Publications

  1. 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; :. doi: 10.1158/0008-5472.CAN-16-0919. PubMed PMID:28108517 .
  2. 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 .
  3. 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 .
  4. 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.
  5. 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):682-90. doi: 10.1038/nsmb.3248. PubMed PMID:27294783 PubMed Central PMC4939079.
  6. Smits, AH, Vermeulen, M. Characterizing Protein-Protein Interactions Using Mass Spectrometry: Challenges and Opportunities. Trends Biotechnol. 2016;34 (10):825-34. doi: 10.1016/j.tibtech.2016.02.014. PubMed PMID:26996615 .
  7. Bogdanović, O, Smits, AH, de la Calle Mustienes, E, Tena, JJ, Ford, E, Williams, R et al.. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat. Genet. 2016;48 (4):417-26. doi: 10.1038/ng.3522. PubMed PMID:26928226 .
  8. Varier, RA, Carrillo de Santa Pau, E, van der Groep, P, Lindeboom, RG, Matarese, F, Mensinga, A et al.. Recruitment of the Mammalian Histone-modifying EMSY Complex to Target Genes Is Regulated by ZNF131. J. Biol. Chem. 2016;291 (14):7313-24. doi: 10.1074/jbc.M115.701227. PubMed PMID:26841866 PubMed Central PMC4817164.
  9. Karemaker, ID, Vermeulen, M. In need of good neighbours: transcription factors require local DNA hypomethylation for target binding. EMBO J. 2016;35 (4):374-5. doi: 10.15252/embj.201593750. PubMed PMID:26758545 PubMed Central PMC4755117.
  10. Makowski, MM, Willems, E, Jansen, PW, Vermeulen, M. Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification. Mol. Cell Proteomics. 2016;15 (3):854-65. doi: 10.1074/mcp.M115.053082. PubMed PMID:26560067 PubMed Central PMC4813705.
  11. Makowski, MM, Willems, E, Fang, J, Choi, J, Zhang, T, Jansen, PW et al.. An interaction proteomics survey of transcription factor binding at recurrent TERT promoter mutations. Proteomics. 2016;16 (3):417-26. doi: 10.1002/pmic.201500327. PubMed PMID:26553150 .
  12. Campos, EI, Smits, AH, Kang, YH, Landry, S, Escobar, TM, Nayak, S et al.. Analysis of the Histone H3.1 Interactome: A Suitable Chaperone for the Right Event. Mol. Cell. 2015;60 (4):697-709. doi: 10.1016/j.molcel.2015.08.005. PubMed PMID:26527279 PubMed Central PMC4656108.
  13. Baymaz, HI, Karemaker, ID, Vermeulen, M. Perspective on unraveling the versatility of 'co-repressor' complexes. Biochim. Biophys. Acta. 2015;1849 (8):1051-6. doi: 10.1016/j.bbagrm.2015.06.012. PubMed PMID:26130598 .
  14. Stunnenberg, HG, Vermeulen, M, Atlasi, Y. Developmental biology. A Me6Age for pluripotency. Science. 2015;347 (6222):614-5. doi: 10.1126/science.aaa6262. PubMed PMID:25657233 .
  15. Spruijt, CG, Vermeulen, M. DNA methylation: old dog, new tricks?. Nat. Struct. Mol. Biol. 2014;21 (11):949-54. doi: 10.1038/nsmb.2910. PubMed PMID:25372310 .
  16. Beck, DB, Narendra, V, Drury, WJ 3rd, Casey, R, Jansen, PW, Yuan, ZF et al.. In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions. J. Proteome Res. 2014;13 (12):6135-43. doi: 10.1021/pr500196b. PubMed PMID:25311790 PubMed Central PMC4261942.
  17. Kloet, SL, Baymaz, HI, Makowski, M, Groenewold, V, Jansen, PW, Berendsen, M et al.. Towards elucidating the stability, dynamics and architecture of the nucleosome remodeling and deacetylase complex by using quantitative interaction proteomics. FEBS J. 2015;282 (9):1774-85. doi: 10.1111/febs.12972. PubMed PMID:25123934 .
  18. Putker, M, Vos, HR, van Dorenmalen, K, de Ruiter, H, Duran, AG, Snel, B et al.. Evolutionary acquisition of cysteines determines FOXO paralog-specific redox signaling. Antioxid. Redox Signal. 2015;22 (1):15-28. doi: 10.1089/ars.2014.6056. PubMed PMID:25069953 PubMed Central PMC4270166.
  19. Baymaz, HI, Spruijt, CG, Vermeulen, M. Identifying nuclear protein-protein interactions using GFP affinity purification and SILAC-based quantitative mass spectrometry. Methods Mol. Biol. 2014;1188 :207-26. doi: 10.1007/978-1-4939-1142-4_15. PubMed PMID:25059614 .
  20. Smits, AH, Lindeboom, RG, Perino, M, van Heeringen, SJ, Veenstra, GJ, Vermeulen, M et al.. Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs. Nucleic Acids Res. 2014;42 (15):9880-91. doi: 10.1093/nar/gku661. PubMed PMID:25056316 PubMed Central PMC4150773.
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