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.Development of bioinformatics methods for data integration from various diagnostic types in clinical oncology

Supervisor: Vojtěch ‚Bystrý, Ph.D.                                         

Consultant: Panagiotis Alexiou, Ph.D.

RG: Bioinformatics Core Facility

Keywords: bioinformatics, next generation sequencing, data integration, oncology, personalized medicine


4. 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


5.Elucidation of novel therapy targets for B-cell malignancies

Supervisor: Michal Šmída, Ph.D.

RG: Michal Šmída Research Group

Keywords: B-cell malignancies; targeted therapy; CRISPR/Cas9; resistance mechanisms


6. 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


7. 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


8. Long non-coding RNAs (lncRNAs) in the pathogenesis of B cell lymphomas

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Keywords: Follicular lymphoma, FL, blood cancer, non-Hodgkin lymphoma, B-cell lymphoma, non-coding RNAs, microRNAs, Next Generation Sequencing, NGS, Illumina, genome editing,Crispr, leukemia, DLBCL


9. 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


10.Migration of malignant B cells and their adaptive response to BCR inhibitor therapy

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Keywords: chronic lymphocytic leukemia, CLL, FCR therapy, NGS technology, BCR signaling inhibitors, genome editing


11.Non-coding RNAs (microRNAS/lncRNAS) and microenvironmental interactions of malignant B-cells

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Keywords: B-cell receptor signaling, BCR, leukemia, lymphoma, B cell malignancies, miRNAs, lncRNAs, mRNAs, NGS data analysis, genome editing, Crispr


12. 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


13.Role of phosphorylated 14-3-3 proteins 

Supervisor: Jozef Hritz, Ph.D.                                                  

Consultant:  prof. Vítězslav Bryja

RG: Lukáš Žídek Research Group

Keywords: Biophysical Chemistry, neurodegenerative diseases, phosphorylation state, 14-3-3 proteins, NMR, ITC, fluorescence


14. 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


15. 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


 16. 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



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.Are Tau fibrils induced by phosphorylation and the interaction with 14-3-3 proteins relevant for Alzheimer disease?

Supervisor: Jozef Hritz, Ph.D.                                                

Consultants: Jiří Nováček, Ph.D.; Jan Přibyl, Ph.D.

RG: Lukáš Žídek Research Group

Keywords: neurodegenerative diseases, Alzheimer disease, protein fibrils, phosphorylation state, 14-3-3 proteins, cryoEM tomography


3. 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


4.Designing modified DNA fragments

Supervisor: prof. Radek Marek

RG: Radek Marek Research Group

Keywords: modified DNA quadruplexes, NMR spectroscopy, structure and biophysical properties


5.Experimental and Theoretical Studies of the Origin of Life on the Earth

Supervisor: prof. Jiří Šponer

Consultants: Judit Šponerová, PhD.

RG: Jiří Šponer Research Group

Keywords: oligonucleotide sequences, quantum chemistry and molecular dynamics simulations, laboratory simulations, prebiotic synthesis, origin of life, abiogenesis of RNA, catalytic activity of RNA


6. 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


7.Interactions underlying physiological function of Microtubule Associated Protein 2c

Supervisor: prof. Lukáš Žídek

Consultants: Jozef Hritz, Ph.D.

RG: Lukáš Žídek Research Group

Keywords: Microtubule Associated Protein 2c, MAP2c, NMR spectroscopy, cryo-electron tomography, 14-3-3 protein


8.Multiscale Modeling of Nucleic Acids

Supervisor: prof. Jiří Šponer

Consultants: prof. Michal Otyepka, Dr. Miroslav Krepl, Dr. Vojtěch Mlýnský

RG: Jiří Šponer Research Group

Keywords: nucleic acids, structural dynamics, multiscale modeling, quantum chemistry, molecular dynamics simulations, protein-RNA complexes, RNA catalysis, quadruplex DNA


9.Protein motif for bacterial affinity

Supervisor: assoc. prof. Robert Vácha

RG: Robert Vácha Research Group

Keywords: membrane parameterizations, antibiotic, peptide affinity, peptide motives, membrane parameterizations, molecular dynamics simulations


10. 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


11. 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


12.RNA as a drug target

Supervisor: Peter Lukavsky, Dr. rer. nat.

RG: Peter Lukavsky Research Group

Keywords: targeting non-coding mRNA, gene expression, neurodegenerative diseases, cancer, mRNA motifs, cryo EM, NMR spectroscopy


13. 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


14. 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


15. 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


16.Structure of parallel forms of nucleic acids studied by NMR spectroscopy and molecular modelling

Supervisor: prof. Radek Marek

Consultant: Jan Novotný, Ph.D.

RG: Radek Marek Research Group

Keywords: oligonucleotides, MD simulations, molecular modelling, NMR spectroscopy


17.Structure, dynamics and interactions of bacterial RNA polymerase subunits and sigma factors

Supervisor: prof. Lukáš Žídek

RG: Lukáš Žídek Research Group

Keywords: RNA polymerase, transcription, bacteria, nuclear magnetic resonance


18.Structure-functional study of proteins involved in host cell recognition

Supervisor: prof. Michaela Wimmerová

RG: Michaela Wimmerová Research Group

Keywords: lectins, pathogens, X-ray crystallography, biomolecular interactions, tissue specific glycosylation


19.Tau conformational changes induced by phosphorylation and 14-3-3 proteins relevant in neurodegenerative diseases

Supervisor: Jozef Hritz, Ph.D.                                                

Consultant: prof. Lukas Žídek, Ph.D.

RG: Lukáš Žídek Research Group

Keywords: Molecular Biophysics, tau protein, phosphorylation, 14-3-3 proteins, neurodegenerative diseases, NMR, computational simulations


Molecular Medicine


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. Elucidation of novel therapy targets for B-cell malignancies

Supervisor: Michal Šmída, Ph.D.

RG: Michal Šmída Research Group

Keywords: B-cell malignancies; targeted therapy; CRISPR/Cas9; resistance mechanisms


3. 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



4.Microenvironmental interactions and non-coding RNAs in the biology of B cell leukemia

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Keywords: cFollicular lymphoma, FL, blood cancer, non-Hodgkin lymphoma, B-cell lymphoma, non-coding RNAs, microRNAs, Next Generation Sequencing, NGS, Illumina, genome editing, Crispr, DLBCL, chronic lymphocytic leukemia, CLL, FCR, BCR signaling inhibitors


 5. 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