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Bioinformatics - algorithms and data analysis

Type of study Follow-up Master
Language of instruction Czech
Code 460-4143/01
Abbreviation BAAD
Course title Bioinformatics - algorithms and data analysis
Credits 4
Coordinating department Department of Computer Science
Course coordinator Ing. Michal Vašinek, Ph.D.

Osnova předmětu

Lectures:
1) Introduction to the principles of functioning of organisms at the DNA level
2) Sequence similarity
3) Data structures
4) Alignment
5) Genome assembly
6) Algorithms for searching in biological databases
7) Prediction of genes
8) Principles of technologies in the analysis of biological data
9) Detection of variants
10) Gene expression
11) Statistical methods for gene expression analysis
12) Phylogenetic data analysis

Exercises in the computer lab:
1) Practicing basic concepts for working with DNA
2) Practicing algorithms for calculating sequence similarity
3) Algorithms for construction of suffix trees
4) Practicing algorithms for global and local alignment
5) Practicing algorithms for genome assembly
6) Access to BLAST databases and practice of algorithms for searching in biological databases
7) Practicing the concepts needed for gene prediction
8) Getting acquainted with various representations of biological data
9) Practicing the concepts needed for the detection of variants
10) Practicing the concepts needed for gene expression
11) Practice of statistical analysis of gene expression data
12) Practicing algorithms for creating evolutionary trees

E-learning

Basic materials are available on the educator's website:
(https://homel.vsb.cz/~vas218/bio)

Selected study materials are published on the e-learning portal (https://www.vsb.cz/e-vyuka/cs/subject/460-4143/02/edison).

Povinná literatura

1) Wing-Kin Sung. Algorithms in Bioinformatics: A Practical Introduction. Chapman & Hall/CRC Mathematical & Computational Biology. 2009
2) Arthur Lesk. Introduction to Bioinformatics. Oxford University Press, 2014.
3) Fatima Cvrčková. Úvod do praktické bioinformatiky. 1. vyd. Praha: Academia, 2006.
4) Pierre Baldi;G. Wesley Hatfield. DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press 2002.

Doporučená literatura

1) Caroline St. Clair, Jonathan E. Visick. Exploring Bioinformatics: A Project-Based Approach. Jones & Bartlett Learning, 2013.