Computational Omics and Systems Biology Group
About
The CompOmics group, headed by Prof. Dr. Lennart Martens, is part of the Department of Biomolecular Medicine of the Faculty of Medicine and Health Sciences of Ghent University, and the VIB-UGent Center for Medical Biotechnology of VIB, both in Ghent, Belgium.
The group has its roots in Ghent, but has active members all over Europe, and specializes in the management, analysis and integration of high-throughput Omics data with an aim towards establishing solid data stores, processing methods and tools to enable downstream systems biology research.
The CompOmics team is always looking for talented people. Go to the jobs section on the VIB website to look for open positions.
Web applications
The following web applications are developed and hosted by the group.
IONBOT
Novel MS/MS search engine
MS²PIP
MS² Peak Intensity Prediction
Unipept
Functional Analysis of Metaproteome Data
Tabloid Proteome
Protein-protein interaction networks
Free and open source software
Here is a selection of our free and open-source tools. A full list can be found on GitHub.
SearchGUI
Combines proteomics search engines in one user-friendly GUI
PeptideShaker
Advanced proteomics data analysis made easy
Colims
LIMS system for proteomics data management and analysis
Thermo Raw File Parser
Convert Thermo Raw files to mzML or MGF on all operating systems
COSS
Fast and user-friendly spectral library search engine
Cellmissy
Data management system for cell migration / invasion data
DeepLC
Retention time prediction for any modified peptide using Deep Learning.
MS²ReScore
Improve Percolator rescoring with MS²PIP-predicted peak intensities.
Latest Tweets
Do you want to identify more than 10,000 immunopeptides in a single shot?
We are thrilled to present Thunder-DDA-PASEF, an optimized LC-MS #immunopeptidomics method tailored to MHC class I ligands, in preprint now at Research Square 🧵(1/n) https://twitter.com/RS_COVID19/status/1633702776428724224
Thunder-DDA-PASEF enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCov-2 spike protein epitopes #covid https://researchsquare.com/article/rs-2625909/latest
And out it is! @compomics @TineClaeys1's paper on a machine learning model that identifies tissue and cell type specific protein patterns.
https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00644#.ZB7o-mnD-RM.twitter
Tutorials
Do you want to learn about Proteomics and Proteomics data analysis? Have a look at our CompOmics tutorials:
Hands-on tutorial using user-friendly proteomics software
Mass spectrometry-based proteomics
Video lecture series
Video lecture series, including practical exercises using Jupyter notebooks
Our team
Dr. Enrico Massignani
Dr. Jasper Zuallaert
Toon Callens
Tine Claeys
Arthur Declercq
Alireza Nameni
Where to find us?
CompOmics moved to a new building!
Computational Omics and Systems Biology GroupDepartment of Biomolecular Medicine, Ghent University
VIB-UGent Center for Medical Biotechnology, VIB
Technologiepark 75
9052 Gent-Zwijnaarde, Belgium
lennart [dot] martens [AT] UGent.be
