prof. Gerben Menschaert (PhD)
Principal investigator - Biobix Lab for Bioinformatics and Computational Genomics (UGent)
Guest professor (Faculty of Bioscience engineering, UGent)
CEO/CSO spinoff company OHMX.bio (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
- Google Scholar
- Prof. Menschaert is involved in
- NXTGNT Sequencing Core facility
- OHMX.bio spinoff UGent - Gerben Menschaert is interested to receive invitations for presentations or talks