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Items: 1 to 20 of 126

1.

Graph rigidity reveals well-constrained regions of chromosome conformation embeddings.

Duggal G, Kingsford C.

BMC Bioinformatics. 2012 Sep 21;13:241. doi: 10.1186/1471-2105-13-241.

2.

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.

3.

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.

4.

Resolving spatial inconsistencies in chromosome conformation measurements.

Duggal G, Patro R, Sefer E, Wang H, Filippova D, Khuller S, Kingsford C.

Algorithms Mol Biol. 2013 Mar 9;8(1):8. doi: 10.1186/1748-7188-8-8.

5.

Inferring 3D chromatin structure using a multiscale approach based on quaternions.

Caudai C, Salerno E, Zoppè M, Tonazzini A.

BMC Bioinformatics. 2015 Jul 29;16:234. doi: 10.1186/s12859-015-0667-0.

6.

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.

7.

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.

8.

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes.

Benedetti F, Dorier J, Burnier Y, Stasiak A.

Nucleic Acids Res. 2014 Mar;42(5):2848-55. doi: 10.1093/nar/gkt1353. Epub 2013 Dec 23.

9.

Inferential modeling of 3D chromatin structure.

Wang S, Xu J, Zeng J.

Nucleic Acids Res. 2015 Apr 30;43(8):e54. doi: 10.1093/nar/gkv100. Epub 2015 Feb 17.

10.

Mapping chromatin interactions by chromosome conformation capture.

Miele A, Gheldof N, Tabuchi TM, Dostie J, Dekker J.

Curr Protoc Mol Biol. 2006 May;Chapter 21:Unit 21.11. doi: 10.1002/0471142727.mb2111s74.

PMID:
18265379
11.

Looping probabilities in model interphase chromosomes.

Rosa A, Becker NB, Everaers R.

Biophys J. 2010 Jun 2;98(11):2410-9. doi: 10.1016/j.bpj.2010.01.054.

12.

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.

13.

Topological domains in mammalian genomes identified by analysis of chromatin interactions.

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B.

Nature. 2012 Apr 11;485(7398):376-80. doi: 10.1038/nature11082.

14.

The statistical-mechanics of chromosome conformation capture.

O'Sullivan JM, Hendy MD, Pichugina T, Wake GC, Langowski J.

Nucleus. 2013 Sep-Oct;4(5):390-8. doi: 10.4161/nucl.26513. Epub 2013 Sep 18. Review.

15.

Exploring the mechanisms of genome-wide long-range interactions: interpreting chromosome organization.

Wang J, Meng X, Chen H, Yuan C, Li X, Zhou Y, Chen M.

Brief Funct Genomics. 2016 Sep;15(5):385-95. doi: 10.1093/bfgp/elv062. Epub 2016 Jan 14. Review.

PMID:
26769147
16.

Capturing pairwise and multi-way chromosomal conformations using chromosomal walks.

Olivares-Chauvet P, Mukamel Z, Lifshitz A, Schwartzman O, Elkayam NO, Lubling Y, Deikus G, Sebra RP, Tanay A.

Nature. 2016 Dec 8;540(7632):296-300. doi: 10.1038/nature20158. Epub 2016 Nov 30.

PMID:
27919068
17.

Reconstruction of 3D genome architecture via a two-stage algorithm.

Segal MR, Bengtsson HL.

BMC Bioinformatics. 2015 Nov 9;16:373. doi: 10.1186/s12859-015-0799-2.

18.

Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions.

Capurso D, Bengtsson H, Segal MR.

Nucleic Acids Res. 2016 Mar 18;44(5):2028-35. doi: 10.1093/nar/gkw070. Epub 2016 Feb 10.

19.

The Hitchhiker's guide to Hi-C analysis: practical guidelines.

Lajoie BR, Dekker J, Kaplan N.

Methods. 2015 Jan 15;72:65-75. doi: 10.1016/j.ymeth.2014.10.031. Epub 2014 Nov 6.

20.

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.

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