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4C technology: protocols and data analysis.
van de Werken HJ, de Vree PJ, Splinter E, Holwerda SJ, Klous P, de Wit E, de Laat W. van de Werken HJ, et al. Among authors: de vree pj, de laat w, de wit e. Methods Enzymol. 2012;513:89-112. doi: 10.1016/B978-0-12-391938-0.00004-5. Methods Enzymol. 2012. PMID: 22929766
Robust 4C-seq data analysis to screen for regulatory DNA interactions.
van de Werken HJ, Landan G, Holwerda SJ, Hoichman M, Klous P, Chachik R, Splinter E, Valdes-Quezada C, Oz Y, Bouwman BA, Verstegen MJ, de Wit E, Tanay A, de Laat W. van de Werken HJ, et al. Among authors: de laat w, de wit e. Nat Methods. 2012 Oct;9(10):969-72. doi: 10.1038/nmeth.2173. Epub 2012 Sep 9. Nat Methods. 2012. PMID: 22961246
Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells.
Holwerda SJ, van de Werken HJ, Ribeiro de Almeida C, Bergen IM, de Bruijn MJ, Verstegen MJ, Simonis M, Splinter E, Wijchers PJ, Hendriks RW, de Laat W. Holwerda SJ, et al. Among authors: de bruijn mj, de laat w, van de werken hj. Nucleic Acids Res. 2013 Aug;41(14):6905-16. doi: 10.1093/nar/gkt491. Epub 2013 Jun 7. Nucleic Acids Res. 2013. PMID: 23748562 Free PMC article.
A large permissive regulatory domain exclusively controls Tbx3 expression in the cardiac conduction system.
van Weerd JH, Badi I, van den Boogaard M, Stefanovic S, van de Werken HJ, Gomez-Velazquez M, Badia-Careaga C, Manzanares M, de Laat W, Barnett P, Christoffels VM. van Weerd JH, et al. Among authors: van den boogaard m, de laat w, van de werken hj. Circ Res. 2014 Aug 1;115(4):432-41. doi: 10.1161/CIRCRESAHA.115.303591. Epub 2014 Jun 24. Circ Res. 2014. PMID: 24963028
Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements.
Kolovos P, van de Werken HJ, Kepper N, Zuin J, Brouwer RW, Kockx CE, Wendt KS, van IJcken WF, Grosveld F, Knoch TA. Kolovos P, et al. Among authors: van ijcken wf, van de werken hj. Epigenetics Chromatin. 2014 Jun 16;7:10. doi: 10.1186/1756-8935-7-10. eCollection 2014. Epigenetics Chromatin. 2014. PMID: 25031611 Free PMC article.
Small chromosomal regions position themselves autonomously according to their chromatin class.
van de Werken HJG, Haan JC, Feodorova Y, Bijos D, Weuts A, Theunis K, Holwerda SJB, Meuleman W, Pagie L, Thanisch K, Kumar P, Leonhardt H, Marynen P, van Steensel B, Voet T, de Laat W, Solovei I, Joffe B. van de Werken HJG, et al. Genome Res. 2017 Jun;27(6):922-933. doi: 10.1101/gr.213751.116. Epub 2017 Mar 24. Genome Res. 2017. PMID: 28341771 Free PMC article.
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