Publications

  1. 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.
  2. 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.
  3. 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.
  4. 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 .
  5. 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.
  6. 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 .
  7. 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.
  8. 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 .
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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 .
  15. 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 .
  16. 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 .
  17. 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.
  18. 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 .
  19. Brinkman, AB, Roelofsen, T, Pennings, SW, Martens, JH, Jenuwein, T, Stunnenberg, HG et al.. Histone modification patterns associated with the human X chromosome. EMBO Rep. 2006;7 (6):628-34. doi: 10.1038/sj.embor.7400686. PubMed PMID:16648823 PubMed Central PMC1479594.
  20. Thaw, P, Sedelnikova, SE, Muranova, T, Wiese, S, Ayora, S, Alonso, JC et al.. Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family. Nucleic Acids Res. 2006;34 (5):1439-49. doi: 10.1093/nar/gkl009. PubMed PMID:16528101 PubMed Central PMC1401507.
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