Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing-Reference-Cited by-同舟云学术

Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing

Published:2016-11-07 Issue:1 Volume:17 Page:
ISSN:1471-2164
Container-title:BMC Genomics
language:en
Short-container-title:BMC Genomics

Author:

Adhikari Badri,Trieu Tuan,Cheng Jianlin

Funder

National Institutes of Health

National Science Foundation

Publisher

Springer Science and Business Media LLC

Subject

Genetics,Biotechnology

Link

http://link.springer.com/content/pdf/10.1186/s12864-016-3210-4.pdf

Reference23 articles.

1. Gasser SM. Visualizing chromatin dynamics in interphase nuclei. Science. 2002;296:1412–6.

2. Lanctôt C, Cheutin T, Cremer M, Cavalli G, Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet. 2007;8:104–15.

3. Mateos-Langerak J, Bohn M, De Leeuw W, Giromus O, Manders EMM, Verschure PJ, et al. Spatially confined folding of chromatin in the interphase nucleus. Proc Natl Acad Sci. 2009;106:3812–7.

4. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–93.

5. Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol. 2012;30:90–8.

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