Publications

  1. 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.
  2. 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 .
  3. 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 .
  4. 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.
  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. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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 .
  14. 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 .
  15. 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 .
  16. Nielsen, FG, Kooyman, M, Kensche, P, Marks, H, Stunnenberg, H, Huynen, M et al.. The PinkThing for analysing ChIP profiling data in their genomic context. BMC Res Notes. 2013;6 :133. doi: 10.1186/1756-0500-6-133. PubMed PMID:23557140 PubMed Central PMC3674928.
  17. Marks, H, Kalkan, T, Menafra, R, Denissov, S, Jones, K, Hofemeister, H et al.. The transcriptional and epigenomic foundations of ground state pluripotency. Cell. 2012;149 (3):590-604. doi: 10.1016/j.cell.2012.03.026. PubMed PMID:22541430 PubMed Central PMC3398752.
  18. 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.
  19. Huang, R, Jaritz, M, Guenzl, P, Vlatkovic, I, Sommer, A, Tamir, IM et al.. An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs. PLoS ONE. 2011;6 (11):e27288. doi: 10.1371/journal.pone.0027288. PubMed PMID:22102886 PubMed Central PMC3213133.
  20. Seitan, VC, Hao, B, Tachibana-Konwalski, K, Lavagnolli, T, Mira-Bontenbal, H, Brown, KE et al.. A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation. Nature. 2011;476 (7361):467-71. doi: 10.1038/nature10312. PubMed PMID:21832993 PubMed Central PMC3179485.
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