dr. Truong Nguyen (PhD)

My research sits at the interface of liquid biopsy, cancer epigenomics, and computational biology, with the aim of turning a routine blood draw into a rich, interpretable readout of tumour biology, and ultimately clinical application. My current focus is circulating cell-free DNA (cfDNA) fragmentomics — the information encoded in how cfDNA is cut and protected rather than only in its sequence. Fragment size distributions, nucleosome occupancy and periodicity, end-motifs, preferred ends, and jagged ends together reflect the (epi)genomic organization of the cells the fragments came from, which makes them a complementary data layer on top of mutation, copy-number, and methylation profiling. Within this space, I develop computational and machine-learning models that push fragmentomics from bulk-sample classification down to the individual read: reproducible, containerized Nextflow pipelines for standardized fragmentomic feature extraction and epigenetic inference from short- and long-read cfDNA WGS; one-class/outlier models of the healthy cfDNA feature space; and supervised and deep sequence-based classifiers (including transformer-style architectures) that sort tumour-derived from healthy-cell-derived fragments. Enriching for the tumoral signal in this way sharpens downstream tasks I care about most — tissue-of-origin inference in cancer of unknown primary, tumour-fraction estimation for residual-disease monitoring, and detection of subtle epigenetic cell-state plasticity such as epithelial-to-mesenchymal transitions under therapeutic pressure. My longer-term goal is to bring these fragmentomics-based, multimodal assays into clinical trials and personalised cancer care.
 

• Lab address VIB:  
  VIB Center for Medical Biotechnology
  UGent Department of Biomolecular Medicine
  Technologiepark-Zwijnaarde 75 - 9052 Ghent
• TOBI lab
• OncoRNALab
• Center for Medical Genetics Ghent
• Centre of Excellence in Mycotoxicology and Public Health
• MYTOX-SOUTH   (UGent): an intercontinental partnership striving to solve mycotoxin problems
• Truong Nguyen is interested to receive invitations for presentations or talks