SubjectsSubjects(version: 854)
Course, academic year 2019/2020
  
Case Studies in Bioinformatics - M143006
Title: Případové studie z bioinformatiky
Guaranteed by: Department of Informatics and Chemistry (143)
Actual: from 2019
Semester: winter
Points: winter s.:3
E-Credits: winter s.:3
Examination process: winter s.:
Hours per week, examination: winter s.:2/0 Ex [hours/week]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type: Master's (post-Bachelor)
Note: course can be enrolled in outside the study plan
enabled for web enrollment
Guarantor: Svozil Daniel doc. Mgr. Ph.D.
Pačes Jan Mgr. Ph.D.
Interchangeability : N143051
Annotation -
Last update: Hladíková Jana (04.01.2018)
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.
Aim of the course -
Last update: Hladíková Jana (04.01.2018)

Students will be able to:

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

Literature -
Last update: Svozil Daniel doc. Mgr. Ph.D. (04.11.2018)

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

Learning resources -
Last update: Hladíková Jana (04.01.2018)

none

Syllabus -
Last update: Hladíková Jana (04.01.2018)

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

Registration requirements -
Last update: Hladíková Jana (04.01.2018)

Biochemistry, Molecular genetics, Bioinformatics

Course completion requirements -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

An oral exam.

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
3 / 3 84 / 84
Coursework assessment
Form Significance
Oral examination 100

 
VŠCHT Praha