PřF:CG920 Genomics - Course Information
CG920 GenomicsFaculty of Science
- Extent and Intensity
- 2/0/0. 2 credit(s) (plus 2 credits for an exam). Type of Completion: zk (examination).
- doc. RNDr. Jan Hejátko, Ph.D. (lecturer), prof. RNDr. Jiří Fajkus, CSc. (deputy)
RNDr. Roman Hobza, Ph.D. (lecturer), doc. RNDr. Jan Hejátko, Ph.D. (deputy)
RNDr. Hana Konečná (lecturer)
Mgr. Markéta Pernisová, Ph.D. (lecturer)
Mgr. Kamil Růžička, Dr. rer. nat. (lecturer)
doc. Mgr. Jan Havliš, Dr. (assistant)
Mgr. Pavla Pospíšilová (assistant)
- prof. RNDr. Jiří Fajkus, CSc.
National Centre for Biomolecular Research - Faculty of Science
Supplier department: National Centre for Biomolecular Research - Faculty of Science
- Mon 17. 9. to Fri 14. 12. Fri 11:00–12:50 A2-211
- Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- Fields of study the course is directly associated with
- Course objectives
- At the end of the course, student will acquire theory of basic approaches in current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (C7301), in frame of which students will be able to practice most of the theory. At the end of this course, students get an overview of modern approaches of functional genomics. Students will be able to use and interpret information deposited in genomic databases and they will be oriented in the modern biology approaches and problems. Student will be able to contribute in a creative way to the further development of modern biology.
- Introduction to genomics.
- Methods of functional genomics.
- Genome databases and basic tools of bioinformatics: (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], search in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analysis of promoter regions of individual genes [ALIBABA], virtual PCR).
- In silico prediction of gene functions.
- Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analysis, physical and chemical mutagenesis, targeted gene silencing using RNA interference).
- Fragmental DNA analysis and positional cloning as tools in forward genetics.
- Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion).
- Phenotype profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches).
- Southern blot and DNA molecular hybridization.
- Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.
- Methods for the gene expression analysis (qualitative and quantitative gene expression profiling, Genevestigator, translational and transcriptional fusions with reporter gene).
- New approaches: Chemical genetics.
- recommended literature
- SAMUELSSON, Tore. Genomics and bioinformatics : an introduction to programming tools for life scientists. Cambridge: Cambridge University Press, 2012. xvii, 338. ISBN 9781107008564. info
- Genomics. Edited by Isidore Rigoutsos - G. Stephanopoulos. New York: Oxford University Press, 2007. xxi, 314 p. ISBN 9780195300819. info
- Teaching methods
- The lecture is based on presentations (pdf format) and individual or group tuition on demand. Presentations themselves will be available as study materials. Subject will be eventually lectured if the number of enrolled students exceeds number 5.
- Assessment methods
- Type of exam: Written exam. The test consists from 40 questions valued according to their difficulties (1-4 points), the total maximum is 100 points. Evaluation criteria of the examination test are as follows: 100-95 points A, 94-88 points B, 87-80 points C, 79-70 points D, 69-58 points E, <58 points F.
- Language of instruction
- Further Comments
- Study Materials
The course is taught annually.