Rate My Professor Stein Aerts

Stein Aerts is a full professor in the Faculty of Medicine at KU Leuven, affiliated with the Department of Human Genetics. He heads the Laboratory of Computational Biology at the VIB-KU Leuven Center for Brain and Disease Research and serves as Scientific Director of VIB.AI, the VIB Center for AI and Computational Biology. Aerts earned his Master in Bioscience Engineering with a focus on Molecular Biology from KU Leuven in 1999, Advanced Studies in Applied Computer Science from the University of Brussels in 2002, and a PhD in Engineering specializing in Bioinformatics from KU Leuven in 2004. Following his doctoral studies, he conducted postdoctoral research at VIB in the laboratory of Bassem Hassan from 2005 to 2009. He joined KU Leuven as Assistant Professor in 2009, progressed to Associate Professor in 2014, Full Professor in 2017, and Gewoon Hoogleraar in 2021. Additionally, he has been a VIB Group Leader since 2016.

Aerts' research program centers on decoding the genomic regulatory code through integrative approaches combining single-cell multi-omics, machine learning, and high-throughput functional genomics, with key applications in neuroscience using Drosophila models and in oncology, particularly melanoma cell state transitions. His laboratory has pioneered bioinformatics methods including SCENIC for single-cell inference of gene regulatory networks and clustering, cisTopic for cis-regulatory topic modeling from single-cell ATAC-seq data, CREsted for predicting cell-type-specific enhancers across species, and experimental platforms like HyDrop for droplet-based single-cell ATAC-seq. Prominent publications encompass 'CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species' (Nature Methods, 2026), 'SCENIC: single-cell regulatory network inference and clustering' (Nature Methods, 2017), 'Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly' (Science, 2022), and 'Robust gene expression programs in melanoma' (Nature Genetics, 2016). His scholarship has amassed over 28,000 citations. Aerts has secured major funding such as the ERC Advanced Grant for Genome2Cells (2022), Methusalem Grant for BioMedAI (2026), ERC Consolidator Grant (2017), EMBO membership (2022), the Biotech Fund Prize for Bioinformatics and Computational Science (2017), and the AstraZeneca Foundation Award for Bioinformatics (2016). He co-founded the Fly Cell Atlas consortium and contributes to steering committees for KU Leuven institutes and the Vlaams Supercomputer Centrum.