Dissertation Topics - Current call

Bio-omics

1. ADAR2 RNA editing in CNS

Supervisor: Liam Keegan, Ph.D.

RG: ERA Chair - Mary O'Connell Research Group

Keywords: RNA modification, ADAR, genetics


2. Characterization of cyclin-dependent kinase 12 (CDK12) substrates and their roles in regulation of transcription and tumorigenesis

Supervisor: Dalibor Blažek, Ph.D.

RG: Dalibor Blažek Research Group

Keywords: cyclin-dependent kinases, Cdk12, transcription, recombination repair pathway genes, genome stability, DNA damage, BRCA1, cancer


3. Dynamics of the Structure Maintenance of Chromosome (SMC) complexes

Supervisor: assoc. prof. Jan Paleček

RG: Jiří Fajkus Research Group

Keywords: Structure Maintenance of Chromosome, SMC complexes, SMC5/6; genome stability, chromatin fibers


4. Functions of cyclin-dependent kinase 11 (CDK11) in regulation of gene expression

Supervisor: Dalibor Blažek, Ph.D.

RG: Dalibor Blažek Research Group

Keywords: cyclin-dependent kinase, Cdk11, transcription, gene expression, cancer


5. Investigating the regulation of the RNA modifying enzyme ADAR1 and how it regulates other biological pathways and diseases

Supervisor: prof. Mary O’Connell

RG: ERA Chair - Mary O'Connell Research Group

Keywords: RNA modification, epitranscriptome, ADAR, innate immunity, cancer


6. Mass spectrometric imaging of biological tissues

Supervisor: prof. Jan Preisler

RG: Jiří Pinkas Research Group

Keywords: mass spectrometry imaging, MSI, matrix-assisted laser desorption/ionization,MALDI, analysis development


7. Microenvironmental interactions and regulation of their crosstalk in malignant B-cells by transcription factors

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Keywords: B-cell receptor, BCR signaling inhibitors, DDR, FOXP1, CD22, chronic lymphocytic leukemia, CLL, NGS technology, genome editing


8. Regulation of BCR signalling by DNA damage response and P53 protein

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Keywords: B-cell receptor, BCR signaling inhibitors, DDR, FOXP1, CD22, chronic lymphocytic leukemia, CLL, NGS technology, genome editing


9. Structure, function and evolution of plant telomere components


Supervisor: prof. Jiří Fajkus

RG: Jiří Fajkus Research Group

Keywords: plant telomere DNA repeats, telomere maintenance, telomerase


10. The role of posttranscriptional RNA modifications in cell differentiation

Supervisor: assoc. prof. Štěpánka Vaňáčová

RG: Štěpánka Vaňáčová Research Group

Keywords: mRNA, protein interactions, posttranscriptional RNA modifications


 11. The role of protein-protein interactions in the dynamics of m6A RNA modification

Supervisor: assoc. prof. Štěpánka Vaňáčová

RG: Štěpánka Vaňáčová Research Group

Keywords: mRNA, protein interactions, m6A RNA, m6Am, RNA modification


12. Search for new regulators of intracellular trafficking in plants

Supervisor: Tomasz Nodzynski, Ph.D.

RG: Tomasz Nodzynski Research Group

Keywords: plants function, intracellular trafficking, endocytic trafficking regulations


Structural Biology

1. A structural basis for the cross-talk between histones and RNA Polymerase II

Supervisor:  assoc. prof. Richard Štefl

RG: Richard Štefl Research Group

Keywords: RNA, posttranslational modifications, CTD, RNAPII, histones, chromatin, C-terminal domain, gene expression


2. Cracking the CTD code

Supervisor: assoc. prof. Richard Štefl

RG: Richard Štefl Research Group

Keywords: CTD, TNAPII, C-terminal domain, CTD code, post-translational modification


3. Integrative structural biology of 3’UTRs

Supervisor: Peter Lukavsky, Dr. rer. nat.

RG: Peter Lukavsky Research Group

Keywords: Three Prime Untranslated Region, 3’UTR, mRNPs, RNA-protein networks, Staufen, RNA-based pulldown, gene expression, 3’UTR mutations, cryo EM, NMR spectroscopy


4. Protein sensitivity of membrane curvature

Supervisor: assoc. prof. Robert Vácha

RG: Robert Vácha Research Group

Keywords: membrane curvature, protein sequencing, protein motifs design, membrane parameterizations


5. Regulation of protein-protein itneractions

Supervisor: assoc. prof. Robert Vácha

RG: Robert Vácha Research Group

Keywords: protein interactions, posttranslational modifications, multi-scale simulations, protein motifs design, protein parameterization


6. Structural and time-resolved studies of phage replication in bacterial biofilm

Supervisor: Pavel Plevka, Ph.D.

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, Ph.D.

RG: Pavel Plevka Research Group

Keywords: enteroviruses, replication cycle, ion beam milling, cryo-electron tomography, cryo-ET, cryo-electron microscopy, virology


8. Structural studies of the TPLATE complex

Supervisor: Konstantinos Tripsianes, Ph.D.

RG: Konstantinos Tripsianes Research Group

Keywords: TPLATE complex, TPC, AP-2, appendage domains, NMR, structural techniques


Molecular Medicine


1. Microenvironmental interactions and regulation of their crosstalk in malignant B-cells by transcription factors

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Description of the topic

Keywords: B-cell receptor, BCR signaling inhibitors, DDR, FOXP1, CD22, chronic lymphocytic leukemia, CLL, NGS technology, genome editing


2. Regulation of BCR signalling by DNA damage response and P53 protein

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Description of the topic

Keywords: B-cell receptor, BCR signaling inhibitors, DDR, FOXP1, CD22, chronic lymphocytic leukemia, CLL, NGS technology, genome editing


 3. The role of protein-protein interactions in the dynamics of m6A RNA modification

Supervisor: assoc. prof. Štěpánka Vaňáčová

RG: Štěpánka Vaňáčová Research Group

Description of the topic

Keywords: mRNA, protein interactions, m6A RNA, m6Am, RNA modification


 4. The role of posttranscriptional RNA modifications in cell differentiation

Supervisor: assoc. prof. Štěpánka Vaňáčová

RG: Štěpánka Vaňáčová Research Group

Description of the topic

Keywords: mRNA, protein interactions, posttranscriptional RNA modifications


Bio-omics


1. Characterization of cyclin-dependent kinase 12 (CDK12) substrates and their roles in regulation of transcription and tumorigenesis
Supervisor : Dalibor Blažek, Ph.D.
RG: Dalibor Blažek Research Group

2. Detailed genomic variant analysis for cancer patient stratification and treatment prognosis
Supervisor: Vojtěch Bystrý, Ph.D.
RG: Šárka Pospíšilová Research Group

3. Development of capillary electrophoresis methods for non-invasive diagnostics of gastroesophageal reflux disease
Supervisor: assoc. prof. Petr Kubáň
RG: František Foret Research Group

4. Development of portable capillary electrophoresis instrumentation for medical diagnostic purposes
Supervisor: assoc. prof. Petr Kubáň
RG: František Foret Research Group

5. Developmental response induced by abiotic stress during seed development in Brassica sp.
Supervisor: Helene Robert Boisivon, Ph.D.
RG: Heléne Robert Boisivon Research Group

6. Dynamics of the Structure Maintenance of Chromosome (SMC) complexes
Supervisor: assoc. prof. Jan Paleček
RG: Jiří Fajkus Research Group

7. Functions of cyclin-dependent kinase 11 (CDK11) in regulation of gene expression
Supervisor: Dalibor Blažek, Ph.D.
RG: Dalibor Blažek Research Group

8. Identification of RNA binding protein function and regulation patterns
Supervisor: Panagiotis Alexiou, Ph.D.
RG: Panagiotis Alexiou Research Group

9. Long non-coding RNAs (lncRNAs) in the pathogenesis of B cell lymphomas
Supervisor: assoc. prof. Marek Mráz
RG: Marek Mráz Research Group

10.Mass spectrometric imaging of biological tissues
Supervisor: prof. Jan Preisler
RG: Jiří Pinkas Research Group

11. Mechanisms controlling germ-line differentiation in plants
Supervisor: Karel Říha, Ph.D.
RG: Karel Říha Research Group

12. Migration of malignant B cells and their adaptive response to BCR inhibitor therapy
Supervisor: assoc. prof. Marek Mráz
RG: Marek Mráz Research Group

13. Multistep Phosphorelay Signaling in Crop Stress
Supervisor : assoc. prof. Jan Hejátko
RG : Jan Hejátko Research Group

14. Non-coding RNAs (microRNAS/lncRNAS) and microenvironmental interactions of malignant B-cells
Supervisor: assoc. prof. Marek Mráz
RG: Marek Mráz Research Group

15. Quality control in diagnostic NGS applications
Supervisor: Boris Tichý, Ph.D.
RG: Core Facility Genomics

16. Regulation of BCR signalling by DNA damage response and P53 protein
Supervisor: assoc. prof. Marek Mráz
RG: Marek Mráz Research Group

17. Search for new regulators of intracellular trafficking in plants
Supervisor: Tomasz Nodzynski, Ph.D.
RG: Tomasz Nodzynski Research Group

18. Structural and functional analysis of cytokinin-regulated DIRIGENT proteins from Arabidopsis thaliana
Supervisor: Blanka Pekárová, Ph.D.
RG: Jan Hejátko Research Group

19. Structure, function and evolution of plant telomere components
Supervisor: prof. Jiří Fajkus
RG: Jiří Fajkus Research Group

20. Syntetic biology in unicellular green algea
Supervisor: Karel Říha, Ph.D.
RG: Karel Říha Research Group

21. Plant signaling at the crossroads of biotic and abiotic interactions
Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.
RG: Břetislav Brzobohatý Research Group

22. Cold-light interaction in Arabidopsis cold acclimation: ontogenic and phyllotactic perspective
Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.
RG: Břetislav Brzobohatý Research Group

23. The impact of changing environmental conditions on seed germination and early plant development: Omics analyses
Supervisor : prof. RNDr. Břetislav Brzobohatý, CSc.
RG: Břetislav Brzobohatý Research Group

24. Metabolic regulation of chromatin modifications and gene expression
Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.
RG: Břetislav Brzobohatý Research Group

25. Abscisic acid – cytokinin crosstalk in regulation of plant development
Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.
RG: Břetislav Brzobohatý Research Group


Structural Biology


1. A structural basis for the cross-talk between histones and RNA Polymerase II
Supervisor:  assoc. prof. Richard Štefl
RG: Richard Štefl Research Group
2.  Characterizing sequence-structure-function relationships: A multi-dimensional approach for evaluating similarity in structural biology data
Supervisor: prof. Jaroslav Koča
RG: Jaroslav Koča Research Group
3. Cracking the CTD code
Supervisor: assoc. prof. Richard Štefl
RG: Richard Štefl Research Group
4. Designing modified DNA fragments
Supervisor: prof. Radek Marek
RG: Radek Marek Research Group
5. Experimental and Theoretical Studies of the Origin of Life on the Earth
Supervisor: prof. Jiří Šponer
RG: Jiří Šponer Research Group
6. Impact of 14-3-3 protein on the formation of protein aggregates involved in neurodegenerative diseases
Supervisor: Jozef Hritz, Ph.D.
RG: Lukáš Žídek Research Group

7. Influence of membrane properties on peptide conformations
Supervisor: assoc. prof. Robert Vácha
RG: Robert Vácha Research Group

8. Integrative structural biology of 3’UTRs
Supervisor: Peter Lukavsky, Dr. rer. nat.
RG: Peter Lukavsky Research Group

9. Interaction of selected phosphor-peptides and organic molecules with 14-3-3 proteins
Supervisor: Jozef Hritz, Ph.D.
RG: Lukáš Žídek Research Group

10.Interactions underlying physiological function of Microtubule Associated Protein 2c
Supervisor : prof. Lukáš Žídek
RG : Lukáš Žídek Research Group

11. Multiscale Modeling of Nucleic Acids
Supervisor: prof. Jiří Šponer
RG: Jiří Šponer Research Group

12. New methods in NMR structure determination to facilitate structural studies of macromolecular complexes
Supervisor: Konstantinos Tripsianes, Ph.D.
RG: Konstantinos Tripsianes Research Group

13. Protein sensitivity of membrane curvature
Supervisor: assoc. prof. Robert Vácha
RG: Robert Vácha Research Group

14. Regulation of protein-protein itneractions
Supervisor : assoc. prof. Robert Vácha
RG : Robert Vácha Research Group

15. Structural basis of function of receiver domains of plant hybrid histidine kinases
Supervisor: prof. Lukáš Žídek
RG: Lukáš Žídek Research Group

16. Structural and time-resolved studies of phage replication in bacterial biofilm
Supervisor: Pavel Plevka, Ph.D.
RG: Pavel Plevka Research Group

17. Structural changes of the selected protein fibrils induced by phosphorylation and the interaction with 14-3-3 proteins
Supervisor: Jozef Hritz, Ph.D.
RG: Lukáš Žídek Research Group

18. Structural characterization of nucleic acid modifying enzymes
Supervisor: prof. Mary Anne O'Connell
RG: ERA Chair - Mary O'Connell Research Group

19. Structural study of enterovirus replication in vivo
Supervisor: Pavel Plevka, Ph.D.
RG: Pavel Plevka Research Group

20. Structure of parallel forms of nucleic acids studied by NMR spectroscopy and molecular modelling
Supervisor: prof. Radek Marek
RG: Radek Marek Research Group

21. Structure, dynamics and interactions of subunits of RNA polymerase of Gram-positive bacteria
Supervisor: prof. Lukáš Žídek
RG: Lukáš Žídek Research Group

22. Structural biology of ion channels
Supervisor: prof. Jaroslav Koča

RG: Jaroslav Koča Research Group

23. Structure-functional study of proteins involved in host cell recognition
Supervisor : prof. RNDr. Michaela Wimmerová, Ph.D.
RG : Michaela Wimmerová Research Group