Publications

  1. 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 .
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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 .
  8. 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 .
  9. 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 .
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. Petkov, SG, Marks, H, Klein, T, Garcia, RS, Gao, Y, Stunnenberg, H et al.. In vitro culture and characterization of putative porcine embryonic germ cells derived from domestic breeds and Yucatan mini pig embryos at Days 20-24 of gestation. Stem Cell Res. 2011;6 (3):226-37. doi: 10.1016/j.scr.2011.01.003. PubMed PMID:21419743 .
  16. Kramer, JM, Kochinke, K, Oortveld, MA, Marks, H, Kramer, D, de Jong, EK et al.. Epigenetic regulation of learning and memory by Drosophila EHMT/G9a. PLoS Biol. 2011;9 (1):e1000569. doi: 10.1371/journal.pbio.1000569. PubMed PMID:21245904 PubMed Central PMC3014924.
  17. Vermeulen, M, Eberl, HC, Matarese, F, Marks, H, Denissov, S, Butter, F et al.. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 2010;142 (6):967-80. doi: 10.1016/j.cell.2010.08.020. PubMed PMID:20850016 .
  18. Marks, H, Veenstra, GJ, Stunnenberg, HG. Insightful tales from single embryonic cells. Cell Stem Cell. 2010;6 (5):397-8. doi: 10.1016/j.stem.2010.04.008. PubMed PMID:20452308 .
  19. Dieu, BT, Marks, H, Zwart, MP, Vlak, JM. Evaluation of white spot syndrome virus variable DNA loci as molecular markers of virus spread at intermediate spatiotemporal scales. J. Gen. Virol. 2010;91 (Pt 5):1164-72. doi: 10.1099/vir.0.018028-0. PubMed PMID:20089797 .
  20. Marks, H, Chow, JC, Denissov, S, Françoijs, KJ, Brockdorff, N, Heard, E et al.. High-resolution analysis of epigenetic changes associated with X inactivation. Genome Res. 2009;19 (8):1361-73. doi: 10.1101/gr.092643.109. PubMed PMID:19581487 PubMed Central PMC2720191.
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