Rate My Professor Stein Aerts

Stein Aerts is a full professor in the Faculty of Medicine at KU Leuven, with an appointment in the Department of Human Genetics. He has headed the Laboratory of Computational Biology at the VIB-KU Leuven Center for Brain and Disease Research since 2009 and serves as Scientific Director of VIB.AI, the VIB Center for AI and Computational Biology, since 2023. Additionally, he is a VIB Group Leader since 2016. Aerts advanced through the faculty ranks at KU Leuven as Assistant Professor from 2009 to 2014, Associate Professor from 2014 to 2017, and Full Professor since 2017. His academic background includes a PhD in Engineering (Bioinformatics) from the Department of Electrical Engineering (ESAT) at KU Leuven in 2004, awarded with greatest distinction and congratulations from the jury, a Master's in Bioscience Engineering (Molecular Biology) from KU Leuven in 1999, and Advanced Studies in Applied Computer Science from the Vrije Universiteit Brussel in 2002. Prior to his faculty position, he conducted postdoctoral research at VIB in the Bassem Hassan laboratory from 2005 to 2009. Earlier professional roles included bioinformatician at Data4s Future Technologies NV from 2000 to 2001 and assistant IT project leader at Janssen Pharmaceutica from 1999 to 2000.

Aerts' research specializes in regulatory genomics, gene regulatory networks, single-cell omics technologies, machine learning in genomics, Drosophila neuroscience, and cancer regulatory heterogeneity. His laboratory develops bioinformatics methods such as SCENIC for single-cell regulatory network inference, cisTopic for cis-regulatory topic modeling on single-cell ATAC-seq data, pySCENIC, CREsted for modeling cell-type-specific enhancers, and SCENIC+ for multiomic inference of enhancers and networks. Key publications include "Cell-type-directed design of synthetic enhancers" (Nature, 2024), "SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks" (Nature Methods, 2023), "Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly" (eLife, 2021), "Cross-species analysis of enhancer logic using deep learning" (Nature Biotechnology, 2020), "A scalable SCENIC workflow for single-cell gene regulatory network analysis" (Genome Biology, 2020), and "SCENIC: single-cell regulatory network inference and clustering" (Nature Methods, 2017). He co-founded the Fly Cell Atlas consortium. Aerts has earned major honors including an ERC Advanced Grant for Genome2Cells (2022), Methusalem Grant for BioMedAI (2026), EMBO membership (2022), ERC Consolidator Grant (2017), Prize for Bioinformatics and Computational Science from the Biotech Fund (2017), AstraZeneca Foundation Award for Bioinformatics (2016), FWO Postdoctoral Fellowships (2005 and 2008), and HFSP Young Investigator Grant (2010). He serves on the board of the KU Leuven Center for Human Genetics and Genomics Core and is a member of Leuven.AI, LISCO - KU Leuven Institute for Single Cell Omics, KU Leuven Brain Institute, and KU Leuven Cancer Institute.