Decoding and controlling cell-state switching: A bottom-up approach based on enhancer logic

Project Information

cis-CONTROL

Grant agreement ID: 724226

DOI

10.3030/724226

Project closed

EC signature date 19 May 2017

Start date 1 June 2017

End date 31 May 2023

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 999 660,00

EU contribution

€ 1 999 660,00

Coordinated by

VIB VZW
Belgium

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (13)

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

Author(s): Carmen Bravo González-Blas, Seppe De Winter, Gert Hulselmans, Nikolai Hecker, Irina Matetovici, Valerie Christiaens, Suresh Poovathingal, Jasper Wouters, Sara Aibar, Stein Aerts
Published in: Nature Methods, 2023, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-023-01938-4

Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads

Author(s): Florian V De Rop; Joy N Ismail; Carmen Bravo González-Blas; Gert J Hulselmans; Christopher Campbell Flerin; Jasper Janssens; Koen Theunis; Valerie M Christiaens; Jasper Wouters; Gabriele Marcassa; Joris de Wit; Suresh Poovathingal; Stein Aerts
Published in: eLife, Issue 10, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.73971

Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning

Author(s): Zeynep Kalender Atak, Ibrahim Ihsan Taskiran, Jonas Demeulemeester, Christopher Flerin, David Mauduit, Liesbeth Minnoye, Gert Hulselmans, Valerie Christiaens, Ghanem-Elias Ghanem, Jasper Wouters, Stein Aerts
Published in: Genome Research, 2021, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.260851.120

Shared enhancer gene regulatory networks between wound and oncogenic programs

Author(s): Swann Floc'hlay, Ramya Balaji, Dimitrije Stanković, Valerie M Christiaens, Carmen Bravo González-Blas, Seppe De Winter, Gert J Hulselmans, Maxime De Waegeneer, Xiaojiang Quan, Duygu Koldere, Mardelle Atkins, Georg Halder, Mirka Uhlirova, Anne-Kathrin Classen, Stein Aerts
Published in: eLife, 2023, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.81173

Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma

Author(s): 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
Published in: Nature Cell Biology, 2020, ISSN 1465-7392
Publisher: Nature Publishing Group
DOI: 10.1038/s41556-020-0547-3

The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes

Author(s): Jelle Jacobs, Mardelle Atkins, Kristofer Davie, Hana Imrichova, Lucia Romanelli, Valerie Christiaens, Gert Hulselmans, Delphine Potier, Jasper Wouters, Ibrahim I. Taskiran, Giulia Paciello, Carmen B. González-Blas, Duygu Koldere, Sara Aibar, Georg Halder, Stein Aerts
Published in: Nature Genetics, Issue 50/7, 2018, Page(s) 1011-1020, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-018-0140-x

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

Author(s): Kristofer Davie, Jasper Janssens, Duygu Koldere, Maxime De Waegeneer, Uli Pech, Łukasz Kreft, Sara Aibar, Samira Makhzami, Valerie Christiaens, Carmen Bravo González-Blas, Suresh Poovathingal, Gert Hulselmans, Katina I. Spanier, Thomas Moerman, Bram Vanspauwen, Sarah Geurs, Thierry Voet, Jeroen Lammertyn, Bernard Thienpont, Sha Liu, Nikos Konstantinides, Mark Fiers, Patrik Verstreken, Stein Aert
Published in: Cell, Issue 174/4, 2018, Page(s) 982-998.e20, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2018.05.057

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

Author(s): Carmen Bravo González-Blas, Liesbeth Minnoye, Dafni Papasokrati, Sara Aibar, Gert Hulselmans, Valerie Christiaens, Kristofer Davie, Jasper Wouters, Stein Aerts
Published in: Nature Methods, Issue 16/5, 2019, Page(s) 397-400, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-019-0367-1

A scalable SCENIC workflow for single-cell gene regulatory network analysis

Author(s): 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
Published in: Nature Protocols, Issue 15/7, 2020, Page(s) 2247-2276, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-020-0336-2

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics

Author(s): Carmen Bravo González‐Blas, Xiao‐Jiang Quan, Ramon Duran‐Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime Waegeneer, David Mauduit, Suresh Poovathingal, Sara Aibar, Stein Aerts
Published in: Molecular Systems Biology, Issue 16/5, 2020, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20209438

Analysis of long and short enhancers in melanoma cell states

Author(s): David Mauduit, Ibrahim Ihsan Taskiran, Liesbeth Minnoye, Maxime de Waegeneer, Valerie Christiaens, Gert Hulselmans, Jonas Demeulemeester, Jasper Wouters, Stein Aerts
Published in: eLife, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.71735

Cross-species analysis of enhancer logic using deep learning

Author(s): Liesbeth Minnoye, Ibrahim Ihsan Taskiran, David Mauduit, Maurizio Fazio, Linde Van Aerschot, Gert Hulselmans, Valerie Christiaens, Samira Makhzami, Monika Seltenhammer, Panagiotis Karras, Aline Primot, Edouard Cadieu, Ellen van Rooijen, Jean-Christophe Marine, Giorgia Egidy, Ghanem Elias Ghanem, Leonard Zon, Jasper Wouters, Stein Aerts
Published in: Genome Research, 2020, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.260844.120

Decoding gene regulation in the fly brain

Author(s): Jasper Janssens, Sara Aibar, Ibrahim Ihsan Taskiran, Joy N. Ismail, Alicia Estacio Gomez, Gabriel Aughey, Katina I. Spanier, Florian V. De Rop, Carmen Bravo González-Blas, Marc Dionne, Krista Grimes, Xiao Jiang Quan, Dafni Papasokrati, Gert Hulselmans, Samira Makhzami, Maxime De Waegeneer, Valerie Christiaens, Tony Southall & Stein Aerts
Published in: Nature, 2022, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-021-04262-z

Other (1)

Enhancer grammar of liver cell types and hepatocyte zonation states

Author(s): Carmen Bravo González-Blas, Irina Matetovici, Hanne Hillen, Ibrahim Ihsan Taskiran, Roel Vandepoel, Valerie Christiaens, Leticia Sansores-García, Elisabeth Verboven, Gert Hulselmans, Suresh Poovathingal, Jonas Demeulemeester, Nikoleta Psatha, David Mauduit, Georg Halder, Stein Aerts
Published in: BioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.12.08.519575