Projects
The regulatory effect of 3D chromatin organization on genes resistant to reprogramming KU Leuven
To understand how cells in our body resist changes in gene expression would be instrumental for better understanding the causes of diseases and designing improved treatments. We have recently identified a possible link between resistance to transcriptional reprogramming and 3D chromatin organization. We hypothesize that genes with low resistance to transcriptional reprogramming occupy accessible 3D positions in the nucleus, while more ...
Transcriptional and epigenomic logic of X chromosome reactivation during factor-induced pluripotency. KU Leuven
In this thesis, I aimed to define the dynamics and the mechanisms that orchestrate the reversal of stable gene silencing during reprogramming of somatic cells into induced pluripotent stem cells (iPSCs). I used X chromosome reactivation as a paradigm to better understand the reversal of silent chromatin. In addition, my goal was also to define the gene regulatory logic of mammalian pre- implantation development and reprogramming, as well as ...
Understanding Early Human Development Using Novel Single-Cell Technologies and Stem-Cell Based Embryo Models KU Leuven
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 ...
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, ...
Early detection of Alzheimer's disease with causal generative AI University of Antwerp
Characterization of iron-chromatin dependent epigenetic regulation of ferroptosis therapy response in multiple myeloma. University of Antwerp
Drosophila allograft screen to identify cis-regulatory variation in cancer genomes. KU Leuven
Title: Dissecting the interplay of chromatin accessibility and enhancer activity
Transcriptional enhancers function as docking platforms for combinations of transcription factors to control gene expression. However, it is not clear how the sequence of an enhancer determines nucleosome occupancy, transcription factor recruitment, and transcriptional activation in vivo. Using ATAC-seq across a panel of Drosophila inbred ...
Exploiting enhancer logic and transcriptional networks to control phenotype switching in melanoma KU Leuven
Enhancers are regulatory genomic regions that play an important role in gene regulatory networks. Through the binding of sequence-specific transcription factors, enhancers cooperatively regulate the expression of their target genes and, ultimately, a cell’s phenotype. Melanoma is one of the most dangerous and difficult to treat human cancers. Both cellular heterogeneity and plasticity of melanoma cell states are thought to contribute to its ...