Search Results - "Van Heeringen, Simon J"

Role of p53 serine 46 in p53 target gene regulation by Smeenk, Leonie, van Heeringen, Simon J, Koeppel, Max, Gilbert, Bianca, Janssen-Megens, Eva, Stunnenberg, Hendrik G, Lohrum, Marion

“…The tumor suppressor p53 plays a crucial role in cellular growth control inducing a plethora of different response pathways. The molecular mechanisms that…”
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p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate by 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

“…Cleft palate is a common congenital disorder that affects up to 1 in 2500 live births and results in considerable morbidity to affected individuals and their…”
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Genome evolution in the allotetraploid frog Xenopus laevis by 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.

“…To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related…”
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MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding by Perino, Matteo, van Mierlo, Guido, Karemaker, Ino D., van Genesen, Siebe, Vermeulen, Michiel, Marks, Hendrik, van Heeringen, Simon J., Veenstra, Gert Jan C.

“…Abstact Polycomb-mediated repression of gene expression is essential for development, with a pivotal role played by trimethylation of histone H3 lysine 27…”
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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] by 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

“…The recent development of single-cell techniques is essential to unravel complex biological systems. By measuring the transcriptome and the accessible genome…”
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Amphioxus functional genomics and the origins of vertebrate gene regulation by Marlétaz, Ferdinand, Firbas, Panos N., Maeso, Ignacio, Tena, Juan J., Bogdanovic, Ozren, Perry, Malcolm, Wyatt, Christopher D. R., de la Calle-Mustienes, Elisa, Bertrand, Stephanie, Burguera, Demian, Acemel, Rafael D., van Heeringen, Simon J., Naranjo, Silvia, Herrera-Ubeda, Carlos, Skvortsova, Ksenia, Jimenez-Gancedo, Sandra, Aldea, Daniel, Marquez, Yamile, Buono, Lorena, Kozmikova, Iryna, Permanyer, Jon, Louis, Alexandra, Albuixech-Crespo, Beatriz, Le Petillon, Yann, Leon, Anthony, Subirana, Lucie, Balwierz, Piotr J., Duckett, Paul Edward, Farahani, Ensieh, Aury, Jean-Marc, Mangenot, Sophie, Wincker, Patrick, Albalat, Ricard, Benito-Gutiérrez, Èlia, Cañestro, Cristian, Castro, Filipe, D’Aniello, Salvatore, Ferrier, David E. K., Huang, Shengfeng, Laudet, Vincent, Marais, Gabriel A. B., Pontarotti, Pierre, Schubert, Michael, Seitz, Hervé, Somorjai, Ildiko, Takahashi, Tokiharu, Mirabeau, Olivier, Xu, Anlong, Yu, Jr-Kai, Carninci, Piero, Martinez-Morales, Juan Ramon, Crollius, Hugues Roest, Kozmik, Zbynek, Weirauch, Matthew T., Garcia-Fernàndez, Jordi, Lister, Ryan, Lenhard, Boris, Holland, Peter W. H., Escriva, Hector, Gómez-Skarmeta, Jose Luis, Irimia, Manuel

“…Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome…”
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ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination by Xu, Quan, Georgiou, Georgios, Frölich, Siebren, van der Sande, Maarten, Veenstra, Gert Jan C, Zhou, Huiqing, van Heeringen, Simon J

“…Abstract Proper cell fate determination is largely orchestrated by complex gene regulatory networks centered around transcription factors. However,…”
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Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation by Kouwenhoven, Evelyn N, Oti, Martin, Niehues, Hanna, van Heeringen, Simon J, Schalkwijk, Joost, Stunnenberg, Hendrik G, van Bokhoven, Hans, Zhou, Huiqing

“…The transcription factor p63 plays a pivotal role in keratinocyte proliferation and differentiation in the epidermis. However, how p63 regulates epidermal…”
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Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates by Bright, Ann Rose, van Genesen, Siebe, Li, Qingqing, Grasso, Alexia, Frölich, Siebren, van der Sande, Maarten, van Heeringen, Simon J, Veenstra, Gert Jan C

“…During vertebrate gastrulation, mesoderm is induced in pluripotent cells, concomitant with dorsal‐ventral patterning and establishing of the dorsal axis. We…”
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GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments by VAN HEERINGEN, Simon J, VEENSTRA, Gert Jan C

“…Accurate prediction of transcription factor binding motifs that are enriched in a collection of sequences remains a computational challenge. Here we report on…”
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Embryonic transcription is controlled by maternally defined chromatin state by Hontelez, Saartje, van Kruijsbergen, Ila, Georgiou, Georgios, van Heeringen, Simon J., Bogdanovic, Ozren, Lister, Ryan, Veenstra, Gert Jan C.

“…Histone-modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origins of the epigenome during…”
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ONECUT2 regulates RANKL-dependent enterocyte and microfold cell differentiation in the small intestine; a multi-omics study by 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

“…Microfold (M) cells reside in the intestinal epithelium of Peyer's patches (PP). Their unique ability to take up and transport antigens from the intestinal…”
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Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis by 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

“…The generation of distinctive cell types that form different tissues and organs requires precise, temporal and spatial control of gene expression. This depends…”
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Identification of the regulatory circuit governing corneal epithelial fate determination and disease by 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

“…The transparent corneal epithelium in the eye is maintained through the homeostasis regulated by limbal stem cells (LSCs), while the nontransparent epidermis…”
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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 by 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

“…Article Usage Stats Services MCB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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fluff: exploratory analysis and visualization of high-throughput sequencing data by Georgiou, Georgios, van Heeringen, Simon J

“…In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data…”
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A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos by Akkers, Robert C., van Heeringen, Simon J., Jacobi, Ulrike G., Janssen-Megens, Eva M., Françoijs, Kees-Jan, Stunnenberg, Hendrik G., Veenstra, Gert Jan C.

“…Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryogenesis…”
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Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis by Lederer, Simone, Heskes, Tom, van Heeringen, Simon J, Albers, Cornelis A

“…Cellular identity and behavior is controlled by complex gene regulatory networks. Transcription factors (TFs) bind to specific DNA sequences to regulate the…”
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Characterization of genome-wide p53-binding sites upon stress response by 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

“…The tumor suppressor p53 is a sequence-specific transcription factor, which regulates the expression of target genes involved in different stress responses. To…”
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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 by 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

“…Heterozygous mutations in p63 are associated with split hand/foot malformations (SHFM), orofacial clefting, and ectodermal abnormalities. Elucidation of the…”
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