Publications

  1. Lindeboom, RGH, Smits, AH, Perino, M, Veenstra, GJC, Vermeulen, M. Mass Spectrometry-Based Absolute Quantification of Single Xenopus Embryo Proteomes. Cold Spring Harb Protoc. 2018; :. doi: 10.1101/pdb.prot098376. PubMed PMID:30104410 .
  2. Kole, K, Lindeboom, RGH, Baltissen, MPA, Jansen, PWTC, Vermeulen, M, Tiesinga, P et al.. Erratum to: Proteomic landscape of the primary somatosensory cortex upon sensory deprivation. Gigascience. 2018;7 (7):. doi: 10.1093/gigascience/giy041. PubMed PMID:30053288 PubMed Central PMC6055539.
  3. Lindeboom, RG, van Voorthuijsen, L, Oost, KC, Rodríguez-Colman, MJ, Luna-Velez, MV, Furlan, C et al.. Integrative multi-omics analysis of intestinal organoid differentiation. Mol. Syst. Biol. 2018;14 (6):e8227. . PubMed PMID:29945941 PubMed Central PMC6018986.
  4. van Buggenum, JAG, Gerlach, JP, Tanis, SEJ, Hogeweg, M, Jansen, PWTC, Middelwijk, J et al.. Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells. Nat Commun. 2018;9 (1):2384. doi: 10.1038/s41467-018-04761-0. PubMed PMID:29921844 PubMed Central PMC6008431.
  5. Perino, M, van Mierlo, G, Karemaker, ID, van Genesen, S, Vermeulen, M, Marks, H et al.. MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding. Nat. Genet. 2018;50 (7):1002-1010. doi: 10.1038/s41588-018-0134-8. PubMed PMID:29808031 .
  6. Karemaker, ID, Vermeulen, M. Single-Cell DNA Methylation Profiling: Technologies and Biological Applications. Trends Biotechnol. 2018;36 (9):952-965. doi: 10.1016/j.tibtech.2018.04.002. PubMed PMID:29724495 .
  7. 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.
  8. 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 .
  9. 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.
  10. 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.
  11. 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 .
  12. 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.
  13. 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.
  14. 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 .
  15. 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.
  16. 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.
  17. 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.
  18. 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 .
  19. 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.
  20. 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 .
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