prof. Gerben Menschaert (PhD)

CRIG member
Gerben Menschaert

Principal investigator - Biobix Lab for Bioinformatics and Computational Genomics (UGent)
Guest professor (Faculty of Bioscience engineering, UGent)
CEO/CSO spinoff company (from UGent)


Research focus

The core expertise of Gerben Menschaert’s group at the BIOBIX lab is the development and application of novel data-analytical methods for omics data.
The current focus is proteogenomics, the integration of both sequencing and mass spectrometry data in a multi-omics manner. NGS-based approaches (RNA-seq, ribosome profiling) and Nanopore-based long read sequencing is combined with mass spectrometry-based proteomics data. One of the applications is the identification and functional validation of so-called SEPS (sORF-encoded polypeptides) unravelling their role in health and (cancer) disease.
Another topic of interest is to try and detect epigenetic biomarkers for ferroptosis, biological rusting towards a possible future therapy for cancer treatment.

Research team

  • prof. Gerben Menschaert – principal investigator, guest professor
  • dr. Steven Verbruggen (PhD) – post-doctoral fellow
  • dr. Jim Clauwaert (PhD) – post-doctoral fellow
  • Gaetan De Waele – doctoral fellow
  • Jeroen Galle – bioinformatician

Key publications

  • TIS Transformer: remapping the human proteome using deep learning. NAR Genomics and Bioinformatics 5 (1), lqad021
  • RIBO-former: leveraging ribosome profiling information to improve the detection of translated open reading frames. bioRxiv, 2023.06. 20.545724
  • Standardized annotation of translated open reading frames. Nature biotechnology 40 (7), 994-999
  • CpG Transformer for imputation of single-cell methylomes. Bioinformatics 38 (3), 597-603, 13, 2022
  • sORF Encoded Peptides in Health and Disease. Frontiers in Genetics 13, 878014
  • Downregulation of the FTO m6A RNA demethylase promotes EMT-mediated progression of epithelial tumors and sensitivity to Wnt inhibitors. Nature cancer 2 (6), 611-628
  • PROTEOFORMER 2.0: further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms. Molecular & Cellular Proteomics 18 (8), S126-S140
  • Deletion 6q drives T-cell leukemia progression by ribosome modulation. Cancer discovery 8 (12), 1614-1631

Contact & links

  • Lab address: Faculty of Bioscience Engineering, Department Data Analysis and Mathematical Modelling, Research Unit BIOBIX: Bioinformatics and Computational Genomics, Campus Coupure, Block A 2nd floor 120.004, Coupure links 653, B-9000 Ghent, Belgium
  • BioBix Lab 
  • LinkedIn 
  • Google Scholar
  • Prof. Menschaert is involved in 
    NXTGNT Sequencing Core facility
    - spinoff UGent
  • Gerben Menschaert is interested to receive invitations for presentations or talks