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Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation Bravo Gonzalez-Blas, Carmen; Matetovici, Irina; Hillen, Hanne; Taskiran, Ibrahim Ihsan; Vandepoel, Roel; Christiaens, Valerie; Sansores-Garcia, Leticia; Verboven, Elisabeth; Hulselmans, Gert; Poovathingal, Suresh; Demeulemeester, Jonas; Psatha, Nikoleta; Mauduit, David; Halder, Georg; Aerts, Stein Share Save
Systematic benchmarking of single-cell ATAC-sequencing protocols De Rop, Florian V.; Hulselmans, Gert; Flerin, Chris; Soler-Vila, Paula; Rafels, Albert; Christiaens, Valerie; Gonzalez-Blas, Carmen Bravo; Marchese, Domenica; Caratu, Ginevra; Poovathingal, Suresh; Rozenblatt-Rosen, Orit; Slyper, Michael; Luo, Wendy; Muus, Christoph; Duarte, Fabiana; Shrestha, Rojesh; Bagdatli, S. Tansu; Corces, M. Ryan; Mamanova, Lira; Knights, Andrew; Meyer, Kerstin B.; Mulqueen, Ryan; Taherinasab, Akram; Maschmeyer, Patrick; Pezoldt, Jörn; Lambert, Camille Lucie Germaine; Iglesias, Marta; Najle, Sebastian R.; Dossani, Zain Y.; Martelotto, Luciano G.; Burkett, Zach; Lebofsky, Ronald; Martin-Subero, Jose Ignacio; Pillai, Satish; Sebe-Pedros, Arnau; Deplancke, Bart; Teichmann, Sarah A.; Ludwig, Leif S.; Braun, Theodore P.; Adey, Andrew C.; Greenleaf, William J.; Buenrostro, Jason D.; Regev, Aviv; Aerts, Stein; Heyn, Holger Share Save
SCENIC plus : single-cell multiomic inference of enhancers and gene regulatory networks Gonzalez-Blas, Carmen Bravo; De Winter, Seppe; Hulselmans, Gert; Hecker, Nikolai; Matetovici, Irina; Christiaens, Valerie; Poovathingal, Suresh; Wouters, Jasper; Aibar, Sara; Aerts, Stein Share Save
Shared enhancer gene regulatory networks between wound and oncogenic programs 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 Share Save
Cell type diversity in a developing octopus brain Styfhals, Ruth; Zolotarov, Grygoriy; Hulselmans, Gert; Spanier, Katina I.; Poovathingal, Suresh; Elagoz, Ali M.; De Winter, Seppe; Deryckere, Astrid; Rajewsky, Nikolaus; Ponte, Giovanna; Fiorito, Graziano; Aerts, Stein; Seuntjens, Eve Share Save
Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads De Rop, Florian, V; Ismail, Joy N.; Bravo Gonzalez-Blas, Carmen; Hulselmans, Gert J.; Flerin, Christopher Campbell; Janssens, Jasper; Theunis, Koen; Christiaens, Valerie M.; Wouters, Jasper; Marcassa, Gabriele; de Wit, Joris; Poovathingal, Suresh; Aerts, Stein Share Save
Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq Mylka, Viacheslav; Matetovici, Irina; Poovathingal, Suresh; Aerts, Jeroen; Vandamme, Niels; Seurinck, Ruth; Verstaen, Kevin; Hulselmans, Gert; van den Hoecke, Silvie; Scheyltjens, Isabelle; Movahedi, Kiavash; Wils, Hans; Reumers, Joke; Van Houdt, Jeroen; Aerts, Stein; Saeys, Yvan Share Save
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Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning Atak, Zeynep Kalender; Taskiran, Ibrahim Ihsan; Demeulemeester, Jonas; Flerin, Christopher; Mauduit, David; Minnoye, Liesbeth; Hulselmans, Gert; Christiaens, Valerie; Ghanem, Ghanem-Elias; Wouters, Jasper; Aerts, Stein Share Save
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; 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 Share Save
Cross-species analysis of enhancer logic using deep learning Minnoye, Liesbeth; Taskiran, Ibrahim Ihsan; Mauduit, David; Fazio, Maurizio; Van Aerschot, Linde; Hulselmans, Gert; Christiaens, Valerie; Makhzami, Samira; Seltenhammer, Monika; Karras, Panagiotis; Primot, Aline; Cadieu, Edouard; van Rooijen, Ellen; Marine, Jean-Christophe; Egidy, Giorgia; Ghanem, Ghanem-Elias; Zon, Leonard; Wouters, Jasper; Aerts, Stein Share Save
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 Share Save
Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics 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 Share Save
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The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes Jacobs, Jelle; Atkins, Mardelle; Davie, Kristofer; Imrichova, Hana; Romanelli, Lucia; Christiaens, Valerie; Hulselmans, Gert; Potier, Delphine; Wouters, Jasper; Taskiran, Ibrahim I.; Paciello, Giulia; Gonzalez-Blas, Carmen B.; Koldere, Duygu; Aibar, Sara; Halder, Georg; Aerts, Stein Share Save
SCENIC: single-cell regulatory network inference and clustering Aibar, Sara; Gonzalez-Blas, Carmen Bravo; Moerman, Thomas; Van Anh Huynh-Thu; Imrichova, Hana; Hulselmans, Gert; Rambow, Florian; Marine, Jean-Christophe; Geurts, Pierre; Aerts, Jan; van den Oord, Joost; Atak, Zeynep Kalender; Wouters, Jasper; Aerts, Stein Share Save
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