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Probing natural molecules with PPAR- to reveal potent agonist against Cancer
Špaková, Adriána ; Bhogal, Inderjeet (oponent) ; Roy, Sudeep (vedoucí práce)
The work focuses on searching for a natural molecule with potential agonistic properties against cancer. The aim of the work was primarily to understand the connection between the peroxisome proliferator-activated receptor gamma (PPAR-) and cancer. Subsequently, molecules from six databases were virtually screened and docked to nuclear receptor PPAR- by using computer aided drug design approach. Hits underwent further exploration, including a dynamic simulation and binding free energy study. Safety verification of the best molecules was performed by ADMET prediction models. An important part of the work was the comparison of newly discovered molecules possessing agonistic properties against cancer with those already known on the market. Specifically, Troglitazone and Rosiglitazone have served as standards, characterized by their high affinity to the PPAR- receptor and demonstrated antineoplastic effects in various human malignant tumors, including breast, colorectal, and pancreatic cancer. On the other hand, these two synthetic molecules face a warning from the FDA (Food and Drug Administration) due to their adverse side effects. Within the study, natural molecules with better properties than the current standards have been discovered. These promising results deserve further attention. One of these molecules could potentially lead to the development of a new drug.
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Bioinformatic analysis of single nucleotide polymorphisms in the 1000 Genomes Project database
Parobková, Viktória ; Roy, Sudeep (oponent) ; Provazník, Ivo (vedoucí práce)
The whole-Genome sequencing and its variations discovery were challenging for many years. The knowledge of all genetic variations is remarkably beneficial in disease research. The bachelor thesis is dedicated to human genetic variations and its two main research projects, the HapMap Project and the 1000 Genomes Project which notably helped the disease analyses. The first part describes both Projects and the following part explains the structure of their databases and presents software which enables to browse and download data from these projects. At last, statistical, population and bioinformatic analyses are performed on structural variant dataset assembled by the 1000 Genomes Project.
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Genetic variations in coronary artery disease
Kocmanová, Klára ; Roy, Sudeep (oponent) ; Provazník, Ivo (vedoucí práce)
This bachelor’s thesis deals with the genetics of coronary artery disease. Studying risk variants helps us identify risk patients and allows us to develop targeted medicine. The first chapter deals with the anatomy, histology, and pathophysiology of CAD. The second chapter focuses on the current knowledge of the genetics of coronary artery disease. The third chapter mentions two genomic projects that have contributed to studying variations in coronary artery disease and the means of reading data from their databases. These projects are the 1000 Genomes Project and CARDIoGRAM plus CD4 consortium. 1000 Genomes-based linkage disequilibrium reference panel was obtained. The selection operator for jointly analyzing multiple variants was applied to the loci discovered in 1000 Genomes-based genome-wide association meta-analysis performed by CARDIoGRAM plus CD4 consortium.
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Genetic variations in coronary artery disease
Kocmanová, Klára ; Roy, Sudeep (oponent) ; Provazník, Ivo (vedoucí práce)
This bachelor’s thesis deals with the genetics of coronary artery disease. Studying risk variants helps us identify risk patients and allows us to develop targeted medicine. The first chapter deals with the anatomy, histology, and pathophysiology of CAD. The second chapter focuses on the current knowledge of the genetics of coronary artery disease. The third chapter mentions two genomic projects that have contributed to studying variations in coronary artery disease and the means of reading data from their databases. These projects are the 1000 Genomes Project and CARDIoGRAM plus CD4 consortium. 1000 Genomes-based linkage disequilibrium reference panel was obtained. The selection operator for jointly analyzing multiple variants was applied to the loci discovered in 1000 Genomes-based genome-wide association meta-analysis performed by CARDIoGRAM plus CD4 consortium.
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Bioinformatic analysis of single nucleotide polymorphisms in the 1000 Genomes Project database
Parobková, Viktória ; Roy, Sudeep (oponent) ; Provazník, Ivo (vedoucí práce)
The whole-Genome sequencing and its variations discovery were challenging for many years. The knowledge of all genetic variations is remarkably beneficial in disease research. The bachelor thesis is dedicated to human genetic variations and its two main research projects, the HapMap Project and the 1000 Genomes Project which notably helped the disease analyses. The first part describes both Projects and the following part explains the structure of their databases and presents software which enables to browse and download data from these projects. At last, statistical, population and bioinformatic analyses are performed on structural variant dataset assembled by the 1000 Genomes Project.
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