Syllabus
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
Annotation
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.