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

lesSDRF logo: Orange text underlined with increasingly opaque arrows pointing to the right

lesSDRF

Streamlining SDRF proteomics metadata annotation

LNCipedia

A comprehensive compendium of human long non-coding RNAs

Scop3D

Sequence Conservation On Protein 3D structure

Scop3P

Phosphosites on protein 3D structure

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

MS²Rescore

Improve Percolator rescoring with MS²PIP-predicted peak intensities.

DeepLC

Retention time prediction for any modified peptide using Deep Learning.

'psm_utils' in a monospaced serif font

psm_utils

Utilities for parsing and handling PSMs and search engine results in Python

Tutorials

Do you want to learn about Proteomics and Proteomics data analysis? Have a look at our CompOmics tutorials:

Bioinformatics for proteomics

Hands-on tutorial using user-friendly proteomics software

Machine learning

Video lecture series, including practical exercises using Jupyter notebooks

Our team

Lennart Martens

Group leader

Sven Degroeve

Staff scientist

Ralf Gabriels

Postdoctoral researcher

Pathmanaban Ramasamy

Postdoctoral researcher

Tim Van Den Bossche

Postdoctoral researcher

Alexander Kensert

Postdoctoral researcher

Robbin Bouwmeester

Postdoctoral researcher

Sakina Bombaywala

Postdoctoral researcher

Enrico Massignani

Postdoctoral researcher

Pieter Verschaffelt

Postdoctoral researcher

Jasper Zuallaert

Postdoctoral researcher

Robbe Devreese

Predoctoral researcher

Harikrishnan Ramadasan

Predoctoral researcher

Toon Callens

Predoctoral researcher

Arthur Declercq

Predoctoral researcher

Alireza Nameni

Predoctoral researcher

Tanja Holstein

Predoctoral researcher

Caroline Jachmann

Predoctoral researcher

Sam van Puyenbroeck

Predoctoral researcher

Tine Claeys

Predoctoral researcher

Lyudmila Kovalchuke

Project manager

Kevin Velghe

Software developer

Natalia Tichshenko

Software developer

Patricia Lefèvre

Group secretary

Latest publications

Harikrishnan Ramadasan

Predoctoral researcher

Tine Claeys

Predoctoral researcher

Tanja Holstein

Predoctoral researcher

Arthur Declercq

Predoctoral researcher

Robbe Devreese

Predoctoral researcher

Caroline Jachmann

Predoctoral researcher

Toon Callens

Predoctoral researcher

Alireza Nameni

Predoctoral researcher

Sam van Puyenbroeck

Predoctoral researcher

Where to find us?

Computational Omics and Systems Biology Group
Department of Biomolecular Medicine, Ghent University
VIB-UGent Center for Medical Biotechnology, VIB
Technologiepark 75
9052 Gent-Zwijnaarde, Belgium
E-mail

lennart [dot] martens [AT] UGent.be

Drone picture of FSVM II building
FSVM II, Zwijnaarde - © UGent, foto Jonas Vandecasteele en Yentl Vandendriessche