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Items: 1 to 20 of 178

1.

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J.

Science. 2009 Oct 9;326(5950):289-93. doi: 10.1126/science.1181369.

2.

Hi-C: a method to study the three-dimensional architecture of genomes.

van Berkum NL, Lieberman-Aiden E, Williams L, Imakaev M, Gnirke A, Mirny LA, Dekker J, Lander ES.

J Vis Exp. 2010 May 6;(39). pii: 1869. doi: 10.3791/1869.

3.

Hi-C: a comprehensive technique to capture the conformation of genomes.

Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J.

Methods. 2012 Nov;58(3):268-76. doi: 10.1016/j.ymeth.2012.05.001. Epub 2012 May 29.

4.

Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide.

Botta M, Haider S, Leung IX, Lio P, Mozziconacci J.

Mol Syst Biol. 2010 Nov 2;6:426. doi: 10.1038/msb.2010.79.

5.

GE Prize essay. Zoom!

Lieberman Aiden E.

Science. 2011 Dec 2;334(6060):1222-3. doi: 10.1126/science.1216288. No abstract available. Erratum in: Science. 2012 Feb 17;335(6070):796.

6.

Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data.

Saberi S, Farré P, Cuvier O, Emberly E.

BMC Bioinformatics. 2015 May 23;16:171. doi: 10.1186/s12859-015-0584-2.

7.
8.

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.

Rousseau M, Fraser J, Ferraiuolo MA, Dostie J, Blanchette M.

BMC Bioinformatics. 2011 Oct 25;12:414. doi: 10.1186/1471-2105-12-414.

9.

Conformation of replicated segments of chromosome fibres in human S-phase nucleus.

Solovjeva L, Svetlova M, Stein G, Chagin V, Rozanov Y, Zannis-Hadjopoulos M, Price G, Tomilin N.

Chromosome Res. 1998 Dec;6(8):595-602.

PMID:
10099872
10.

Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila.

Grob S, Schmid MW, Grossniklaus U.

Mol Cell. 2014 Sep 4;55(5):678-93. doi: 10.1016/j.molcel.2014.07.009. Epub 2014 Aug 14.

11.

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.

Dekker J, Marti-Renom MA, Mirny LA.

Nat Rev Genet. 2013 Jun;14(6):390-403. doi: 10.1038/nrg3454. Epub 2013 May 9. Review.

12.

Complexity of chromatin folding is captured by the strings and binders switch model.

Barbieri M, Chotalia M, Fraser J, Lavitas LM, Dostie J, Pombo A, Nicodemi M.

Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16173-8. doi: 10.1073/pnas.1204799109. Epub 2012 Sep 17.

13.

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).

Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W.

Nat Genet. 2006 Nov;38(11):1348-54. Epub 2006 Oct 8.

PMID:
17033623
14.

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.

Sanborn AL, Rao SS, Huang SC, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6456-65. doi: 10.1073/pnas.1518552112. Epub 2015 Oct 23.

15.

Iterative correction of Hi-C data reveals hallmarks of chromosome organization.

Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA.

Nat Methods. 2012 Oct;9(10):999-1003. doi: 10.1038/nmeth.2148. Epub 2012 Sep 2.

16.

Spatial confinement is a major determinant of the folding landscape of human chromosomes.

Gürsoy G, Xu Y, Kenter AL, Liang J.

Nucleic Acids Res. 2014 Jul;42(13):8223-30. doi: 10.1093/nar/gku462. Epub 2014 Jul 2.

17.

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.

Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P.

Nature. 2013 Oct 3;502(7469):59-64. doi: 10.1038/nature12593. Epub 2013 Sep 25.

18.

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C.

Ay F, Vu TH, Zeitz MJ, Varoquaux N, Carette JE, Vert JP, Hoffman AR, Noble WS.

BMC Genomics. 2015 Feb 25;16:121. doi: 10.1186/s12864-015-1236-7.

19.
20.

Chromatin globules: a common motif of higher order chromosome structure?

Sanyal A, Baù D, Martí-Renom MA, Dekker J.

Curr Opin Cell Biol. 2011 Jun;23(3):325-31. doi: 10.1016/j.ceb.2011.03.009. Epub 2011 Apr 12. Review.

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