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

by 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
Published in Genome Res (2021)

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

by 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
Published in Mol Syst Biol (2020)

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

by Jacobs, Jelle, Atkins, Mardelle, Davie, Kristofer, Imrichova, Hana, Romanelli, Lucia, Christiaens, Valerie, Hulselmans, Gert, Potier, Delphine, Wouters, Jasper, Taskiran, Ibrahim Ihsan, Paciello, Giulia, González-Blas, Carmen Bravo, Koldere, Duygu, Aibar, Sara, Halder, Georg, Aerts, Stein
Published in Nat Genet (2018)

Cross-species analysis of enhancer logic using deep learning

by 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
Published in Genome Res (2020)