Publications

  1. Richardson, R, Mitchell, K, Hammond, NL, Mollo, MR, Kouwenhoven, EN, Wyatt, ND et al.. p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate. PLoS Genet. 2017;13 (6):e1006828. doi: 10.1371/journal.pgen.1006828. PubMed PMID:28604778 PubMed Central PMC5484519.
  2. Gudde, AEEG, van Heeringen, SJ, de Oude, AI, van Kessel, IDG, Estabrook, J, Wang, ET et al.. Antisense transcription of the myotonic dystrophy locus yields low-abundant RNAs with and without (CAG)n repeat. RNA Biol. 2017; :1-15. doi: 10.1080/15476286.2017.1279787. PubMed PMID:28102759 .
  3. Novakovic, B, Habibi, E, Wang, SY, Arts, RJ, Davar, R, Megchelenbrink, W et al.. β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance. Cell. 2016;167 (5):1354-1368.e14. doi: 10.1016/j.cell.2016.09.034. PubMed PMID:27863248 .
  4. Session, AM, Uno, Y, Kwon, T, Chapman, JA, Toyoda, A, Takahashi, S et al.. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 2016;538 (7625):336-343. doi: 10.1038/nature19840. PubMed PMID:27762356 PubMed Central PMC5313049.
  5. Suzuki, A, Yoshida, H, van Heeringen, SJ, Takebayashi-Suzuki, K, Veenstra, GJC, Taira, M et al.. Genomic organization and modulation of gene expression of the TGF-β and FGF pathways in the allotetraploid frog Xenopus laevis. Dev. Biol. 2017;426 (2):336-359. doi: 10.1016/j.ydbio.2016.09.016. PubMed PMID:27692744 .
  6. Bogdanovic, O, van Heeringen, SJ. ChIP-seq Data Processing for PcG Proteins and Associated Histone Modifications. Methods Mol. Biol. 2016;1480 :37-53. doi: 10.1007/978-1-4939-6380-5_4. PubMed PMID:27659973 .
  7. van Kruijsbergen, I, Hontelez, S, Elurbe, DM, van Heeringen, SJ, Huynen, MA, Veenstra, GJC et al.. Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos. Dev. Biol. 2017;426 (2):460-471. doi: 10.1016/j.ydbio.2016.08.031. PubMed PMID:27639284 PubMed Central PMC5350053.
  8. Georgiou, G, van Heeringen, SJ. fluff: exploratory analysis and visualization of high-throughput sequencing data. PeerJ. 2016;4 :e2209. doi: 10.7717/peerj.2209. PubMed PMID:27547532 PubMed Central PMC4957989.
  9. Hontelez, S, van Kruijsbergen, I, Georgiou, G, van Heeringen, SJ, Bogdanovic, O, Lister, R et al.. Erratum: Embryonic transcription is controlled by maternally defined chromatin state. Nat Commun. 2016;7 :12208. doi: 10.1038/ncomms12208. PubMed PMID:27378471 PubMed Central PMC4935964.
  10. San, B, Chrispijn, ND, Wittkopp, N, van Heeringen, SJ, Lagendijk, AK, Aben, M et al.. Normal formation of a vertebrate body plan and loss of tissue maintenance in the absence of ezh2. Sci Rep. 2016;6 :24658. doi: 10.1038/srep24658. PubMed PMID:27145952 PubMed Central PMC4857124.
  11. Hontelez, S, van Kruijsbergen, I, Georgiou, G, van Heeringen, SJ, Bogdanovic, O, Lister, R et al.. Embryonic transcription is controlled by maternally defined chromatin state. Nat Commun. 2015;6 :10148. doi: 10.1038/ncomms10148. PubMed PMID:26679111 PubMed Central PMC4703837.
  12. Kouwenhoven, EN, Oti, M, Niehues, H, van Heeringen, SJ, Schalkwijk, J, Stunnenberg, HG et al.. Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation. EMBO Rep. 2015;16 (7):863-78. doi: 10.15252/embr.201439941. PubMed PMID:26034101 PubMed Central PMC4515125.
  13. 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.
  14. van Heeringen, SJ, Akkers, RC, van Kruijsbergen, I, Arif, MA, Hanssen, LL, Sharifi, N et al.. Principles of nucleation of H3K27 methylation during embryonic development. Genome Res. 2014;24 (3):401-10. doi: 10.1101/gr.159608.113. PubMed PMID:24336765 PubMed Central PMC3941105.
  15. Paranjpe, SS, Jacobi, UG, van Heeringen, SJ, Veenstra, GJ. A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development. BMC Genomics. 2013;14 :762. doi: 10.1186/1471-2164-14-762. PubMed PMID:24195446 PubMed Central PMC3907017.
  16. Shen, J, van den Bogaard, EH, Kouwenhoven, EN, Bykov, VJ, Rinne, T, Zhang, Q et al.. APR-246/PRIMA-1(MET) rescues epidermal differentiation in skin keratinocytes derived from EEC syndrome patients with p63 mutations. Proc. Natl. Acad. Sci. U.S.A. 2013;110 (6):2157-62. doi: 10.1073/pnas.1201993110. PubMed PMID:23355676 PubMed Central PMC3568378.
  17. Bogdanovic, O, Fernandez-Miñán, A, Tena, JJ, de la Calle-Mustienes, E, Hidalgo, C, van Kruysbergen, I et al.. Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Res. 2012;22 (10):2043-53. doi: 10.1101/gr.134833.111. PubMed PMID:22593555 PubMed Central PMC3460198.
  18. Boergesen, M, Pedersen, TÅ, Gross, B, van Heeringen, SJ, Hagenbeek, D, Bindesbøll, C et al.. Genome-wide profiling of liver X receptor, retinoid X receptor, and peroxisome proliferator-activated receptor α in mouse liver reveals extensive sharing of binding sites. Mol. Cell. Biol. 2012;32 (4):852-67. doi: 10.1128/MCB.06175-11. PubMed PMID:22158963 PubMed Central PMC3272984.
  19. Bogdanović, O, van Heeringen, SJ, Veenstra, GJ. The epigenome in early vertebrate development. Genesis. 2012;50 (3):192-206. doi: 10.1002/dvg.20831. PubMed PMID:22139962 PubMed Central PMC3294079.
  20. Bogdanovic, O, Long, SW, van Heeringen, SJ, Brinkman, AB, Gómez-Skarmeta, JL, Stunnenberg, HG et al.. Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Genome Res. 2011;21 (8):1313-27. doi: 10.1101/gr.114843.110. PubMed PMID:21636662 PubMed Central PMC3149498.
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