Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 39

1.

Single-cell RNA-seq identifies a reversible mesodermal activation in abnormally specified epithelia of p63 EEC syndrome.

Soares E, Xu Q, Li Q, Qu J, Zheng Y, Raeven HHM, Brandao KO, Petit I, van den Akker WMR, van Heeringen SJ, Aberdam D, Tang F, Zhou H.

Proc Natl Acad Sci U S A. 2019 Aug 27;116(35):17361-17370. doi: 10.1073/pnas.1908180116. Epub 2019 Aug 14.

PMID:
31413199
2.

WDR5, BRCA1, and BARD1 Co-regulate the DNA Damage Response and Modulate the Mesenchymal-to-Epithelial Transition during Early Reprogramming.

Peñalosa-Ruiz G, Bousgouni V, Gerlach JP, Waarlo S, van de Ven JV, Veenstra TE, Silva JCR, van Heeringen SJ, Bakal C, Mulder KW, Veenstra GJC.

Stem Cell Reports. 2019 Apr 9;12(4):743-756. doi: 10.1016/j.stemcr.2019.02.006. Epub 2019 Mar 14.

3.

Amphioxus functional genomics and the origins of vertebrate gene regulation.

Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M.

Nature. 2018 Dec;564(7734):64-70. doi: 10.1038/s41586-018-0734-6. Epub 2018 Nov 21.

4.

Splicing and Chromatin Factors Jointly Regulate Epidermal Differentiation.

Tanis SEJ, Jansen PWTC, Zhou H, van Heeringen SJ, Vermeulen M, Kretz M, Mulder KW.

Cell Rep. 2018 Oct 30;25(5):1292-1303.e5. doi: 10.1016/j.celrep.2018.10.017.

5.

Dendritic Cells Actively Limit Interleukin-10 Production Under Inflammatory Conditions via DC-SCRIPT and Dual-Specificity Phosphatase 4.

Søndergaard JN, van Heeringen SJ, Looman MWG, Tang C, Triantis V, Louche P, Janssen-Megens EM, Sieuwerts AM, Martens JWM, Logie C, Stunnenberg HG, Ansems M, Adema GJ.

Front Immunol. 2018 Jun 22;9:1420. doi: 10.3389/fimmu.2018.01420. eCollection 2018.

6.

MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding.

Perino M, van Mierlo G, Karemaker ID, van Genesen S, Vermeulen M, Marks H, van Heeringen SJ, Veenstra GJC.

Nat Genet. 2018 Jul;50(7):1002-1010. doi: 10.1038/s41588-018-0134-8. Epub 2018 May 28.

PMID:
29808031
7.

Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development.

Toenhake CG, Fraschka SA, Vijayabaskar MS, Westhead DR, van Heeringen SJ, Bártfai R.

Cell Host Microbe. 2018 Apr 11;23(4):557-569.e9. doi: 10.1016/j.chom.2018.03.007.

8.

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.

Elurbe DM, Paranjpe SS, Georgiou G, van Kruijsbergen I, Bogdanovic O, Gibeaux R, Heald R, Lister R, Huynen MA, van Heeringen SJ, Veenstra GJC.

Genome Biol. 2017 Oct 24;18(1):198. doi: 10.1186/s13059-017-1335-7.

9.

p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate.

Richardson R, Mitchell K, Hammond NL, Mollo MR, Kouwenhoven EN, Wyatt ND, Donaldson IJ, Zeef L, Burgis T, Blance R, van Heeringen SJ, Stunnenberg HG, Zhou H, Missero C, Romano RA, Sinha S, Dixon MJ, Dixon J.

PLoS Genet. 2017 Jun 12;13(6):e1006828. doi: 10.1371/journal.pgen.1006828. eCollection 2017 Jun.

10.

Antisense transcription of the myotonic dystrophy locus yields low-abundant RNAs with and without (CAG)n repeat.

Gudde AEEG, van Heeringen SJ, de Oude AI, van Kessel IDG, Estabrook J, Wang ET, Wieringa B, Wansink DG.

RNA Biol. 2017 Oct 3;14(10):1374-1388. doi: 10.1080/15476286.2017.1279787. Epub 2017 Jan 19.

11.

β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance.

Novakovic B, Habibi E, Wang SY, Arts RJW, Davar R, Megchelenbrink W, Kim B, Kuznetsova T, Kox M, Zwaag J, Matarese F, van Heeringen SJ, Janssen-Megens EM, Sharifi N, Wang C, Keramati F, Schoonenberg V, Flicek P, Clarke L, Pickkers P, Heath S, Gut I, Netea MG, Martens JHA, Logie C, Stunnenberg HG.

Cell. 2016 Nov 17;167(5):1354-1368.e14. doi: 10.1016/j.cell.2016.09.034.

12.

Genome evolution in the allotetraploid frog Xenopus laevis.

Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS.

Nature. 2016 Oct 20;538(7625):336-343. doi: 10.1038/nature19840.

13.

Genomic organization and modulation of gene expression of the TGF-β and FGF pathways in the allotetraploid frog Xenopus laevis.

Suzuki A, Yoshida H, van Heeringen SJ, Takebayashi-Suzuki K, Veenstra GJC, Taira M.

Dev Biol. 2017 Jun 15;426(2):336-359. doi: 10.1016/j.ydbio.2016.09.016. Epub 2016 Sep 28.

14.

ChIP-seq Data Processing for PcG Proteins and Associated Histone Modifications.

Bogdanovic O, van Heeringen SJ.

Methods Mol Biol. 2016;1480:37-53. doi: 10.1007/978-1-4939-6380-5_4.

PMID:
27659973
15.

Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos.

van Kruijsbergen I, Hontelez S, Elurbe DM, van Heeringen SJ, Huynen MA, Veenstra GJC.

Dev Biol. 2017 Jun 15;426(2):460-471. doi: 10.1016/j.ydbio.2016.08.031. Epub 2016 Sep 14.

16.

fluff: exploratory analysis and visualization of high-throughput sequencing data.

Georgiou G, van Heeringen SJ.

PeerJ. 2016 Jul 19;4:e2209. doi: 10.7717/peerj.2209. eCollection 2016.

17.

Erratum: Embryonic transcription is controlled by maternally defined chromatin state.

Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJ.

Nat Commun. 2016 Jul 5;7:12208. doi: 10.1038/ncomms12208. No abstract available.

18.

Normal formation of a vertebrate body plan and loss of tissue maintenance in the absence of ezh2.

San B, Chrispijn ND, Wittkopp N, van Heeringen SJ, Lagendijk AK, Aben M, Bakkers J, Ketting RF, Kamminga LM.

Sci Rep. 2016 May 5;6:24658. doi: 10.1038/srep24658.

19.

Embryonic transcription is controlled by maternally defined chromatin state.

Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJC.

Nat Commun. 2015 Dec 18;6:10148. doi: 10.1038/ncomms10148. Erratum in: Nat Commun. 2016 Jul 05;7:12208.

20.

Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation.

Kouwenhoven EN, Oti M, Niehues H, van Heeringen SJ, Schalkwijk J, Stunnenberg HG, van Bokhoven H, Zhou H.

EMBO Rep. 2015 Jul;16(7):863-78. doi: 10.15252/embr.201439941. Epub 2015 Jun 1.

21.

Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs.

Smits AH, Lindeboom RG, Perino M, van Heeringen SJ, Veenstra GJ, Vermeulen M.

Nucleic Acids Res. 2014 Sep;42(15):9880-91. doi: 10.1093/nar/gku661. Epub 2014 Jul 23.

22.

Principles of nucleation of H3K27 methylation during embryonic development.

van Heeringen SJ, Akkers RC, van Kruijsbergen I, Arif MA, Hanssen LL, Sharifi N, Veenstra GJ.

Genome Res. 2014 Mar;24(3):401-10. doi: 10.1101/gr.159608.113. Epub 2013 Dec 11.

23.

A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development.

Paranjpe SS, Jacobi UG, van Heeringen SJ, Veenstra GJ.

BMC Genomics. 2013 Nov 6;14:762. doi: 10.1186/1471-2164-14-762.

24.

APR-246/PRIMA-1(MET) rescues epidermal differentiation in skin keratinocytes derived from EEC syndrome patients with p63 mutations.

Shen J, van den Bogaard EH, Kouwenhoven EN, Bykov VJ, Rinne T, Zhang Q, Tjabringa GS, Gilissen C, van Heeringen SJ, Schalkwijk J, van Bokhoven H, Wiman KG, Zhou H.

Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2157-62. doi: 10.1073/pnas.1201993110. Epub 2013 Jan 25.

25.

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.

Bogdanovic O, Fernandez-Miñán A, Tena JJ, de la Calle-Mustienes E, Hidalgo C, van Kruysbergen I, van Heeringen SJ, Veenstra GJ, Gómez-Skarmeta JL.

Genome Res. 2012 Oct;22(10):2043-53. doi: 10.1101/gr.134833.111. Epub 2012 May 16.

26.

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.

Boergesen M, Pedersen TÅ, Gross B, van Heeringen SJ, Hagenbeek D, Bindesbøll C, Caron S, Lalloyer F, Steffensen KR, Nebb HI, Gustafsson JÅ, Stunnenberg HG, Staels B, Mandrup S.

Mol Cell Biol. 2012 Feb;32(4):852-67. doi: 10.1128/MCB.06175-11. Epub 2011 Dec 12.

27.

The epigenome in early vertebrate development.

Bogdanović O, van Heeringen SJ, Veenstra GJ.

Genesis. 2012 Mar;50(3):192-206. doi: 10.1002/dvg.20831. Epub 2011 Dec 27. Review.

28.

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis.

Bogdanovic O, Long SW, van Heeringen SJ, Brinkman AB, Gómez-Skarmeta JL, Stunnenberg HG, Jones PL, Veenstra GJ.

Genome Res. 2011 Aug;21(8):1313-27. doi: 10.1101/gr.114843.110. Epub 2011 Jun 2.

29.

Crosstalk between c-Jun and TAp73alpha/beta contributes to the apoptosis-survival balance.

Koeppel M, van Heeringen SJ, Kramer D, Smeenk L, Janssen-Megens E, Hartmann M, Stunnenberg HG, Lohrum M.

Nucleic Acids Res. 2011 Aug;39(14):6069-85. doi: 10.1093/nar/gkr028. Epub 2011 Mar 31.

30.

Role of p53 serine 46 in p53 target gene regulation.

Smeenk L, van Heeringen SJ, Koeppel M, Gilbert B, Janssen-Megens E, Stunnenberg HG, Lohrum M.

PLoS One. 2011 Mar 4;6(3):e17574. doi: 10.1371/journal.pone.0017574.

31.

Nucleotide composition-linked divergence of vertebrate core promoter architecture.

van Heeringen SJ, Akhtar W, Jacobi UG, Akkers RC, Suzuki Y, Veenstra GJ.

Genome Res. 2011 Mar;21(3):410-21. doi: 10.1101/gr.111724.110. Epub 2011 Jan 10.

32.

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments.

van Heeringen SJ, Veenstra GJ.

Bioinformatics. 2011 Jan 15;27(2):270-1. doi: 10.1093/bioinformatics/btq636. Epub 2010 Nov 15.

33.

Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.

Kouwenhoven EN, van Heeringen SJ, Tena JJ, Oti M, Dutilh BE, Alonso ME, de la Calle-Mustienes E, Smeenk L, Rinne T, Parsaulian L, Bolat E, Jurgelenaite R, Huynen MA, Hoischen A, Veltman JA, Brunner HG, Roscioli T, Oates E, Wilson M, Manzanares M, Gómez-Skarmeta JL, Stunnenberg HG, Lohrum M, van Bokhoven H, Zhou H.

PLoS Genet. 2010 Aug 19;6(8):e1001065. doi: 10.1371/journal.pgen.1001065.

34.

ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation.

Akkers RC, van Heeringen SJ, Manak JR, Green RD, Stunnenberg HG, Veenstra GJ.

PLoS One. 2010 Jan 21;5(1):e8820. doi: 10.1371/journal.pone.0008820.

35.

A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.

Akkers RC, van Heeringen SJ, Jacobi UG, Janssen-Megens EM, Françoijs KJ, Stunnenberg HG, Veenstra GJ.

Dev Cell. 2009 Sep;17(3):425-34. doi: 10.1016/j.devcel.2009.08.005.

36.

ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands.

Welboren WJ, van Driel MA, Janssen-Megens EM, van Heeringen SJ, Sweep FC, Span PN, Stunnenberg HG.

EMBO J. 2009 May 20;28(10):1418-28. doi: 10.1038/emboj.2009.88. Epub 2009 Apr 4.

37.

The novel p53 target gene IRF2BP2 participates in cell survival during the p53 stress response.

Koeppel M, van Heeringen SJ, Smeenk L, Navis AC, Janssen-Megens EM, Lohrum M.

Nucleic Acids Res. 2009 Feb;37(2):322-35. doi: 10.1093/nar/gkn940. Epub 2008 Nov 28.

38.

Genetic identification of a network of factors that functionally interact with the nucleosome remodeling ATPase ISWI.

Burgio G, La Rocca G, Sala A, Arancio W, Di Gesù D, Collesano M, Sperling AS, Armstrong JA, van Heeringen SJ, Logie C, Tamkun JW, Corona DF.

PLoS Genet. 2008 Jun 6;4(6):e1000089. doi: 10.1371/journal.pgen.1000089.

39.

Characterization of genome-wide p53-binding sites upon stress response.

Smeenk L, van Heeringen SJ, Koeppel M, van Driel MA, Bartels SJ, Akkers RC, Denissov S, Stunnenberg HG, Lohrum M.

Nucleic Acids Res. 2008 Jun;36(11):3639-54. doi: 10.1093/nar/gkn232. Epub 2008 May 12.

Supplemental Content

Loading ...
Support Center