Projects
Dissecting tissue spatial organization using machine learning and spatial transcriptomics Ghent University
In this project, we aim to better functionally characterize different spatial contexts within tissues. To this end we will develop novel bioinformatics pipelines to process and integrate several “omics” and imaging data types. Novel machine learning methods will be explored that aim to combine the high spatial resolution of imaging techniques with the deep phenotyping capabilities of current scRNAseq methods.
Identifying virulence-associated genes in the head blight pathogen Fusarium poae via a comparative pathogenomics and transcriptomics approach Ghent University
This project proposal uses the high quality genome assembly of F. poae in a comparative pathogenomics and transcriptomics study with the aggressive pathogen F. graminearum and the cryptic pathogen F. langsethiae. The goal of this project is to get insight in the role of secondary metabolites, virulence- and effector genes in the cryptic pathogenesis of the ubiquitous pathogen F. poae.
Mining the Musa biodiversity for drought tolerance: allele discovery via integrated phenomics, proteomics and transcriptomics KU Leuven
Banana (Musa spp.) is one of the most produced fruits in the world, the production exceeded 122 million tons in 2013. For optimal production the crop requires: 1200–2690 mm water/year, depending on the agro-ecological zone. The limited genetic diversity in commercial plantations renders the crop extremely vulnerable for (a)biotic stress, like drought. However, worldwide a huge (uncharacterized) biodiversity is available, and we ...
A transcriptomics based kinetic model of pectin modifications in relation to apple softening. KU Leuven
Enzyme-induced pectin modifications are thought to be the main cause of softening in apples. To understand the molecular basis of softening, we characterized the cell wall pectin of apples during storage, and correlated changes in pectin molecular with the activities of four key enzymes that are thought to be implicated in pectin modifications during softening. Currently, we are looking at ...
Differential transcriptomics in the regulation of digestion and uptake of protease inhibitors in the desert locust, Schistocerca gregaria KU Leuven
Insects are among the most successful organisms on the planet. One explanation for their success is their extraordinary ability to successfully consume a wide range of foods. Like all heterotrophic organisms, insects need to acquire vital nutrients from their diet. The central organ for food digestion and absorption of nutrients is the gastrointestinal tract. This organ’s principal functions are to mediate the efficient digestion of food and ...
Venomics and transcriptomics of Conus spp.: an untapped treasure for drug discovery. KU Leuven
Combined dual transcriptomic, proteomic and functional investigations to reveal host-pathogen interactions behind the virulence of foodborne pathogen Bacillus cereus Ghent University
A toxin-mediated infection of foodborne Bacillus cereus requires direct contact of viable B. cereus with its host for in-situ production of diarrheal enterotoxins. This direct contact leads to a cross-talk between a pathogen and its host. The interaction will be investigated by functional, cytotoxic and
transcriptomic approaches, using tools such as Seahorse flux analysis, RNAseq, microarrays, RTPCR, ELISA and mass-spectrometry.