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Methods of functional genomics - MB140P86
Title: Methods of functional genomics
Czech title: Metody funkční genomiky
Guaranteed by: Department of Genetics and Microbiology (31-140)
Faculty: Faculty of Science
Actual: from 2019
Semester: summer
E-Credits: 3
Examination process: summer s.:combined
Hours per week, examination: summer s.:4/0, Ex [DS]
Capacity: unlimited
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: English
Level: specialized
Note: enabled for web enrollment
Guarantor: RNDr. Vladimír Beneš, CSc.
Teacher(s): RNDr. Vladimír Beneš, CSc.
RNDr. Martin Pospíšek, Ph.D.
Annotation -
Last update: RNDr. Martin Pospíšek, Ph.D. (04.01.2019)
The course will sequentially cover all current cutting-edge approaches used by molecular biologists and bioinformaticians during genome sequencing, annotation and functional analysis. Course will be equally focused both on wet-bench as well as data analysis methods. Students will be provided with short introduction into the each topic covered, so only common knowledge in molecular and cellular biology corresponding roughly to the finished bachelor studies in biology, biochemistry and other related science will be required. The course is aimed mainly for Mgr. and Ph.D. students and will be run in co-operation with University of South Bohemia in Ceske Budejovice and students will be guided by 5-7 top-notch scientists from the European Molecular Biology Laboratory, Heidelberg, Germany (http://www.embl.org/).
The course will be complemented with practical tutorials mainly focused on genomics and proteomics data analysis.
Literature
Last update: RNDr. Martin Pospíšek, Ph.D. (04.04.2012)

Lectures reflect development in technologies and our current knowledge and change every year. Therefore teachers will prepare a new batch of recommended literature for each course. The recommended literature will be available for students enrolled to the course on http://web.natur.cuni.cz/~pospisek/vyuka/vyuka.htm in advance.

Requirements to the exam -
Last update: RNDr. Martin Pospíšek, Ph.D. (04.04.2012)

Final exam will be performed preferentially as a computer test but might comprise an oral exam or combination of both. The exam scope is bounded by the syllabus and information provided during the course.

Syllabus -
Last update: RNDr. Martin Pospíšek, Ph.D. (01.04.2012)

2011 lecturer team will comprise (without titles):

Vladimir Benes [benes@embl.de] - genomics

http://www.embl.de/services/core_facilities/genecore/members/index.php?s_personId=147

Jeroen Krijgveld [jeroen.krijgsveld@embl.de] - proteomics

http://www.embl.de/research/units/genome_biology/krijgsveld/index.html

Jonathon Blake [blake@embl.de] - bioinformatics

http://www.embl.de/services/core_facilities/genecore/index.html

Andy Riddell [riddell@embl.de] - flow cytometry

http://fccfweb.embl-heidelberg.de/fccfweb/index.php?option=com_contact&task=view&contact_id=1&Itemid=93

Beate Neumann [bneumann@embl.de] - systematic siRNA approaches

http://www.embl.de/almf/almf_services/contact/neumann/

Tobias Rausch [rausch@embl.de] - bioinformatics

http://www.embl.de/~rausch/

Hüseyin Besir [besir@embl.de] - protein expression and purification

http://www.embl.de/services/core_facilities/pepcore/members/index.php?s_personId=CP-60003254


The covered topics will include:

Genomics:

Microarrays - overview of technologies & applications;

Massively parallel sequencing - overview of technologies & applications; comparison with microarrays

qPCR - principles, applications, data

Proteomics:

Mass spectrometry: what?s the purpose?

MS instrumentation

Peptide fingerprinting: protein identification by MS

Peptide sequencing by MS

Identification of post-translational modifications

LC-MSMS and large-scale proteomics, incl. examples

Stable-isotope labeling and quantitative proteomics

Analysis of intact proteins

Bioinformatics:

Introduction: Biologists and Bioinformatics

>What bioinformatics is

>What bioinformatics can do

>What it can?t do

>Current Challenges for bioinformatics

>Data sizes, Read lengths

Application 1: Microarrays

>Analysis

>Normalization

>Design

>Data Repositories and Mining

Application 2: Next Generation Sequencing

>The range of applications

>Data analysis by application

>What can go wrong and biases with counts

Flow cytometry:

The principles of flow cytometry

Technology overview

Assays, applications

siRNA

The principles of siRNAs

Technology overview

Applications, examples, including high-throughput screenings

Protein expression and purification

Introduction to various protein expression systems and technologies

Applications, examples, troubleshooting
 
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