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Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures.
Published in:
eLife, 2016, p. 1, doi. 10.7554/eLife.10557
By:
- Xinchen Wang;
- Tucker, Nathan R.;
- Rizki, Gizem;
- Mills, Robert;
- Krijger, Peter H. L.;
- de Wit, Elzo;
- Subramanian, Vidya;
- Bartell, Eric;
- Xinh-Xinh Nguyen;
- Jiangchuan Ye;
- Leyton-Mange, Jordan;
- Dolmatova, Elena V.;
- van der Harst, Pim;
- de Laat, Wouter;
- Ellinor, Patrick T.;
- Newton-Cheh, Christopher;
- Milan, David J.;
- Kellis, Manolis;
- Boyer, Laurie A.
Publication type:
Article
peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data.
Published in:
Nucleic Acids Research, 2018, v. 46, n. 15, p. e91, doi. 10.1093/nar/gky443
By:
- Geeven, Geert;
- Teunissen, Hans;
- de Laat, Wouter;
- de Wit, Elzo
Publication type:
Article
A Mediator-cohesin axis controls heterochromatin domain formation.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28377-7
By:
- Haarhuis, Judith H. I.;
- van der Weide, Robin H.;
- Blomen, Vincent A.;
- Flach, Koen D.;
- Teunissen, Hans;
- Willems, Laureen;
- Brummelkamp, Thijn R.;
- Rowland, Benjamin D.;
- de Wit, Elzo
Publication type:
Article
Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping.
Published in:
Nature Biotechnology, 2014, v. 32, n. 10, p. 1019, doi. 10.1038/nbt.2959
By:
- de Vree, Paula J P;
- de Wit, Elzo;
- Yilmaz, Mehmet;
- van de Heijning, Monique;
- Klous, Petra;
- Verstegen, Marjon J A M;
- Wan, Yi;
- Teunissen, Hans;
- Krijger, Peter H L;
- Geeven, Geert;
- Eijk, Paul P;
- Sie, Daoud;
- Ylstra, Bauke;
- Hulsman, Lorette O M;
- van Dooren, Marieke F;
- van Zutven, Laura J C M;
- van den Ouweland, Ans;
- Verbeek, Sjef;
- van Dijk, Ko Willems;
- Cornelissen, Marion
Publication type:
Article
Pioneer activity distinguishes activating from non‐activating SOX2 binding sites.
Published in:
EMBO Journal, 2023, v. 42, n. 20, p. 1, doi. 10.15252/embj.2022113150
By:
- Maresca, Michela;
- van den Brand, Teun;
- Li, Hangpeng;
- Teunissen, Hans;
- Davies, James;
- de Wit, Elzo
Publication type:
Article
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C).
Published in:
Nature Genetics, 2006, v. 38, n. 11, p. 1348, doi. 10.1038/ng1896
By:
- Simonis, Marieke;
- Klous, Petra;
- Splinter, Erik;
- Moshkin, Yuri;
- Willemsen, Rob;
- de Wit, Elzo;
- van Steensel, Bas;
- de Laat, Wouter
Publication type:
Article
Characterization of the Drosophila melanogaster genome at the nuclear lamina.
Published in:
Nature Genetics, 2006, v. 38, n. 9, p. 1005, doi. 10.1038/ng1852
By:
- Pickersgill, Helen;
- Kalverda, Bernike;
- de Wit, Elzo;
- Talhout, Wendy;
- Fornerod, Maarten;
- van Steensel, Bas
Publication type:
Article
Corrigendum: Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster.
Published in:
2006
By:
- Tolhuis, Bas;
- Muijrers, Inhua;
- de Wit, Elzo;
- Teunissen, Hans;
- Talhout, Wendy;
- van Steensel, Bas;
- van Lohuizen, Maarten
Publication type:
Correction Notice
Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster.
Published in:
Nature Genetics, 2006, v. 38, n. 6, p. 694, doi. 10.1038/ng1792
By:
- Tolhuis, Bas;
- Muijrers, Inhua;
- de Wit, Elzo;
- Teunissen, Hans;
- Talhout, Wendy;
- van Steensel, Bas;
- van Lohuizen, Maarten
Publication type:
Article
Robust 4C-seq data analysis to screen for regulatory DNA interactions.
Published in:
Nature Methods, 2012, v. 9, n. 10, p. 969, doi. 10.1038/nmeth.2173
By:
- van de Werken, Harmen J G;
- Landan, Gilad;
- Holwerda, Sjoerd J B;
- Hoichman, Michael;
- Klous, Petra;
- Chachik, Ran;
- Splinter, Erik;
- Valdes-Quezada, Christian;
- Öz, Yuva;
- Bouwman, Britta A M;
- Verstegen, Marjon J A M;
- de Wit, Elzo;
- Tanay, Amos;
- de Laat, Wouter
Publication type:
Article
Limitations and possibilities of small RNA digital gene expression profiling.
Published in:
2009
By:
- Linsen, Sam E. V.;
- de Wit, Elzo;
- Janssens, Georges;
- Heater, Sheila;
- Chapman, Laura;
- Parkin, Rachael K.;
- Fritz, Brian;
- Wyman, Stacia K.;
- de Bruijn, Ewart;
- Voest, Emile E.;
- Kuersten, Scott;
- Tewari, Muneesh;
- Cuppen, Edwin
Publication type:
Letter
SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-43498-3
By:
- Liu, Ning Qing;
- Paassen, Irene;
- Custers, Lars;
- Zeller, Peter;
- Teunissen, Hans;
- Ayyildiz, Dilara;
- He, Jiayou;
- Buhl, Juliane Laura;
- Hoving, Eelco Wieger;
- van Oudenaarden, Alexander;
- de Wit, Elzo;
- Drost, Jarno
Publication type:
Article
Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.
Published in:
BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2137-5
By:
- Zepeda-Mendoza, Cinthya J.;
- Mukhopadhyay, Swagatam;
- Wong, Emily S.;
- Harder, Nathalie;
- Splinter, Erik;
- de Wit, Elzo;
- Eckersley-Maslin, Melanie A.;
- Ried, Thomas;
- Eils, Roland;
- Rohr, Karl;
- Mills, Alea;
- de Laat, Wouter;
- Flicek, Paul;
- Sengupta, Anirvan M.;
- Spector, David L.
Publication type:
Article
Dynamic chromosomal interactions and control of heterochromatin positioning by Ki‐67.
Published in:
EMBO Reports, 2022, v. 23, n. 12, p. 1, doi. 10.15252/embr.202255782
By:
- van Schaik, Tom;
- Manzo, Stefano G;
- Vouzas, Athanasios E;
- Liu, Ning Qing;
- Teunissen, Hans;
- de Wit, Elzo;
- Gilbert, David M;
- van Steensel, Bas
Publication type:
Article
Unexpected gene activation following CRISPR‐Cas9‐mediated genome editing.
Published in:
EMBO Reports, 2022, v. 23, n. 2, p. 1, doi. 10.15252/embr.202153902
By:
- Manjón, Anna G;
- Linder, Simon;
- Teunissen, Hans;
- Friskes, Anoek;
- Zwart, Wilbert;
- de Wit, Elzo;
- Medema, René H
Publication type:
Article
A natural WNT signaling variant potently synergizes with Cdkn2ab loss in skin carcinogenesis.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09321-8
By:
- Krimpenfort, Paul;
- Snoek, Margriet;
- Lambooij, Jan-Paul;
- Song, Ji-Ying;
- van der Weide, Robin;
- Bhaskaran, Rajith;
- Teunissen, Hans;
- Adams, David J.;
- de Wit, Elzo;
- Berns, Anton
Publication type:
Article
HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila.
Published in:
EMBO Journal, 2007, v. 26, n. 3, p. 741, doi. 10.1038/sj.emboj.7601527
By:
- Greil, Frauke;
- de Wit, Elzo;
- Bussemaker, Harmen J.;
- van Steensel, Bas
Publication type:
Article
Variegated gene expression caused by cell-specific long-range DNA interactions.
Published in:
Nature Cell Biology, 2011, v. 13, n. 8, p. 944, doi. 10.1038/ncb2278
By:
- Noordermeer, Daan;
- de Wit, Elzo;
- Klous, Petra;
- van de Werken, Harmen;
- Simonis, Marieke;
- Lopez-Jones, Melissa;
- Eussen, Bert;
- de Klein, Annelies;
- Singer, Robert H.;
- de Laat, Wouter
Publication type:
Article
Genome-wide analysis of FOXO3 mediated transcription regulation through RNA polymerase II profiling.
Published in:
Molecular Systems Biology, 2013, v. 9, n. 1, p. 1, doi. 10.1038/msb.2012.74
By:
- Eijkelenboom, Astrid;
- Mokry, Michal;
- de Wit, Elzo;
- Smits, Lydia M;
- Polderman, Paulien E;
- van Triest, Miranda H;
- van Boxtel, Ruben;
- Schulze, Almut;
- de Laat, Wouter;
- Cuppen, Edwin;
- Burgering, Boudewijn M T
Publication type:
Article
CTCF and cohesin promote focal detachment of DNA from the nuclear lamina.
Published in:
Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02754-3
By:
- van Schaik, Tom;
- Liu, Ning Qing;
- Manzo, Stefano G.;
- Peric-Hupkes, Daan;
- de Wit, Elzo;
- van Steensel, Bas
Publication type:
Article
DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus.
Published in:
Genome Biology, 2013, v. 14, n. 5, p. 1, doi. 10.1186/gb-2013-14-5-r50
By:
- Kaaij, Lucas T. J.;
- van de Wetering, Marc;
- Fang, Fang;
- Decato, Benjamin;
- Molaro, Antoine;
- van de Werken, Harmen J. G.;
- van Es, Johan H.;
- Schuijers, Jurian;
- de Wit, Elzo;
- de Laat, Wouter;
- Hannon, Gregory J.;
- Clevers, Hans C.;
- Smith, Andrew D.;
- Ketting, René F.
Publication type:
Article
CTCF: a Swiss-army knife for genome organization and transcription regulation.
Published in:
Essays in Biochemistry, 2019, v. 63, n. 1, p. 157, doi. 10.1042/EBC20180069
By:
- Braccioli, Luca;
- de Wit, Elzo
Publication type:
Article
The pluripotent genome in three dimensions is shaped around pluripotency factors.
Published in:
Nature, 2013, v. 501, n. 7466, p. 227, doi. 10.1038/nature12420
By:
- de Wit, Elzo;
- Bouwman, Britta A. M.;
- Zhu, Yun;
- Klous, Petra;
- Splinter, Erik;
- Verstegen, Marjon J. A. M.;
- Krijger, Peter H. L.;
- Festuccia, Nicola;
- Nora, Elphège P.;
- Welling, Maaike;
- Heard, Edith;
- Geijsen, Niels;
- Poot, Raymond A.;
- Chambers, Ian;
- de Laat, Wouter
Publication type:
Article
A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation.
Published in:
Nucleic Acids Research, 2019, v. 47, n. 18, p. 9557, doi. 10.1093/nar/gkz675
By:
- Korkmaz, Gozde;
- Manber, Zohar;
- Lopes, Rui;
- Prekovic, Stefan;
- Schuurman, Karianne;
- Kim, Yongsoo;
- Teunissen, Hans;
- Flach, Koen;
- Wit, Elzo de;
- Galli, Giorgio G;
- Zwart, Wilbert;
- Elkon, Ran;
- Agami, Reuven
Publication type:
Article
Global Chromatin Domain Organization of the Drosophila Genome.
Published in:
PLoS Genetics, 2008, v. 4, n. 3, p. 1, doi. 10.1371/journal.pgen.1000045
By:
- de Wit, Elzo;
- Braunschweig, Ulrich;
- Greil, Frauke;
- Bussemaker, Harmen J.;
- van Steensel, Bas
Publication type:
Article
High-Resolution Mapping Reveals Links of HP1 with Active and Inactive Chromatin Components.
Published in:
PLoS Genetics, 2007, v. 3, n. 3, p. 0346, doi. 10.1371/journal.pgen.0030038
By:
- de Wit, Elzo;
- Greil, Frauke;
- Steensel, Bas van
Publication type:
Article
Small RNA expression and strain specificity in the rat.
Published in:
BMC Genomics, 2010, v. 11, p. 249, doi. 10.1186/1471-2164-11-249
By:
- Linsen, Sam E. V.;
- de Wit, Elzo;
- de Bruijn, Ewart;
- Edwin Cuppen
Publication type:
Article

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