Laboratory of Computational Biology

Research in our lab is focusing on gene and genome regulation, with applications in neuroscience (Drosophila melanogaster) and cancer.

Stein Aerts

Group Leader
VIB Group Leader since 2016
Associate Professor University of Leuven, 2014-2017
Assistant Professor University of Leuven, 2009-2014
Postdoc at VIB, Bassem Hassan lab, 2005-2009, Leuven
Visiting postdoc at Developmental Biology Institute of Marseille, Luminy (IBDML), Marseille, France (2006), with Denis Thieffry and Carl Herrmann
PhD Bioinformatics, School of Engineering (ESAT), University of Leuven, 2001-2004

Research areas

Computational biology Molecular neurology

Research focus

In the lab of computational biology 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.

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. Our favorite model systems include Drosophila (the brain and the eye-antennal imaginal disc) as well as human cancer cells (short-term cultures, cell lines, primary cells, xenografts, and organ-on-chip).

Dry Lab

We use bioinformatics methods for network inference and computational modeling of enhancers, such as machine learning and advanced motif discovery. Some of the bioinformatics methods we have developed and made available to the community include TOUCAN, ENDEAVOUR, iRegulon, i-cisTarget, mu-cisTarget, and SCENIC.

Tech Lab

We develop microfluidics chips, including droplet microfluidics for single-cell assays. We also develop microfluidic devices to analyse 3D tumoroids (organ-on-chip) and single-cell migration, in combination with lens-free imaging.

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Publications

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Jobs

We are always on the lookout for highly motivated colleagues to join our team. If you are interested to work on single-cell regulatory genomics - computational or experimental, please contact us.
 

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Team

The Stein Aerts Lab can only thrive thanks to the dedication and commitment of its people, no matter what their function or seniority.

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Events

To stay up to date in rapidly developing fields, scientists regularly interact with (international) colleagues. Conferences and other (scientific) events are an excellent way to facilitate such a continent-spanning knowledge exchange.

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