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Items: 15

1.

METHimpute: imputation-guided construction of complete methylomes from WGBS data.

Taudt A, Roquis D, Vidalis A, Wardenaar R, Johannes F, Colomé-Tatché M.

BMC Genomics. 2018 Jun 7;19(1):444. doi: 10.1186/s12864-018-4641-x.

2.

Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids.

Lauss K, Wardenaar R, Oka R, van Hulten MHA, Guryev V, Keurentjes JJB, Stam M, Johannes F.

Plant Physiol. 2018 Feb;176(2):1627-1645. doi: 10.1104/pp.17.01054. Epub 2017 Dec 1.

3.

Erratum to: Methylome Evolution in plants.

Vidalis A, Živković D, Wardenaar R, Roquis D, Tellier A, Johannes F.

Genome Biol. 2017 Feb 27;18(1):41. doi: 10.1186/s13059-017-1176-4. No abstract available.

4.

Methylome evolution in plants.

Vidalis A, Živković D, Wardenaar R, Roquis D, Tellier A, Johannes F.

Genome Biol. 2016 Dec 20;17(1):264. doi: 10.1186/s13059-016-1127-5. Review. Erratum in: Genome Biol. 2017 Feb 27;18(1):41.

5.

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.

Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, Coe BP, Deelen P, de Ligt J, Lameijer EW, van Dijk F, Hormozdiari F; Genome of the Netherlands Consortium, Uitterlinden AG, van Duijn CM, Eichler EE, de Bakker PI, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Ye K, Guryev V.

Nat Commun. 2016 Oct 6;7:12989. doi: 10.1038/ncomms12989.

6.

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations.

van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ, Colomé-Tatché M, Johannes F.

Proc Natl Acad Sci U S A. 2015 May 26;112(21):6676-81. doi: 10.1073/pnas.1424254112. Epub 2015 May 11.

7.

Epigenetic basis of morphological variation and phenotypic plasticity in Arabidopsis thaliana.

Kooke R, Johannes F, Wardenaar R, Becker F, Etcheverry M, Colot V, Vreugdenhil D, Keurentjes JJ.

Plant Cell. 2015 Feb;27(2):337-48. doi: 10.1105/tpc.114.133025. Epub 2015 Feb 10.

8.

Mapping the epigenetic basis of complex traits.

Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury JM, Wincker P, Roudier F, Jansen RC, Colot V, Johannes F.

Science. 2014 Mar 7;343(6175):1145-8. doi: 10.1126/science.1248127. Epub 2014 Feb 6.

PMID:
24505129
9.

Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip.

Cortijo S, Wardenaar R, Colomé-Tatché M, Johannes F, Colot V.

Methods Mol Biol. 2014;1112:125-49. doi: 10.1007/978-1-62703-773-0_9.

PMID:
24478012
10.

Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis.

Wardenaar R, Liu H, Colot V, Colomé-Tatché M, Johannes F.

Methods Mol Biol. 2013;1067:203-24. doi: 10.1007/978-1-62703-607-8_13.

PMID:
23975794
11.

Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia.

Lendvai Á, Johannes F, Grimm C, Eijsink JJ, Wardenaar R, Volders HH, Klip HG, Hollema H, Jansen RC, Schuuring E, Wisman GB, van der Zee AG.

Epigenetics. 2012 Nov;7(11):1268-78. doi: 10.4161/epi.22301. Epub 2012 Sep 27.

12.

Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation.

Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Sarazin A, Etcheverry M, Martin A, Feng S, Duvernois-Berthet E, Labadie K, Wincker P, Jacobsen SE, Jansen RC, Colot V, Johannes F.

Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16240-5. doi: 10.1073/pnas.1212955109. Epub 2012 Sep 17.

13.

Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature.

Roux F, Colomé-Tatché M, Edelist C, Wardenaar R, Guerche P, Hospital F, Colot V, Jansen RC, Johannes F.

Genetics. 2011 Aug;188(4):1015-7. doi: 10.1534/genetics.111.128744. Epub 2011 May 19.

14.

Undifferentiated embryonic cell transcription factor 1 regulates ESC chromatin organization and gene expression.

Kooistra SM, van den Boom V, Thummer RP, Johannes F, Wardenaar R, Tesson BM, Veenhoff LM, Fusetti F, O'Neill LP, Turner BM, de Haan G, Eggen BJ.

Stem Cells. 2010 Oct;28(10):1703-14. doi: 10.1002/stem.497.

15.

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.

Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HT, Cuppen E, Jansen RC.

Bioinformatics. 2010 Apr 15;26(8):1000-6. doi: 10.1093/bioinformatics/btq087. Epub 2010 Mar 5.

PMID:
20208068

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