Publications

  1. Glodzik, D, Morganella, S, Davies, H, Simpson, PT, Li, Y, Zou, X et al.. Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers. Nat. Genet. 2017;49 (11):1661. doi: 10.1038/ng1117-1661a. PubMed PMID:29074948 .
  2. Glodzik, D, Morganella, S, Davies, H, Simpson, PT, Li, Y, Zou, X et al.. A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers. Nat. Genet. 2017;49 (3):341-348. doi: 10.1038/ng.3771. PubMed PMID:28112740 .
  3. 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.
  4. 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.
  5. 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.
  6. Deplus, R, Blanchon, L, Rajavelu, A, Boukaba, A, Defrance, M, Luciani, J et al.. Regulation of DNA methylation patterns by CK2-mediated phosphorylation of Dnmt3a. Cell Rep. 2014;8 (3):743-53. doi: 10.1016/j.celrep.2014.06.048. PubMed PMID:25066127 .
  7. Menafra, R, Brinkman, AB, Matarese, F, Franci, G, Bartels, SJ, Nguyen, L et al.. Genome-wide binding of MBD2 reveals strong preference for highly methylated loci. PLoS ONE. 2014;9 (6):e99603. doi: 10.1371/journal.pone.0099603. PubMed PMID:24927503 PubMed Central PMC4057170.
  8. Habibi, E, Brinkman, AB, Arand, J, Kroeze, LI, Kerstens, HH, Matarese, F et al.. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell. 2013;13 (3):360-9. doi: 10.1016/j.stem.2013.06.002. PubMed PMID:23850244 .
  9. Castel, D, Mourikis, P, Bartels, SJ, Brinkman, AB, Tajbakhsh, S, Stunnenberg, HG et al.. Dynamic binding of RBPJ is determined by Notch signaling status. Genes Dev. 2013;27 (9):1059-71. doi: 10.1101/gad.211912.112. PubMed PMID:23651858 PubMed Central PMC3656323.
  10. Spruijt, CG, Gnerlich, F, Smits, AH, Pfaffeneder, T, Jansen, PW, Bauer, C et al.. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell. 2013;152 (5):1146-59. doi: 10.1016/j.cell.2013.02.004. PubMed PMID:23434322 .
  11. Simmer, F, Brinkman, AB, Assenov, Y, Matarese, F, Kaan, A, Sabatino, L et al.. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics. 2012;7 (12):1355-67. doi: 10.4161/epi.22562. PubMed PMID:23079744 PubMed Central PMC3528691.
  12. Brinkman, AB, Gu, H, Bartels, SJ, Zhang, Y, Matarese, F, Simmer, F et al.. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 2012;22 (6):1128-38. doi: 10.1101/gr.133728.111. PubMed PMID:22466170 PubMed Central PMC3371717.
  13. Bartels, SJ, Spruijt, CG, Brinkman, AB, Jansen, PW, Vermeulen, M, Stunnenberg, HG et al.. A SILAC-based screen for Methyl-CpG binding proteins identifies RBP-J as a DNA methylation and sequence-specific binding protein. PLoS ONE. 2011;6 (10):e25884. doi: 10.1371/journal.pone.0025884. PubMed PMID:21991380 PubMed Central PMC3185043.
  14. Bogdanovic, O, Long, SW, van Heeringen, SJ, Brinkman, AB, Gómez-Skarmeta, JL, Stunnenberg, HG et al.. Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Genome Res. 2011;21 (8):1313-27. doi: 10.1101/gr.114843.110. PubMed PMID:21636662 PubMed Central PMC3149498.
  15. Bock, C, Tomazou, EM, Brinkman, AB, Müller, F, Simmer, F, Gu, H et al.. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat. Biotechnol. 2010;28 (10):1106-14. doi: 10.1038/nbt.1681. PubMed PMID:20852634 PubMed Central PMC3066564.
  16. Brinkman, AB, Simmer, F, Ma, K, Kaan, A, Zhu, J, Stunnenberg, HG et al.. Whole-genome DNA methylation profiling using MethylCap-seq. Methods. 2010;52 (3):232-6. doi: 10.1016/j.ymeth.2010.06.012. PubMed PMID:20542119 .
  17. Spruijt, CG, Bartels, SJ, Brinkman, AB, Tjeertes, JV, Poser, I, Stunnenberg, HG et al.. CDK2AP1/DOC-1 is a bona fide subunit of the Mi-2/NuRD complex. Mol Biosyst. 2010;6 (9):1700-6. doi: 10.1039/c004108d. PubMed PMID:20523938 .
  18. Martens, JH, Brinkman, AB, Simmer, F, Francoijs, KJ, Nebbioso, A, Ferrara, F et al.. PML-RARalpha/RXR Alters the Epigenetic Landscape in Acute Promyelocytic Leukemia. Cancer Cell. 2010;17 (2):173-85. doi: 10.1016/j.ccr.2009.12.042. PubMed PMID:20159609 .
  19. Brinkman, AB, Pennings, SW, Braliou, GG, Rietveld, LE, Stunnenberg, HG. DNA methylation immediately adjacent to active histone marking does not silence transcription. Nucleic Acids Res. 2007;35 (3):801-11. doi: 10.1093/nar/gkl1014. PubMed PMID:17202157 PubMed Central PMC1807972.
  20. Ettema, TJ, Brinkman, AB, Lamers, PP, Kornet, NG, de Vos, WM, van der Oost, J et al.. Molecular characterization of a conserved archaeal copper resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2. Microbiology (Reading, Engl.). 2006;152 (Pt 7):1969-79. doi: 10.1099/mic.0.28724-0. PubMed PMID:16804172 .
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