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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. Last update: Pospíšek Martin, RNDr., Ph.D. (04.01.2019)
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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. Last update: Pospíšek Martin, RNDr., Ph.D. (04.04.2012)
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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. Last update: Pospíšek Martin, RNDr., Ph.D. (04.04.2012)
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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 Last update: Pospíšek Martin, RNDr., Ph.D. (01.04.2012)
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