After obtaining my Master’s degree in 1998, I worked for several years in pharmaceutical and biotech companies (Janssens Pharmaceutica & deVGen) as a bioinformatician. In 2006 I decided to “start over” in an academic setting. I joined the BioBix lab (Lab of Bioinformatics and Computational Genomics, Faculty of Bioscience Engineering, Ghent University) and did my PhD within the frame of a Strategic Fundamental Research Project (IWT-SBO) on Functional Peptidomics, a cross-university collaboration between groups of the University of Ghent, University of Leuven and Antwerp University, wherein our group was responsible for the bioinformatics and data analysis. I was supervising the tasks performed by our group within the project. Afterwards I worked as a postdoctoral researcher in both the BioBix lab and Prometa (Interfaculty Centre for Proteomics and Metabolomics, KULeuven) and was granted a postdoctoral fellowship from the FWO (The Research Foundation Flanders) in 2012.

In 2013 I stayed as a visiting scientist at the New York University Langone Medical Center (US), in the lab of Prof. David Fenyö, focussing on proteogenomics. Later in 2016, I was also granted a ½ year stay at the Queensland Univeristy, Brisbane, Australia, collaborating with Prof. Joseph Rothnagel on SEPs (short ORF-encoded polypeptides).

Currently, my main research focus is to combine different high throughput technologies and to integrate resulting information to address different biological questions, this in strong collaboration with partners such as NXTGNT and VIB-Ugent Center for Medical Biotechnology:

  • combination of ribosome profiling (RIBOseq) and mass spectrometry (MS) for improved protein/peptide identification (see also Steven Verbruggen and Elvis Ndah).
  • genome-wide identification of a new class of bio-active peptides, termed SEPs small open reading frames (ORF)-encoded polypeptides, using RNAseq, RIBOseq and MS (see also Volodimir Olexiouk and Marlies Peeters).
  • genome-wide investigation of gene regulation at transcriptional and translational level using MS, RIBOseq and RNAseq measuring overall expression and translation, MBDseq and RRBS measuring DNA methylation, m6Aseq and BS-RNA-seq measuring RNA methylation. Also novel sequencing technologies such as the Oxford Nanopore are investigated.

In total, I have published a total of 39 articles in international peer reviewed journals, such as Nucleic Acids Research, Genome Biology,  Nature Chemical Biology, Molecular & Cellular Proteomics, and Bioinformatics.  Since 2008, I (co-)supervise(d) 10 Master’s degree students and 6 PhD students and 1 postdoctoral fellow and was granted 4 FWO research grants.


Publications on Google Scholar.
Research Media: ResearchGate – LinkedIn.

ASMS Meeting, Saint Louis, US -2015
NYU Medical School, New York, US – 2015

Gerben Menschaert

Tenured Academic Staff

Mass Spectrometry, NGS, Ribosome Profiling, Oxford NanoPore, Proteogenomics, Multi-omics data analysis, sORF(-encoded polypeptides), Epigenetics, Epitranscriptomics