Lennart Martens Lab

Research focus

​The development of several high-throughput Omics fields (genomics, transcriptomics, proteomics, metabolomics) over the past few years has already resulted in a wealth of data on these various stages in the flow of biological information (from genes to proteins, and on to their metabolic functions). Yet this large amount of information is also rather challenging; indeed, making sense of such volumes of data is no longer straightforward. Initial data processing to obtain results, along with the required quality control of these results, has to be automated. Additionally, storage and retrieval of multi-experiment data also requires a specific informatics infrastructure. On a more global level, dissemination of the (published) data to the scientific community also requires the construction of publicly accessible, domain-specific repositories. Finally, integration of the various results obtained across the different domains remains very much an ongoing research effort in the life sciences.

Throughout the technological maturation process of the Omics fields, one of the key roles of bioinformatics has been to analyze the information after it was obtained from an experiment: the so-called data-driven approach. As the various fields have matured, however, targeted methodologies that start with more focused questions are again gaining prominence. Accordingly, bioinformatics analyses have to morph into computational planning approaches, where the brunt of the informatics effort is expended prior to running the experiment.

This exciting transition is in turn a prerequisite to collecting sufficiently comprehensive and reliable data to allow the fine-tuning of systems biology models of reactions and pathways. Indeed, modeling efforts today are in part restricted by the limited amount of available data, resulting in poor coverage of the genes, proteins, or metabolites involved. Other aspects of the models, such as catalogs of protein-protein interactions, often have to deal with the converse problem of sometimes noisy data.

We therefore focus on three key points, aimed at enabling systems biology modeling:
- Data collection and integration across the various Omics fields
- (Semi-)automatic quality control of the obtained data using configurable expert systems
- Development of computational Omics to help set up and guide experiments based on a user-supplied list of target entities

Our team is also coordinator of "MULTIMOT", a H2020 EU funded project that aims to build an open data ecosystem for cell migration research, through standardization, dissemination and meta-analysis efforts.


Mass spectrometrists should search for all peptides, but assess only the ones they care aboutSticker A Martens L* Clement L*NATURE METHODS, 14, 643-644, 2017* or °: authors contributed equally
moFF: a robust and automated approach to extract peptide ion intensitiesArgentini Andrea Goeminne Ludger Verheggen Kenneth Hulstaert Niels Staes An Clement l Martens LennartNATURE METHODS, 13, 964-966, 2016
PeptideShaker enables reanalysis of MS-derived proteomics data setsVaudel Marc Burkhart J. M Zahedi R. P Oveland E Berven F. S Sickmann A Martens Lennart Barsnes HNATURE BIOTECHNOLOGY, 33, 22-4, 2015
ProteomeXchange provides globally coordinated proteomics data submission and disseminationVizcaino J. A Deutsch E. W. Wang R Csordas A Reisinger F Rios D Dianes J. A Sun Z Farrah T Bandeira N Binz P. Xenarios I. Eisenacher M Mayer G Gatto L Campos A Chalkley R. J Kraus H. J Albar J. P Martinez-Bartolomé S Apweiler R Omenn G. S. Martens Lennart Jones Angharad Hermjakob HNATURE BIOTECHNOLOGY, 32, 223-6, 2014
MS2PIP: a tool for MS/MS peak intensity predictionDegroeve Sven Martens LennartBIOINFORMATICS, 29, 3199-203, 2013

Job openings


Ten Million Euro for Access to European Proteomics Facilities

12/01/2019 - The European Union has awarded 10 million euro to a consortium of eighteen European research groups in the field of mass spectrometry based proteomics research throughout Europe. Three VIB-UGent groups are actively involved in this project

New tools raise the bar for protein research

02/03/2015 - ​Two recent publications by Lennart Martens, associated with VIB and Ghent University, have launched a new eco system for life sciences data.

Lennart Martens

Lennart Martens

Research area(s)


​PhD: Ghent University, Ghent, Belgium, 2006
Postdoc: EMBL-EBI, Cambridge, UK, 2006-09
VIB Group leader since October 2009

Contact Info

VIB-UGent Center for Medical BiotechnologyAlbert Baertsoenkaai 3 9000 GENTRoute description