Developing reproducible and efficient computational tools for modeling and analysis of dynamic multi-level 3D genome
2024
Rossini, Roberto
Characterizing the genomes of living organisms increasingly involves extensive use of computational tools for data processing and analysis. During my PhD, I have developed and utilized computational tools to improve our understanding of how genomes are organized in three dimensions (3D). During my PhD, I developed MoDLE, a rapid computational tool that simulates a process known as DNA loop extrusion, a crucial biochemical process playing a key role in organizing the genome, regulating gene expression, and repairing DNA. Further, I developed hictk, a toolkit to efficiently process 3D genome mapping data such as Hi-C, enabling researchers to operate on multiple file formats, something that was not previously possible. Finally, in the last part of my PhD, I studied how the 3D genome is disorganized in breast cancer cells. From our analyses, we uncovered that the 3D genome organization is compromised during breast cancer progression, revealing a multi-level genome disorganization that disrupts oncogene regulation, potentially driving breast cancer progression. Taken together, my work highlights the importance of high-quality and high-performance computational tools, as these are crucial to characterizing biological processes such as the progression of cancer.
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