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

Informazioni relative al progetto

cis-CONTROL

ID dell’accordo di sovvenzione: 724226

DOI

10.3030/724226

Progetto chiuso

Data della firma CE 19 Maggio 2017

Data di avvio 1 Giugno 2017

Data di completamento 31 Maggio 2023

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 999 660,00

Contributo UE

€ 1 999 660,00

Coordinato da

VIB VZW
Belgium

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (13)

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

Autori: Carmen Bravo González-Blas, Seppe De Winter, Gert Hulselmans, Nikolai Hecker, Irina Matetovici, Valerie Christiaens, Suresh Poovathingal, Jasper Wouters, Sara Aibar, Stein Aerts
Pubblicato in: Nature Methods, 2023, ISSN 1548-7091
Editore: 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

Autori: 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
Pubblicato in: eLife, Numero 10, 2022, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.73971

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

Autori: 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
Pubblicato in: Genome Research, 2021, ISSN 1088-9051
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.260851.120

Shared enhancer gene regulatory networks between wound and oncogenic programs

Autori: 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
Pubblicato in: eLife, 2023, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.81173

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

Autori: 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
Pubblicato in: Nature Cell Biology, 2020, ISSN 1465-7392
Editore: Nature Publishing Group
DOI: 10.1038/s41556-020-0547-3

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

Autori: 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
Pubblicato in: Nature Genetics, Numero 50/7, 2018, Pagina/e 1011-1020, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-018-0140-x

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

Autori: 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
Pubblicato in: Cell, Numero 174/4, 2018, Pagina/e 982-998.e20, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2018.05.057

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

Autori: Carmen Bravo González-Blas, Liesbeth Minnoye, Dafni Papasokrati, Sara Aibar, Gert Hulselmans, Valerie Christiaens, Kristofer Davie, Jasper Wouters, Stein Aerts
Pubblicato in: Nature Methods, Numero 16/5, 2019, Pagina/e 397-400, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-019-0367-1

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

Autori: 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
Pubblicato in: Nature Protocols, Numero 15/7, 2020, Pagina/e 2247-2276, ISSN 1754-2189
Editore: Nature Publishing Group
DOI: 10.1038/s41596-020-0336-2

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

Autori: 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
Pubblicato in: Molecular Systems Biology, Numero 16/5, 2020, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.20209438

Analysis of long and short enhancers in melanoma cell states

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

Cross-species analysis of enhancer logic using deep learning

Autori: 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
Pubblicato in: Genome Research, 2020, ISSN 1088-9051
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.260844.120

Decoding gene regulation in the fly brain

Autori: 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
Pubblicato in: Nature, 2022, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-021-04262-z

Other (1)

Enhancer grammar of liver cell types and hepatocyte zonation states

Autori: 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
Pubblicato in: BioRxiv, 2022, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.12.08.519575