GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks von Moerman, Thomas, Aibar Santos, Sara, Bravo González-Blas, Carmen, Simm, Jaak, Moreau, Yves, Aerts, Jan, 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, Sara, Seurinck, Ruth, Saelens, Wouter, Cannoodt, Robrecht, Rouchon, Quentin, Verbeiren, Toni, De Maeyer, Dries, Reumers, Joke, Saeys, Yvan, Aerts, Stein

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cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data von Bravo González-Blas, Carmen, Minnoye, Liesbeth, Papasokrati, Dafni, Aibar, Sara, Hulselmans, Gert, Christiaens, Valerie, Davie, Kristofer, Wouters, Jasper, Aerts, Stein

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Phenotype molding of stromal cells in the lung tumor microenvironment von Lambrechts, Diether, Wauters, Els, Boeckx, Bram, Aibar, Sara, Nittner, David, Burton, Oliver, Bassez, Ayse, Decaluwé, Herbert, Pircher, Andreas, Van den Eynde, Kathleen, Weynand, Birgit, Verbeken, Erik, De Leyn, Paul, Liston, Adrian, Vansteenkiste, Johan, Carmeliet, Peter, Aerts, Stein, Thienpont, Bernard

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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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Toward Minimal Residual Disease-Directed Therapy in Melanoma von Rambow, Florian, Rogiers, Aljosja, Marin-Bejar, Oskar, Aibar, Sara, Femel, Julia, Dewaele, Michael, Karras, Panagiotis, Brown, Daniel, Chang, Young Hwan, Debiec-Rychter, Maria, Adriaens, Carmen, Radaelli, Enrico, Wolter, Pascal, Bechter, Oliver, Dummer, Reinhard, Levesque, Mitchell, Piris, Adriano, Frederick, Dennie T., Boland, Genevieve, Flaherty, Keith T., van den Oord, Joost, Voet, Thierry, Aerts, Stein, Lund, Amanda W., Marine, Jean-Christophe

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Actuation enhances patterning in human neural tube organoids von Abdel Fattah, Abdel Rahman, Daza, Brian, Rustandi, Gregorius, Berrocal-Rubio, Miguel Ángel, Gorissen, Benjamin, Poovathingal, Suresh, Davie, Kristofer, Barrasa-Fano, Jorge, Cóndor, Mar, Cao, Xuanye, Rosenzweig, Derek Hadar, Lei, Yunping, Finnell, Richard, Verfaillie, Catherine, Sampaolesi, Maurilio, Dedecker, Peter, Van Oosterwyck, Hans, Aerts, Stein, Ranga, Adrian

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Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling von Davie, Kristofer, Jacobs, Jelle, Atkins, Mardelle, Potier, Delphine, Christiaens, Valerie, Halder, Georg, Aerts, Stein

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i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules von Herrmann, Carl, Van de Sande, Bram, Potier, Delphine, Aerts, Stein

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Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics von Bates, Alexander Shakeel, Janssens, Jasper, Jefferis, Gregory SXE, 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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i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly von Imrichová, Hana, Hulselmans, Gert, Atak, Zeynep Kalender, Potier, Delphine, Aerts, Stein

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Melanoma addiction to the long non-coding RNA SAMMSON von Leucci, Eleonora, Vendramin, Roberto, Spinazzi, Marco, Laurette, Patrick, Fiers, Mark, Wouters, Jasper, Radaelli, Enrico, Eyckerman, Sven, Leonelli, Carina, Vanderheyden, Katrien, Rogiers, Aljosja, Hermans, Els, Baatsen, Pieter, Aerts, Stein, Amant, Frederic, Van Aelst, Stefan, van den Oord, Joost, de Strooper, Bart, Davidson, Irwin, Lafontaine, Denis L. J., Gevaert, Kris, Vandesompele, Jo, Mestdagh, Pieter, Marine, Jean-Christophe

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iRegulon: from a gene list to a gene regulatory network using large motif and track collections von Janky, Rekin's, Verfaillie, Annelien, Imrichová, Hana, Van de Sande, Bram, Standaert, Laura, Christiaens, Valerie, Hulselmans, Gert, Herten, Koen, Naval Sanchez, Marina, Potier, Delphine, Svetlichnyy, Dmitry, Kalender Atak, Zeynep, Fiers, Mark, Marine, Jean-Christophe, Aerts, Stein

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Gitools: analysis and visualisation of genomic data using interactive heat-maps von Perez-Llamas, Christian, Lopez-Bigas, Nuria

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Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells von Laurette, Patrick, Strub, Thomas, Koludrovic, Dana, Keime, Céline, Le Gras, Stéphanie, Seberg, Hannah, Van Otterloo, Eric, Imrichova, Hana, Siddaway, Robert, Aerts, Stein, Cornell, Robert A, Mengus, Gabrielle, Davidson, Irwin

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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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Mapping gene regulatory networks from single-cell omics data von Fiers, Mark W E J, Minnoye, Liesbeth, Aibar, Sara, Bravo González-Blas, Carmen, Kalender Atak, Zeynep, Aerts, Stein

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Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state von Verfaillie, Annelien, Imrichova, Hana, Atak, Zeynep Kalender, Dewaele, Michael, Rambow, Florian, Hulselmans, Gert, Christiaens, Valerie, Svetlichnyy, Dmitry, Luciani, Flavie, Van den Mooter, Laura, Claerhout, Sofie, Fiers, Mark, Journe, Fabrice, Ghanem, Ghanem-Elias, Herrmann, Carl, Halder, Georg, Marine, Jean-Christophe, Aerts, Stein

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An Ectopic Network of Transcription Factors Regulated by Hippo Signaling Drives Growth and Invasion of a Malignant Tumor Model von Atkins, Mardelle, Potier, Delphine, Romanelli, Lucia, Jacobs, Jelle, Mach, Jana, Hamaratoglu, Fisun, Aerts, Stein, Halder, Georg

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