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.
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).
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.
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.
To showcase the world-class scientific research of the Stein Aerts Lab, you can discover their scientific papers in more detail.
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.
The Stein Aerts Lab can only thrive thanks to the dedication and commitment of its people, no matter what their function or seniority.
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.