Role of p53 serine 46 in p53 target gene regulation
Smeenk, Leonie, van Heeringen, Simon J, Koeppel, Max, Gilbert, Bianca, Janssen-Megens, Eva, Stunnenberg, Hendrik G, Lohrum, Marion
Published in PloS one (04.03.2011)
Published in PloS one (04.03.2011)
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p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate
Richardson, Rose, Mitchell, Karen, Hammond, Nigel L, Mollo, Maria Rosaria, Kouwenhoven, Evelyn N, Wyatt, Niki D, Donaldson, Ian J, Zeef, Leo, Burgis, Tim, Blance, Rognvald, van Heeringen, Simon J, Stunnenberg, Hendrik G, Zhou, Huiqing, Missero, Caterina, Romano, Rose Anne, Sinha, Satrajit, Dixon, Michael J, Dixon, Jill
Published in PLoS genetics (12.06.2017)
Published in PLoS genetics (12.06.2017)
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Genome evolution in the allotetraploid frog Xenopus laevis
Session, Adam M., Uno, Yoshinobu, Kwon, Taejoon, Chapman, Jarrod A., Toyoda, Atsushi, Takahashi, Shuji, Fukui, Akimasa, Hikosaka, Akira, Suzuki, Atsushi, Kondo, Mariko, van Heeringen, Simon J., Quigley, Ian, Heinz, Sven, Ogino, Hajime, Ochi, Haruki, Hellsten, Uffe, Lyons, Jessica B., Simakov, Oleg, Putnam, Nicholas, Stites, Jonathan, Kuroki, Yoko, Tanaka, Toshiaki, Michiue, Tatsuo, Watanabe, Minoru, Bogdanovic, Ozren, Lister, Ryan, Georgiou, Georgios, Paranjpe, Sarita S., van Kruijsbergen, Ila, Shu, Shengquiang, Carlson, Joseph, Kinoshita, Tsutomu, Ohta, Yuko, Mawaribuchi, Shuuji, Jenkins, Jerry, Grimwood, Jane, Schmutz, Jeremy, Mitros, Therese, Mozaffari, Sahar V., Suzuki, Yutaka, Haramoto, Yoshikazu, Yamamoto, Takamasa S., Takagi, Chiyo, Heald, Rebecca, Miller, Kelly, Haudenschild, Christian, Kitzman, Jacob, Nakayama, Takuya, Izutsu, Yumi, Robert, Jacques, Fortriede, Joshua, Burns, Kevin, Lotay, Vaneet, Karimi, Kamran, Yasuoka, Yuuri, Dichmann, Darwin S., Flajnik, Martin F., Houston, Douglas W., Shendure, Jay, DuPasquier, Louis, Vize, Peter D., Zorn, Aaron M., Ito, Michihiko, Marcotte, Edward M., Wallingford, John B., Ito, Yuzuru, Asashima, Makoto, Ueno, Naoto, Matsuda, Yoichi, Veenstra, Gert Jan C., Fujiyama, Asao, Harland, Richard M., Taira, Masanori, Rokhsar, Daniel S.
Published in Nature (London) (20.10.2016)
Published in Nature (London) (20.10.2016)
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MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding
Perino, Matteo, van Mierlo, Guido, Karemaker, Ino D., van Genesen, Siebe, Vermeulen, Michiel, Marks, Hendrik, van Heeringen, Simon J., Veenstra, Gert Jan C.
Published in Nature genetics (01.07.2018)
Published in Nature genetics (01.07.2018)
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scANANSE gene regulatory network and motif analysis of single-cell clusters [version 1; peer review: 1 approved, 1 approved with reservations]
Smits, Jos G.A., Arts, Julian A., Frölich, Siebren, Snabel, Rebecca R., Heuts, Branco M.H., Martens, Joost H.A., van Heeringen, Simon J., Zhou, Huiqing
Published in F1000 research (2023)
Published in F1000 research (2023)
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ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination
Xu, Quan, Georgiou, Georgios, Frölich, Siebren, van der Sande, Maarten, Veenstra, Gert Jan C, Zhou, Huiqing, van Heeringen, Simon J
Published in Nucleic acids research (20.08.2021)
Published in Nucleic acids research (20.08.2021)
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Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation
Kouwenhoven, Evelyn N, Oti, Martin, Niehues, Hanna, van Heeringen, Simon J, Schalkwijk, Joost, Stunnenberg, Hendrik G, van Bokhoven, Hans, Zhou, Huiqing
Published in EMBO reports (01.07.2015)
Published in EMBO reports (01.07.2015)
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Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates
Bright, Ann Rose, van Genesen, Siebe, Li, Qingqing, Grasso, Alexia, Frölich, Siebren, van der Sande, Maarten, van Heeringen, Simon J, Veenstra, Gert Jan C
Published in The EMBO journal (03.05.2021)
Published in The EMBO journal (03.05.2021)
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ONECUT2 regulates RANKL-dependent enterocyte and microfold cell differentiation in the small intestine; a multi-omics study
Luna Velez, Maria V, Neikes, Hannah K, Snabel, Rebecca R, Quint, Yarah, Qian, Chen, Martens, Aniek, Veenstra, Gert Jan C, Freeman, Michael R, van Heeringen, Simon J, Vermeulen, Michiel
Published in Nucleic acids research (22.02.2023)
Published in Nucleic acids research (22.02.2023)
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Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
Bogdanovic, Ozren, Fernandez-Miñán, Ana, Tena, Juan J, de la Calle-Mustienes, Elisa, Hidalgo, Carmen, van Kruysbergen, Ila, van Heeringen, Simon J, Veenstra, Gert Jan C, Gómez-Skarmeta, José Luis
Published in Genome research (01.10.2012)
Published in Genome research (01.10.2012)
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Identification of the regulatory circuit governing corneal epithelial fate determination and disease
Smits, Jos G A, Cunha, Dulce Lima, Amini, Maryam, Bertolin, Marina, Laberthonnière, Camille, Qu, Jieqiong, Owen, Nicholas, Latta, Lorenz, Seitz, Berthold, Roux, Lauriane N, Stachon, Tanja, Ferrari, Stefano, Moosajee, Mariya, Aberdam, Daniel, Szentmary, Nora, van Heeringen, Simon J, Zhou, Huiqing
Published in PLoS biology (19.10.2023)
Published in PLoS biology (19.10.2023)
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Genome-Wide Profiling of Liver X Receptor, Retinoid X Receptor, and Peroxisome Proliferator-Activated Receptor α in Mouse Liver Reveals Extensive Sharing of Binding Sites
Boergesen, Michael, Pedersen, Thomas Åskov, Gross, Barbara, van Heeringen, Simon J., Hagenbeek, Dik, Bindesbøll, Christian, Caron, Sandrine, Lalloyer, Fanny, Steffensen, Knut R., Nebb, Hilde I., Gustafsson, Jan-Åke, Stunnenberg, Hendrik G., Staels, Bart, Mandrup, Susanne
Published in Molecular and Cellular Biology (01.02.2012)
Published in Molecular and Cellular Biology (01.02.2012)
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A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos
Akkers, Robert C., van Heeringen, Simon J., Jacobi, Ulrike G., Janssen-Megens, Eva M., Françoijs, Kees-Jan, Stunnenberg, Hendrik G., Veenstra, Gert Jan C.
Published in Developmental cell (01.09.2009)
Published in Developmental cell (01.09.2009)
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Characterization of genome-wide p53-binding sites upon stress response
Smeenk, Leonie, van Heeringen, Simon J, Koeppel, Max, van Driel, Marc A, Bartels, Stefanie J.J, Akkers, Robert C, Denissov, Sergei, Stunnenberg, Hendrik G, Lohrum, Marion
Published in Nucleic acids research (01.06.2008)
Published in Nucleic acids research (01.06.2008)
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Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus
Kouwenhoven, Evelyn N, van Heeringen, Simon J, Tena, Juan J, Oti, Martin, Dutilh, Bas E, Alonso, M Eva, de la Calle-Mustienes, Elisa, Smeenk, Leonie, Rinne, Tuula, Parsaulian, Lilian, Bolat, Emine, Jurgelenaite, Rasa, Huynen, Martijn A, Hoischen, Alexander, Veltman, Joris A, Brunner, Han G, Roscioli, Tony, Oates, Emily, Wilson, Meredith, Manzanares, Miguel, Gómez-Skarmeta, José Luis, Stunnenberg, Hendrik G, Lohrum, Marion, van Bokhoven, Hans, Zhou, Huiqing
Published in PLoS genetics (01.08.2010)
Published in PLoS genetics (01.08.2010)
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Regulatory remodeling in the allo-tetraploid frog Xenopus laevis
Elurbe, Dei M, Paranjpe, Sarita S, Georgiou, Georgios, van Kruijsbergen, Ila, Bogdanovic, Ozren, Gibeaux, Romain, Heald, Rebecca, Lister, Ryan, Huynen, Martijn A, van Heeringen, Simon J, Veenstra, Gert Jan C
Published in Genome Biology (24.10.2017)
Published in Genome Biology (24.10.2017)
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