Current doctoral students

Narendran Annadurai

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Supervisor: Das Viswanath M.Sc., Ph.D.
Status: Ongoing
Specialization:

Tau aggregation inhibitors in the treatment of neurodegenerative diseases Understanding the mechanisms of tau aggregation, propagation and cellular machinery involved in aggregated tau degradation would help in identifying therapeutic targets for tauopathies (Alzheimer’s disease, PSP, CTE, FTLD, etc.) and other neurodegenerative diseases. The thesis is focused on studying tau aggregate spreading mechanisms, identifying small molecule inhibitors of tau misfolding and aggregation using in vitro aggregation assays, cell and molecular biology, biochemistry and microscopy techniques. I am also working on the validation of small molecules (selected from in vitro MARK4 kinase activity inhibition assay) on inhibiting microtubule affinity regulating kinase 4 (MARK4) mediated tau phosphorylation using a cell line model.

Jan Bachořík

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Supervisor: Urban Milan Ph.D.
Status: Ongoing
Specialization:

Preparation of semisynthetic triterpenes -

Zuzana Barbuščáková

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Supervisor: Hlaváč Jan Ph.D.
Status: Ongoing
Specialization:

Molecular system for multiple detection of enzymes inside the cell -

Kateřina Bendová

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Supervisor: Petřík Miloš Ph.D.
Status: Ongoing
Specialization:

Multimodal imaging for in vivo testing of selected biomolecules -

Ondřej Bouška

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Supervisor: Koudeláková Vladimíra PhD.
Status: Ongoing
Specialization:

miRNA as a triage test in HPV-positive patients -

Tereza Buchtová

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Supervisor: Mistrík Martin Ph.D.
Status: Ongoing
Specialization:

Proteotoxic stress -

Zdeněk Dostál

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Supervisor: Modrianský Martin Ph.D.
Status: Ongoing
Specialization:

Modulation of expression of microRNAs flavonoids -

Dominika Flašarová

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Supervisor: Mohelníková Duchoňová Beatrice M.D., Ph.D.
Status: Ongoing
Specialization:

Effect and toxicity of HIPEC -

Mária Gamratová

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Supervisor: Brychtová Světlana M.D., Ph.D.
Status: Ongoing
Specialization: Pathological anatomy and forensic medicine

The role of cancer microenvironment in prognosis of Hodgkin lymfomas -

Veronika Grešáková

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Supervisor:
Status: Ongoing
Specialization:

Functional characterization of FAM208a -

Anahit Hakobjanyan

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Supervisor: Petřek Martin M.D., CSc.
Status: Ongoing
Specialization:

Expression and regulation of cytokines or signaling molecules at the interface of bone and joint replacement: a contribution to the immunopathogenesis osteolysis/ periprosthetic infection -

Jiří Hodoň

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Supervisor: Urban Milan Ph.D.
Status: Ongoing
Specialization:

Cytotoxic active triterpenes and their mechanism of action -

Denisa Hrčková Drozdková

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Supervisor: Smešný Trtková Kateřina Ph.D.
Status: Ongoing
Specialization: Medical biology

Effect of histone deacetylase inhibitors on apoptosis and proliferative activity of cancer cells -

Zlata Hušková

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Supervisor: Steigerová Jana Ph.D.
Status: Ongoing
Specialization:

Molecular mechanisms of action of plant steroids on tumor cells -

Alžběta Chabroňová

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Supervisor: Navrátilová Zdenka Ph.D.
Status: Ongoing
Specialization: Physiology and pathophysiology

Exosomal miRNAs in chronic obstructive lung disease This study will be focused on identifying mechanisms of post-transcriptional regulation in COPD pathogenesis by measuring expression of selected miRNAs and determining differentially expressed miRNAs in patients vs controls.

Jaroslava Jáčová

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Supervisor: Adam Tomáš Ph.D.
Status: Ongoing
Specialization:

Metabolomic GC×GC-TOF MS analysis of biofluids The thesis is focused on metabolomic analysis of biofluids, using comprehesnive two-dimensional gas chromatography coupled with time of flight mass spectrometry (GC×GC-TOF MS). The optimal column combination suitable for given biofluid has been evaluated, GC×GC TOF-MS analysis has been optimized, separation efficiency has been determined, data processing method has been developed.

Jana Jiravová

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Supervisor: Bartoň Tománková Kateřina Ph.D.
Status: Ongoing
Specialization:

The study of nanomaterials using modern microscopic techniques The thesis is focused on the characterisation of nanoparticles properties and detection effect of nanoparticles on biological systems included tumor and non-tumor cell lines. For detection of nanoparticles are used modern microscopic techniques (e.g. atomic force microscopy, Raman spectroscopy, confocal and electron microscopy). Nanoparticles are massively used in daily life, so it is important to know their properties.

Jana Juráňová

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Supervisor:
Status: Ongoing
Specialization:

The mechanism of wound healing -

Barbora Koblihová

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Supervisor: Slavkovský Rastislav Ph.D.
Status: Ongoing
Specialization:

Genetic biomarkers of tumors and aging Clonal hematopoiesis of indeterminate potential (CHIP) has recently been described as an age-related condition manifested by the accumulation of somatic mutations in cells of the hematopoietic system. Although this condition is not accompanied by any morphological features of hematological neoplasia, the incidence of CHIP correlates with increased overall mortality and the risk of developing malignant transformation of hematopoietic cells, as well as cardiovascular disease. The investigation of possible links between CHIP, aging, and ischemic stroke is the main aim of this study. We will use various techniques, including FACS, MACS, and advanced deep sequencing allowing highly sensitive detection of mutations in samples of stroke patients. The analysis of immune cells in the blood and also cells in atherosclerotic plaques will be of special interest.

Lenka Kocourková

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Supervisor: Smešný Trtková Kateřina Ph.D.
Status: Ongoing
Specialization:

Effect of coregulators on the androgen receptor activity in cells derived from prostate cancer after their treatment with histone deacetylase inhibitor The thesis is focused on the detection of coregulator expressions in cancer and normal prostate cells. Coregulators, coactivators as well as coregulators, play an important role in androgen receptor-mediated progression of the prostate cancer. There is a competition between coactivators and corepressors for binding on the androgen receptor and therefore, the changes and the expression ratio between could be important for prostate cancer growth and progression. We focus on two regulators: SMRT (silencing mediator for retinoid and thyroid hormone receptors) as corepressor, and p300 as coactivator.

Kateřina Kolářová

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Supervisor: Mohelníková Duchoňová Beatrice M.D., Ph.D.
Status: Ongoing
Specialization:

Biomarkers of the risk of developing, effect and toxicity of treatment in gastrointestinal malignancies -

Markéta Kolečková

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Supervisor: Kolář Zdeněk M.D., CSc.
Status: Ongoing
Specialization:

New diagnostic biomarkers and tumor progression -

Lucie Kotková

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Supervisor: Drábek Jiří Ph.D.
Status: Ongoing
Specialization:

Genetic and Epigenetic Biomarkers in cancer -

Jana Kotulová

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Supervisor: Džubák Petr M.D., Ph.D.
Status: Ongoing
Specialization:

Adenosine receptor inhibitors, the development and optimization Adenosine receptors are involved in several cellular processes and can play significant role in development of various diseases, including cancer. The aim of the thesis is to study the role of adenosine receptors in cell physiology as well as in pathological state. This work is focused on screening of potential ligands of adenosine receptors and characterization of their molecular interactions using high-throughput screening approach and further validation by methods of molecular biology. Novel potent inhibitors can be beneficial for cancer therapy in the future.

Stepan Kouril

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Supervisor: Friedecký David Ph.D.
Status: Ongoing
Specialization: Medical chemistry and clinical biochemistry

Lipidomic analysis of biological samples by HR-MS -

Leona Krátká

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Supervisor: Hlaváč Jan Ph.D.
Status: Ongoing
Specialization:

Stereoselective synthesis on solid support -

Patricia Kriegelsteinová

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Supervisor: Soural Miroslav Ph.D.
Status: Ongoing
Specialization:

Synthesis of benzothiadiazepines using solid-phase synthesis -

Agáta Kubíčková

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Supervisor: Hajdúch Marián M.D., Ph.D.
Status: Ongoing
Specialization: Oncology

Cellular models for optical screening of biologically active compounds -

Natálie Kudlová

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Supervisor: Hajdúch Marián M.D., Ph.D.
Status: Ongoing
Specialization:

High throughput sequencing methods in biomarker identification and validation High throughput sequencing is rapidly improving in its quality, speed and cost. This scientific approach increases our ability to characterise diseases at the genomic, transcriptomic and epigenetic levels. The aim of the thesis is to use this technique for studying cells under ribosomal stress. The work is focused on the identification and validation of biomarkers that are in connection with ribosomal stress caused diseases.

Alina Kutlushina

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Supervisor: Polishchuk Pavlo Ph.D., M.Sc.
Status: Ongoing
Specialization:

Development of 3D pharmacophore signatures and their application in drug design -

Radmila Lemstrová

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Supervisor: Mohelníková Duchoňová Beatrice M.D., Ph.D.
Status: Ongoing
Specialization:

Prognostic and predictive factors for pancreatic cancer -

Dávid Lukáč

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Supervisor: Moudrý Pavel Ph.D.
Status: Ongoing
Specialization:

DNA replication and cancer -

Petra Lužná

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Supervisor: Smešný Trtková Kateřina Ph.D.
Status: Ongoing
Specialization:

Methylation status in patients with multiple myeloma -

Zuzana Macečková

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Supervisor: Hajdúch Marián M.D., Ph.D.
Status: Ongoing
Specialization:

Molecular pathology of Diamond-Blackfan anemia Diamon-Blacfan anemia is a rare congenital red cell aplasia, often associated with congenital malformations, particularly of upper limbs and craniofacial region. As a cause, mutations in genes for ribosomal proteins have been reported in approximately 50% of the cases. Mutations in ribosomal proteins lead to defects during ribosome biogenesis and thus ribosome stress, which in turn leads to cell cycle arrest or apoptosis in erythroid progenitors.In my study, I focus on discovering and validation of new possible molecular causes of Diamond-Blackfan anemia and other ribosomopathies by NGS approach followed by functional studies of chosen genes.

Lucie Mádrová

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Supervisor: Adam Tomáš Ph.D.
Status: Ongoing
Specialization:

Study of the effect of selected cancerostatics on the cell metabolome The thesis is focused on the development of both targeted and untargeted metabolomics methods (liquid chromatography coupled with high resolution mass spectrometry) for the study of the effects of various anticancer drugs on model cell lines. The main goal is to quantitatively analyse changes in metabolome’s composition for the comprehensive characterization of metabolic networks.

Zuzana Malá

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Supervisor: Kolářová Hana Ph.D.
Status: Ongoing
Specialization:

Nanomaterials and the study of cell damage fluorescence methods The thesis is focused on the study of effect of various porphyrin and phtalocyanin photosensitizers during different light intensity on cell and bacterial lines using fluorescent, molecular and microscopis methods. Further the thesis is focused on the characterisation of nanoparticles properties combinated with photodynamic therapy.

Lukáš Malina

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Supervisor: Bartoň Tománková Kateřina Ph.D.
Status: Ongoing
Specialization:

Study of cell destruction using physical and chemical methods The thesis is focused on the study of effect of various porphyrin and phtalocyanin photosensitizers during different light intensity on G361 (human skin melanoma) and NIH3T3 (mouse fibroblasts) cell lines using fluorescent, molecular and microscopic methods. Main aim is on the dependence of photodynamic therapy on photosensitizer type, its concentration and light doses on tumorous and non-tumorous lines to choose best fitting photosensitizer.

Martina Matějková

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Supervisor: Džubák Petr M.D., Ph.D.
Status: Ongoing
Specialization: Oncology

Expression profiling effects of anticancer drugs -

Mariia Matveieva

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Supervisor: Polishchuk Pavlo Ph.D., M.Sc.
Status: Ongoing
Specialization: Pediatrics

Automatic mining of relationships between structure and activity in chemical databases The thesis is focused on the development of methods and tools for mining valuable structural features of compounds in chemical databases. Those methods are being developed with the main goal to explain observed structure-activity relationships and to design new molecules with improved properties.

Marcel Matzenauer

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Supervisor: Vrána David Ph.D.
Status: Ongoing
Specialization:

Evaluation of the effectiveness and toxicity of stereotactic radiotherapy -

Martina Medvedíková

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Supervisor: Mašek Vlastimil Ph.D.
Status: Ongoing
Specialization:

Study of interaction of biologically active small molecules with selected target macromolecules The thesis is focused on the study of the interaction potential anticancer drugs with target macromolecules (DNA, proteins). These interactions are analyzed using various methods, such as isothermal titration calorimetry, confocal Raman microscopy and molecular biology methods.

Alena Mičková

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Supervisor: Bouchal Jan Ph.D.
Status: Ongoing
Specialization:

Monitoring characteristics of tumor stem cells from prostate cancer -

Jaroslav Michálek

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Supervisor: Brychtová Světlana M.D., Ph.D.
Status: Ongoing
Specialization:

Molecular aspects of atherosclerosis (focusing on microRNA) -

Aleksandra Nikonenko

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Supervisor: Polishchuk Pavlo Ph.D., M.Sc.
Status: Ongoing
Specialization:

xxx -

Eva Novosadová

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Supervisor: Petřek Martin M.D., CSc.
Status: Ongoing
Specialization:

Role of RBPs (RNA- binding proteins) in regulation of immune reactions In this thesis will be studied RNA- binding proteins on their expression level. Further will be investigated their possible role of biomarkers in patients with inflammatory lung diseases.

Martin Ondra

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Supervisor: Hajdúch Marián M.D., Ph.D.
Status: Ongoing
Specialization:

Role of ribosomal proteins and ribosomal stress in case of DNA damage -

Róbert Ondruššek

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Supervisor: Brychtová Světlana M.D., Ph.D.
Status: Ongoing
Specialization: Pathological anatomy and forensic medicine

The role of cancer microenvironment in cancer prognosis -

Zuzana Pastorková

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Supervisor: Škarda Jozef M.D., Ph.D.
Status: Ongoing
Specialization:

Influence of microRNA to metastasis -

Martin Pola

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Supervisor: Bajgar Robert M.D., Ph.D.
Status: Ongoing
Specialization:

The role of oxygen in the effectiveness of photodynamic therapy on cellular models in the presence of sensitizers -

Julie Rendlová

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Supervisor: Hron Karel Ph.D.
Status: Ongoing
Specialization: Applied mathematics

Advanced methods of compositional data analysis -

Lenka Roubalová

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Supervisor: Vrba Jiří Ph.D.
Status: Ongoing
Specialization:

Molecular mechanisms of the protective effect of natural substances -

Patrik Rulíšek

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Supervisor: Überall Ivo Ph.D.
Status: Ongoing
Specialization: Pathological anatomy and forensic medicine

Computer image analysis in pathology -

Lenka Řeháčková

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Supervisor: Džubák Petr M.D., Ph.D.
Status: Ongoing
Specialization:

Mechanism of multidrug resistance (MDR) in cancer cells -

Alona Řehulková

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Supervisor: Srovnal Josef M.D., Ph.D.
Status: Ongoing
Specialization:

Prognostic and predictive factors in solid tumors Cancer cells can be released from primary tumors and transported through the body via blood or lymphatic vessels. These circulating tumor cells (CTCs) can settle and cause the formation of micrometastases in suitable conditions. Numerous studies have shown that CTCs have negative prognostic significance in several types of cancer. CTCs reflect current states of tumors, thus they can provide convenient biomarkers. Furthermore, assessment of their presence and status can facilitate understanding of tumor progression (and/or the development of clinical cancer dormancy), thereby greatly assisting prognostic considerations and therapeutic decisions. Diverse methods are available for detecting, isolating, and characterizing them, which differ in specificity, utility, costs, and sensitivity. We work with RT-qPCR and CytoTrack technology.

Jakub Schůrek

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Supervisor: Hajdúch Marián M.D., Ph.D.
Status: Ongoing
Specialization:

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Kateřina Sikorová

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Supervisor: Petřek Martin M.D., CSc.
Status: Ongoing
Specialization:

Genetic variability of bio markers of inflammation in patients with early manifestation of coronary artery disease -

Jan Skácel

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Supervisor: Mohelníková Duchoňová Beatrice M.D., Ph.D.
Status: Ongoing
Specialization:

Prognostic and predictive markers of ovarian cancer in relation to cytoreductive surgery and hyperthermic intraperitoneal chemotherapy -

Hanuš Slavík

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Supervisor: Srovnal Josef M.D., Ph.D.
Status: Ongoing
Specialization:

Minimal residual disease in solid cancers The main goal of this thesis is to discover new biomarkers on the level of RNA. These biomarkers can be tested for usage in predictive and prognostic medicine and they can help in early diagnostic or in postoperative identification of the risk of recurrence. The methods used for this purpose are RT-qRCR and microarray assays (cytoscan).

Martin Sněhota

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Supervisor: Vachutka Jaromír
Status: Ongoing
Specialization:

Objectification of quality of ultrasound imaging -

Martina Spisarová

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Supervisor: Melichar Bohuslav M.D., Ph.D.
Status: Ongoing
Specialization:

Infulence of chemotherpy and radiotherapy on the immune system -

Jarmila Stanková

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Supervisor: Džubák Petr M.D., Ph.D.
Status: Ongoing
Specialization:

Cytotoxic drugs molecular target identification by methods of cell biology and proteomics Molecular target identification of biologically active molecules is a key factor facilitating rational design and preclinical development of potential drugs. Methods of cellular biology, chemical proteomics and mass spectrometry are developed and used for its purposes.

Pavel Stejskal

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Supervisor: Srovnal Josef M.D., Ph.D.
Status: Ongoing
Specialization:

Circulating tumor cells detection -

Karolína Světlíková

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Supervisor: Petřková Jana Ph.D.
Status: Ongoing
Specialization:

Pathophysiology of selected internal diseases -

Veronika Šlachtová

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Supervisor: Brulíková Lucie Ph.D.
Status: Ongoing
Specialization: Organic chemistry

Design and synthesis of compounds with potential anti-TB properties -

Zuzana Šporiková

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Supervisor: Trojanec Radek Ph.D., MBA
Status: Ongoing
Specialization:

Cytogenetics changes in solid tumors The thesis is focused on the identification of molecular and genetic changes in solid tumors focusing on glial tumors especially on a group of recurrent glioblastoma. The main goal is to identify molecular and genetic aberrations which are responsible for glioblastoma progression and recurrence by comprehensive, complementary molecular genetic methods and high-throughput technologies.

Jan Václavík

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Supervisor: Adam Tomáš Ph.D.
Status: Ongoing
Specialization:

Metabolomic tools for diagnosis of inherited metabolic disorders Inherited metabolic disorders of purine and pyrimidine (PP) metabolism exhibit broad neurological, hematological, immunological and renal manifestations. They are characterized by increased concentrations of PP metabolites in body fluids caused by abnormal or missing activity of particular enzyme which is involved in their metabolism. Liquid chromatography coupled to tandem mass spectrometry (LC‐MS/MS) is method of choice in the last 15 years for diagnoses of PP metabolic disorders. Due to instrumental price drop high‐resolution mass spectrometry (HRMS) is starting to be increasingly used in clinical laboratories. The aim of this work is to compare diagnostic efficacy of these two approaches.

Jana Václavková

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Supervisor: Džubák Petr M.D., Ph.D.
Status: Ongoing
Specialization:

Identification of mechanisms of action of molecules with anticancer effect The thesis is focused on optimization of the method for identifying cellular targets of anticancer drugs. The aim of the work is to optimize affinity purification using streptavidin coated plates. Next the new drugs will be tested to find their molecular target and the validation studies will be performed.

Zuzana Valachová

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Supervisor: Vrána David Ph.D.
Status: Ongoing
Specialization:

Predictive and prognostic factors in breast cancer -

David Vanda

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Supervisor: Soural Miroslav Ph.D.
Status: Ongoing
Specialization:

Synthesis of heterocyclic compounds as ligands of serotonine receptors and phosphodiesterases -

Monika Vidlařová

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Supervisor: Srovnal Josef M.D., Ph.D.
Status: Ongoing
Specialization:

Detection and clinical importance of circulating tumor cells in solid tumours The thesis is focused on the detection of circulating tumour cells (CTCs) by different approaches and the clinical importance of their presence in solid tumours, especially in lung, pancreatic and colorectal cancer patients. The main goal is to identify patients with high risk of disease recurrence and in need of adjuvant therapy. The second goal is to participate in the research and development of novel methods of CTCs detection and characterization.

Dominik Vítek

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Supervisor: Voller Jiří Ph.D.
Status: Ongoing
Specialization:

Study of neurodegeneration and aging on model organisms -

Zuzana Vlachova

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Supervisor: Vrána David Ph.D.
Status: Ongoing
Specialization:

Prognostic and predictive factors of breast cancer -

Tomáš Zemánek

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Supervisor: Mohelníková Duchoňová Beatrice M.D., Ph.D.
Status: Ongoing
Specialization:

Prognostic and predictive markers of pancreatic carcinoma -

Ludmila Žárská

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Supervisor: Kolářová Hana Ph.D.
Status: Ongoing
Specialization:

Photodynamically active substances possibility of their use for photodynamic therapy of tumors The thesis is focused on the study of effect of various porphyrin and phtalocyanin photosensitizers during different light intensity on cell lines using molecular and microscopic methods.

Vladimír Židlík

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Supervisor: Brychtová Světlana M.D., Ph.D.
Status: Ongoing
Specialization: Pathological anatomy and forensic medicine

The role of cancer microenvironment in prognosis of malignant melanomas -

Patrícia Žižkovičová

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Supervisor: Hajdúch Marián M.D., Ph.D.
Status: Ongoing
Specialization:

Molecular and cellular changes in the process of aging Somatic mutations occur during aging in cells. Most of these mutations are harmless and passively accumulate in the human body. However, some somatic mutations obtained at the beginning of growth may cause developmental disorders and their accumulation is also responsible for the formation of cancer and may contribute to the aging process. As the sensitivity of methods for detection of low-frequency mutations has evolved, it is now possible to monitor the development of clonal mutations and to understand their occurrence in normal cells, respectively their connection with the development of the pathological state. The aim of the dissertation thesis is to monitor population aging and collection of acquired clonal mutations using deep whole exome sequencing and panel sequencing.