Title: "Impact of 2D sampling on the characterization of cellular structures in tissues"

In my master’s thesis, I studied how standard two-dimensional sampling in tissue imaging can bias the characterization of cellular spatial organization. Using multiplexed 3D imaging datasets from various tissues and organisms, I developed a computational pipeline to preprocess, cluster, and annotate millions of cells, and applied spatial statistics such as the Clark–Evans index and pair correlation function. By comparing full 3D data to simulated 2D dissections, I found that while 2D sampling efficiently recovers cell-type diversity, it systematically misestimates both short- and long-range cell–cell interaction patterns, especially in anisotropic structures. I further validated these findings with geometric models and biological simulations of nodular and vascular tissues. This work not only highlights a fundamental limitation of current spatial omics workflows but also lays the groundwork for developing tools to correct spatial bias in biomedical imaging analysis.

Key words: statistics, transcriptomics, mathematics, machine learning

Title: "Modification of HoxD locus spatial structure by recruiting a truncated form of CTCF protein"

In my undergraduate project I was working on the problem of pathologies associated with abnormalities in the 3D genome. Using the HoxD locus as a model system we were trying to alter the local genome topology by dCas9-mediated recruitment of a truncated form of CTCF to the specific positions in the locus. Based on the contact heatmaps from Hi-C experiments, we showed the appearance of new loops and even the formation of a new topologically associated domain in the loci where our epigenetic construction was applied. The effect was in accordance with changes in the ChiP-seq profile. These results are promising and valuable not only in terms of fundamental science but also for medical applications. The ability to manipulate 3D architecture of the genome can potentially be used in the future to cure certain diseases, like certain types of cancer.

Key words: molecular biology, epigenetics, 3D genome

Title: "Phylogenetic and Domain Analysis of Thg1-like Proteins from Bacteria"

In this project, I performed a phylogenetic and domain analysis of Thg1-like proteins across bacteria, and additionally archaea and viruses. I reconstructed 3D protein structure, marked conserved domains and active site residues critical for magnesium coordination and GTP binding. Through phylogenetic tree construction and sequence alignment, I explored evolutionary relationships and sequence variability within active sites, aiming to understand potential horizontal gene transfer events and identify diverse protein variants for future studies.

Key words: phylogenetics, protein analysis, domain structure, Thg1