Publications

  1. Smits, JPH, Dirks, RAM, Qu, J, Oortveld, MAW, Brinkman, AB, Zeeuwen, PLJM et al.. Terminal keratinocyte differentiation in vitro is associated with a stable DNA methylome. Exp Dermatol. 2020; :. doi: 10.1111/exd.14153. PubMed PMID:32681572 .
  2. Nederlof, I, De Bortoli, D, Bareche, Y, Nguyen, B, de Maaker, M, Hooijer, GKJ et al.. Comprehensive evaluation of methods to assess overall and cell-specific immune infiltrates in breast cancer. Breast Cancer Res. 2019;21 (1):151. doi: 10.1186/s13058-019-1239-4. PubMed PMID:31878981 PubMed Central PMC6933637.
  3. Brinkman, AB, Nik-Zainal, S, Simmer, F, Rodríguez-González, FG, Smid, M, Alexandrov, LB et al.. Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation. Nat Commun. 2019;10 (1):1749. doi: 10.1038/s41467-019-09828-0. PubMed PMID:30988298 PubMed Central PMC6465362.
  4. Nik-Zainal, S, Davies, H, Staaf, J, Ramakrishna, M, Glodzik, D, Zou, X et al.. Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature. 2019;566 (7742):E1. doi: 10.1038/s41586-019-0883-2. PubMed PMID:30659290 .
  5. van Mierlo, G, Dirks, RAM, De Clerck, L, Brinkman, AB, Huth, M, Kloet, SL et al.. Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency. Cell Stem Cell. 2019;24 (1):123-137.e8. doi: 10.1016/j.stem.2018.10.017. PubMed PMID:30472157 .
  6. 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 .
  7. 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 PubMed Central PMC5988034.
  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. 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.
  10. 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.
  11. 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 .
  12. 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.
  13. 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 .
  14. 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.
  15. 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 .
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
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