Publications

  1. Xu, Q, Georgiou, G, Frölich, S, van der Sande, M, Veenstra, GJC, Zhou, H et al.. ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination. Nucleic Acids Res. 2021; :. doi: 10.1093/nar/gkab598. PubMed PMID:34244796 .
  2. Bright, AR, van Genesen, S, Li, Q, Grasso, A, Frölich, S, van der Sande, M et al.. Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates. EMBO J. 2021;40 (9):e104913. doi: 10.15252/embj.2020104913. PubMed PMID:33555045 PubMed Central PMC8090851.
  3. van Mierlo, G, Jansen, JRG, Wang, J, Poser, I, van Heeringen, SJ, Vermeulen, M et al.. Predicting protein condensate formation using machine learning. Cell Rep. 2021;34 (5):108705. doi: 10.1016/j.celrep.2021.108705. PubMed PMID:33535034 .
  4. Lederer, S, Heskes, T, van Heeringen, SJ, Albers, CA. Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis. PLoS One. 2020;15 (5):e0231824. doi: 10.1371/journal.pone.0231824. PubMed PMID:32357166 PubMed Central PMC7194367.
  5. Soares, E, Xu, Q, Li, Q, Qu, J, Zheng, Y, Raeven, HHM et al.. Single-cell RNA-seq identifies a reversible mesodermal activation in abnormally specified epithelia of p63 EEC syndrome. Proc Natl Acad Sci U S A. 2019;116 (35):17361-17370. doi: 10.1073/pnas.1908180116. PubMed PMID:31413199 PubMed Central PMC6717277.
  6. Peñalosa-Ruiz, G, Bousgouni, V, Gerlach, JP, Waarlo, S, van de Ven, JV, Veenstra, TE et al.. WDR5, BRCA1, and BARD1 Co-regulate the DNA Damage Response and Modulate the Mesenchymal-to-Epithelial Transition during Early Reprogramming. Stem Cell Reports. 2019;12 (4):743-756. doi: 10.1016/j.stemcr.2019.02.006. PubMed PMID:30880078 PubMed Central PMC6449870.
  7. Marlétaz, F, Firbas, PN, Maeso, I, Tena, JJ, Bogdanovic, O, Perry, M et al.. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. 2018;564 (7734):64-70. doi: 10.1038/s41586-018-0734-6. PubMed PMID:30464347 PubMed Central PMC6292497.
  8. Tanis, SEJ, Jansen, PWTC, Zhou, H, van Heeringen, SJ, Vermeulen, M, Kretz, M et al.. Splicing and Chromatin Factors Jointly Regulate Epidermal Differentiation. Cell Rep. 2018;25 (5):1292-1303.e5. doi: 10.1016/j.celrep.2018.10.017. PubMed PMID:30380419 .
  9. Søndergaard, JN, van Heeringen, SJ, Looman, MWG, Tang, C, Triantis, V, Louche, P et al.. Dendritic Cells Actively Limit Interleukin-10 Production Under Inflammatory Conditions via DC-SCRIPT and Dual-Specificity Phosphatase 4. Front Immunol. 2018;9 :1420. doi: 10.3389/fimmu.2018.01420. PubMed PMID:29988341 PubMed Central PMC6023963.
  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. Toenhake, CG, Fraschka, SA, Vijayabaskar, MS, Westhead, DR, van Heeringen, SJ, Bártfai, R et al.. Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development. Cell Host Microbe. 2018;23 (4):557-569.e9. doi: 10.1016/j.chom.2018.03.007. PubMed PMID:29649445 PubMed Central PMC5899830.
  12. Elurbe, DM, Paranjpe, SS, Georgiou, G, van Kruijsbergen, I, Bogdanovic, O, Gibeaux, R et al.. Regulatory remodeling in the allo-tetraploid frog Xenopus laevis. Genome Biol. 2017;18 (1):198. doi: 10.1186/s13059-017-1335-7. PubMed PMID:29065907 PubMed Central PMC5655803.
  13. 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.
  14. 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;14 (10):1374-1388. doi: 10.1080/15476286.2017.1279787. PubMed PMID:28102759 PubMed Central PMC5711456.
  15. Novakovic, B, Habibi, E, Wang, SY, Arts, RJW, 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 PubMed Central PMC5927328.
  16. 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.
  17. 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 .
  18. 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 .
  19. 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.
  20. 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.
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