Bi7201 Genomics - a basic course

Faculty of Science
Autumn 2009
Extent and Intensity
1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
doc. RNDr. Jan Hejátko, Ph.D. (lecturer)
RNDr. Hana Konečná (lecturer)
Mgr. Eva Paděrová (lecturer)
Guaranteed by
prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology - Biology Section - Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.
Fri 8:00–9:50 BR3
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 / plans 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 (Bi7201c), 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 analyzis 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 analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference).
  • Fragmental DNA analyzis 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 quantitaive gene expression profiling, Genevestigator, transaltional and transcriptional fusions with reporter gene).
  • New approaches: Chemical genetics.
  • Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
  • Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175
Teaching methods
The main teaching method are lectures that include particular examples from the own scientific praxis and demonstration of the solution of particular problems via individual tools of functional genomics.
Assessment methods
Type of lectures: The lectures are facultative, however, the presence of students is highly desirable for complete understanding of principles of functional genomics approaches; the teaching materials available on-line are rather supporting. Type of exam: Written exam.
Language of instruction
Follow-Up Courses
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 2010 - only for the accreditation, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012.
  • Enrolment Statistics (Autumn 2009, recent)
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