Gerben Menschaert

gerbenm2After obtaining my master degree in 1998, I worked for several years as a database developer and bioinformatician in pharmaceutical and biotech companies (Janssens Pharmaceutica & deVGen). In 2006 I decided to “start over” in an academic setting. I did my PhD within the frame of a Strategic Fundamental Research Project on Functional Peptidomics, a cross-university collaboration between groups of the Ghent University, University of Leuven, and Antwerp University, wherein we were responsible for the bioinformatics and data analysis.

This work resulted in tools aiding the bio-active peptide identification process in peptidomics experiments (Bonanza for peptidomics and IggyPep). Moreover an optimized identification process was devised gathering conventional and aforementioned new tools into one pipeline. This doctoral thesis was supervised by Prof. Wim Van Criekinge in close collaboration with Prof. Walter Luyten. In february 2010, I successfully obtained my PhD in Applied Biological Science.

Since then, I started working as post-doctoral researcher in both the Lab of Bioinformatics and Computational Genomics (BioBix), and Prometa, Interfaculty Center for Proteomics & Metabolomics, recently renamed to Sybioma. From January 2012 on, I work full-time at the Biobix lab, since October 2012 as an FWO postdoctoral fellow. My main interest is to combine two of my favorite research technologies: mass spectrometry and next generation sequencing (NGS) and their data analysis. It is my strong belief that combined results from both technology platforms yield sound scientific output, which I’m trying to obtain in the following research projects:

•                Combining ribosome profiling (NGS of ribosome-captured mRNA sequences) and mass spectrometry into an improved protein/peptide identification pipeline (see also Steven Verbruggen).

•                Genome-wide identification and validation of a new class of bio-active peptides, termed micropeptides, by combining valuable information obtained by mass spectrometry data combined with several high throughput sequencing data sources, RNA-seq for gene expression, and ribosome profiling (RNA-seq of ribosome-captured mRNA fragments) for revealing true coding sequences (see also Volodimir Olexiouk and Jeroen Crappé).

•                Genome-wide investigation of the potential influence of epigenetics on gene transcription and translation by combining valuable information obtained by mass spectrometry based quantitative proteomics data and multiple high throughput sequencing data sources, MBD-seq for DNA methylation, RNA-seq for gene expression, and ribosome profiling (RNA-seq of ribosome captured mRNA fragments) for revealing the true coding sequences (see also Alexander Koch and Sandra Steyaert).

•                Genome-wide investigation of the potential post-transcriptional regulatory effect of the epitranscriptome on the proteome complexity, by combining m6A-seq and RIBO-seq data.

Publications: Bibliography Gent University – Google Scholar.
Research Media: ResearchGateLinkedIn.

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

 

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