polymorphisms • prediction models • mapping analysis • approaches for preparing sequencing libraries • Checking data quality

Conditions for subject completion

Full-time form (validity from: 2019/2020 Winter semester)
Task nameType of taskMax. number of points
(act. for subtasks)
Min. number of points
Examination Examination  
Mandatory attendence parzicipation:

Show history

Occurrence in study plans

Academic yearProgrammeField of studySpec.ZaměřeníFormStudy language Tut. centreYearWSType of duty
2020/2021 (P0588D140004) Bioinformatics and Computational Biology P English Ostrava Choice-compulsory type B study plan
2020/2021 (P0588D140004) Bioinformatics and Computational Biology K English Ostrava Choice-compulsory type B study plan

Occurrence in special blocks

Block nameAcademic yearForm of studyStudy language YearWSType of blockBlock owner