PhD defense - Melanie Nijs
Non-negative Matrix Factorization for the Analysis of Mass Spectrometry Imaging Data - with applications to other omics modalities
Start: 5/07/2024, 14:00
Location: Aula van de Tweede Hoofdwet
Abstract
Molecular biology delves into how DNA controls cell functions, aiming to understand complex processes at a molecular level. Thanks to recent technological advances, we can now study biomolecules like DNA, RNA, proteins, and metabolites on a large scale using "omics" technologies. These advances have led to significant improvements in diagnostics, treatments, genetically modified organisms, and personalized medicine. "Omics" refers to fields such as genomics (DNA), transcriptomics (RNA), proteomics (proteins), and metabolomics (metabolites). Each generates vast amounts of data that require sophisticated analysis tools. This thesis focuses on three advanced techniques—mass spectrometry imaging (MSI), multiplexed immunohistochemistry (mIHC), and chromatin conformation capture (3C)—and addresses the challenge of analyzing these complex data sets. To simplify and interpret these data, we utilized non-negative matrix factorization (NMF), which breaks down large data sets into smaller, understandable components. In MSI, used to study proteins and metabolites in tissues, we found that NMF methods considering Poisson noise performed best. We also employed a visualization tool to reveal detailed structures in mouse pancreas data and developed a hierarchical NMF approach to uncover subtle signals. For the analysis of mIHC data, which measures protein markers with high spatial resolution, we created a pipeline combining NMF with machine learning to analyze melanoma and kidney samples more efficiently. Finally, for chromatin structure analysis in mouse brain cells, we used NMF to identify crucial chromatin contacts linked to specific cell types, despite noisy data.
Overall, this research demonstrates how advanced computational methods like NMF can extract valuable insights from complex biological data, enhancing our understanding of molecular biology.
URL: https://www.kuleuven.be/doctoraatsverdediging/fiches/3E22/3E220098.htm
PDF: PDF
Organized by: Melanie Nijs