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Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques P�, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JH, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Rep. 2016 Nov 15;17(8):2137-2150. doi: 10.1016/j.celrep.2016.10.059.
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Joshi O, Wang SY, Kuznetsova T, Atlasi Y, Peng T, Fabre PJ, Habibi E, Shaik J, Saeed S, Handoko L, Richmond T, Spivakov M, Burgess D, Stunnenberg HG. Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency. Cell Stem Cell. 2015 Dec 3;17(6):748-57. doi: 10.1016/j.stem.2015.11.010
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Saeed S, Quintin J, Kerstens HH, Rao NA, Aghajanirefah A, Matarese F, Cheng SC, Ratter J, Berentsen K, van der Ent MA, Sharifi N, Janssen-Megens EM, Ter Huurne M, Mandoli A, van Schaik T, Ng A, Burden F, Downes K, Frontini M, Kumar V, Giamarellos-Bourboulis EJ, Ouwehand WH, van der Meer JW, Joosten LA, Wijmenga C, Martens JH, Xavier RJ, Logie C, Netea MG, Stunnenberg HG. Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science. 2014 Sep 26;345(6204):1251086. doi: 10.1126/science.1251086.
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Saeed S, Logie C, Stunnenberg HG, Martens JH. Genome-wide functions of PML-RARalpha in acute promyelocytic leukaemia. Review British J Cancer. 2011; 104:554-558.
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Cheng SC, Quintin J, Cramer RA, Shepardson KM, Saeed S, Kumar V, Giamarellos-Bourboulis EJ, Martens JH, Rao NA, Aghajanirefah A, Manjeri GR, Li Y, Ifrim DC, Arts RJ, van der Meer BM, Deen PM, Logie C, O'Neill LA, Willems P, van de Veerdonk FL, van der Meer JW, Ng A, Joosten LA, Wijmenga C, Stunnenberg HG, Xavier RJ, Netea MG. mTOR- and HIF-1?-mediated aerobic glycolysis as metabolic basis for trained immunity. Science. 2014 Sep 26;345(6204):1250684. doi: 10.1126/science.1250684.
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Mandoli A, Singh AA, Jansen PW, Wierenga AT, Riahi H, Franci G, Prange K, Saeed S, Vellenga E, Vermeulen M, Stunnenberg HG, Martens JH. 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. Leukemia. 2014 Apr;28(4):770-8. doi: 10.1038/leu.2013.257. Epub 2013 Sep 4.
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Saeed S, Logie C, Francoijs KJ, Frige G, Romanenghi M, Nielsen FG, Raats L, Shahhoseini M, Huynen M, Altucci L, Minucci S, Martens JH, Stunnenberg HG. Chromatin accessibility, p300 and histone acetylation define PML-RAR? and AML1-ETO binding sites in acute myeloid leukemia. Blood. 2012 Aug 24. doi: 10.1182/blood-2011-10-386086.
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Quintin J, Saeed S, Martens JH, Giamarellos-Bourboulis EJ, Ifrim DC, Logie C, Jacobs L, Jansen T, Kullberg BJ, Wijmenga C, Joosten LA, Xavier RJ, van der Meer JW, Stunnenberg HG, Netea MG. Candida albicans Infection Affords Protection against Reinfection via Functional Reprogramming of Monocytes. Cell Host Microbe. 2012 Aug 16;12(2):223-32. (*both authors contributed equally)
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Martens JH, Mandoli A, Simmer F, Wierenga BJ, Saeed S, Singh AA, Altucci L, Vellenga E, Stunnenberg HG. ERG and FLI1 binding sites demarcate targets for aberrant epigenetic regulation by AML1-ETO in acute myeloid leukemia. Blood. 2012 Sep 14. doi: 10.1182/blood-2012-05-429050.
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Kleinnijenhuis J, Quintin J, Preijers F, Joosten LA, Ifrim DC, Saeed S, Jacobs C, van Loenhout J, de Jong D, Stunnenberg HG, Xavier RJ, van der Meer JW, van Crevel R, Netea MG. Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes. Proc Natl Acad Sci U S A (PNAS) 2012 Sep 17. doi: 10.1073/pnas.1202870109.
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