Publications

  1. Astle, WJ, Elding, H, Jiang, T, Allen, D, Ruklisa, D, Mann, AL et al.. The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease. Cell. 2016;167 (5):1415-1429.e19. doi: 10.1016/j.cell.2016.10.042. PubMed PMID:27863252 .
  2. Chen, L, Ge, B, Casale, FP, Vasquez, L, Kwan, T, Garrido-Martín, D et al.. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Cell. 2016;167 (5):1398-1414.e24. doi: 10.1016/j.cell.2016.10.026. PubMed PMID:27863251 PubMed Central PMC5119954.
  3. Novakovic, B, Habibi, E, Wang, SY, Arts, RJ, Davar, R, Megchelenbrink, W et al.. β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance. Cell. 2016;167 (5):1354-1368.e14. doi: 10.1016/j.cell.2016.09.034. PubMed PMID:27863248 .
  4. Breeze, CE, Paul, DS, van Dongen, J, Butcher, LM, Ambrose, JC, Barrett, JE et al.. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Rep. 2016;17 (8):2137-2150. doi: 10.1016/j.celrep.2016.10.059. PubMed PMID:27851974 PubMed Central PMC5120369.
  5. Schuyler, RP, Merkel, A, Raineri, E, Altucci, L, Vellenga, E, Martens, JH et al.. Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems. Cell Rep. 2016;17 (8):2101-2111. doi: 10.1016/j.celrep.2016.10.054. PubMed PMID:27851971 .
  6. Mandoli, A, Singh, AA, Prange, KH, Tijchon, E, Oerlemans, M, Dirks, R et al.. The Hematopoietic Transcription Factors RUNX1 and ERG Prevent AML1-ETO Oncogene Overexpression and Onset of the Apoptosis Program in t(8;21) AMLs. Cell Rep. 2016;17 (8):2087-2100. doi: 10.1016/j.celrep.2016.08.082. PubMed PMID:27851970 .
  7. Queirós, AC, Beekman, R, Vilarrasa-Blasi, R, Duran-Ferrer, M, Clot, G, Merkel, A et al.. Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage. Cancer Cell. 2016;30 (5):806-821. doi: 10.1016/j.ccell.2016.09.014. PubMed PMID:27846393 .
  8. Smid, M, Rodríguez-González, FG, Sieuwerts, AM, Salgado, R, Prager-Van der Smissen, WJ, Vlugt-Daane, MV et al.. Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. Nat Commun. 2016;7 :12910. doi: 10.1038/ncomms12910. PubMed PMID:27666519 PubMed Central PMC5052682.
  9. Angela, N, Carafa, V, Conte, M, Tambaro, FP, Abbondanza, C, Martens, JH et al.. c-Myc modulation & acetylation is a key HDAC inhibitor target in cancer. Clin. Cancer Res. 2016; :. doi: 10.1158/1078-0432.CCR-15-2388. PubMed PMID:27358484 .
  10. Vegi, NM, Klappacher, J, Oswald, F, Mulaw, MA, Mandoli, A, Thiel, VN et al.. MEIS2 Is an Oncogenic Partner in AML1-ETO-Positive AML. Cell Rep. 2016;16 (2):498-507. doi: 10.1016/j.celrep.2016.05.094. PubMed PMID:27346355 .
  11. Morganella, S, Alexandrov, LB, Glodzik, D, Zou, X, Davies, H, Staaf, J et al.. The topography of mutational processes in breast cancer genomes. Nat Commun. 2016;7 :11383. doi: 10.1038/ncomms11383. PubMed PMID:27136393 PubMed Central PMC5001788.
  12. Nik-Zainal, S, Davies, H, Staaf, J, Ramakrishna, M, Glodzik, D, Zou, X et al.. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature. 2016;534 (7605):47-54. doi: 10.1038/nature17676. PubMed PMID:27135926 PubMed Central PMC4910866.
  13. van den Boom, V, Maat, H, Geugien, M, Rodríguez López, A, Sotoca, AM, Jaques, J et al.. Non-canonical PRC1.1 Targets Active Genes Independent of H3K27me3 and Is Essential for Leukemogenesis. Cell Rep. 2016;14 (2):332-46. doi: 10.1016/j.celrep.2015.12.034. PubMed PMID:26748712 .
  14. Kuznetsova, T, Wang, SY, Rao, NA, Mandoli, A, Martens, JH, Rother, N et al.. Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization. Genome Biol. 2015;16 :264. doi: 10.1186/s13059-015-0832-9. PubMed PMID:26619937 PubMed Central PMC4665721.
  15. Kretzmer, H, Bernhart, SH, Wang, W, Haake, A, Weniger, MA, Bergmann, AK et al.. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nat. Genet. 2015;47 (11):1316-25. doi: 10.1038/ng.3413. PubMed PMID:26437030 .
  16. Sotoca, AM, Prange, KH, Reijnders, B, Mandoli, A, Nguyen, LN, Stunnenberg, HG et al.. 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. Oncogene. 2016;35 (15):1965-76. doi: 10.1038/onc.2015.261. PubMed PMID:26148230 PubMed Central PMC4833872.
  17. Agirre, X, Castellano, G, Pascual, M, Heath, S, Kulis, M, Segura, V et al.. Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers. Genome Res. 2015;25 (4):478-87. doi: 10.1101/gr.180240.114. PubMed PMID:25644835 PubMed Central PMC4381520.
  18. Saeed, S, Quintin, J, Kerstens, HH, Rao, NA, Aghajanirefah, A, Matarese, F et al.. Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science. 2014;345 (6204):1251086. doi: 10.1126/science.1251086. PubMed PMID:25258085 PubMed Central PMC4242194.
  19. Chen, L, Kostadima, M, Martens, JH, Canu, G, Garcia, SP, Turro, E et al.. Transcriptional diversity during lineage commitment of human blood progenitors. Science. 2014;345 (6204):1251033. doi: 10.1126/science.1251033. PubMed PMID:25258084 PubMed Central PMC4254742.
  20. Cheng, SC, Quintin, J, Cramer, RA, Shepardson, KM, Saeed, S, Kumar, V et al.. mTOR- and HIF-1α-mediated aerobic glycolysis as metabolic basis for trained immunity. Science. 2014;345 (6204):1250684. doi: 10.1126/science.1250684. PubMed PMID:25258083 PubMed Central PMC4226238.
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