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| nationality = Belgian
| nationality = Belgian
| alma_mater = University of Leuven
| alma_mater = University of Leuven
| known_for = Research on regulatory genomics and gene regulation networks
| known_for = Research on gene regulation and computational biology
| title = Professor
| title = Professor
}}
}}


'''Stein Aerts''' is a Belgian bio-engineer and computational biologist. He leads the lab for Laboratory of Computational Biology at [[Vlaams Instituut voor Biotechnologie|VIB]] and [[KU Leuven]] ([[KU Leuven|University of Leuven]]), and has received several accolades for his pioneering research into the workings of the human [[genome]].
'''Stein Aerts''' is a Belgian bio-engineer and computational biologist. He leads the Laboratory of Computational Biology<ref>{{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}}</ref> at [[Vlaams Instituut voor Biotechnologie|VIB]] and [[KU Leuven]] ([[KU Leuven|University of Leuven]]), and has received several accolades for his pioneering research into the workings of the the genomic regulatory code.


== Early life and education ==
== Early life and education ==
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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 [[Vlaams Instituut voor Biotechnologie|VIB]] in [[Leuven]], including a research visit at the Developmental Biology Institute of [[Marseille]], Luminy (IBDML), in [[France]], with [[Denis Thierry]] and Carl Herrmann.
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 [[Vlaams Instituut voor Biotechnologie|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 [[KU Leuven|University of Leuven]], where he is now [[Professor|full professor]], and heads the Laboratory of [[Computational biology|Computational Biology]] at the [[KU Leuven]] Department of Human Genetics. Since 2016, he was also appointed [[Vlaams Instituut voor Biotechnologie|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 [[KU Leuven|University of Leuven]]. His research focuses on deciphering the genomic regulatory code, using a combination of single-cell, [[Machine learning|machine-learning]], and experimental approaches.<ref>{{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}}</ref>
In 2009, Aerts was appointed [[assistant professor]] at the [[KU Leuven|University of Leuven]], where he is now [[Professor|full professor]], and heads the Laboratory of [[Computational biology|Computational Biology]] at the [[KU Leuven]] Department of Human Genetics. Since 2016, he was also appointed [[Vlaams Instituut voor Biotechnologie|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 [[KU Leuven|University of Leuven]]. His research focuses on deciphering the genomic regulatory code, using a combination of single-cell, [[Machine learning|machine-learning]], and high-throughput experimental approaches.<ref>{{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}}</ref>


== Research ==
== Research ==
Aerts research interest in regulatory genomics and gene regulatory networks cover a wide-range of experimental approaches, applied in the context of neuronal development, neurodegeneration, as well as cancer.<ref>{{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}}</ref><ref>{{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}}</ref>
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.<ref>{{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}}</ref><ref>{{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}}</ref>


His scientific contributions include new bioinformatics methods for the analysis of single-cell gene regulatory networks, namely SCENIC<ref>{{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}}</ref> and [[cisTopic]];<ref>{{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}}</ref> a new experimental technique for enhancer reporter assays (CHEQ-seq); and a deep learning implementation for enhancer modelling (DeepMEL).<ref>{{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}}</ref>
During his PhD research, Aerts invented one of the first bioinformatics algorithms for the prediction of genomic enhancers (ModuleSearcher)<ref>{{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}}</ref> and developed several bioinformatics tools for the analysis of cis-regulatory sequences (TOUCAN)<ref>{{Cite journal |last=Aerts |first=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 |url=https://pubmed.ncbi.nlm.nih.gov/12626717/ |journal=Nucleic Acids Research |volume=31 |issue=6 |pages=1753–1764 |doi=10.1093/nar/gkg268 |issn=1362-4962 |pmid=12626717}}</ref><ref>{{Cite journal |last=Aerts |first=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 |url=https://pubmed.ncbi.nlm.nih.gov/15980497/ |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}}</ref><ref>{{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}}</ref> and for gene prioritisation (Endeavour).<ref>{{Cite journal |last=Aerts |first=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=2006-05 |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}}</ref> Other scientific contributions include new bioinformatics methods for the analysis of single-cell gene regulatory networks, namely iRegulon,<ref>{{Cite journal |last=Janky |first=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=2014-07 |title=iRegulon: from a gene list to a gene regulatory network using large motif and track collections |url=https://pubmed.ncbi.nlm.nih.gov/25058159/ |journal=PLoS computational biology |volume=10 |issue=7 |pages=e1003731 |doi=10.1371/journal.pcbi.1003731 |issn=1553-7358 |pmc=4109854 |pmid=25058159}}</ref> SCENIC<ref>{{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}}</ref> and [[cisTopic]];<ref>{{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}}</ref> a new experimental technique for massively parallel enhancer reporter assays (CHEQ-seq); and a deep learning implementation for enhancer modelling (DeepMEL<ref>{{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}}</ref> and DeepFlyBrain<ref>{{Cite journal |last=Janssens |first=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=2022-01 |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}}</ref>).


Aerts co-founded the Fly Cell Atlas consortium<ref>{{Cite web |title=FLY CELL ATLAS |url=http://flycellatlas.org/ |access-date=2022-05-03 |website=FLY CELL ATLAS |language=en}}</ref> and generated a single-cell atlas of the ageing [[Drosophila melanogaster|Drosophila]] brain.<ref>{{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}}</ref> In 2022, the consortium announced the completion of a single-nucleus transcriptomic atlas of the adult fruit fly,<ref>{{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}}</ref><ref>{{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 |language=en}}</ref> 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.<ref>{{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 |language=en}}</ref>
Aerts co-founded the Fly Cell Atlas consortium<ref>{{Cite web |title=FLY CELL ATLAS |url=http://flycellatlas.org/ |access-date=2022-05-03 |website=FLY CELL ATLAS |language=en}}</ref> and generated a single-cell atlas of the ageing [[Drosophila melanogaster|Drosophila]] brain.<ref>{{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}}</ref> In 2022, the consortium announced the completion of a single-nucleus transcriptomic atlas of the adult fruit fly,<ref>{{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}}</ref><ref>{{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 |language=en}}</ref> 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.<ref>{{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 |language=en}}</ref>
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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.<ref>{{Cite web |title=aertslab |url=https://github.com/aertslab |access-date=2022-05-03 |website=GitHub |language=en}}</ref>
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.<ref>{{Cite web |title=aertslab |url=https://github.com/aertslab |access-date=2022-05-03 |website=GitHub |language=en}}</ref>


MedelCraft, a [[Minecraft|MineCraft]] mod developed by the Aerts lab, is a video game designed to teach children about [[DNA]], [[genetics]], and the laws of [[Mendelian inheritance|Mendel]], by allowing them to cross and clone different breeds of virtual chickens.<ref>{{Cite web |title=MendelCraft |url=https://mendelcraft.aertslab.org/ |access-date=2022-05-03 |website=mendelcraft.aertslab.org}}</ref>
MendelCraft, a [[Minecraft|MineCraft]] mod developed by the Aerts lab, is a video game designed to teach children about [[DNA]], [[genetics]], and the laws of [[Mendelian inheritance|Mendel]], by allowing them to cross and clone different breeds of virtual chickens.<ref>{{Cite web |title=MendelCraft |url=https://mendelcraft.aertslab.org/ |access-date=2022-05-03 |website=mendelcraft.aertslab.org}}</ref>


== Awards ==
== Awards ==

Revision as of 20:39, 4 May 2022

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 has received several accolades for his pioneering research into the workings of the the genomic regulatory code.

Early life and education

Aerts was born and raised in Heusden-Zolder, Belgium, where he completed his secondary education at Heilig-Hart College.[2] 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.[3]

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.[4]

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.[5][6]

During his PhD research, Aerts invented one of the first bioinformatics algorithms for the prediction of genomic enhancers (ModuleSearcher)[7] and developed several bioinformatics tools for the analysis of cis-regulatory sequences (TOUCAN)[8][9][10] and for gene prioritisation (Endeavour).[11] Other scientific contributions include new bioinformatics methods for the analysis of single-cell gene regulatory networks, namely iRegulon,[12] SCENIC[13] and cisTopic;[14] a new experimental technique for massively parallel enhancer reporter assays (CHEQ-seq); and a deep learning implementation for enhancer modelling (DeepMEL[15] and DeepFlyBrain[16]).

Aerts co-founded the Fly Cell Atlas consortium[17] and generated a single-cell atlas of the ageing Drosophila brain.[18] In 2022, the consortium announced the completion of a single-nucleus transcriptomic atlas of the adult fruit fly,[19][20] 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.[21]

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.[22]

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.[23]

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.[24]

Awards

  • Francqui Chair at ULB 2022[25]
  • ERC Consolidator Grant[26]
  • 2017 Prize for Bioinformatics and Computational Science from the Biotech Fund
  • 2016 Astrazeneca Foundation Award Bioinformatics[27]

References

  1. ^ Aerts, lab. "Stein Aerts Lab - VIB - KULeuven". aertslab.org. Retrieved 2022-05-04.
  2. ^ "Limburgse topwetenschapper Stein Aerts: "Eigenlijk is dit een onmogelijke job"". www.hbvl.be (in Flemish). Retrieved 2022-05-03.
  3. ^ "Stein Aerts Lab - VIB - KULeuven". aertslab.org. Retrieved 2022-05-03.
  4. ^ name, Your. "Stein Aerts Lab - VIB - KULeuven". aertslab.org. Retrieved 2022-05-03.
  5. ^ Leuven, K. U. "Computer program detects differences between human cells". phys.org. Retrieved 2022-05-03.
  6. ^ 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.
  7. ^ "ModuleSearcher". gbiomed.kuleuven.be. Retrieved 2022-05-04.
  8. ^ 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. PMID 12626717.
  9. ^ 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.
  10. ^ "TOUCAN - Regulatory Sequence Analysis - Gene Regulation Bioinformatics". toucan.aertslab.org. Retrieved 2022-05-04.
  11. ^ 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 (2006-05). "Gene prioritization through genomic data fusion". Nature Biotechnology. 24 (5): 537–544. doi:10.1038/nbt1203. ISSN 1087-0156. PMID 16680138. {{cite journal}}: Check date values in: |date= (help)
  12. ^ 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 (2014-07). "iRegulon: from a gene list to a gene regulatory network using large motif and track collections". PLoS computational biology. 10 (7): e1003731. doi:10.1371/journal.pcbi.1003731. ISSN 1553-7358. PMC 4109854. PMID 25058159. {{cite journal}}: Check date values in: |date= (help)CS1 maint: unflagged free DOI (link)
  13. ^ 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.
  14. ^ 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.
  15. ^ 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.
  16. ^ 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 (2022-01). "Decoding gene regulation in the fly brain". Nature. 601 (7894): 630–636. doi:10.1038/s41586-021-04262-z. ISSN 1476-4687. PMID 34987221. {{cite journal}}: Check date values in: |date= (help)
  17. ^ "FLY CELL ATLAS". FLY CELL ATLAS. Retrieved 2022-05-03.
  18. ^ 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.
  19. ^ 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.
  20. ^ "Tiny Hero, Big Map". hms.harvard.edu. Retrieved 2022-05-03.
  21. ^ "The fruit fly: tiny research hero now fully mapped". press.vib.be. Retrieved 2022-05-03.
  22. ^ 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.
  23. ^ "aertslab". GitHub. Retrieved 2022-05-03.
  24. ^ "MendelCraft". mendelcraft.aertslab.org. Retrieved 2022-05-03.
  25. ^ ULB (25 January 2022). "Francqui Chair 2021 - "Decoding gene regulation in the single-cell era"".
  26. ^ "ERC-2016 Consolidator Grants for Stein Aerts, Phillip Lemey and Tom Van Doorsselaere". www.kuleuven.be. Retrieved 2022-05-03.
  27. ^ AstraZenecaFoundation. "Award winners - AZ Foundation & FWO/F.R.S.-FNRS". Retrieved 3 May 2022.


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