Publications

  1. Karemaker, ID, Vermeulen, M. Single-Cell DNA Methylation Profiling: Technologies and Biological Applications. Trends Biotechnol. 2018; :. doi: 10.1016/j.tibtech.2018.04.002. PubMed PMID:29724495 .
  2. Makowski, MM, Gräwe, C, Foster, BM, Nguyen, NV, Bartke, T, Vermeulen, M et al.. Global profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry. Nat Commun. 2018;9 (1):1653. doi: 10.1038/s41467-018-04084-0. PubMed PMID:29695722 PubMed Central PMC5916898.
  3. Fang, J, Jia, J, Makowski, M, Xu, M, Wang, Z, Zhang, T et al.. Publisher correction: Functional characterization of a multi-cancer risk locus on chr5p15.33 reveals regulation of TERT by ZNF148. Nat Commun. 2018;9 :16159. doi: 10.1038/ncomms16159. PubMed PMID:29596408 .
  4. Pines, A, Dijk, M, Makowski, M, Meulenbroek, EM, Vrouwe, MG, van der Weegen, Y et al.. TRiC controls transcription resumption after UV damage by regulating Cockayne syndrome protein A. Nat Commun. 2018;9 (1):1040. doi: 10.1038/s41467-018-03484-6. PubMed PMID:29531219 PubMed Central PMC5847541.
  5. Di Costanzo, A, Del Gaudio, N, Conte, L, Dell'Aversana, C, Vermeulen, M, de Thé, H et al.. The HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia. Oncogene. 2018;37 (19):2559-2572. doi: 10.1038/s41388-018-0143-1. PubMed PMID:29467492 PubMed Central PMC5945585.
  6. Zhang, X, Smits, AH, van Tilburg, GB, Ovaa, H, Huber, W, Vermeulen, M et al.. Proteome-wide identification of ubiquitin interactions using UbIA-MS. Nat Protoc. 2018;13 (3):530-550. doi: 10.1038/nprot.2017.147. PubMed PMID:29446774 .
  7. Karemaker, ID, Vermeulen, M. ZBTB2 reads unmethylated CpG island promoters and regulates embryonic stem cell differentiation. EMBO Rep. 2018;19 (4):. doi: 10.15252/embr.201744993. PubMed PMID:29437775 PubMed Central PMC5891434.
  8. Oost, KC, van Voorthuijsen, L, Fumagalli, A, Lindeboom, RGH, Sprangers, J, Omerzu, M et al.. Specific Labeling of Stem Cell Activity in Human Colorectal Organoids Using an ASCL2-Responsive Minigene. Cell Rep. 2018;22 (6):1600-1614. doi: 10.1016/j.celrep.2018.01.033. PubMed PMID:29425513 PubMed Central PMC5847189.
  9. Kebede, AF, Nieborak, A, Shahidian, LZ, Le Gras, S, Richter, F, Gómez, DA et al.. Histone propionylation is a mark of active chromatin. Nat. Struct. Mol. Biol. 2017;24 (12):1048-1056. doi: 10.1038/nsmb.3490. PubMed PMID:29058708 .
  10. Kole, K, Lindeboom, RGH, Baltissen, MPA, Jansen, PWTC, Vermeulen, M, Tiesinga, P et al.. Proteomic landscape of the primary somatosensory cortex upon sensory deprivation. Gigascience. 2017;6 (10):1-10. doi: 10.1093/gigascience/gix082. PubMed PMID:29020746 PubMed Central PMC5632293.
  11. Edupuganti, RR, Geiger, S, Lindeboom, RGH, Shi, H, Hsu, PJ, Lu, Z et al.. N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis. Nat. Struct. Mol. Biol. 2017;24 (10):870-878. doi: 10.1038/nsmb.3462. PubMed PMID:28869609 PubMed Central PMC5725193.
  12. Krishnan, S, Smits, AH, Vermeulen, M, Reinberg, D. Phospho-H1 Decorates the Inter-chromatid Axis and Is Evicted along with Shugoshin by SET during Mitosis. Mol. Cell. 2017;67 (4):579-593.e6. doi: 10.1016/j.molcel.2017.07.008. PubMed PMID:28781233 PubMed Central PMC5562512.
  13. Choi, J, Xu, M, Makowski, MM, Zhang, T, Law, MH, Kovacs, MA et al.. A common intronic variant of PARP1 confers melanoma risk and mediates melanocyte growth via regulation of MITF. Nat. Genet. 2017;49 (9):1326-1335. doi: 10.1038/ng.3927. PubMed PMID:28759004 .
  14. Fang, J, Jia, J, Makowski, M, Xu, M, Wang, Z, Zhang, T et al.. Functional characterization of a multi-cancer risk locus on chr5p15.33 reveals regulation of TERT by ZNF148. Nat Commun. 2017;8 :15034. doi: 10.1038/ncomms15034. PubMed PMID:28447668 PubMed Central PMC5414179.
  15. Zhang, X, Smits, AH, van Tilburg, GB, Jansen, PW, Makowski, MM, Ovaa, H et al.. An Interaction Landscape of Ubiquitin Signaling. Mol. Cell. 2017;65 (5):941-955.e8. doi: 10.1016/j.molcel.2017.01.004. PubMed PMID:28190767 .
  16. Zhang, T, Xu, M, Makowski, MM, Lee, C, Kovacs, M, Fang, J et al.. SDHD Promoter Mutations Ablate GABP Transcription Factor Binding in Melanoma. Cancer Res. 2017;77 (7):1649-1661. doi: 10.1158/0008-5472.CAN-16-0919. PubMed PMID:28108517 .
  17. Smits, AH, Borrmann, A, Roosjen, M, van Hest, JC, Vermeulen, M. Click-MS: Tagless Protein Enrichment Using Bioorthogonal Chemistry for Quantitative Proteomics. ACS Chem. Biol. 2016;11 (12):3245-3250. doi: 10.1021/acschembio.6b00520. PubMed PMID:27643597 .
  18. Spruijt, CG, Luijsterburg, MS, Menafra, R, Lindeboom, RG, Jansen, PW, Edupuganti, RR et al.. ZMYND8 Co-localizes with NuRD on Target Genes and Regulates Poly(ADP-Ribose)-Dependent Recruitment of GATAD2A/NuRD to Sites of DNA Damage. Cell Rep. 2016;17 (3):783-798. doi: 10.1016/j.celrep.2016.09.037. PubMed PMID:27732854 .
  19. Miller, A, Ralser, M, Kloet, SL, Loos, R, Nishinakamura, R, Bertone, P et al.. Sall4 controls differentiation of pluripotent cells independently of the Nucleosome Remodelling and Deacetylation (NuRD) complex. Development. 2016;143 (17):3074-84. doi: 10.1242/dev.139113. PubMed PMID:27471257 PubMed Central PMC5047675.
  20. Kloet, SL, Makowski, MM, Baymaz, HI, van Voorthuijsen, L, Karemaker, ID, Santanach, A et al.. The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation. Nat. Struct. Mol. Biol. 2016;23 (7):682-690. doi: 10.1038/nsmb.3248. PubMed PMID:27294783 PubMed Central PMC4939079.
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