Jan 18, 2020   12:37 p.m. Bohdana
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Course syllabus N426A0_4I - Applied Genomics, Proteomics and Bioinformatics (FCFT - WS 2020/2021)

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University: Slovak University of Technology in Bratislava
Faculty: Faculty of Chemical and Food Technology
Course unit title: Applied Genomics, Proteomics and Bioinformatics
Course unit code: N426A0_4I
Mode of completion and Number of ECTS credits: Exam (3 credits)
Name of lecturer: doc. Ing. Boris Lakatoš, PhD. (person responsible for course) - slovak, english
Learning outcomes of the course unit:
Subject the Applied Genomics, Proteomics and Bioinformatics deals with a rapidly evolving scientific area that introduces students into genomes, proteomes and databases that store various data about genes, proteins, genomes and proteomes. Students would learn about genomics, proteomics and bioinformatics and offer basic knowledge of genome sequencing, major differences between prokaryotic and eukaryotic genomes, basic proteomics and its applications. Students woul gain skills in applied bioinformatics, comparative, evolutionary, human genomics and functional genomics. The acquired knowledge during the course would be helpful to those students who want to work in core facilities and commercial biological and medical laboratories as well as in their postgraduate studies.
Prerequisites and co-requisites: none
Course contents:
1. Classification of genomics. Sequencing of genomes and sequencing methods („next-generation sequencing“). General/main databases of genomes.
2. Structure, organization and composition of prokaryotic genomes. Microbial genomics and genome epidemiology.
3. Function genomics, metagenomics and methods of metagenomics.
4. Evolution and structure of mitochondrial genomes, mtDNA and mitochondrial diseases.
5. Structure, organization and composition of eukaryotic genomes. Repetitive a transponable genetic elements and their effect on genome. Telomeric and subtelomeric regions.
6. DNA methylations, RNAi and silencing of genes expresion.
7. History of human genome sequencing. Evolution of human genome and structure variations (STR, VNTR, SNP).
8. Genomics of human diseases, nutritional genomics, epigenomics and methods of epigenomics.
9. Malditof and ESI, their use in proteomics, spectra and their analysis.
10. Tandem mass spectrometry, peptide sequencing by means of tandem mass spectrometry.
11. Affinity purification of proteins and TAP tag.
12. Main online databases (InterPro, UniProt, Pride, Pfam). Similarity, homology, local and global sequences assignment.
13. Substitution matrices (PAM, BLOSUM). Prediction of protein structure and RNA and structure alignment of proteins.
Recommended or required reading:
CVRČKOVÁ, F. Úvod do praktické bioinformatiky. Česko: Academia, 2006. 148 p. ISBN 80-200-1360-1.
HEYER, L. -- CAMPBELL, A. Discovering Genomics, Proteomics and Bioinformatics. USA: Cold Spring Harbor Lab. Press, 2006. 352 p. ISBN 0-8053-4722-4.
BREJOVÁ, B. -- NEBOHÁČOVÁ, M. -- NOSEK, J. Genomika. Univerzita Komenského: CreateSpace Independent Publishing Platform, 2013. 276 p. ISBN 1-49373-133-5.
HAWLEY, S. -- MORI, C. The human genome. Kanada: Academic Press, 2011. 420 p. ISBN 0-12333-445-4.

Planned learning activities and teaching methods: Lectures
Assesment methods and criteria: Written exam.
Language of instruction: Slovak, English
Work placement(s): There is no compulsory work placement in the course unit.

Last modification made by Ing. Tomáš Molnár on 05/20/2019.

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