PřF GEPR Genomics and Proteomics
Name in Czech: Genomika a proteomika
doctoral full-time
Included in the programme: PřF D-GEPR_ Genomics and Proteomics

Final state doctoral examination and defence of the doctoral thesis

Student must pass the Final State Exam, which is to prove student's professional orientation in the field of genomics and proteomics and other related disciplines, particularly in molecular and cellular biology, structural biology, bioinformatics, and in the experimental approaches used in the field. The exam topics are selected by supervisor and approved by Doctoral board (or its chairman) in advance. The student should especially be able to prove sufficient general knowledge in the field studied and in-depth knowledge in areas related to his/her Ph.D. thesis, including being familiar with recent major publications in their field of expertise.

Before the dissertation thesis defence can take place, student must publish first-author paper (or the manuscript must be accepted for publication) in impacted international journal indexed in Web of Science (WoS) with impact factor above the subject median (or two publications must be published if the IF is below the median).

The dissertation thesis defence starts with presentation of major scientific achievements and is followed by discussions with referees and committee members. Student must prove her/his ability to work and develop research independently, to present and defend her/his results and conclusions.

Requirements of the study

Research activities:
Dissertation thesis preparation – runs throughout the whole studies (at least 60% of the workload)
Read relevant literature
Publication activity – student must publish first-author paper in impacted international journal indexed in Web of Science (WoS) with impact factor above the subject median, 10% of the workload
Dissertation thesis defence
Active participation at an international conference
Internship abroad - student must spend 1 month in a lab abroad (can be cumulated)

Education activities:
Special subjects - to complement and extend the student's topic (defined in Study plan section - 20% of the workload at most)
Mandatory Genomics and Proteomics seminar
Teaching activity – student can participate in supervision of bachelor and master students, and in regular teaching activities (not more than 150 hours - 10% of the workload at most)
Soft skills - e.g. Academic writing,
Scientific English

Suggestion of theses topics and the topics of defended theses

Examples of (10 selected) successfully defended dissertations:

Veronika Pavlištová: Effect of chromatin assembly on genome stability (https://is.muni.cz/auth/th/wx0ba/)

Kateřina Zábrady: Analysis of MAGE (Melanoma AntiGEn) proteins and their interaction partners (https://is.muni.cz/auth/th/ap968/)

Eliška Janoušková: Dynamics of Telomeric Proteins (https://is.muni.cz/auth/th/pm7q7/)

Kateřina Šedová: Characterisation of Protein Modifications by Mass Spectrometry (https://is.muni.cz/auth/th/eypvg/)

Zuzana Vrzalová: Complex molecular diagnostics of congenital adrenal hyperplasia (https://is.muni.cz/auth/th/x4k2c/)

Karin Jaške: Crossroads of genetics and epigenetics: nucleosome assembly and chromosome integrity (https://is.muni.cz/auth/th/laaa5/)

Markéta Žďárská: Differential proteomics and phosphoproteomics of hormonal regulations in plants (https://is.muni.cz/auth/th/dhio8/)

Michal Zimmermann: Protein-DNA interactions involved in regulation of telomere maintenance (https://is.muni.cz/auth/th/fsxl1/)

Marc Guerineau: Analysis of SMC5-6 complex subunits and their functional homologs (https://is.muni.cz/auth/th/uccar/)

Eva Majerová: Epigenetic mechanisms in the regulation of telomere maintenance (https://is.muni.cz/auth/th/eyt2h/)

Recommended progress through the study plan

Povinné

Code Name Guarantor Type of Completion Extent and Intensity Credits Term Profile Cat.
PřF:C9950Seminar of the Dept. Functional Genomics and Proteomics J. Fajkusz 0/22 --
2 credits

Povinně volitelné

Code Name Guarantor Type of Completion Extent and Intensity Credits Term Profile Cat.
PřF:CG020Genomics J. Hejátkozk 2/0/02+2 --
PřF:C7301Genomics - practice J. Hejátkok 0/0/33 --
PřF:C9025Evolutionary and comparative plant genomics J. Fajkuszk 2/02+2 --
PřF:C9035Evolutionary and comparative plant cytogenetics - practice J. Fajkusk 0/2/02 --
PřF:C9041Structure and function of eukaryotic chromosomes J. Fajkuszk 2/0/02+2 --
PřF:C9042Analysis of chromatin structure - practical training J. Fajkusz 0/0/22 --
PřF:C2131Introduction to bioinformatics M. Wimmerovázk 2/0/02+2 --
PřF:C2132Introduction to bioinformatics - seminar M. Wimmerováz 0/1/01 --
PřF:C2135Bioinformatics for practice M. Wimmerovák 0/2/02+1 --
PřF:C2138Advanced bioinformatics M. Wimmerovázk 2/0/02+2 --
PřF:C2139Advanced bioinformatics - seminary M. Wimmerováz 0/1/01 --
PřF:C8202Proteomics - a basic course J. Fajkuszk 1/0/01+2 --
PřF:C8302Proteomics - practice J. Hejátkok 0/0/33 --
PřF:C9530Structure of biomacromolecules L. Žídekzk 2/0/02+2 --
PřF:C9531Structure of biomacromolecules L. Žídekz 0/2/02 --
PřF:CG010Proteomics J. Havlišzk 2/0/02+2 --
PřF:CG080Methods in genomics J. Fajkuszk 2/0/02+2 --
PřF:CG090Methods in proteomics Z. Zdráhalzk 2/0/02+2 --
PřF:CG030Structure and function of protein complexes J. Palečekzk 2/02+2 --
PřF:CG031Practical course in modelling of complexes J. Palečekz 0/2/02 --
PřF:C7250Protein characterisation using mass spectrometry Z. Zdráhalk 1/0/01+1 --
PřF:C7350Protein characterisation using mass spectrometry - practice Z. Zdráhalz 0/1/01 --
65 credits

Volitelné

Code Name Guarantor Type of Completion Extent and Intensity Credits Term Profile Cat.
PřF:C3900Molecular mechanisms of cell ageing P. Procházková Schrumpfovázk 2/0/02+2 --
PřF:C6210Biotechnology M. Mandlzk 2/0/02+2 --
PřF:C7073Bioanalytics I - Biomacromolecules J. Havlišzk 2/0/02+2 --
PřF:C7250Protein characterisation using mass spectrometry Z. Zdráhalk 1/0/01+1 --
PřF:C7490Molecular diagnostics of inherited diseases J. Fajkuszk 1/0/01+2 --
PřF:C9085Protein-RNA interactions R. Šteflzk 1/0/01+2 --
PřF:C9285Praxis of science and research - publication and projects J. Fajkusk 2/0/02 --
PřF:JA003English for Science - Elective Course H. Němcovák 0/2/0 + online.3 --
PřF:C7230Fluorescence methods in life sciences - a journey from molecules to cells J. Fajkuszk 2/0/02+2 --
PřF:C7235Fluorescence methods in life sciences - excercise J. Fajkusk 0/2/02+1 --
PřF:C8980Protein Preparation and Characterization I - Expression and Purification L. Žídekzk 2/0/02+2 --
PřF:C9045Biology of yeasts J. Palečekzk 2/0/02+2 --
PřF:C8857Protein Preparation and Characterization III - Protein-mediated interactions L. Krejčízk 1/0/01+2 --
PřF:C9142Biology of yeasts - practice J. Palečekz 0/2/02 --
PřF:Bi8350Evolutionary genomics E. Kejnovskýzk 2/0/02+2 --
PřF:C7072Bioanalytics II - Analytical methods in clinical praxis J. Havlišzk 2/0/02+2 --
PřF:F8310The molecular interactions in biology and chemistry V. Brabeck 2/03+1 --
PřF:S1001Chemical properties, structure and interactions of nucleic acids M. Fojtazk 3/03+2 --
PřF:S2008Developmental and cellular biology of plants J. Frimlzk 4/0/04+2 --
PřF:S2011Hormones in plant development J. Fajkuszk 2/0/02+2 --
PřF:S4001International performance L. Štěpánekzk 2/02+2 --
PřF:S4002Law, ethics and philosophy of science J. Havlišzk 2/0/02+2 --
PřF:S2009Mendel Centre Seminars in the Bio-omics J. Havlišz 0/2/02 --
PřF:S5020Life Science PI Seminars V. Sklenářz 2/0/0- --
PřF:XD010Masaryk University Life Sciences Seminar sponsored by CEITEC and ICRC V. Bryjaz 0/2/02 --
84 credits