Stein Aerts Lab

Research focus

​We are interested in decoding the genomic regulatory code and understanding how genomic regulatory programs drive dynamic changes in cellular states, both in normal and disease processes. Transcriptional states emerge from complex gene regulatory networks. The nodes in these networks are cis-regulatory regions such as enhancers and promoters, where usually multiple transcription factors bind to regulate the expression of their target genes.

Our lab is a “humid” lab, half wet and half dry. In the wet-lab we apply high-throughput technologies to decipher enhancer logic and map gene regulatory networks, such as RNA-seq for transcriptomics and ATAC-seq and ChIP-seq for epigenomic profiling. To test the activities of promoters and enhancers we use massively parallel enhancer-reporter assays. Finally, to map high-resolution landscapes of possible cellular states we use single-cell transcriptomics and single-cell epigenomics.

We are interested in a variety of biological problems, and use as main model system the fruit fly Drosophila melanogaster, with a focus on the retina and the brain. Our fly lab houses multiple Drosophila species, natural inbred strains, and mutant lines, allowing to incorporate evolutionary models, natural variation (Quantitative Trait Loci), and disease mutations in our studies of the genomic regulatory code.

We are also interested in deciphering regulatory programs of cellular state switches in mammalian systems, including human and mouse. To study the cis-regulatory code in mammalian genomes we mainly use cancer as model system. During cancer progression, gene expression profiles of cancer cells can change, causing regulatory heterogeneity in tumors. This heterogeneity has an important impact on therapy response, since some cell states may be more or less vulnerable to a particular drug therapy.

In our dry lab we use bioinformatics methods for network inference and computational modeling of enhancers, such as Random Forest machine learning and Deep neural networks. Some of the bioinformatics methods we have developed and made available to the community include TOUCAN, ENDEAVOUR, iRegulon and i-cisTarget.



cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data.Bravo González-Blas Carmen* Minnoye Liesbeth* Papasokrati Dafni Aibar Sara Hulselmans Gert Christiaens Valerie Davie Kristofer Wouters Jasper Aerts Stein@NATURE METHODS, 16, 397-400, 2019* or °: authors contributed equally@: corresponding authors
A Single-Cell Transcriptome Atlas of the Aging Drosophila BrainDavie K* Janssens J* Koldere D* De Waegeneer M Pech U Kreft L Aibar Santos S Makhzami S Christiaens V Bravo Gonzalez Blas M Poovathingal S Hulselmans G Spanier K Moerman T Vanspauwen B Geurs S Voet T Lammertyn J Thienpont B Liu S Konstantinides N Fiers M Verstreken P Aerts SCELL, 174, 982-998 e20, 2018* or °: authors contributed equally
The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomesJacobs Jelle Atkins Mardelle Davie Kristofer Imrichova Hana Romanelli Lucia Christiaens Valerie Hulselmans Gert Potier D Wouters Jasper Taskiran Ibrahim Ihsan Paciello G Bravo Gonzalez Blas Maria Del Carmen Koldere Duygu Aibar Santos Sara Halder Georg Aerts SteinNATURE GENETICS, 50, 1011-1020, 2018
SCENIC: single-cell regulatory network inference and clusteringAibar Santos Sara Bravo Gonzalez Blas Maria Del Carmen Moerman T Huynh-Thu Va Imrichova Hana Hulselmans Gert Rambow Florian Marine Jean-Christophe Geurts P Aerts J. Van Den Oord J Kalender Zeynep Wouters Jasper Aerts SteinNATURE METHODS, 14, 1083-1086, 2017
Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logicVerfaillie A Svetlichnyy D Imrichova H Davie K Fiers Mark Kalender Atak Z Hulselmans G Christiaens V. Aerts SGENOME RESEARCH, 26, 882-95, 2016

Job openings


Mapping cellular diversity by looking for common topics of gene control

09/04/2019 - A Belgian team of computational biologists led by Stein Aerts (VIB-KU Leuven) has developed a new bioinformatics method called cisTopic. The results are published in Nature Methods.

Europe looks to cells for a healthier future

15/01/2019 - The body’s cells are constantly changing. But which of these changes are healthy developments and which lead to serious diseases? This is what LifeTime, a transnational and interdisciplinary initiative of leading European researchers, wants to figure out.

Human and artificial intelligence join forces to study complexity of the brain

14/06/2018 - A team of scientists lead by Stein Aerts (VIB-KU Leuven) is the first to map the gene expression of each individual brain cell during aging, though they started small: with the brain of a fruit fly.

Unlocking the genome

04/06/2018 - A team led by Stein Aerts (VIB-KU Leuven) uncovers how access to relevant DNA regions is orchestrated in epithelial cells. These findings shed new light on biological mechanisms of gene regulation & open up potential new avenues for cellular reprogramming

European scientists unite to track all cells in the human body

22/03/2018 - ​A consortium of European researchers will develop & apply new technologies to profile virtually all individual cells within the human body & track how they change during ageing & disease. Stein Aerts and Chris Marine (VIB-KU Leuven) are Belgian partners

Who’s afraid of bioRxiv: Weighing the pros and cons of preprint publishing

14/12/2017 - ​BioRxiv, a free online archive where scientists can post draft papers known as preprints, is causing quite a stir in the world of life sciences.

3 accomplished VIB Scientists receive ERC Consolidator grants

14/03/2017 - In November of 2016, three of our very own top researchers, Stein Aerts, Martin Guilliams and Rouslan Efremov were awarded Consolidator Grants, bringing the total number of such ERC grants won by VIB scientists up to 43.

ERC Consolidator Grants for three VIB scientists

30/11/2016 - The European Research Council (ERC) has awarded 3 VIB scientists a consolidator grant: Stein Aerts (VIB-KU Leuven), Martin Guilliams (VIB-UGent) and Rouslan Efremov (VIB-VUB).

Stein Aerts

Stein Aerts

Research area(s)

Model organism(s)


PhD: Dept. of Electrical Engineering (ESAT), KULeuven, Leuven, Belgium, 2004
Postdoc: VIB-KULeuven, Belgium, 2004-09
Visiting postdoc: Inst. for Developmental Biol., Luminy, Marseille, France, 2006
KULeuven Professor since 2009
VIB Group leader since September 2016

Contact Info

VIB-KU Leuven Center for Brain & Disease ResearchO&N 4, 6e verdCampus GasthuisbergHerestraat 49, bus 602 3000 LEUVENRoute description