A scalable SCENIC workflow for single-cell gene regulatory network analysis
Van de Sande, Bram, Flerin, Christopher, Davie, Kristofer, De Waegeneer, Maxime, Hulselmans, Gert, Aibar, Sara, Seurinck, Ruth, Saelens, Wouter, Cannoodt, Robrecht, Rouchon, Quentin, Verbeiren, Toni, De Maeyer, Dries, Reumers, Joke, Saeys, Yvan, Aerts, Stein
Published in Nature protocols (01.07.2020)
Published in Nature protocols (01.07.2020)
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Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma
Wouters, Jasper, Kalender-Atak, Zeynep, Minnoye, Liesbeth, Spanier, Katina I, De Waegeneer, Maxime, Bravo González-Blas, Carmen, Mauduit, David, Davie, Kristofer, Hulselmans, Gert, Najem, Ahmad, Dewaele, Michael, Pedri, Dennis, Rambow, Florian, Makhzami, Samira, Christiaens, Valerie, Ceyssens, Frederik, Ghanem, Ghanem, Marine, Jean-Christophe, Poovathingal, Suresh, Aerts, Stein
Published in Nature cell biology (01.08.2020)
Published in Nature cell biology (01.08.2020)
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Shared enhancer gene regulatory networks between wound and oncogenic programs
Floc'hlay, Swann, Balaji, Ramya, Stanković, Dimitrije, Christiaens, Valerie M, Bravo González-Blas, Carmen, De Winter, Seppe, Hulselmans, Gert J, De Waegeneer, Maxime, Quan, Xiaojiang, Koldere, Duygu, Atkins, Mardelle, Halder, Georg, Uhlirova, Mirka, Classen, Anne-Kathrin, Aerts, Stein
Published in eLife (03.05.2023)
Published in eLife (03.05.2023)
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Journal Article
Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
Bravo González‐Blas, Carmen, Quan, Xiao‐Jiang, Duran‐Romaña, Ramon, Taskiran, Ibrahim Ihsan, Koldere, Duygu, Davie, Kristofer, Christiaens, Valerie, Makhzami, Samira, Hulselmans, Gert, Waegeneer, Maxime, Mauduit, David, Poovathingal, Suresh, Aibar, Sara, Aerts, Stein
Published in Molecular systems biology (01.05.2020)
Published in Molecular systems biology (01.05.2020)
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Journal Article
Analysis of long and short enhancers in melanoma cell states
Mauduit, David, Taskiran, Ibrahim Ihsan, Minnoye, Liesbeth, de Waegeneer, Maxime, Christiaens, Valerie, Hulselmans, Gert, Demeulemeester, Jonas, Wouters, Jasper, Aerts, Stein
Published in eLife (07.12.2021)
Published in eLife (07.12.2021)
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Journal Article
A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain
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, Hulselmans, Gert, Spanier, Katina I., Moerman, Thomas, Vanspauwen, Bram, Geurs, Sarah, Voet, Thierry, Lammertyn, Jeroen, Thienpont, Bernard, Liu, Sha, Konstantinides, Nikos, Fiers, Mark, Verstreken, Patrik, Aerts, Stein
Published in Cell (09.08.2018)
Published in Cell (09.08.2018)
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Peritumoral activation of the Hippo pathway effectors YAP and TAZ suppresses liver cancer in mice
Moya, Iván M, Castaldo, Stéphanie A, Van den Mooter, Laura, Soheily, Soheil, Sansores-Garcia, Leticia, Jacobs, Jelle, Mannaerts, Inge, Xie, Jun, Verboven, Elisabeth, Hillen, Hanne, Algueró-Nadal, Ana, Karaman, Ruchan, Van Haele, Matthias, Kowalczyk, Weronika, De Waegeneer, Maxime, Verhulst, Stefaan, Karras, Panagiotis, van Huffel, Leen, Zender, Lars, Marine, Jean-Christophe, Roskams, Tania, Johnson, Randy, Aerts, Stein, van Grunsven, Leo A, Halder, Georg
Published in Science (American Association for the Advancement of Science) (22.11.2019)
Published in Science (American Association for the Advancement of Science) (22.11.2019)
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Journal Article
Decoding gene regulation in the fly brain
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, Quan, Xiao Jiang, Papasokrati, Dafni, Hulselmans, Gert, Makhzami, Samira, De Waegeneer, Maxime, Christiaens, Valerie, Southall, Tony, Aerts, Stein
Published in Nature (London) (27.01.2022)
Published in Nature (London) (27.01.2022)
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Journal Article
Developmental transcriptional control of mitochondrial homeostasis is required for activity-dependent synaptic connectivity
Mohylyak, Iryna, Bengochea, Mercedes, Pascual-Caro, Carlos, Asfogo, Noemi, Fonseca-Topp, Sara, Danda, Natasha, Atak, Zeynep Kalender, De Waegeneer, Maxime, Plaçais, Pierre-Yves, Preat, Thomas, Aerts, Stein, Corti, Olga, de Juan-Sanz, Jaime, Hassan, Bassem A
Published in bioRxiv : the preprint server for biology (11.06.2023)
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Published in bioRxiv : the preprint server for biology (11.06.2023)
Journal Article
Decoding gene regulation in the fly brain
Janssens, Jasper, Aibar, Sara, Ibrahim Ihsan Taskiran, Ismail, Joy N, Spanier, Katina I, Carmen Bravo Gonzalez-Blas, Xiao Jiang Quan, Dafni Papasokrati, Hulselmans, Gert, Makhzami, Samira, De Waegeneer, Maxime, Christiaens, Valerie, Aerts, Stein
Published in bioRxiv (12.08.2021)
Published in bioRxiv (12.08.2021)
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Paper
Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics
Carmen Bravo González-Blas, Xiao-Jiang, Quan, Duran-Romaña, Ramon, Ibrahim Ihsan Taskiran, Koldere, Duygu, Davie, Kristofer, Christiaens, Valerie, Makhzami, Samira, Hulselmans, Gert, De Waegeneer, Maxime, Mauduit, David, Poovathingal, Suresh, Aibar, Sara, Aerts, Stein
Published in bioRxiv (20.12.2019)
Published in bioRxiv (20.12.2019)
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Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly
Li, Hongjie, Janssens, Jasper, De Waegeneer, Maxime, Kolluru, Sai Saroja, Davie, Kristofer, Gardeux, Vincent, Sealens, Wouter, Fabrice, David, Brbic, Maria, Leskovec, Jure, Mclaughlin, Colleen, Xie, Qijing, Jones, Robert, Brueckner, Katja, Shim, Jiwon, Tattikota, Sudhir Gopal, Schnorrer, Frank, Rust, Katja, Nystul, Todd, Carvalho-Santos, Zita, Ribeiro, Carlos, Pal, Soumitra, Przytycka, Teresa Maria, Allen, Aaron, Goodwin, Stephen, Berry, Cameron, Margaret T (Minx) Fuller, White-Cooper, Helen, Matunis, Erika, Dinardo, Stephen, Galenza, Anthony, O'brien, Lucy Erin, Julian At Dow, Fca Consortium, Jasper, Heinrich, Oliver, Brian, Perrimon, Norbert, Deplancke, Bart, Quake, Stephen, Luo, Liqun, Aerts, Stein
Published in bioRxiv (05.07.2021)
Published in bioRxiv (05.07.2021)
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Paper
Single-cell gene regulatory network analysis reveals new melanoma cell states and transition trajectories during phenotype switching
Wouters, Jasper, Zeynep Kalender Atak, Minnoye, Liesbeth, Spanier, Katina, De Waegeneer, Maxime, Carmen Bravo Gonzalez-Blas, Mauduit, David, Davie, Kristofer, Hulselmans, Gert, Najem, Ahmad, Dewaele, Michael, Rambow, Florian, Makhzami, Samira, Christiaens, Valerie, Ceyssens, Frederik, Ghanem, Ghanem, Jean-Christophe Marine, Poovathingal, Suresh, Aerts, Stein
Published in bioRxiv (08.08.2019)
Published in bioRxiv (08.08.2019)
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A single-cell catalogue of regulatory states in the ageing Drosophila brain
Davie, Kristofer, Janssens, Jasper, Koldere, Duygu, Pech, Uli, Aibar, Sara, De Waegeneer, Maxime, Makhzami, Samira, Christiaens, Valerie, Carmen Bravo Gonzalez-Blas, Hulselmans, Gert, Spanier, Katina, Moerman, Thomas, Vanspauwen, Bram, Lammertyn, Jeroen, Thienpont, Bernard, Liu, Sha, Verstreken, Patrik, Aerts, Stein
Published in bioRxiv (21.12.2017)
Published in bioRxiv (21.12.2017)
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