SubjectsSubjects(version: 954)
Course, academic year 2023/2024
  
Case Studies in Bioinformatics - M143006
Title: Případové studie z bioinformatiky
Guaranteed by: Department of Informatics and Chemistry (143)
Faculty: Faculty of Chemical Technology
Actual: from 2023
Semester: winter
Points: winter s.:3
E-Credits: winter s.:3
Examination process: winter s.:
Hours per week, examination: winter s.:2/0, C [HT]
Capacity: unlimited / unknown (unknown)
Min. number of students: unlimited
State of the course: taught
Language: Czech
Teaching methods: full-time
Teaching methods: full-time
Level:  
Note: course can be enrolled in outside the study plan
enabled for web enrollment
Guarantor: Svozil Daniel prof. Mgr. Ph.D.
Pačes Jan Mgr. Ph.D.
Interchangeability : N143051
This subject contains the following additional online materials
Annotation -
This course summarizes acquired bioinformatics knowledge, and puts bioinformatics skills into a context. Lecturers will demonstrate individual methods and approaches using well documented and well performed experiments. Possible solutions will be compared, and their efficiency will be discussed.
Last update: Hladíková Jana (04.01.2018)
Aim of the course -

Students will be able to:

  • Gain general knowledge of bioinformatics methods and approaches employed in solving real-life scientific projects.

Last update: Hladíková Jana (04.01.2018)
Literature -

R: Zvárová J, Mazura I (eds.), Metody molekulární biologie a bioinformatiky, Karolinum, Praha 2013, ISBN: 978-8024621500

R: Rodriguez-Ezpeleta N., Hackenberg M., Aransay A. M. (Eds.), Bioinformatics for High Throughput Sequencing, Springer 2012, ISBN 978-1-4614-0781-2

A: Cristianini N., Hahn W., Introduction to Computational Genomics. A case studies approach, Cambridge University Press 2012, ISBN: 978-0-521-67191-0

A: Brown S. M. (Ed.), Next-Generation DNA Sequencing Informatics, Cold Spring Harbor Laboratory Press 2012, ISBN: 978-1-936113-87-3

A: Hahne F., Huber W., Gentleman R., Falcon S., Bioconductor Case Studies, Springer 2008, ISBN: 978-0-387-77240-0

Last update: Svozil Daniel (04.11.2018)
Learning resources -

none

Last update: Hladíková Jana (04.01.2018)
Requirements to the exam - Czech

Předmět je zakončen ústní zkouškou.

Last update: Cibulková Jana (13.09.2023)
Syllabus -

1. Introduction

2. Bacterial genome assembly - Achromobacter

3. Eukaryotic genome project I - Mastigamoeba, assembly from z 454, Illumina and PacBio sequences

4. Eukaryotic genome project II - repeats and other problematic stretches, assembly evaluation

5. Eukaryotic genome project III - gene prediction, annotation

6. RNA-Seq of the known genome, analysis of gene expression

7. Exploratory RNA-Seq of unknown genomes - Cobitis

8. Analysis of gene expression of tumorous tissues using microarrays

9. Metagenomics, analysis of poluted ground water

10. Phylogenetic analysis of the SARS epidemic

11. Comparative genomics, Burkholderia

12. Epigenetic analysis, melanomes

13. ENSEMBLE API

14. Genotyping analysis, porphyria

Last update: Hladíková Jana (04.01.2018)
Registration requirements -

Biochemistry, Molecular genetics, Bioinformatics

Last update: Hladíková Jana (04.01.2018)
Course completion requirements -

An oral exam.

Last update: Svozil Daniel (26.01.2018)
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
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VŠCHT Praha