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

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Shared enhancer gene regulatory networks between wound and oncogenic programs von 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

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Analysis of long and short enhancers in melanoma cell states von Mauduit, David, Taskiran, Ibrahim Ihsan, Minnoye, Liesbeth, de Waegeneer, Maxime, Christiaens, Valerie, Hulselmans, Gert, Demeulemeester, Jonas, Wouters, Jasper, Aerts, Stein

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A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain von 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

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

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Peritumoral activation of the Hippo pathway effectors YAP and TAZ suppresses liver cancer in mice von 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

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Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics von Bravo González‐Blas, Carmen, Quan, Xiao‐Jiang, Duran‐Romaña, Ramon, Taskiran, Ibrahim Ihsan, Koldere, Duygu, Davie, Kristofer, Christiaens, Valerie, Makhzami, Samira, Hulselmans, Gert, de Waegeneer, Maxime, Mauduit, David, Poovathingal, Suresh, Aibar, Sara, Aerts, Stein

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Decoding gene regulation in the fly brain von 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

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Analysis of long and short enhancers in melanoma cell states von Mauduit, David, Taskiran, Ibrahim Ihsan, Minnoye, Liesbeth, de Waegeneer, Maxime, Christiaens, Valerie, Hulselmans, Gert, Demeulemeester, Jonas, Wouters, Jasper, Aerts, Stein

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Analysis of long and short enhancers in melanoma cell states von Mauduit, David, Taskiran, Ibrahim Ihsan, Minnoye, Liesbeth, de Waegeneer, Maxime, Christiaens, Valerie, Hulselmans, Gert, Demeulemeester, Jonas, Wouters, Jasper, Aerts, Stein

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Shared enhancer gene regulatory networks between wound and oncogenic programs von Floc'hlay, Swann, Balaji, Ramya, Stankovic, Dimitrije, Christiaens, Valerie M, Gonzalez-Blas, Carmen Bravo, De Winter, Seppe, Hulselmans, Gert J, De Waegeneer, Maxime, Quan, Xiaojiang, Koldere, Duygu, Atkins, Mardelle, Halder, Georg, Uhlirova, Mirka, Classen, Anne-Kathrin, Aerts, Stein

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Decoding gene regulation in the fly brain von Janssens, Jasper, Aibar, Sara, Taskiran, Ibrahim Ihsan, Ismail, Joy N, Gomez, Alicia Estacio, Aughey, Gabriel, Spanier, Katina, De Rop, Florian, Gonzalez-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

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A scalable SCENIC workflow for single-cell gene regulatory network analysis von Van de Sande, Bram, Flerin, Christopher, Davie, Kristofer, De Waegeneer, Maxime, Hulselmans, Gert, Aibar Santos, Sara, Seurinck, Ruth, Saelens, Wouter, Cannoodt, Robrecht, Rouchon, Quentin, Verbeiren, Toni, De Maeyer, Dries, Reumers, Joke, Saeys, Yvan, Aerts, Stein

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Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics von Gonzalez-Blas, Carmen Bravo, Quan, Xiao-Jiang, Duran-Romana, Ramon, Taskiran, Ibrahim Ihsan, Koldere, Duygu, Davie, Kristofer, Christiaens, Valerie, Makhzami, Samira, Hulselmans, Gert, de Waegeneer, Maxime, Mauduit, David, Poovathingal, Suresh, Aibar, Sara, Aerts, Stein

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Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly von Li, Hongjie, Janssens, Jasper, De Waegeneer, Maxime, Kolluru, Sai Saroja, Davie, Kristofer, Gardeux, Vincent, Saelens, Wouter, David, Fabrice, Brbic, Maria, Leskovec, Jure, McLaughlin, Colleen N, Xie, Qijing, Jones, Robert C, Brueckner, Katja, Shim, Jiwon, Tattikota, Sudhir Gopal, Schnorrer, Frank, Rust, Katja, Nystul, Todd G, Carvalho-Santos, Zita, Ribeiro, Carlos, Pal, Soumitra, Mahadevaraju, Sharvani, Przytycka, Teresa M, Allen, Aaron M, Goodwin, Stephen F, Berry, Cameron W, Fuller, Margaret T, White-Cooper, Helen, Matunis, Erika L, DiNardo, Stephen, Galenza, Anthony, O'Brien, Lucy Erin, Dow, Julian A.T, Jasper, Heinrich, Oliver, Brian, Perrimon, Norbert, Deplancke, Bart, Quake, Stephen R, Luo, Liqun, Aerts, Stein

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Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma von Wouters, Jasper, Kalender-Atak, Zeynep, Minnoye, Liesbeth, Spanier, Katina, De Waegeneer, Maxime, Gonzalez-Blas, Carmen Bravo, 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

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Peritumoral activation of the Hippo pathway effectors YAP and TAZ suppresses liver cancer in mice von Moya, Ivan M, Castaldo, Stephanie A, Van den Mooter, Laura, Soheily, Soheil, Sansores-Garcia, Leticia, Jacobs, Jelle, Mannaerts, Inge, Xie, Jun, Verboven, Elisabeth, Hillen, Hanne, Alguero-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

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A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain von Davie, Kristofer, Janssens, Jasper, Koldere, Duygu, De Waegeneer, Maxime, Pech, Uli, Kreft, Lukasz, 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

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PySCENIC reduced test dataset for workflow testing von De Waegeneer, Maxime, Moreno, Pablo

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Decoding gene regulation in the fly brain von 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

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