Projects
MAGE – Modelling of Allelic Gene Expression in health and disease. Ghent University
Studying expression of individual alleles could learn us more about possible molecular causes of diseases such as cancer, yet existing methods are too expensive or yield only incomplete information. In this project we will develop a novel, cheaper and more comprehensive methodology, based on population genetics concepts and statistical modelling, and demonstrate its relevance in a cancer case study.
High resolution examination of the topological and cell-type specific expression differences of an Alzheimer risk gene. University of Antwerp
Integration of long read genome sequencing and single-cell multi-omics to identify genetic variation underlying Parkinson’s disease KU Leuven
In recent years, there have been major developments in ’omics technologies. Long read sequencing now produces highly accurate reads from single molecules with theoretically unlimited length. Long reads enable us to assemble whole human genomes de novo, study complex genomic regions and large structural variants, all of which are particularly difficult through conventional short read technologies. It also allows us to directly study DNA ...
Cross-fertilization, self-fertilization and parthenocarpy in European pear (Pyrus communis) and their effects on fruit quality KU Leuven
Unpredictable fruit set and poor yield are important problems in commercial pear production worldwide and are often the result of a combination of self-incompatibility and poor (insect) pollination. The S-RNase dependent self-incompatibility mechanism in pear inhibits growth of genetically incompatible pollen tubes and thereby prevents fertilization and fruit set after self-pollination. In order to ensure adequate fruit set, growers may aim ...
Targeted treatment for KCNQ related encephalopathies: retigabine analogues, repurposed drugs and allele specific knock down (TREATKCNQ). University of Antwerp
EXPLORING THE CODE OF LIFE: FROM DECODING TO DESIGNING CELL TYPE-SPECIFIC ENHANCERS WITH DEEP LEARNING KU Leuven
Cellular identity, which is defined by the activity of certain genes, is provided by the transcriptional enhancer code combined with differential and combinatorial expression of transcription factors. This code plays a central role in the regulation of gene expression. To understand the functional impact of noncoding genome variation and to develop cell type-specific drivers, decoding the code of enhancers is essential. Here in this thesis, ...
The development of a cost-efficient eQTL scanning strategy to unravel the broad transcriptional response of a generalist pest to novel hosts. Ghent University
Finding genetic variants that explain transcriptional variation underlying phenotypes of interest is of major relevance for the biological sciences However, state-of-the-art methods to comprehensively scan for such expression - quantitative trait loci (eQTLs) throughout the genome are prohibitively expensive for common applications Here, we propose to develop a novel strategy that is based on statistically modelling allele-specific RNA-seq ...
Single-molecule multi-omics to study tumour heterogeneity and evolution KU Leuven
Cancer is a chiefly genetic disease, originating from the acquisition of somatic mutations in cells throughout our life. While most of these mutations are innocuous passengers, a handful unlock the typical hallmarks of cancer. The latter endow a cell with a fitness advantage relative to neighbouring cells, leading to a clonal outgrowth. Clonal expansions can be shaped by the evolutionary processes of selection and drift, which act on the ...
Study of yeast invertases for changing fructan levels in bread KU Leuven
Saccharomyces cerevisiae invertase (ScInv) is a β-fructofuranosidase encoded by different, closely related SUC genes and classified within the family 32 of glycoside hydrolases. ScInv prefers sucrose as a substrate but also hydrolyses raffinose, fructo-oligosaccharide (FOS) and short-chain fructans. Invertase produced by baker’s yeast plays and important role during breadmaking. It is responsible for setting free those sugars that yield most ...