Publications

  1. van Mierlo, G, Wester, RA, Marks, H. A Mass Spectrometry Survey of Chromatin-Associated Proteins in Pluripotency and Early Lineage Commitment. Proteomics. 2019;19 (14):e1900047. doi: 10.1002/pmic.201900047. PubMed PMID:31219242 .
  2. van Mierlo, G, Veenstra, GJC, Vermeulen, M, Marks, H. The Complexity of PRC2 Subcomplexes. Trends Cell Biol. 2019;29 (8):660-671. doi: 10.1016/j.tcb.2019.05.004. PubMed PMID:31178244 .
  3. Atlasi, Y, Megchelenbrink, W, Peng, T, Habibi, E, Joshi, O, Wang, SY et al.. Publisher Correction: Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. Nat. Cell Biol. 2019;21 (7):911-912. doi: 10.1038/s41556-019-0341-2. PubMed PMID:31097792 .
  4. Atlasi, Y, Megchelenbrink, W, Peng, T, Habibi, E, Joshi, O, Wang, SY et al.. Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. Nat. Cell Biol. 2019;21 (5):568-578. doi: 10.1038/s41556-019-0310-9. PubMed PMID:31036938 .
  5. Furlan, C, Dirks, RAM, Thomas, PC, Jones, RC, Wang, J, Lynch, M et al.. Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements. Nat Commun. 2019;10 (1):1525. doi: 10.1038/s41467-019-09533-y. PubMed PMID:30948724 PubMed Central PMC6449397.
  6. Dirks, RAM, van Mierlo, G, Kerstens, HHD, Bernardo, AS, Kobolák, J, Bock, I et al.. Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states. Epigenetics Chromatin. 2019;12 (1):14. doi: 10.1186/s13072-019-0259-8. PubMed PMID:30767785 PubMed Central PMC6376749.
  7. 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 .
  8. van Mierlo, G, Wester, RA, Marks, H. Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in the pluripotent ground state. Stem Cell Res. 2018;33 :135-145. doi: 10.1016/j.scr.2018.09.017. PubMed PMID:30352361 .
  9. Bernardo, AS, Jouneau, A, Marks, H, Kensche, P, Kobolak, J, Freude, K et al.. Mammalian embryo comparison identifies novel pluripotency genes associated with the naïve or primed state. Biol Open. 2018;7 (8):. doi: 10.1242/bio.033282. PubMed PMID:30026265 PubMed Central PMC6124576.
  10. 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 .
  11. Fisher, CL, Marks, H, Cho, LT, Andrews, R, Wormald, S, Carroll, T et al.. An efficient method for generation of bi-allelic null mutant mouse embryonic stem cells and its application for investigating epigenetic modifiers. Nucleic Acids Res. 2017;45 (21):e174. doi: 10.1093/nar/gkx811. PubMed PMID:28981838 PubMed Central PMC5716182.
  12. Kalkan, T, Olova, N, Roode, M, Mulas, C, Lee, HJ, Nett, I et al.. Tracking the embryonic stem cell transition from ground state pluripotency. Development. 2017;144 (7):1221-1234. doi: 10.1242/dev.142711. PubMed PMID:28174249 PubMed Central PMC5399622.
  13. Dirks, RA, Stunnenberg, HG, Marks, H. Genome-wide epigenomic profiling for biomarker discovery. Clin Epigenetics. 2016;8 :122. doi: 10.1186/s13148-016-0284-4. PubMed PMID:27895806 PubMed Central PMC5117701.
  14. Marks, H, Kerstens, HH, Barakat, TS, Splinter, E, Dirks, RA, van Mierlo, G et al.. Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq. Genome Biol. 2016;17 :22. doi: 10.1186/s13059-016-0885-4. PubMed PMID:26850229 PubMed Central PMC4743200.
  15. Marks, H, Kerstens, HH, Barakat, TS, Splinter, E, Dirks, RA, van Mierlo, G et al.. Dynamics of gene silencing during X inactivation using allele-specific RNA-seq. Genome Biol. 2015;16 :149. doi: 10.1186/s13059-015-0698-x. PubMed PMID:26235224 PubMed Central PMC4546214.
  16. Yang, SH, Kalkan, T, Morissroe, C, Marks, H, Stunnenberg, H, Smith, A et al.. Otx2 and Oct4 drive early enhancer activation during embryonic stem cell transition from naive pluripotency. Cell Rep. 2014;7 (6):1968-81. doi: 10.1016/j.celrep.2014.05.037. PubMed PMID:24931607 PubMed Central PMC4074343.
  17. Veillard, AC, Marks, H, Bernardo, AS, Jouneau, L, Laloë, D, Boulanger, L et al.. Stable methylation at promoters distinguishes epiblast stem cells from embryonic stem cells and the in vivo epiblasts. Stem Cells Dev. 2014;23 (17):2014-29. doi: 10.1089/scd.2013.0639. PubMed PMID:24738887 PubMed Central PMC4142781.
  18. Denissov, S, Hofemeister, H, Marks, H, Kranz, A, Ciotta, G, Singh, S et al.. Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant. Development. 2014;141 (3):526-37. doi: 10.1242/dev.102681. PubMed PMID:24423662 .
  19. Marks, H, Stunnenberg, HG. Transcription regulation and chromatin structure in the pluripotent ground state. Biochim. Biophys. Acta. 2014;1839 (3):129-37. doi: 10.1016/j.bbagrm.2013.09.005. PubMed PMID:24096207 .
  20. 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 .
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