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

Información del proyecto

cis-CONTROL

Identificador del acuerdo de subvención: 724226

DOI

10.3030/724226

Proyecto cerrado

Fecha de la firma de la CE 19 Mayo 2017

Fecha de inicio 1 Junio 2017

Fecha de finalización 31 Mayo 2023

Financiado con arreglo a

• EXCELLENT SCIENCE - European Research Council (ERC)

Coste total

€ 1 999 660,00

Aportación de la UE

€ 1 999 660,00

Coordinado por

VIB VZW
Belgium

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Publicaciones

Peer reviewed articles (13)

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

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

Autores: 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
Publicado en: eLife, Edición 10, 2022, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.73971

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

Autores: 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
Publicado en: Genome Research, 2021, ISSN 1088-9051
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.260851.120

Shared enhancer gene regulatory networks between wound and oncogenic programs

Autores: 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
Publicado en: eLife, 2023, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.81173

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

Autores: 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
Publicado en: Nature Cell Biology, 2020, ISSN 1465-7392
Editor: Nature Publishing Group
DOI: 10.1038/s41556-020-0547-3

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

Autores: 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
Publicado en: Nature Genetics, Edición 50/7, 2018, Página(s) 1011-1020, ISSN 1061-4036
Editor: Nature Publishing Group
DOI: 10.1038/s41588-018-0140-x

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

Autores: 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
Publicado en: Cell, Edición 174/4, 2018, Página(s) 982-998.e20, ISSN 0092-8674
Editor: Cell Press
DOI: 10.1016/j.cell.2018.05.057

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

Autores: Carmen Bravo González-Blas, Liesbeth Minnoye, Dafni Papasokrati, Sara Aibar, Gert Hulselmans, Valerie Christiaens, Kristofer Davie, Jasper Wouters, Stein Aerts
Publicado en: Nature Methods, Edición 16/5, 2019, Página(s) 397-400, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/s41592-019-0367-1

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

Autores: 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
Publicado en: Nature Protocols, Edición 15/7, 2020, Página(s) 2247-2276, ISSN 1754-2189
Editor: Nature Publishing Group
DOI: 10.1038/s41596-020-0336-2

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

Autores: 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
Publicado en: Molecular Systems Biology, Edición 16/5, 2020, ISSN 1744-4292
Editor: Nature Publishing Group
DOI: 10.15252/msb.20209438

Analysis of long and short enhancers in melanoma cell states

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

Cross-species analysis of enhancer logic using deep learning

Autores: 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
Publicado en: Genome Research, 2020, ISSN 1088-9051
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.260844.120

Decoding gene regulation in the fly brain

Autores: 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
Publicado en: Nature, 2022, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-021-04262-z

Other (1)

Enhancer grammar of liver cell types and hepatocyte zonation states

Autores: 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
Publicado en: BioRxiv, 2022, ISSN 2692-8205
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.12.08.519575