Henk Stunnenberg

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1978 …2023

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  • 2016

    Histone Methylation by the Kleefstra Syndrome Protein EHMT1 Mediates Homeostatic Synaptic Scaling

    Benevento, M., Iacono, G., Selten, M., Ba, W., Oudakker, A., Frega, M., Keller, J., Mancini, R., Lewerissa, E., Kleefstra, T., Stunnenberg, H. G., Zhou, H., van Bokhoven, H. & Nadif Kasri, N., 20 Jul 2016, In: Neuron. 91, 2, p. 341-355 15 p.

    Research output: Contribution to journalArticlepeer-review

    56 Citations (Scopus)
  • Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells

    von Meyenn, F., Iurlaro, M., Habibi, E., Liu, N. Q., Salehzadeh-Yazdi, A., Santos, F., Petrini, E., Milagre, I., Yu, M., Xie, Z., Kroeze, L. I., Nesterova, T. B., Jansen, J. H., Xie, H., He, C., Reik, W. & Stunnenberg, H. G., 16 Jun 2016, In: Molecular Cell. 62, 6, p. 848-861 14 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    141 Citations (Scopus)
  • Information recovery from low coverage whole-genome bisulfite sequencing

    Libertini, E., Heath, S. C., Hamoudi, R. A., Gut, M., Ziller, M. J., Czyz, A., Ruotti, V., Stunnenberg, H. G., Frontini, M., Ouwehand, W. H., Meissner, A., Gut, I. G. & Beck, S., 27 Jun 2016, In: Nature Communications. 7, 11306.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    30 Citations (Scopus)
  • Landscape of somatic mutations in 560 breast cancer whole-genome sequences

    Nik-Zainal, S., Davies, H., Staaf, J., Ramakrishna, M., Glodzik, D., Zou, X., Martincorena, I., Alexandrov, L. B., Martin, S., Wedge, D. C., Van Loo, P., Ju, Y. S., Smid, M., Brinkman, A. B., Morganella, S., Aure, M. R., Lingjærde, O. C., Langerød, A., Ringnér, M., Ahn, S. M., & 68 othersBoyault, S., Brock, J. E., Broeks, A., Butler, A., Desmedt, C., Dirix, L., Dronov, S., Fatima, A., Foekens, J. A., Gerstung, M., Hooijer, G. K. J., Jang, S. J., Jones, D. R., Kim, H. Y., King, T. A., Krishnamurthy, S., Lee, H. J., Lee, J. Y., Li, Y., McLaren, S., Menzies, A., Mustonen, V., O'Meara, S., Pauporté, I., Pivot, X., Purdie, C. A., Raine, K., Ramakrishnan, K., Rodríguez-González, F. G., Romieu, G., Sieuwerts, A. M., Simpson, P. T., Shepherd, R., Stebbings, L., Stefansson, O. A., Teague, J., Tommasi, S., Treilleux, I., Van Den Eynden, G. G., Vermeulen, P., Vincent-Salomon, A., Yates, L., Caldas, C., Veer, L. V. T., Tutt, A., Knappskog, S., Tan, B. K. T., Jonkers, J., Borg, Å., Ueno, N. T., Sotiriou, C., Viari, A., Futreal, P. A., Campbell, P. J., Span, P. N., Van Laere, S., Lakhani, S. R., Eyfjord, J. E., Thompson, A. M., Birney, E., Stunnenberg, H. G., Van De Vijver, M. J., Martens, J. W. M., Børresen-Dale, A. L., Richardson, A. L., Kong, G., Thomas, G. & Stratton, M. R., 2 May 2016, In: Nature. 534, 7605, p. 47-54 8 p.

    Research output: Contribution to journalArticlepeer-review

    1476 Citations (Scopus)
  • Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

    Javierre, B. M., Sewitz, S., Cairns, J., Wingett, S. W., Várnai, C., Thiecke, M. J., Freire-Pritchett, P., Spivakov, M., Fraser, P., Burren, O. S., Cutler, A. J., Todd, J. A., Wallace, C., Wilder, S. P., Kreuzhuber, R., Kostadima, M., Zerbino, D. R., Stegle, O., Burden, F., Farrow, S., & 19 othersRehnström, K., Downes, K., Grassi, L., Ouwehand, W. H., Frontini, M., Hill, S. M., Wang, F., Stunnenberg, H. G., Martens, J. H., Kim, B., Sharifi, N., Janssen-Megens, E. M., Yaspo, M. L., Linser, M., Kovacsovics, A., Clarke, L., Richardson, D., Datta, A. & Flicek, P., 17 Nov 2016, In: Cell. 167, 5, p. 1369-1384.e19

    Research output: Contribution to journalArticlepeer-review

    Open Access
    615 Citations (Scopus)
  • MEIS2 Is an Oncogenic Partner in AML1-ETO-Positive AML

    Vegi, N. M., Klappacher, J., Oswald, F., Mulaw, M. A., Mandoli, A., Thiel, V. N., Bamezai, S., Feder, K., Martens, J. H. A., Rawat, V. P. S., Mandal, T., Quintanilla-Martinez, L., Spiekermann, K., Hiddemann, W., Döhner, K., Döhner, H., Stunnenberg, H. G., Feuring-Buske, M. & Buske, C., 12 Jul 2016, In: Cell Reports. 16, 2, p. 498-507 10 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    32 Citations (Scopus)
  • Non-canonical PRC1.1 Targets Active Genes Independent of H3K27me3 and Is Essential for Leukemogenesis

    van den Boom, V., Maat, H., Geugien, M., Rodríguez López, A., Sotoca, A. M., Jaques, J., Brouwers-Vos, A. Z., Fusetti, F., Groen, R. W. J., Yuan, H., Martens, A. C. M., Stunnenberg, H. G., Vellenga, E., Martens, J. H. A. & Schuringa, J. J., 12 Jan 2016, In: Cell Reports. 14, 2, p. 332-346 15 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    108 Citations (Scopus)
  • Recruitment of the mammalian histone-modifying EMSY complex to target genes is regulated by ZNF131

    Varier, R. A., De Santa Pau, E. C., Van Der Groep, P., Lindeboom, R. G. H., Matarese, F., Mensinga, A., Smits, A. H., Edupuganti, R. R., Baltissen, M. P., Jansen, P. W. T. C., Hoeve, N. T., Van Weely, D. R., Poser, I., Van Diest, P. J., Stunnenberg, H. G. & Vermeulen, M., 1 Apr 2016, In: Journal of Biological Chemistry. 291, 14, p. 7313-7324 12 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    29 Citations (Scopus)
  • The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

    Astle, W. J., Elding, H., Jiang, T., Allen, D., Ruklisa, D., Mann, A. L., Mead, D., Bouman, H., Riveros-Mckay, F., Kostadima, M. A., Lambourne, J. J., Sivapalaratnam, S., Downes, K., Kundu, K., Bomba, L., Berentsen, K., Bradley, J. R., Daugherty, L. C., Delaneau, O., Freson, K., & 54 othersGarner, S. F., Grassi, L., Guerrero, J., Haimel, M., Janssen-Megens, E. M., Kaan, A., Kamat, M., Kim, B., Mandoli, A., Marchini, J., Martens, J. H. A., Meacham, S., Megy, K., O'Connell, J., Petersen, R., Sharifi, N., Sheard, S. M., Staley, J. R., Tuna, S., van der Ent, M., Walter, K., Wang, S. Y., Wheeler, E., Wilder, S. P., Iotchkova, V., Moore, C., Sambrook, J., Stunnenberg, H. G., Di Angelantonio, E., Kaptoge, S., Kuijpers, T. W., Carrillo-de-Santa-Pau, E., Juan, D., Rico, D., Valencia, A., Chen, L., Ge, B., Vasquez, L., Kwan, T., Garrido-Martín, D., Watt, S., Yang, Y., Guigo, R., Beck, S., Paul, D. S., Pastinen, T., Bujold, D., Bourque, G., Frontini, M., Danesh, J., Roberts, D. J., Ouwehand, W. H., Butterworth, A. S. & Soranzo, N., 17 Nov 2016, In: Cell. 167, 5, p. 1415-1429.e19

    Research output: Contribution to journalArticlepeer-review

    Open Access
    736 Citations (Scopus)
  • The Hematopoietic Transcription Factors RUNX1 and ERG Prevent AML1-ETO Oncogene Overexpression and Onset of the Apoptosis Program in t(8;21) AMLs

    Mandoli, A., Singh, A. A., Prange, K. H. M., Tijchon, E., Oerlemans, M., Dirks, R., Ter Huurne, M., Wierenga, A. T. J., Janssen-Megens, E. M., Berentsen, K., Sharifi, N., Kim, B., Matarese, F., Nguyen, L. N., Hubner, N. C., Rao, N. A., van den Akker, E., Altucci, L., Vellenga, E., Stunnenberg, H. G., & 1 othersMartens, J. H. A., 15 Nov 2016, In: Cell Reports. 17, 8, p. 2087-2100 14 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    45 Citations (Scopus)
  • The oncofusion protein FUS-ERG targets key hematopoietic regulators and modulates the all-trans retinoic acid signaling pathway in t(16;21) acute myeloid leukemia

    Sotoca, A. M., Prange, K. H. M., Reijnders, B., Mandoli, A., Nguyen, L. N., Stunnenberg, H. G. & Martens, J. H. A., 14 Apr 2016, In: Oncogene. 35, 15, p. 1965-1976 12 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    34 Citations (Scopus)
  • The topography of mutational processes in breast cancer genomes

    Morganella, S., Alexandrov, L. B., Glodzik, D., Zou, X., Davies, H., Staaf, J., Sieuwerts, A. M., Brinkman, A. B., Martin, S., Ramakrishna, M., Butler, A., Kim, H. Y., Borg, Å., Sotiriou, C., Futreal, P. A., Campbell, P. J., Span, P. N., Van Laere, S., Lakhani, S. R., Eyfjord, J. E., & 13 othersThompson, A. M., Stunnenberg, H. G., Van De Vijver, M. J., Martens, J. W. M., Børresen-Dale, A. L., Richardson, A. L., Kong, G., Thomas, G., Sale, J., Rada, C., Stratton, M. R., Birney, E. & Nik-Zainal, S., 2 May 2016, In: Nature Communications. 7, 11383.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    193 Citations (Scopus)
  • Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells

    De Simone, M., Arrigoni, A., Rossetti, G., Gruarin, P., Ranzani, V., Politano, C., Bonnal, R. J. P., Provasi, E., Sarnicola, M. L., Panzeri, I., Moro, M., Crosti, M., Mazzara, S., Vaira, V., Bosari, S., Palleschi, A., Santambrogio, L., Bovo, G., Zucchini, N., Totis, M., & 11 othersGianotti, L., Cesana, G., Perego, R. A., Maroni, N., Pisani Ceretti, A., Opocher, E., De Francesco, R., Geginat, J., Stunnenberg, H. G., Abrignani, S. & Pagani, M., 15 Nov 2016, In: Immunity. 45, 5, p. 1135-1147 13 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    448 Citations (Scopus)
  • ZMYND8 Co-localizes with NuRD on Target Genes and Regulates Poly(ADP-Ribose)-Dependent Recruitment of GATAD2A/NuRD to Sites of DNA Damage

    Spruijt, C. G., Luijsterburg, M. S., Menafra, R., Lindeboom, R. G. H., Jansen, P. W. T. C., Edupuganti, R. R., Baltissen, M. P., Wiegant, W. W., Voelker-Albert, M. C., Matarese, F., Mensinga, A., Poser, I., Vos, H. R., Stunnenberg, H. G., van Attikum, H. & Vermeulen, M., 11 Oct 2016, In: Cell Reports. 17, 3, p. 783-798 16 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    80 Citations (Scopus)
  • β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance

    Novakovic, B., Habibi, E., Wang, S. Y., Arts, R. J. W., Davar, R., Megchelenbrink, W., Kim, B., Kuznetsova, T., Kox, M., Zwaag, J., Matarese, F., van Heeringen, S. J., Janssen-Megens, E. M., Sharifi, N., Wang, C., Keramati, F., Schoonenberg, V., Flicek, P., Clarke, L., Pickkers, P., & 6 othersHeath, S., Gut, I., Netea, M. G., Martens, J. H. A., Logie, C. & Stunnenberg, H. G., 17 Nov 2016, In: Cell. 167, 5, p. 1354-1368.e14

    Research output: Contribution to journalArticlepeer-review

    Open Access
    391 Citations (Scopus)
  • 2015

    A quantitative proteomics tool to identify DNA-protein interactions in primary cells or blood

    Hubner, N. C., Nguyen, L. N., Hornig, N. C. & Stunnenberg, H. G., 6 Feb 2015, In: Journal of Proteome Research. 14, 2, p. 1315-1329 15 p.

    Research output: Contribution to journalArticlepeer-review

    28 Citations (Scopus)
  • Conditional depletion of intellectual disability and Parkinsonism candidate gene ATP6AP2 in fly and mouse induces cognitive impairment and neurodegeneration

    Dubos, A., Castells-Nobau, A., Meziane, H., Oortveld, M. A. W., Houbaert, X., Iacono, G., Martin, C., Mittelhaeuser, C., Lalanne, V., Kramer, J. M., Bhukel, A., Quentin, C., Slabbert, J., Verstreken, P., Sigrist, S. J., Messaddeq, N., Birling, M. C., Selloum, M., Stunnenberg, H. G., Humeau, Y., & 2 othersSchenck, A. & Herault, Y., 1 Dec 2015, In: Human Molecular Genetics. 24, 23, p. 6736-6755 20 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    49 Citations (Scopus)
  • DNA Methylation of the Aryl Hydrocarbon Receptor Repressor Associations with Cigarette Smoking and Subclinical Atherosclerosis

    Reynolds, L. M., Wan, M., Ding, J., Taylor, J. R., Lohman, K., Su, D., Bennett, B. D., Porter, D. K., Gimple, R., Pittman, G. S., Wang, X., Howard, T. D., Siscovick, D., Psaty, B. M., Shea, S., Burke, G. L., Jacobs, D. R., Rich, S. S., Hixson, J. E., Stein, J. H., & 8 othersStunnenberg, H., Barr, R. G., Kaufman, J. D., Post, W. S., Hoeschele, I., Herrington, D. M., Bell, D. A. & Liu, Y., 1 Oct 2015, In: Circulation: Cardiovascular Genetics. 8, 5, p. 707-716 10 p.

    Research output: Contribution to journalArticlepeer-review

    98 Citations (Scopus)
  • DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control

    Kretzmer, H., Bernhart, S. H., Wang, W., Haake, A., Weniger, M. A., Bergmann, A. K., Betts, M. J., Carrillo-de-Santa-Pau, E., Doose, G., Gutwein, J., Richter, J., Hovestadt, V., Huang, B., Rico, D., Jühling, F., Kolarova, J., Lu, Q., Otto, C., Wagener, R., Arnolds, J., & 40 othersBurkhardt, B., Claviez, A., Drexler, H. G., Eberth, S., Eils, R., Flicek, P., Haas, S., Hummel, M., Karsch, D., Kerstens, H. H. D., Klapper, W., Kreuz, M., Lawerenz, C., Lenze, D., Loeffler, M., López, C., MacLeod, R. A. F., Martens, J. H. A., Kulis, M., Martín-Subero, J. I., Möller, P., Nagel, I., Picelli, S., Vater, I., Rohde, M., Rosenstiel, P., Rosolowski, M., Russell, R. B., Schilhabel, M., Schlesner, M., Stadler, P. F., Szczepanowski, M., Trümper, L., Stunnenberg, H. G., Küppers, R., Ammerpohl, O., Lichter, P., Siebert, R., Hoffmann, S. & Radlwimmer, B., 1 Nov 2015, In: Nature Genetics. 47, 11, p. 1316-1325 10 p.

    Research output: Contribution to journalArticlepeer-review

    108 Citations (Scopus)
  • Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency

    Joshi, O., Wang, S. Y., Kuznetsova, T., Atlasi, Y., Peng, T., Fabre, P. J., Habibi, E., Shaik, J., Saeed, S., Handoko, L., Richmond, T., Spivakov, M., Burgess, D. & Stunnenberg, H. G., 3 Dec 2015, In: Cell Stem Cell. 17, 6, p. 748-757 10 p.

    Research output: Contribution to journalArticlepeer-review

    143 Citations (Scopus)
  • Dynamics of gene silencing during X inactivation using allele-specific RNA-seq

    Marks, H., Kerstens, H. H. D., Barakat, T. S., Splinter, E., Dirks, R. A. M., van Mierlo, G., Joshi, O., Wang, S. Y., Babak, T., Albers, C. A., Kalkan, T., Smith, A., Jouneau, A., de Laat, W., Gribnau, J. & Stunnenberg, H. G., 3 Aug 2015, In: Genome Biology. 16, 1, 149.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    81 Citations (Scopus)
  • Epigenome data release: A participant-centered approach to privacy protection

    Dyke, S. O. M., Cheung, W. A., Joly, Y., Ammerpohl, O., Lutsik, P., Rothstein, M. A., Caron, M., Busche, S., Bourque, G., Rönnblom, L., Flicek, P., Beck, S., Hirst, M., Stunnenberg, H., Siebert, R., Walter, J. & Pastinen, T., 17 Jul 2015, In: Genome Biology. 16, 1, 142.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    33 Citations (Scopus)
  • Epigenomics: Roadmap for regulation

    Romanoski, C. E., Glass, C. K., Stunnenberg, H. G., Wilson, L. & Almouzni, G., 19 Feb 2015, In: Nature. 518, 7539, p. 314-316 3 p.

    Research output: Contribution to journalArticlepeer-review

    163 Citations (Scopus)
  • Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays

    Honkela, A., Peltonen, J., Topa, H., Charapitsa, I., Matarese, F., Grote, K., Stunnenberg, H. G., Reid, G., Lawrence, N. D. & Rattray, M., 20 Oct 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 42, p. 13115-13120 6 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    64 Citations (Scopus)
  • Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization

    Kuznetsova, T., Wang, S. Y., Rao, N. A., Mandoli, A., Martens, J. H. A., Rother, N., Aartse, A., Groh, L., Janssen-Megens, E. M., Li, G., Ruan, Y., Logie, C. & Stunnenberg, H. G., 1 Dec 2015, In: Genome Biology. 16, 1, 264.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    40 Citations (Scopus)
  • MINCR is a MYC-induced lncRNA able to modulate MYC's transcriptional network in Burkitt lymphoma cells

    Doose, G., Haake, A., Bernhart, S. H., López, C., Duggimpudi, S., Wojciech, F., Bergmann, A. K., Borkhardt, A., Burkhardt, B., Claviez, A., Dimitrova, L., Haas, S., Hoell, J. I., Hummel, M., Karsch, D., Klapper, W., Kleo, K., Kretzmer, H., Kreuz, M., Küppers, R., & 22 othersLawerenz, C., Lenze, D., Loeffler, M., Mantovani-Löffler, L., Möller, P., Ott, G., Richter, J., Rohde, M., Rosenstiel, P., Rosenwald, A., Schilhabel, M., Schneider, M., Scholz, I., Stilgenbauer, S., Stunnenberg, H. G., Szczepanowski, M., Trümper, L., Weniger, M. A., Hoffmann, S., Siebert, R., Iaccarino, I. & Eisenman, R. N., 22 Sept 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 38, p. E5261-E5270

    Research output: Contribution to journalArticlepeer-review

    89 Citations (Scopus)
  • Non-coding recurrent mutations in chronic lymphocytic leukaemia

    Puente, X. S., Beà, S., Valdés-Mas, R., Villamor, N., Gutiérrez-Abril, J., Martín-Subero, J. I., Munar, M., Rubio-Pérez, C., Jares, P., Aymerich, M., Baumann, T., Beekman, R., Belver, L., Carrio, A., Castellano, G., Clot, G., Colado, E., Colomer, D., Costa, D., Delgado, J., & 37 othersEnjuanes, A., Estivill, X., Ferrando, A. A., Gelpí, J. L., González, B., González, S., González, M., Gut, M., Hernández-Rivas, J. M., López-Guerra, M., Martín-García, D., Navarro, A., Nicolás, P., Orozco, M., Payer, Á. R., Pinyol, M., Pisano, D. G., Puente, D. A., Queirós, A. C., Quesada, V., Romeo-Casabona, C. M., Royo, C., Royo, R., Rozman, M., Russiñol, N., Salaverría, I., Stamatopoulos, K., Stunnenberg, H. G., Tamborero, D., Terol, M. J., Valencia, A., López-Bigas, N., Torrents, D., Gut, I., López-Guillermo, A., López-Otín, C. & Campo, E., 22 Oct 2015, In: Nature. 526, 7574, p. 519-524 6 p.

    Research output: Contribution to journalArticlepeer-review

    657 Citations (Scopus)
  • Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation

    Kouwenhoven, E. N., Oti, M., Niehues, H., Van Heeringen, S. J., Schalkwijk, J., Stunnenberg, H. G., Van Bokhoven, H. & Zhou, H., 1 Jul 2015, In: EMBO Reports. 16, 7, p. 863-878 16 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    112 Citations (Scopus)
  • Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers

    Agirre, X., Castellano, G., Pascual, M., Heath, S., Kulis, M., Segura, V., Bergmann, A., Esteve, A., Merkel, A., Raineri, E., Agueda, L., Blanc, J., Richardson, D., Clarke, L., Datta, A., Russiñol, N., Queirós, A. C., Beekman, R., Rodríguez-Madoz, J. R., José-Enériz, E. S., & 18 othersFang, F., Gutiérrez, N. C., García-Verdugo, J. M., Robson, M. I., Schirmer, E. C., Guruceaga, E., Martens, J. H. A., Gut, M., Calasanz, M. J., Flicek, P., Siebert, R., Campo, E., San Miguel, J. F., Melnick, A., Stunnenberg, H. G., Gut, I. G., Prosper, F. & Martín-Subero, J. I., 1 Apr 2015, In: Genome Research. 25, 4, p. 478-487 10 p.

    Research output: Contribution to journalArticlepeer-review

    105 Citations (Scopus)
  • Whole-genome fingerprint of the DNA methylome during human B cell differentiation

    Kulis, M., Merkel, A., Heath, S., Queirós, A. C., Schuyler, R. P., Castellano, G., Beekman, R., Raineri, E., Esteve, A., Clot, G., Verdaguer-Dot, N., Duran-Ferrer, M., Russiñol, N., Vilarrasa-Blasi, R., Ecker, S., Pancaldi, V., Rico, D., Agueda, L., Blanc, J., Richardson, D., & 22 othersClarke, L., Datta, A., Pascual, M., Agirre, X., Prosper, F., Alignani, D., Paiva, B., Caron, G., Fest, T., Muench, M. O., Fomin, M. E., Lee, S. T., Wiemels, J. L., Valencia, A., Gut, M., Flicek, P., Stunnenberg, H. G., Siebert, R., Küppers, R., Gut, I. G., Campo, E. & Martín-Subero, J. I., 26 Jun 2015, In: Nature Genetics. 47, 7, p. 746-756 11 p.

    Research output: Contribution to journalArticlepeer-review

    239 Citations (Scopus)
  • 2014

    A comprehensive evaluation of rodent malaria parasite genomes and gene expression

    Otto, T. D., Böhme, U., Jackson, A. P., Hunt, M., Franke-Fayard, B., Hoeijmakers, W. A. M., Religa, A. A., Robertson, L., Sanders, M., Ogun, S. A., Cunningham, D., Erhart, A., Billker, O., Khan, S. M., Stunnenberg, H. G., Langhorne, J., Holder, A. A., Waters, A. P., Newbold, C. I., Pain, A., & 2 othersBerriman, M. & Janse, C. J., 2014, In: BMC Medicine. 12, 1, 86.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    195 Citations (Scopus)
  • Age-related variations in the methylome associated with gene expression in human monocytes and T cells

    Reynolds, L. M., Taylor, J. R., Ding, J., Lohman, K., Johnson, C., Siscovick, D., Burke, G., Post, W., Shea, S., Jacobs, D. R., Stunnenberg, H., Kritchevsky, S. B., Hoeschele, I., McCall, C. E., Herrington, D. M., Tracy, R. P. & Liu, Y., 2014, In: Nature Communications. 5, 5366.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    130 Citations (Scopus)
  • Analysis of Chromatin–Nuclear Receptor Interactions by Laser-Chromatin Immunoprecipitation

    Benedetti, R., Conte, M., Carafa, V., Ventura, B. D., Altucci, C., Velotta, R., Stunnenberg, H. G., Altucci, L. & Nebbioso, A., 2014, In: Methods in molecular biology (Clifton, N.J.). 1204, p. 25-34 10 p.

    Research output: Contribution to journalArticlepeer-review

    2 Citations (Scopus)
  • A polymorphic enhancer near GREM1 influences bowel cancer risk through differential CDX2 and TCF7L2 binding

    Lewis, A., Freeman-Mills, L., delaCalle-Mustienes, E., Giráldez-Pérez, R. M., Davis, H., Jaeger, E., Becker, M., Hubner, N. C., Nguyen, L. N., Zeron-Medina, J., Bond, G., Stunnenberg, H. G., Carvajal, J. J., Gomez-Skarmeta, J. L., Leedham, S. & Tomlinson, I., 21 Aug 2014, In: Cell Reports. 8, 4, p. 983-990 8 p.

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    41 Citations (Scopus)
  • CBFB-MYH11/RUNX1 together with a compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupies self-renewal genes in inv(16) acute myeloid leukemia

    Mandoli, A., Singh, A. A., Jansen, P. W. T. C., Wierenga, A. T. J., Riahi, H., Franci, G., Prange, K., Saeed, S., Vellenga, E., Vermeulen, M., Stunnenberg, H. G. & Martens, J. H. A., Apr 2014, In: Leukemia. 28, 4, p. 770-778 9 p.

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    Open Access
    68 Citations (Scopus)
  • Context-selective death of acute myeloid leukemia cells triggered by the novel hybrid retinoid-HDAC inhibitor MC2392

    De Bellis, F., Carafa, V., Conte, M., Rotili, D., Petraglia, F., Matarese, F., Françoijs, K. J., Ablain, J., Valente, S., Castellano, R., Goubard, A., Collette, Y., Mandoli, A., Martens, J. H. A., De Thé, H., Nebbioso, A., Mai, A., Stunnenberg, H. G. & Altucci, L., 15 Apr 2014, In: Cancer Research. 74, 8, p. 2328-2339 12 p.

    Research output: Contribution to journalArticlepeer-review

    33 Citations (Scopus)
  • Dual promoter usage as regulatory mechanism of let-7c expression in leukemic and solid tumors

    Pelosi, A., Careccia, S., Sagrestani, G., Nanni, S., Manni, I., Schinzari, V., Martens, J. H. A., Farsetti, A., Stunnenberg, H. G., Gentileschi, M. P., Del Bufalo, D., De Maria, R., Piaggio, G. & Rizzo, M. G., Jun 2014, In: Molecular Cancer Research. 12, 6, p. 878-889 12 p.

    Research output: Contribution to journalArticlepeer-review

    13 Citations (Scopus)
  • Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity

    Saeed, S., Quintin, J., Kerstens, H. H. D., Rao, N. A., Aghajanirefah, A., Matarese, F., Cheng, S. C., Ratter, J., Berentsem, K., Van Der Ent, M. A., Sharifi, N., Jamssern-Megens, E. M., Ter Huurne, M., Mandoli, A., Van Schaik, T., Ng, A., Burden, F., Downes, K., Frontini, M., Kumar, V., & 10 othersGiamarellos-Bourboulis, E. J., Ouwehand, W. H., Van Der Meer, J. W. M., Joosten, L. A. B., Wijmenga, C., Martens, J. H. A., Xavier, R. J., Logie, C., Netea, M. G. & Stunnenberg, H. G., 26 Sept 2014, In: Science. 345, 6204, 1251086.

    Research output: Contribution to journalArticlepeer-review

    1124 Citations (Scopus)
  • Genome-wide binding of MBD2 reveals strong preference for highly methylated loci

    Menafra, R., Brinkman, A. B., Matarese, F., Franci, G., Bartels, S. J. J., Nguyen, L., Shimbo, T., Wade, P. A., Hubner, N. C. & Stunnenberg, H. G., 13 Jun 2014, In: PLoS ONE. 9, 6, e99603.

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    Open Access
    38 Citations (Scopus)
  • Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data

    wa Maina, C., Honkela, A., Matarese, F., Grote, K., Stunnenberg, H. G., Reid, G., Lawrence, N. D. & Rattray, M., May 2014, In: PLoS Computational Biology. 10, 5, e1003598.

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    Open Access
    19 Citations (Scopus)
  • Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant

    Denissov, S., Hofemeister, H., Marks, H., Kranz, A., Ciotta, G., Singh, S., Anastassiadis, K., Stunnenberg, H. G. & Stewart, A. F., Jan 2014, In: Development. 141, 3, p. 526-537 12 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    193 Citations (Scopus)
  • mTOR- and HIF-1α-mediated aerobic glycolysis as metabolic basis for trained immunity

    Cheng, S. C., Quintin, J., Cramer, R. A., Shepardson, K. M., Saeed, S., Kumar, V., Giamarellos-Bourboulis, E. J., Martens, J. H. A., Rao, N. A., Aghajanirefah, A., Manjeri, G. R., Li, Y., Ifrim, D. C., Arts, R. J. W., Van Der Meer, B. M. J. W., Deen, P. M. T., Logie, C., O'Neill, L. A., Willems, P., Van De Veerdonk, F. L., & 7 othersVan Der Meer, J. W. M., Ng, A., Joosten, L. A. B., Wijmenga, C., Stunnenberg, H. G., Xavier, R. J. & Netea, M. G., 7 Nov 2014, In: Science. 345, 6204, 1250684.

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    Open Access
    1282 Citations (Scopus)
  • Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency

    Yang, S. H., Kalkan, T., Morissroe, C., Marks, H., Stunnenberg, H., Smith, A. & Sharrocks, A. D., 26 Jun 2014, In: Cell Reports. 7, 6, p. 1968-1981 14 p.

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    99 Citations (Scopus)
  • Processed pseudogenes acquired somatically during cancer development

    Cooke, S. L., Shlien, A., Marshall, J., Pipinikas, C. P., Martincorena, I., Tubio, J. M. C., Li, Y., Menzies, A., Mudie, L., Ramakrishna, M., Yates, L., Davies, H., Bolli, N., Bignell, G. R., Tarpey, P. S., Behjati, S., Nik-Zainal, S., Papaemmanuil, E., Teixeira, V. H., Raine, K., & 72 othersOameara, S., Dodoran, M. S., Teague, J. W., Butler, A. P., Iacobuzio-Donahue, C., Santarius, T., Grundy, R. G., Malkin, D., Greaves, M., Munshi, N., Flanagan, A. M., Bowtell, D., Martin, S., Larsimont, D., Reis-Filho, J. S., Boussioutas, A., Taylor, J. A., Hayes, N. D., Janes, S. M., Futreal, P. A., Stratton, M. R., McDermott, U., Campbell, P. J., Provenzano, E., van de Vijver, M., Richardson, A. L., Purdie, C., Pinder, S., Grogan, G. M., Vincent-Salomon, A., Larsimont, D., Grabau, D., Sauer, T., Garred, Ø., Ehinger, A., Van den Eynden, G. G., van Deurzen, C. H. M., Salgado, R., Brock, J. E., Lakhani, S. R., Giri, D. D., Arnould, L., Jacquemier, J., Treilleux, I., Caldas, C., Chin, S. F., Fatima, A., Thompson, A. M., Stenhouse, A., Foekens, J., Martens, J., Sieuwerts, A., Brinkman, A., Stunnenberg, H., Span, P. N., Sweep, F., Desmedt, C., Sotiriou, C., Thomas, G., Broeks, A., Langerod, A., Aparicio, S., Simpson, P. T., van ’t Veer, L., Eyfjord, J. E., Hilmarsdottir, H., Jonasson, J. G., Børresen-Dale, A. L., Ta Michael Lee, M., Wong, B. H., Tee Tan, B. K. & Hooijer, G. K. J., 9 Apr 2014, In: Nature Communications. 5, 3644.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    73 Citations (Scopus)
  • Regulation of DNA methylation patterns by CK2-mediated phosphorylation of Dnmt3a

    Deplus, R., Blanchon, L., Rajavelu, A., Boukaba, A., Defrance, M., Luciani, J., Rothé, F., Dedeurwaerder, S., Denis, H., Brinkman, A. B., Simmer, F., Müller, F., Bertin, B., Berdasco, M., Putmans, P., Calonne, E., Litchfield, D. W., De Launoit, Y., Jurkowski, T. P., Stunnenberg, H. G., & 6 othersBock, C., Sotiriou, C., Fraga, M. F., Esteller, M., Jeltsch, A. & Fuks, F., 7 Aug 2014, In: Cell Reports. 8, 3, p. 743-753 11 p.

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    63 Citations (Scopus)
  • Relationship between genome and epigenome - challenges and requirements for future research

    Almouzni, G., Altucci, L., Amati, B., Ashley, N., Baulcombe, D., Beaujean, N., Bock, C., Bongcam-Rudloff, E., Bousquet, J., Braun, S., Paillerets, B. B. D., Bussemakers, M., Clarke, L., Conesa, A., Estivill, X., Fazeli, A., Grgurević, N., Gut, I., Heijmans, B. T., Hermouet, S., & 41 othersHouwing-Duistermaat, J., Iacobucci, I., Ilaš, J., Kandimalla, R., Krauss-Etschmann, S., Lasko, P., Lehmann, S., Lindroth, A., Majdič, G., Marcotte, E., Martinelli, G., Martinet, N., Meyer, E., Miceli, C., Mills, K., Moreno-Villanueva, M., Morvan, G., Nickel, D., Niesler, B., Nowacki, M., Nowak, J., Ossowski, S., Pelizzola, M., Pochet, R., Potočnik, U., Radwanska, M., Raes, J., Rattray, M., Robinson, M. D., Roelen, B., Sauer, S., Schinzer, D., Slagboom, E., Spector, T., Stunnenberg, H. G., Tiligada, E., Torres-Padilla, M. E., Tsonaka, R., Soom, A. V., Vidaković, M. & Widschwendter, M., 18 Jun 2014, In: BMC Genomics. 15, 1, 487.

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    25 Citations (Scopus)
  • Stable methylation at promoters distinguishes epiblast stem cells from embryonic stem cells and the in vivo epiblasts

    Veillard, A. C., Marks, H., Bernardo, A. S., Jouneau, L., Laloë, D., Boulanger, L., Kaan, A., Brochard, V., Tosolini, M., Pedersen, R., Stunnenberg, H. & Jouneau, A., 1 Sept 2014, In: Stem Cells and Development. 23, 17, p. 2014-2029 16 p.

    Research output: Contribution to journalArticlepeer-review

    26 Citations (Scopus)
  • Transcriptional diversity during lineage commitment of human blood progenitors

    Clien, L., Kostadraia, M., Martens, J. H. A., Canu, G., Garcia, S. P., Torro, E., Downes, K., Macaolay, L. C., Bielczyk-Maezynska, E., Coe, S., Farrow, S., Poudel, P., Borden, F., Jansen, S. B. G., Astle, W. J., Attwood, A., Bariana, T., De Bono, B., Bresechi, A., Chambers, J. C., & 46 othersChoudry, F. A., Clarke, L., Coupland, P., Van Der Ent, M., Erber, W. N., Jansen, J. H., Favier, R., Fenech, M. E., Foad, N., Freson, K., Van Geet, C., Gomez, K., Guigo, R., Hampshire, D., Kelly, A. M., Kerstens, H. H. D., Kooner, J. S., Laffan, M., Lentaigne, C., Labalette, C., Martin, T., Meaeham, S., Mumford, A., Nuiirnberg, S., Palumbo, E., Van Der Reijden, B. A., Richardson, D., Sammut, S. J., Slodkowicz, G., Tamuri, A. U., Vasquez, L., Voss, K., Watt, S., Westbury, S., Flicek, P., Loos, R., Goldman, N., Bertone, P., Read, R. J., Richardson, S., Cvejic, A., Soranzo, N., Onwehand, W. H., Stunnenberg, H. G., Frontini, M. & Rendon, A., 26 Sept 2014, In: Science. 345, 6204, 1251033.

    Research output: Contribution to journalArticlepeer-review

    209 Citations (Scopus)
  • 2013

    De novo mutations in the genome organizer CTCF cause intellectual disability

    Gregor, A., Oti, M., Kouwenhoven, E. N., Hoyer, J., Sticht, H., Ekici, A. B., Kjaergaard, S., Rauch, A., Stunnenberg, H. G., Uebe, S., Vasileiou, G., Reis, A., Zhou, H. & Zweier, C., 11 Jul 2013, In: American Journal of Human Genetics. 93, 1, p. 124-131 8 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    119 Citations (Scopus)
  • Dynamic binding of RBPJ is determined by notch signaling status

    Castel, D., Mourikis, P., Bartels, S. J. J., Brinkman, A. B., Tajbakhsh, S. & Stunnenberg, H. G., 1 May 2013, In: Genes and Development. 27, 9, p. 1059-1071 13 p.

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    Open Access
    187 Citations (Scopus)