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Stein Aerts

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Stein Aerts
NationalityBelgian
Alma materUniversity of Leuven
Known forResearch on gene regulation and computational biology
TitleProfessor

Stein Aerts is a Belgian bio-engineer and computational biologist. He leads the Laboratory of Computational Biology[1] at VIB and KU Leuven (University of Leuven), and is director of VIB.AI, the VIB Center for AI & Computational Biology. He has received several accolades for his research into the workings of the genomic regulatory code.[2]

Early life and education

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Aerts was born and raised in Heusden-Zolder, Belgium, where he completed his secondary education at Heilig-Hart College.[3] He obtained a Master's degree in Bioscience Engineering (Molecular Biology) from the University of Leuven, and subsequently combined a job as Assistant IT Project Leader at Janssen Pharmaceutica with advanced studies in Applied Computer Science at the University of Brussels. He obtained a PhD in Engineering (Bioinformatics), working at the Department of Electrical Engineering ESAT-SCD at the University of Leuven.[4]

Academic career

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Aerts completed his postdoc training working on the genomics of gene regulation in the fruit fly model Drosophila melanogaster in the lab of Bassem Hassan at VIB in Leuven, including a research visit at the Developmental Biology Institute of Marseille, Luminy (IBDML), in France, with Denis Thierry and Carl Herrmann.

In 2009, Aerts was appointed assistant professor at the University of Leuven, where he is now full professor, and heads the Laboratory of Computational Biology at the KU Leuven Department of Human Genetics. Since 2016, he was also appointed VIB group leader. Aerts teaches several courses, including Introduction to Bioinformatics, Bioinformatics: Structural and Comparative Genomics, Bioinformatics and Systems Biology: Sequence, Structure & Evolution and Bioinformatics and Systems Biology: Expression, Regulation and Networks at the University of Leuven. His research focuses on deciphering the genomic regulatory code, using a combination of single-cell, machine-learning, and high-throughput experimental approaches.[5]

Research

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Aerts research interest in regulatory genomics and gene regulatory networks cover a wide range of experimental and computational approaches, applied in the context of neuronal development, neurodegeneration, as well as cancer.[6][7]

During his PhD research, Aerts invented one of the first bioinformatics algorithms for the prediction of genomic enhancers (ModuleSearcher)[8] and developed several bioinformatics tools for the analysis of cis-regulatory sequences (TOUCAN)[9][10][11] and for gene prioritisation (Endeavour).[12] Other scientific contributions include new bioinformatics methods for the analysis of single-cell gene regulatory networks, namely iRegulon,[13] SCENIC[14] and cisTopic;[15] a new experimental technique for massively parallel enhancer reporter assays (CHEQ-seq); and a deep learning implementation for enhancer modelling (DeepMEL[16] and DeepFlyBrain[17]).

Aerts co-founded the Fly Cell Atlas consortium[18] and generated a single-cell atlas of the ageing Drosophila brain.[19] In 2022, the consortium announced the completion of a single-nucleus transcriptomic atlas of the adult fruit fly,[20][21] which they hope will serve as a valuable resource for the research community and as a reference for studies of gene function at single-cell resolution.[22]

The generation of cell and tissue atlases help research to study biological processes, not only in flies but also for modeling human diseases at a whole-organism level with cell-type resolution. Aerts is also part of a pan-European research consortium called LifeTime, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution.[23]

Outreach

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As an advocate for open science, Aerts deposits the data and methods developed by his team on open repositories, or makes them freely available as open source software and databases.[24]

MendelCraft, a MineCraft mod developed by the Aerts lab, is a video game designed to teach children about DNA, genetics, and the laws of Mendel, by allowing them to cross and clone different breeds of virtual chickens.[25]

Awards

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  • ERC Advanced Grant 2023
  • Elected EMBO member 2022[26]
  • Francqui Chair at ULB 2022[27]
  • ERC Consolidator Grant[28]
  • 2017 Prize for Bioinformatics and Computational Science from the Biotech Fund
  • 2016 Astrazeneca Foundation Award Bioinformatics[29]

References

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  1. ^ Aerts, lab. "Stein Aerts Lab - VIB - KULeuven". aertslab.org. Retrieved 2022-05-04.
  2. ^ Marx, Vivien (2019-05-01). "Stein Aerts". Nature Methods. 16 (5): 355. doi:10.1038/s41592-019-0397-8. ISSN 1548-7105. PMID 30971811. S2CID 106411505.
  3. ^ "Limburgse topwetenschapper Stein Aerts: "Eigenlijk is dit een onmogelijke job"". www.hbvl.be (in Flemish). 6 November 2018. Retrieved 2022-05-03.
  4. ^ "Stein Aerts Lab - VIB - KULeuven". aertslab.org. Retrieved 2022-05-03.
  5. ^ name, Your. "Stein Aerts Lab - VIB - KULeuven". aertslab.org. Retrieved 2022-05-03.
  6. ^ Leuven, K. U. "Computer program detects differences between human cells". phys.org. Retrieved 2022-05-03.
  7. ^ Sterling, John (2022-01-06). / "AI Used to Study Cell Diversity in the Brain of Drosophila melanogaster". GEN - Genetic Engineering and Biotechnology News. Retrieved 2022-05-03.
  8. ^ "ModuleSearcher". gbiomed.kuleuven.be. Retrieved 2022-05-04.
  9. ^ Aerts, Stein; Thijs, Gert; Coessens, Bert; Staes, Mik; Moreau, Yves; De Moor, Bart (2003-03-15). "Toucan: deciphering the cis-regulatory logic of coregulated genes". Nucleic Acids Research. 31 (6): 1753–1764. doi:10.1093/nar/gkg268. ISSN 1362-4962. PMC 152870. PMID 12626717.
  10. ^ Aerts, Stein; Van Loo, Peter; Thijs, Gert; Mayer, Herbert; de Martin, Rainer; Moreau, Yves; De Moor, Bart (2005-07-01). "TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis". Nucleic Acids Research. 33 (Web Server issue): W393–396. doi:10.1093/nar/gki354. ISSN 1362-4962. PMC 1160115. PMID 15980497.
  11. ^ "TOUCAN - Regulatory Sequence Analysis - Gene Regulation Bioinformatics". toucan.aertslab.org. Retrieved 2022-05-04.
  12. ^ Aerts, Stein; Lambrechts, Diether; Maity, Sunit; Van Loo, Peter; Coessens, Bert; De Smet, Frederik; Tranchevent, Leon-Charles; De Moor, Bart; Marynen, Peter; Hassan, Bassem; Carmeliet, Peter (May 2006). "Gene prioritization through genomic data fusion". Nature Biotechnology. 24 (5): 537–544. doi:10.1038/nbt1203. ISSN 1087-0156. PMID 16680138. S2CID 2303897.
  13. ^ Janky, Rekin's; Verfaillie, Annelien; Imrichová, Hana; Van de Sande, Bram; Standaert, Laura; Christiaens, Valerie; Hulselmans, Gert; Herten, Koen; Naval Sanchez, Marina; Potier, Delphine; Svetlichnyy, Dmitry (July 2014). "iRegulon: from a gene list to a gene regulatory network using large motif and track collections". PLOS Computational Biology. 10 (7): e1003731. Bibcode:2014PLSCB..10E3731J. doi:10.1371/journal.pcbi.1003731. ISSN 1553-7358. PMC 4109854. PMID 25058159.
  14. ^ Aibar, Sara; González-Blas, Carmen Bravo; Moerman, Thomas; Huynh-Thu, Vân Anh; Imrichova, Hana; Hulselmans, Gert; Rambow, Florian; Marine, Jean-Christophe; Geurts, Pierre; Aerts, Jan; van den Oord, Joost (November 2017). "SCENIC: single-cell regulatory network inference and clustering". Nature Methods. 14 (11): 1083–1086. doi:10.1038/nmeth.4463. ISSN 1548-7105. PMC 5937676. PMID 28991892.
  15. ^ Bravo González-Blas, Carmen; Minnoye, Liesbeth; Papasokrati, Dafni; Aibar, Sara; Hulselmans, Gert; Christiaens, Valerie; Davie, Kristofer; Wouters, Jasper; Aerts, Stein (May 2019). "cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data". Nature Methods. 16 (5): 397–400. doi:10.1038/s41592-019-0367-1. ISSN 1548-7105. PMC 6517279. PMID 30962623.
  16. ^ Minnoye, Liesbeth; Taskiran, Ibrahim Ihsan; Mauduit, David; Fazio, Maurizio; Van Aerschot, Linde; Hulselmans, Gert; Christiaens, Valerie; Makhzami, Samira; Seltenhammer, Monika; Karras, Panagiotis; Primot, Aline (December 2020). "Cross-species analysis of enhancer logic using deep learning". Genome Research. 30 (12): 1815–1834. doi:10.1101/gr.260844.120. ISSN 1549-5469. PMC 7706731. PMID 32732264.
  17. ^ Janssens, Jasper; Aibar, Sara; Taskiran, Ibrahim Ihsan; Ismail, Joy N.; Gomez, Alicia Estacio; Aughey, Gabriel; Spanier, Katina I.; De Rop, Florian V.; González-Blas, Carmen Bravo; Dionne, Marc; Grimes, Krista (January 2022). "Decoding gene regulation in the fly brain". Nature. 601 (7894): 630–636. Bibcode:2022Natur.601..630J. doi:10.1038/s41586-021-04262-z. ISSN 1476-4687. PMID 34987221. S2CID 245771324.
  18. ^ "FLY CELL ATLAS". FLY CELL ATLAS. Retrieved 2022-05-03.
  19. ^ Davie, Kristofer; Janssens, Jasper; Koldere, Duygu; De Waegeneer, Maxime; Pech, Uli; Kreft, Łukasz; Aibar, Sara; Makhzami, Samira; Christiaens, Valerie; Bravo González-Blas, Carmen; Poovathingal, Suresh (2018-08-09). "A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain". Cell. 174 (4): 982–998.e20. doi:10.1016/j.cell.2018.05.057. ISSN 1097-4172. PMC 6086935. PMID 29909982.
  20. ^ Li, Hongjie; Janssens, Jasper; De Waegeneer, Maxime; Kolluru, Sai Saroja; Davie, Kristofer; Gardeux, Vincent; Saelens, Wouter; David, Fabrice P. A.; Brbić, Maria; Spanier, Katina; Leskovec, Jure (2022-03-04). "Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly". Science. 375 (6584): eabk2432. doi:10.1126/science.abk2432. ISSN 1095-9203. PMC 8944923. PMID 35239393.
  21. ^ "Tiny Hero, Big Map". hms.harvard.edu. 9 March 2022. Retrieved 2022-05-03.
  22. ^ "The fruit fly: tiny research hero now fully mapped". press.vib.be. 3 March 2022. Retrieved 2022-05-03.
  23. ^ Rajewsky, Nikolaus; Almouzni, Geneviève; Gorski, Stanislaw A.; Aerts, Stein; Amit, Ido; Bertero, Michela G.; Bock, Christoph; Bredenoord, Annelien L.; Cavalli, Giacomo; Chiocca, Susanna; Clevers, Hans (November 2020). "LifeTime and improving European healthcare through cell-based interceptive medicine". Nature. 587 (7834): 377–386. Bibcode:2020Natur.587..377R. doi:10.1038/s41586-020-2715-9. ISSN 1476-4687. PMC 7656507. PMID 32894860.
  24. ^ "aertslab". GitHub. Retrieved 2022-05-03.
  25. ^ "MendelCraft". mendelcraft.aertslab.org. Retrieved 2022-05-03.
  26. ^ "Find people in the EMBO Communities". people.embo.org. Retrieved 2023-06-22.
  27. ^ ULB (25 January 2022). "Francqui Chair 2021 - "Decoding gene regulation in the single-cell era"".
  28. ^ "ERC-2016 Consolidator Grants for Stein Aerts, Phillip Lemey and Tom Van Doorsselaere". www.kuleuven.be. Retrieved 2022-05-03.
  29. ^ AstraZenecaFoundation. "Award winners - AZ Foundation & FWO/F.R.S.-FNRS". Retrieved 3 May 2022.
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