| Course title | Methods of Functional Genomic |
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| Course code | KMB/217 |
| Organizational form of instruction | Lecture |
| Level of course | Bachelor |
| Year of study | 2 |
| Frequency of the course | In each academic year, in the summer semester. |
| Semester | Summer |
| Number of ECTS credits | 5 |
| Language of instruction | English |
| Status of course | Compulsory-optional |
| Form of instruction | Face-to-face |
| Work placements | This is not an internship |
| Recommended optional programme components | None |
| Lecturer(s) |
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| Course content |
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Content of lectures 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 Mass spectrometry as a discovery tool in proteomics Mass spectrometry as a screening tool - from research to clinic? Mass spectrometry for structural biology 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 Genomics: Microarrays - overview of technologies & applications; Massively parallel sequencing - overview of technologies & applications; comparison with microarrays Principles of MPS data analysis Discovery and implications of genome structural variants qPCR - principles, applications, data. RNAi technology: Overview about silencing reagents used in RNAi screens siRNA design Transfection methods used for RNAi Genome-wide RNAi screen to identify cell division genes as an example for high-throughput applications Validation of RNAi results
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| Learning activities and teaching methods |
Monologic (reading, lecture, briefing), Skills training, Work activities (workshops)
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| Learning outcomes |
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Objectives of the course: a) to provide students with a comprehensive overview of current methods used in functional genomics with an emphasis on their practical aspects; b) to increase students' awareness through examples from real scientific projects about methods' potential they offer for solution of tasks the students may encounter during work on their diploma/PhD thesis.
Obtaining basic educaion in following fields: Proteomics, transcriptomics, genomics, |
| Prerequisites |
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Basic understanding of cell and molecular biology. Special course for Ph.D. study field Molecular and Cell Biology and Genetics
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| Assessment methods and criteria |
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Test
The exam is a multiple-choice test. Minimal score necessary is 50%. |
| Recommended literature |
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| Study plans that include the course |
| Faculty | Study plan (Version) | Category of Branch/Specialization | Recommended semester |
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