Dissertation Topics - CALL SPRING 2022

CALL SPRING 2022

Life Sciences

1. Modelling binding specificities of RBPs using Artificial Neural Networks

Supervisor : Panagiotis Alexiou, PhD

RG : Panagiotis Alexiou Research Group

Keywords : Bioinformatics, RBP, Machine Learning, Deep Learning

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 : CDK12, transcription, mRNA processing, RNA polymerase II, cancer, genomics, proteomics, kinase inhibitors

3. Functions of cyclin-dependent kinase 11 (CDK11) in regulation of gene expression and tumorigenesis

Supervisor : Dalibor Blažek, Ph.D.

RG : Dalibor Blažek Research Group

Keywords : CDK11, transcription, mRNA processing, RNA polymerase II, cancer, genomics, proteomics, kinase inhibitors

4. Structural studies of various states of direct and bridged transcription-translation coupling in vitro and in vivo

Supervisor : Gabriel Demo, Ph.D.

RG : Gabriel Demo Research Group

Keywords : RNA polymerase, ribosome, coupling, structure, cryo-EM, cryo-ET

5. Designing modified DNA fragments

Supervisor: Prof. Radek Marek, Ph.D.

RG : Radek Marek Research Group

Keywords : DNA, base pairing, molecular modelling, quantum chemistry

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

Supervisor : Prof. Radek Marek, Ph.D.

RG : Radek Marek Research Group

Keywords: DNA, base pairing, NMR spectroscopy, molecular modelling

7. Subcellular trafficking in plant adaptation

Supervisor : Tomasz Nodzynski, Ph.D.

RG : Tomasz Nodzynski Research Group

Keywords: vesicular trafficking; intracellular localization; stress response; adaptation

8. The role of the intracellular environment in modulation of biomolecular structure, dynamics and interactions.

Supervisor : Lukáš Trantírek, Ph.D.

RG : Lukáš Trantírek Research Group

Keywords: protein/DNA; structure; dynamics; protein/DNA-drug interactions; (in-cell) NMR spectroscopy.

9. Basic principles of DNA quadruplex folding landscape studied by advanced simulations.

Supervisor :Prof. Dr. Jiří Šponer, D.Sc & Lukáš Trantírek, Ph.D.

RG : Lukáš Trantírek Research Group

Keywords:  G quadruplex, Molecular dynamics, DNA folding

​10. AFM Extension Modules to Study Cell Mechanics and Electrophysiology.

Supervisor : Jan Přibyl

CF : Jan Přibyl Core Facility

Keywords: Atomic Force Microscopy, Fluid FM, Multielectrode Array, biomechanics, cell cultures

11. Structural Biology of WNT Signalling.

Supervisor : Konstantinos Tripsianes, Ph.D.

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.

12. Role of protein disorder in bacterial transcription.

Supervisor : Prof. Lukáš Žídek, Ph.D.

RG : Lukáš Žídek Research Group

Keywords: bacterial RNA polymerase, intrinsically disordered proteins, nuclear magnetic resonance, cryo-electron microscopy

13. Characterization of components of cytokinin metabolism involved in shoot regeneration.

​Supervisor: Mgr. Markéta Pernisová, Ph.D.

CF : Markéta Pernisová CF

Keywords: in vitro regeneration, shoot, cytokinins, CRISPR/Cas, Arabidopsis, crops

14.  Lymphoid microenvironment models and their use to study targeted therapy and resistance in B cell malignancies

​Supervisor: doc. MUDr. Mgr. Marek Mráz, Ph.D.

RG:  Marek Mraz Research Group

Keywords:  in vitro regeneration, shoot, cytokinins, CRISPR/Cas, Arabidopsis, crops

15.  Regulation of cell migration in B cell leukemias and lymphomas

​Supervisor:  doc. MUDr. Mgr. Marek Mráz, Ph.D.

RG:  Marek Mraz Research Group

Keywords:  in vitro regeneration, shoot, cytokinins, CRISPR/Cas, Arabidopsis, crops

16.  RNA as a drug target

​Supervisor:  Mgr. PharmDr. Peter Lukavsky, Dr. rer. nat.

RG:  Peter Lukavsky Research Group

Keywords:  3'untranslated region; small molecule drugs; RNA as drug target; cancer; high-throughput screening; RNA-based pulldown; translational control; mRNA decay, RNA-protein interactions; NMR spectroscopy; structural biology

17. Antimicrobial peptides and the role of line tension.

Supervisor : doc. RNDr. Robert Vácha, Ph.D.

RG : Robert Vácha Research Group

Keywords: Antimicrobial peptides, membrane pore formation, molecular dynamics, free energy calculations

18. Antimicrobial peptides and the role of membrane asymmetry.

Supervisor : doc. RNDr. Robert Vácha, Ph.D.

RG : Robert Vácha Research Group

Keywords: Antimicrobial peptides, membrane pore formation, molecular dynamics, free energy calculations

Molecular Medicine

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

​Supervisor:  doc. MUDr. Mgr. Marek Mráz, Ph.D.

RG:  Marek Mraz Research Group

Keywords:  Long non-coding RNA, lymphomas, DLBCL, miRNA

2.  Prioritizing drug combinations in leukemia based on analysis of targetted therapy in vivo

​Supervisor:  Mgr. Miroslav Boudny, Ph.D.

​Consultant:  doc. MUDr. Mgr. Marek Mráz, Ph.D.

RG:  Marek Mraz Research Group

Keywords:  CLL, BCR signalling, therapy, BTK/PI3K inhibitors

3. 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 : CDK12, transcription, mRNA processing, RNA polymerase II, cancer, genomics, proteomics, kinase inhibitors

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

Supervisor : Dalibor Blažek, Ph.D.

RG : Dalibor Blažek Research Group

Keywords : CDK11, transcription, mRNA processing, RNA polymerase II, cancer, genomics, proteomics, kinase inhibitors