
Dissertation Topics
Topics for the call SPRING 2021
Bio-omics
Supervisor : Dalibor Blažek
RG : Dalibor Blažek Research Group
Keywords : transcription, DNA damage, cancer, genomics, proteomics
2. Functions of cyclin-dependent kinase 11 (CDK11) in regulationof gene expression
Supervisor : Dalibor Blažek
RG : Dalibor Blažek Research Group
Keywords : CDK11, histone genes, cancer, proteomics, genomics
3. Plant telomeres and telomerases
Supervisor : Jiří Fajkus
RG : Jiří Fajkus Research Group
Keywords : Telomeres, telomerase, RNA-protein interactions, bioinformatics, evolution
4. REGULATION OF BCR SIGNALLING BY DNA DAMAGE RESPONSE AND P53 PROTEIN
Supervisor : Marek Mráz
Co-supervisor : Miroslav Boudný
RG : Marek Mráz Research Group
Keywords : B-cell receptor signaling, BCR, leukemia, lymphoma, B cell malignancies,
miRNAs, p53, FOXP1, CD22 sh, CLL
5. LONG NON-CODING RNAs (lncRNAs) IN LEUKEMIAS
Supervisor: Marek Mráz
RG : Marek Mráz Research Group
Keywords : Follicular lymphoma, FL, non-Hodgkin lymphoma, B-cell lymphoma, NGS,
Illumina, genome editing, CRISPR, DLBCL, leukemia, CLL, FCR, BCR signaling
inhibitors
6. REGULATION OF CELL MIGRATION IN B CELL LEUKEMIAS ANDLYMPHOMAS
Supervisor : Marek Mráz
RG : Marek Mráz Research Group
Keywords: Follicular lymphoma, FL, non-Hodgkin lymphoma, B-cell lymphoma, NGS,
Illumina, genome editing, CRISPR, DLBCL, leukemia, CLL, FCR, BCR signaling
inhibitors
7. ROLE OF TRANSCRIPTION FACTORS IN ONSET AND PROGRESSIONOF B-CELL MALIGNANCIES
Supervisor : Marek Mráz
Co-supervisor : Josef Večeřa
RG : Marek Mráz Research Group
Keywords: leukemia, lymphoma, B cell malignancies, TFs, CLL3
8. Subcellular trafficking in plant survival
Supervisor : Tomasz Nodzynski
RG : Tomasz Nodzynski Research Group
Keywords: vesicular trafficking; intracellular localization; stress response; adaptation
Supervisor : Mary O’Connell
RG : Mary O’Connell Research Group
Keywords: RNA modification, epitranscriptome, ADAR, innate immunity, cancer
10. Complexes Maintaining Chromatin Structure
Supervisor : Jan Paleček
RG : Jiří Fajkus Research Group
Keywords: Chromatin structure, genome stability, SMC complexes
11. Proteins involved in the regulation of telomeric repeats
Supervisor : Petra Prochazkova Schrumpfova
RG : Jiří Fajkus Research Group
Keywords: telomerase; telomeres; proteins; telo-box; regulatory elements; telomerase assembly; plant
development
Supervisor : Michal Šmída
RG : Michal Šmída Research Group
Keywords: CRISPR/Cas9, CAR-T cell, B-cell malignancy, genetic screening
13 . The role of protein-protein interactions in the dynamics of m6A RNA modification
Supervisor : Štěpánka Vaňáčová
RG : Štěpánka Vaňáčová Research Group
Keywords: mRNA, protein interactions, m6A RNA, m6Am, RNA modification
Structural Biology
Supervisor : Gabriel Demo
RG : Gabriel Demo Research Group
Keywords : RNA polymerase, ribosome, coupling, structure, cryo-EM, cryo-ET
Supervisor : Gabriel Demo
RG : Gabriel Demo Research Group
Keywords : Poxviruses, viral RNA polymerase, ribosome, coupling, cryo-ET
Supervisor : Peter Lukavsky
RG : Peter Lukavsky Research Group
Keywords : mRNAs, 3’UTRs, non-coding mRNA
4. Designing modified DNA fragments
Supervisor : Radek Marek
RG : Radek Marek Research Group
Keywords : DNA, base pairing, molecular modelling, quantum chemistry
5. Structure of parallel forms of nucleic acids studied by NMR spectroscopy and molecular modelling
Supervisor : Radek Marek
RG : Radek Marek Research Group
Keywords : DNA, base pairing, NMR spectroscopy, molecular modelling
6. Structural and time-resolved studies of phage replication in bacterial biofilm
Supervisor : Pavel Plevka
RG : Pavel Plevka Research Group
Keywords : bacterial biofilm, phage therapy, ion beam milling, cryo-electron tomography, cryo-ET,
fluorescence microscopy, cryo-electron microscopy, virology, antibiotic-resistance
7. Structural study of enterovirus replication in vivo
Supervisor : Pavel Plevka
RG : Pavel Plevka Research Group
Keywords : enteroviruses, replication cycle, ion beam milling, cryo-electron tomography, cryo-ET, virology,
cryo-electron microscopy
8. Structural Biology of WNT Signalling
Supervisor : Konstantinos Tripsianes
RG : Konstantinos Tripsianes Research Group
Keywords : Wnt signaling, Dishevelled, Casein kinase, interactions, conformations, phosphorylations,
dynamics, allostery, NMR, X-ray crystallography, SAXS, FRET, cryo-EM, native MS, MS-HDX
9. Association of proteins in phospholipid membranes
Supervisor : Robert Vácha
RG : Robert Vácha Research Group
10. Selectivity of translocation across lipid membranes
Supervisor : Robert Vácha
RG : Robert Vácha Research Group
11. Structural characterization of hybrid proteinsinvolved in neurodegenerative diseases
Supervisor : Jozef Hritz
Consultant : Lukáš Žídek
RG : Lukáš Žídek Research Group
Keywords : hydrid proteins, disordered region, NMR spectroscopy, neurodegenerative diseases
phosphorylation, computational simulations
12. Structural properties of human carbonic anhydrase IX and design of its inhibitors
Supervisor : Jozef Hritz
RG : Lukáš Žídek Research Group
Keywords : carbonic anhydrase, cancer, intrinsically disordered region, NMR, inhibitors
13. Characterization of biomolecules in living cells using NMR spectroscopy
Supervisor : Lukáš Trantírek
RG : Lukáš Trantírek Research Group
Keywords : in-cell NMR spectroscopy; cell-cycle; drug screening; protein
14. The role of the hnRNP C protein in RNA regulation
Supervisor : Jiří Nováček
CF : Cryo-Electron Microscopy and Tomography Core Facility
Keywords : hnRNP C, 40S particle, cryo-EM, cryo-FIBM
Molecular Medicine
Supervisor : Dalibor Blažek
RG : Dalibor Blažek Research Group
2. Functions of cyclin-dependent kinase 11 (CDK11) in regulation of gene expression
Supervisor: Dalibor Blažek
RG : Dalibor Blažek Research Group
3. PRIORITIZING DRUG COMBINATIONS IN LEUKEMIA BASED ON ANALYSIS OF TARGETTED THERAPY IN VIVO
Supervisor : Marek Mráz
Co-supervisor : Miroslav Boudný
RG : Marek Mráz Research Group
4. LONG NON-CODING RNAs (lncRNAs) IN THE PATHOGENESIS OF B CELL LYMPHOMAS
Supervisor : Marek Mráz
RG : Marek Mráz Research Group
Supervisor : Michal Šmída
RG : Michal Šmída Research Group
6. The role of posttranscriptional RNA modifications in cell differentiation
Supervisor : Štěpánka Vaňáčová
RG : Štěpánka Vaňáčová Research Group
Keywords: mRNA, protein interactions, posttranscriptional RNA modifications