Thu Nguyen
Doctoral student – Lab for Computational Biology, Integromics and Gene Regulation (CBIGR) – Department of Biomedical Molecular Biology, Faculty of Sciences & Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, UGent
Principal investigator: prof. Vanessa Vermeirssen (PhD)
Research focus
Gene expression in human cells is tightly controlled by regulatory DNA elements such as enhancers and transcription factors. Enhancers can activate genes that are located far away along the genome by forming physical contacts through the three-dimensional folding of chromatin. These long-range enhancer–gene interactions play a crucial role in determining cell identity and controlling normal cellular functions. Disruptions in these regulatory mechanisms are increasingly recognized as an important driver of cancer development, including aggressive brain tumors such as glioblastoma. Understanding how distant regulatory elements control gene activity in cancer cells is therefore essential for identifying disease mechanisms and potential therapeutic targets.
Current computational approaches that study gene regulation using single-cell data typically connect regulatory elements to nearby genes based only on their linear distance along the genome. However, many enhancers regulate genes located hundreds of thousands of base pairs away through 3D chromatin contacts. Because most existing methods ignore this spatial genome organization, many important long-range regulatory interactions remain undetected or are incorrectly assigned.
This research aims to develop a computational framework to better identify long-range enhancer–gene interactions in glioblastoma. A deep learning model will first predict chromatin contacts from widely available omics datasets. These predicted 3D interactions will then be integrated with single-cell regulatory data to link enhancers with their target genes and reconstruct regulatory relationships.
By incorporating genome structure into the analysis of gene regulation, this project will provide a more accurate understanding of how distant regulatory elements influence gene activity in cancer. Importantly, predicting chromatin contacts from existing omics data reduces the need for costly Hi-C experiments and enables broader application in cancer research.
Contact & links
- Lab address: CBIGR: Zwijnaarde-Technologiepark 71, 9052 Ghent
- IRC
- Center for Medical Genetics Ghent
- HINT
- Hoang Thien Thu Nguyen is interested to receive invitations for presentations or talks