Stein Aerts
{{Short description|Belgian bio-engineer and computational biologist}}
{{Infobox person
| name = Stein Aerts
| image = Stein-aerts.jpg
| nationality = Belgian
| alma_mater = University of Leuven
| known_for = Research on gene regulation and computational biology
| title = Professor
}}
Stein Aerts is a Belgian bio-engineer and computational biologist. He leads the Laboratory of Computational Biology{{Cite web |last=Aerts |first=lab |title=Stein Aerts Lab - VIB - KULeuven |url=http://aertslab.org/ |access-date=2022-05-04 |website=aertslab.org |language=en-us}} 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.{{Cite journal |last=Marx |first=Vivien |date=2019-05-01 |title=Stein Aerts |journal=Nature Methods |language=en |volume=16 |issue=5 |pages=355 |doi=10.1038/s41592-019-0397-8 |pmid=30971811 |s2cid=106411505 |issn=1548-7105|doi-access=free }}
Early life and education
Aerts was born and raised in Heusden-Zolder, Belgium, where he completed his secondary education at Heilig-Hart College.{{Cite web |title=Limburgse topwetenschapper Stein Aerts: "Eigenlijk is dit een onmogelijke job" |url=https://www.hbvl.be/cnt/dmf20181106_03911737 |access-date=2022-05-03 |website=www.hbvl.be |date=6 November 2018 |language=nl-BE}} 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.{{Cite web |title=Stein Aerts Lab - VIB - KULeuven |url=https://aertslab.org/ |access-date=2022-05-03 |website=aertslab.org}}
Academic career
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.{{Cite web |last=name |first=Your |title=Stein Aerts Lab - VIB - KULeuven |url=http://aertslab.org/ |access-date=2022-05-03 |website=aertslab.org |language=en-us}}
Research
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.{{Cite web |last=Leuven |first=K. U. |title=Computer program detects differences between human cells |url=https://phys.org/news/2017-10-differences-human-cells.html |access-date=2022-05-03 |website=phys.org |language=en}}{{Cite web |last=Sterling |first=John |date=2022-01-06 |title=AI Used to Study Cell Diversity in the Brain of Drosophila melanogaster |url=https://www.genengnews.com/news/ai-used-to-study-cell-diversity-in-the-brain-of-drosophila-melanogaster / |access-date=2022-05-03 |website=GEN - Genetic Engineering and Biotechnology News |language=en-US}}
During his PhD research, Aerts invented one of the first bioinformatics algorithms for the prediction of genomic enhancers (ModuleSearcher){{Cite web |title=ModuleSearcher |url=https://gbiomed.kuleuven.be/apps/lcb/toucan/help/WebServices/modulesearcher.htm |access-date=2022-05-04 |website=gbiomed.kuleuven.be}} and developed several bioinformatics tools for the analysis of cis-regulatory sequences (TOUCAN){{Cite journal |last1=Aerts |first1=Stein |last2=Thijs |first2=Gert |last3=Coessens |first3=Bert |last4=Staes |first4=Mik |last5=Moreau |first5=Yves |last6=De Moor |first6=Bart |date=2003-03-15 |title=Toucan: deciphering the cis-regulatory logic of coregulated genes |journal=Nucleic Acids Research |volume=31 |issue=6 |pages=1753–1764 |doi=10.1093/nar/gkg268 |issn=1362-4962 |pmid=12626717|pmc=152870 }}{{Cite journal |last1=Aerts |first1=Stein |last2=Van Loo |first2=Peter |last3=Thijs |first3=Gert |last4=Mayer |first4=Herbert |last5=de Martin |first5=Rainer |last6=Moreau |first6=Yves |last7=De Moor |first7=Bart |date=2005-07-01 |title=TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis |journal=Nucleic Acids Research |volume=33 |issue=Web Server issue |pages=W393–396 |doi=10.1093/nar/gki354 |issn=1362-4962 |pmc=1160115 |pmid=15980497}}{{Cite web |title=TOUCAN - Regulatory Sequence Analysis - Gene Regulation Bioinformatics |url=http://toucan.aertslab.org/software/toucan.php |access-date=2022-05-04 |website=toucan.aertslab.org}} and for gene prioritisation (Endeavour).{{Cite journal |last1=Aerts |first1=Stein |last2=Lambrechts |first2=Diether |last3=Maity |first3=Sunit |last4=Van Loo |first4=Peter |last5=Coessens |first5=Bert |last6=De Smet |first6=Frederik |last7=Tranchevent |first7=Leon-Charles |last8=De Moor |first8=Bart |last9=Marynen |first9=Peter |last10=Hassan |first10=Bassem |last11=Carmeliet |first11=Peter |date=May 2006 |title=Gene prioritization through genomic data fusion |url=https://pubmed.ncbi.nlm.nih.gov/16680138/ |journal=Nature Biotechnology |volume=24 |issue=5 |pages=537–544 |doi=10.1038/nbt1203 |issn=1087-0156 |pmid=16680138|s2cid=2303897 }} Other scientific contributions include new bioinformatics methods for the analysis of single-cell gene regulatory networks, namely iRegulon,{{Cite journal |last1=Janky |first1=Rekin's |last2=Verfaillie |first2=Annelien |last3=Imrichová |first3=Hana |last4=Van de Sande |first4=Bram |last5=Standaert |first5=Laura |last6=Christiaens |first6=Valerie |last7=Hulselmans |first7=Gert |last8=Herten |first8=Koen |last9=Naval Sanchez |first9=Marina |last10=Potier |first10=Delphine |last11=Svetlichnyy |first11=Dmitry |date=July 2014 |title=iRegulon: from a gene list to a gene regulatory network using large motif and track collections |journal=PLOS Computational Biology |volume=10 |issue=7 |pages=e1003731 |doi=10.1371/journal.pcbi.1003731 |issn=1553-7358 |pmc=4109854 |pmid=25058159|bibcode=2014PLSCB..10E3731J |doi-access=free }} SCENIC{{Cite journal |last1=Aibar |first1=Sara |last2=González-Blas |first2=Carmen Bravo |last3=Moerman |first3=Thomas |last4=Huynh-Thu |first4=Vân Anh |last5=Imrichova |first5=Hana |last6=Hulselmans |first6=Gert |last7=Rambow |first7=Florian |last8=Marine |first8=Jean-Christophe |last9=Geurts |first9=Pierre |last10=Aerts |first10=Jan |last11=van den Oord |first11=Joost |date=November 2017 |title=SCENIC: single-cell regulatory network inference and clustering |journal=Nature Methods |volume=14 |issue=11 |pages=1083–1086 |doi=10.1038/nmeth.4463 |issn=1548-7105 |pmc=5937676 |pmid=28991892}} and cisTopic;{{Cite journal |last1=Bravo González-Blas |first1=Carmen |last2=Minnoye |first2=Liesbeth |last3=Papasokrati |first3=Dafni |last4=Aibar |first4=Sara |last5=Hulselmans |first5=Gert |last6=Christiaens |first6=Valerie |last7=Davie |first7=Kristofer |last8=Wouters |first8=Jasper |last9=Aerts |first9=Stein |date=May 2019 |title=cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data |journal=Nature Methods |volume=16 |issue=5 |pages=397–400 |doi=10.1038/s41592-019-0367-1 |issn=1548-7105 |pmc=6517279 |pmid=30962623}} a new experimental technique for massively parallel enhancer reporter assays (CHEQ-seq); and a deep learning implementation for enhancer modelling (DeepMEL{{Cite journal |last1=Minnoye |first1=Liesbeth |last2=Taskiran |first2=Ibrahim Ihsan |last3=Mauduit |first3=David |last4=Fazio |first4=Maurizio |last5=Van Aerschot |first5=Linde |last6=Hulselmans |first6=Gert |last7=Christiaens |first7=Valerie |last8=Makhzami |first8=Samira |last9=Seltenhammer |first9=Monika |last10=Karras |first10=Panagiotis |last11=Primot |first11=Aline |date=December 2020 |title=Cross-species analysis of enhancer logic using deep learning |journal=Genome Research |volume=30 |issue=12 |pages=1815–1834 |doi=10.1101/gr.260844.120 |issn=1549-5469 |pmc=7706731 |pmid=32732264}} and DeepFlyBrain{{Cite journal |last1=Janssens |first1=Jasper |last2=Aibar |first2=Sara |last3=Taskiran |first3=Ibrahim Ihsan |last4=Ismail |first4=Joy N. |last5=Gomez |first5=Alicia Estacio |last6=Aughey |first6=Gabriel |last7=Spanier |first7=Katina I. |last8=De Rop |first8=Florian V. |last9=González-Blas |first9=Carmen Bravo |last10=Dionne |first10=Marc |last11=Grimes |first11=Krista |date=January 2022 |title=Decoding gene regulation in the fly brain |url=https://pubmed.ncbi.nlm.nih.gov/34987221/ |journal=Nature |volume=601 |issue=7894 |pages=630–636 |doi=10.1038/s41586-021-04262-z |issn=1476-4687 |pmid=34987221|bibcode=2022Natur.601..630J |s2cid=245771324 }}).
Aerts co-founded the Fly Cell Atlas consortium{{Cite web |title=FLY CELL ATLAS |url=http://flycellatlas.org/ |access-date=2022-05-03 |website=FLY CELL ATLAS |language=en}} and generated a single-cell atlas of the ageing Drosophila brain.{{Cite journal |last1=Davie |first1=Kristofer |last2=Janssens |first2=Jasper |last3=Koldere |first3=Duygu |last4=De Waegeneer |first4=Maxime |last5=Pech |first5=Uli |last6=Kreft |first6=Łukasz |last7=Aibar |first7=Sara |last8=Makhzami |first8=Samira |last9=Christiaens |first9=Valerie |last10=Bravo González-Blas |first10=Carmen |last11=Poovathingal |first11=Suresh |date=2018-08-09 |title=A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain |journal=Cell |volume=174 |issue=4 |pages=982–998.e20 |doi=10.1016/j.cell.2018.05.057 |issn=1097-4172 |pmc=6086935 |pmid=29909982}} In 2022, the consortium announced the completion of a single-nucleus transcriptomic atlas of the adult fruit fly,{{Cite journal |last1=Li |first1=Hongjie |last2=Janssens |first2=Jasper |last3=De Waegeneer |first3=Maxime |last4=Kolluru |first4=Sai Saroja |last5=Davie |first5=Kristofer |last6=Gardeux |first6=Vincent |last7=Saelens |first7=Wouter |last8=David |first8=Fabrice P. A. |last9=Brbić |first9=Maria |last10=Spanier |first10=Katina |last11=Leskovec |first11=Jure |date=2022-03-04 |title=Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly |journal=Science |volume=375 |issue=6584 |pages=eabk2432 |doi=10.1126/science.abk2432 |issn=1095-9203 |pmc=8944923 |pmid=35239393}}{{Cite web |title=Tiny Hero, Big Map |url=https://hms.harvard.edu/news/tiny-hero-big-map |access-date=2022-05-03 |website=hms.harvard.edu |date=9 March 2022 |language=en}} 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.{{Cite web |title=The fruit fly: tiny research hero now fully mapped |url=https://press.vib.be/the-fruit-fly-tiny-research-hero-now-fully-mapped |access-date=2022-05-03 |website=press.vib.be |date=3 March 2022 |language=en}}
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.{{Cite journal |last1=Rajewsky |first1=Nikolaus |last2=Almouzni |first2=Geneviève |last3=Gorski |first3=Stanislaw A. |last4=Aerts |first4=Stein |last5=Amit |first5=Ido |last6=Bertero |first6=Michela G. |last7=Bock |first7=Christoph |last8=Bredenoord |first8=Annelien L. |last9=Cavalli |first9=Giacomo |last10=Chiocca |first10=Susanna |last11=Clevers |first11=Hans |date=November 2020 |title=LifeTime and improving European healthcare through cell-based interceptive medicine |journal=Nature |language=en |volume=587 |issue=7834 |pages=377–386 |doi=10.1038/s41586-020-2715-9 |pmid=32894860 |pmc=7656507 |bibcode=2020Natur.587..377R |issn=1476-4687}}
Outreach
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.{{Cite web |title=aertslab |url=https://github.com/aertslab |access-date=2022-05-03 |website=GitHub |language=en}}
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.{{Cite web |title=MendelCraft |url=https://mendelcraft.aertslab.org/ |access-date=2022-05-03 |website=mendelcraft.aertslab.org}}
Awards
- ERC Advanced Grant 2023
- Elected EMBO member 2022{{Cite web |title=Find people in the EMBO Communities |url=https://people.embo.org/profile/stein-aerts |access-date=2023-06-22 |website=people.embo.org}}
- Francqui Chair at ULB 2022{{cite web |last=ULB |date=25 January 2022 |title=Francqui Chair 2021 - "Decoding gene regulation in the single-cell era" |url=https://actus.ulb.be/fr/agenda/francqui-chair-2021-decoding-gene-regulation-in-the-single-cell-era}}
- ERC Consolidator Grant{{cite web |title=ERC-2016 Consolidator Grants for Stein Aerts, Phillip Lemey and Tom Van Doorsselaere |url=https://www.kuleuven.be/english/research/EU/p/erc/news/161216-erc-cog |access-date=2022-05-03 |website=www.kuleuven.be }}
- 2017 Prize for Bioinformatics and Computational Science from the Biotech Fund
- 2016 Astrazeneca Foundation Award Bioinformatics{{cite web |last=AstraZenecaFoundation |date=|access-date= 3 May 2022 |title=Award winners - AZ Foundation & FWO/F.R.S.-FNRS |url=https://www.azfoundation.be/the-awards/fwo-fnrs/2016.html}}