Stein Aerts

27.3k citations

101 papers · 11.7k · 6 hit papers · h-index 45

Impact in

Cancer Research top 0.5%
Molecular Biology top 0.5%
- Single-cell and spatial transcriptomics
- Genomics and Chromatin Dynamics
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Gene Regulatory Network Analysis
- Epigenetics and DNA Methylation
- RNA Research and Splicing

Papers in

Molecular Biology 87
- Genomics and Chromatin Dynamics 43
- Single-cell and spatial transcriptomics 20
- RNA Research and Splicing 16
- Developmental Biology and Gene Regulation 12
- Gene expression and cancer classification 11
- RNA and protein synthesis mechanisms 10
Cancer Research 14
- Cancer Genomics and Diagnostics 10

Co-authors: Gert Hulselmans (30 shared papers)Sara Aibar (12 shared papers)Zeynep Kalender Atak (18 shared papers)Carmen Bravo González‐Blas (14 shared papers)Hana Imrichová (10 shared papers)Jasper Wouters (12 shared papers)Jean‐Christophe Marine (7 shared papers)Jan Aerts (2 shared papers)
Journals: eLife (7 papers)Nucleic Acids Research (5 papers)Nature Communications (4 papers)Genome biology (4 papers)PLoS Genetics (4 papers)
Partner nations: Belgium United States United Kingdom

In The Last Decade

Stein Aerts

99 papers receiving 11.6k citations

Stein Aerts's Hit Papers

6 papers align trajectories log scale

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks 2023 · 231 citations

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if any of the following hold:

it has ≥500 total citations;
it reaches ≥1.5× the top-1% citation threshold for papers in the same subfield and year (the threshold is the minimum needed to enter the top 1%, not the average within it);
it reaches the top citation threshold in at least one of its specific research topics.

2023 Nature Methods
2020 Nature Protocols
2018 Nature Medicine
2017 Nature Methods
2014 PLoS Computational Biology
2006 Nature Biotechnology

Peers

Countries citing papers authored by Stein Aerts

Since Specialization

Citations

This map shows the geographic impact of Stein Aerts's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Stein Aerts with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Stein Aerts more than expected).

Fields of papers citing papers by Stein Aerts

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Stein Aerts. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Stein Aerts. The network helps show where Stein Aerts may publish in the future.

Co-authors

The 25 scholars most cited alongside Stein Aerts, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Stein Aerts Line = papers co-authored together Stein Aerts links everyone, so they are left out of the graph.

All Works

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20 of 20 papers shown

Showing the 20 most-cited of 101 papers — load more, or switch the sort, to bring in the rest.

#	Work
1	SCENIC: single-cell regulatory network inference and clustering Nature Methods ·Sara Aibar, Carmen Bravo González‐Blas, Thomas Moerman, Vân Anh Huynh‐Thu, Hana Imrichová, Gert Hulselmans, Florian Rambow, Jean‐Christophe Marine, Pierre Geurts, Jan Aerts, Joost van den Oord, Zeynep Kalender Atak, Jasper Wouters, Stein Aerts Hit paper breakdown →	2017	3087
2	Phenotype molding of stromal cells in the lung tumor microenvironment Nature Medicine ·Diether Lambrechts, Els Wauters, Bram Boeckx, Sara Aibar, David Nittner, Oliver T. Burton, Ayse Bassez, Herbert Decaluwé, Andreas Pircher, Kathleen Van den Eynde, Birgit Weynand, Erik Verbeken, Paul De Leyn, Adrian Liston, Johan Vansteenkiste, Peter Carmeliet, Stein Aerts, Bernard Thienpont Hit paper breakdown →	2018	1037
3	A scalable SCENIC workflow for single-cell gene regulatory network analysis Nature Protocols ·Bram Van de Sande, Christopher Flerin, Kristofer Davie, Maxime De Waegeneer, Gert Hulselmans, Sara Aibar, Ruth Seurinck, Wouter Saelens, Robrecht Cannoodt, Quentin Rouchon, Toni Verbeiren, Dries De Maeyer, Joke Reumers, Yvan Saeys, Stein Aerts Hit paper breakdown →	2020	723
4	Gene prioritization through genomic data fusion Nature Biotechnology ·Stein Aerts, Diether Lambrechts, Sunit Maity, Peter Van Loo, Bert Coessens, Frederik De Smet, Léon-Charles Tranchevent, Bart De Moor, Peter Marynen, Bassem A. Hassan, Peter Carmeliet, Yves Moreau Hit paper breakdown →	2006	661
5	iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections PLoS Computational Biology ·Rekin’s Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval-Sánchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean‐Christophe Marine, Stein Aerts Hit paper breakdown →	2014	610
6	Alteration of the micro RNA network during the progression of Alzheimer's disease EMBO Molecular Medicine ·Pierre Lau, Koen Bossers, Rekin’s Janky, Evgenia Salta, Carlo Sala Frigerio, Shahar Barbash, Roy Rothman, Annerieke Sierksma, Amantha Thathiah, David Greenberg, Aikaterini S. Papadopoulou, Tilmann Achsel, Torik Ayoubi, Hermona Soreq, Joost Verhaagen, Dick F. Swaab, Stein Aerts, Bart De Strooper	2013	377
7	GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks Bioinformatics ·Thomas Moerman, Sara Aibar, Carmen Bravo González‐Blas, Jaak Simm, Yves Moreau, Jan Aerts, Stein Aerts	2018	292
8	Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state Nature Communications ·Annelien Verfaillie, Hana Imrichová, Zeynep Kalender Atak, Michael Dewaele, Florian Rambow, Gert Hulselmans, Valerie Christiaens, Dmitry Svetlichnyy, Flavie Luciani, Laura Van den Mooter, Sofie Claerhout, Mark Fiers, Fabrice Journé, Ghanem-Elias Ghanem, Carl Herrmann, Georg Halder, Jean‐Christophe Marine, Stein Aerts	2015	280
9	cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data Nature Methods ·Carmen Bravo González‐Blas, Liesbeth Minnoye, Dafni Papasokrati, Sara Aibar, Gert Hulselmans, Valerie Christiaens, Kristofer Davie, Jasper Wouters, Stein Aerts	2019	244
10	SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks Nature Methods ·Carmen Bravo González‐Blas, Seppe De Winter, Gert Hulselmans, Nikolai Hecker, Irina Matetovici, Valerie Christiaens, Suresh Poovathingal, Jasper Wouters, Sara Aibar, Stein Aerts Hit paper breakdown →	2023	231
11	Toucan: deciphering the cis-regulatory logic of coregulated genes Nucleic Acids Research ·Stein Aerts	2003	161
12	ENDEAVOUR update: a web resource for gene prioritization in multiple species Nucleic Acids Research ·Léon-Charles Tranchevent, Roland Barriot, Shuguang Yu, Steven Van Vooren, Peter Van Loo, Bert Coessens, Bart De Moor, Stein Aerts, Yves Moreau	2008	160
13	Mapping gene regulatory networks from single-cell omics data Briefings in Functional Genomics ·Mark Fiers, Liesbeth Minnoye, Sara Aibar, Carmen Bravo González‐Blas, Zeynep Kalender Atak, Stein Aerts	2017	147
14	Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma Nature Cell Biology ·Jasper Wouters, Zeynep Kalender Atak, Liesbeth Minnoye, Katina I. Spanier, Maxime De Waegeneer, Carmen Bravo González‐Blas, David Mauduit, Kristofer Davie, Gert Hulselmans, Ahmad Najem, Michael Dewaele, Dennis Pedri, Florian Rambow, Samira Makhzami, Valerie Christiaens, Frederik Ceyssens, Ghanem Ghanem, Jean‐Christophe Marine, Suresh Poovathingal, Stein Aerts	2020	137
15	Comparison and meta-analysis of microarray data: from the bench to the computer desk Trends in Genetics ·Yves Moreau, Stein Aerts, Bart De Moor, Bart De Strooper, Michał Dąbrowski	2003	131
16	Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling PLoS Genetics ·Kristofer Davie, Jelle Jacobs, Mardelle Atkins, Delphine Potier, Valerie Christiaens, Georg Halder, Stein Aerts	2015	122
17	i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules Nucleic Acids Research ·Carl Herrmann, Bram Van de Sande, Delphine Potier, Stein Aerts	2012	122
18	TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis Nucleic Acids Research ·Stein Aerts, Peter Van Loo, Gert Thijs, Herbert Mayer, Rainer de Martin, Yves Moreau, Bart De Moor	2005	118
19	i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly Nucleic Acids Research ·Hana Imrichová, Gert Hulselmans, Zeynep Kalender Atak, Delphine Potier, Stein Aerts	2015	116
20	JAK3 mutants transform hematopoietic cells through JAK1 activation, causing T-cell acute lymphoblastic leukemia in a mouse model Blood ·Sandrine Degryse, Charles E. de Bock, Luk Cox, Sofie Demeyer, Olga Gielen, Nicole Mentens, Kris Jacobs, Ellen Geerdens, Valentina Gianfelici, Gert Hulselmans, Mark Fiers, Stein Aerts, Jules P.P. Meijerink, Thomas Tousseyn, Jan Cools	2014	109

About Stein Aerts

Stein Aerts is a scholar working on Molecular Biology, Cancer Research, Cellular and Molecular Neuroscience, Genetics and Cell Biology, having authored 101 papers that have together received 11.7k indexed citations. Recurring topics across this work include Genomics and Chromatin Dynamics (43 papers), Single-cell and spatial transcriptomics (20 papers), RNA Research and Splicing (16 papers), Developmental Biology and Gene Regulation (12 papers), Neurobiology and Insect Physiology Research (11 papers), Gene expression and cancer classification (11 papers), Cancer Genomics and Diagnostics (10 papers) and RNA and protein synthesis mechanisms (10 papers). The work is most often cited by research in Cancer Research (2.0k citations), Molecular Biology (8.3k citations), Immunology (2.3k citations), Aging (167 citations) and Oncology (1.9k citations). Stein Aerts has collaborated with scholars based in Belgium, United States and United Kingdom. Frequent co-authors include Gert Hulselmans, Sara Aibar, Zeynep Kalender Atak, Carmen Bravo González‐Blas, Hana Imrichová, Jasper Wouters, Jean‐Christophe Marine, Jan Aerts, Thomas Moerman and Florian Rambow. Their work appears in journals such as eLife, Nucleic Acids Research, Nature Communications, Genome biology and PLoS Genetics.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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Stein Aerts

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In The Last Decade

Stein Aerts

Stein Aerts's Hit Papers

Peers

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Fields of papers citing papers by Stein Aerts

All Works

About Stein Aerts

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