460-6028/02 – Computational Genomics (VG)
| Gurantor department | Department of Computer Science | Credits | 10 |
| Subject guarantor | doc. MUDr. František Mrázek, Ph.D. | Subject version guarantor | doc. MUDr. František Mrázek, Ph.D. |
| Study level | postgraduate | Requirement | Choice-compulsory type B |
| Year | | Semester | winter + summer |
| | Study language | English |
| Year of introduction | 2019/2020 | Year of cancellation | |
| Intended for the faculties | FEI | Intended for study types | Doctoral |
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
Additional study materials
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.
Oral exam.
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
Occurrence in study plans
Occurrence in special blocks
Assessment of instruction
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