Projects
Comparative genomics of pathogenic bacteria KU Leuven
Omics techniques and bioinformatics analyses have become an integral part of modern biological investigation. In this dissertation, we focus on their application to the field of microbiology, more
specifically to the domain of bacteria and their viruses (phages). The work presented can be broadly divided into three sections: i) the development of new bioinformatics methods made possible by the introduction of long read sequencing ...
Drought stress physiology of banana linked to a functional genomics approach. KU Leuven
Assessing the sensitivity of forest plant populations to climate change using microclimate modeling and landscape genomics KU Leuven
Climate change has been identified as one of the most important human-induced global drivers of biodiversity loss. Moreover, climate models predict increases in frequency, intensity, and duration of climate-related disturbances in the next few decades. One of the main consequences of climate change is that temperature isoclines move towards the poles with unprecedented speed, driving species out of parts of their current distribution range. ...
The evolutionary genomics of Lassa Virus virulence and persistence KU Leuven
Lassa virus (LASV) is an endemic virus in West Africa that infects hundreds of thousands of individuals each year. Humans primarily become infected through contact with rodents of the genus Mastomys that shed viruses in their urine and faeces. About 80% of people who become infected remain asymptomatic, but 1 in 5 LASV infections result in an acute viral haemorrhagic illness. No effective treatments or vaccines exist and little is known about ...
Deciphering the evolution of gene regulatory networks and enhancer architectures in neuronal cell types using single-cell deep learning and comparative genomics KU Leuven
Genomic enhancers are key players in gene regulatory networks (GRNs), underlying the differentiation of cell types. On the one hand, genomic regulatory blocks (GRBs) reflect conservation of enhancer-gene pairs for key developmental genes. On the other hand, rewiring of GRNs through the birth, erosion, and repurposing of enhancers is a key driver for evolution across mammals, including the emergence of the neocortex. Recent single cell ATACseq ...
Genomics and transcriptomics of auto-immune and autoinflammatory conditions KU Leuven
In this scientific research project we aim to help a group of patients with rare auto-immune and auto-inflamatory conditions by unravelling the pathogenic mutation underlying their disease. These patients may suffer from recurrent fevers, severe arthritis and generalized illness. We will do this by first implementing a screening assay which identifies a rare group of disorders, called interferonopathies. Second, patients identified in this ...
Deep-learning data fusion for patient screening and clustering from genomics liquid biopsies and its application for presymptomatic cancer detection and stratified medicine KU Leuven
My PhD research relates to the design of an Artificial Intelligence (AI) framework for learning complex relations between the DNA profile of a liquid biopsy (i.e., DNA extracted from a blood sample) and the diagnosis, prognosis, or relapse of a tumor. This AI framework will be able to continuously integrate information from DNA profiles from tens of thousands of liquid biopsies. In particular, it will allow building models for the early ...