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Items: 1 to 20 of 144

1.

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.

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.

Quantitative Analysis of Intra-chromosomal Contacts: The 3C-qPCR Method.

Ea V, Court F, Forné T.

Methods Mol Biol. 2017;1589:75-88. doi: 10.1007/7651_2015_269.

PMID:
26025624
4.

Detecting Spatial Chromatin Organization by Chromosome Conformation Capture II: Genome-Wide Profiling by Hi-C.

Vietri Rudan M, Hadjur S, Sexton T.

Methods Mol Biol. 2017;1589:47-74. doi: 10.1007/7651_2015_261.

PMID:
26900130
5.

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.

6.

Normalization of a chromosomal contact map.

Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J.

BMC Genomics. 2012 Aug 30;13:436. doi: 10.1186/1471-2164-13-436.

7.

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.

8.

Generation and Analysis of Chromosomal Contact Maps of Bacteria.

Marbouty M, Koszul R.

Methods Mol Biol. 2017;1624:75-84. doi: 10.1007/978-1-4939-7098-8_7.

PMID:
28842877
9.

Generation and Analysis of Chromosomal Contact Maps of Yeast Species.

Cournac A, Marbouty M, Mozziconacci J, Koszul R.

Methods Mol Biol. 2016;1361:227-45. doi: 10.1007/978-1-4939-3079-1_13.

10.

Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions.

Stadhouders R, Kolovos P, Brouwer R, Zuin J, van den Heuvel A, Kockx C, Palstra RJ, Wendt KS, Grosveld F, van Ijcken W, Soler E.

Nat Protoc. 2013 Mar;8(3):509-24. doi: 10.1038/nprot.2013.018. Epub 2013 Feb 14.

PMID:
23411633
11.

Comparison of computational methods for Hi-C data analysis.

Forcato M, Nicoletti C, Pal K, Livi CM, Ferrari F, Bicciato S.

Nat Methods. 2017 Jul;14(7):679-685. doi: 10.1038/nmeth.4325. Epub 2017 Jun 12.

12.

UMI-4C for quantitative and targeted chromosomal contact profiling.

Schwartzman O, Mukamel Z, Oded-Elkayam N, Olivares-Chauvet P, Lubling Y, Landan G, Izraeli S, Tanay A.

Nat Methods. 2016 Aug;13(8):685-91. doi: 10.1038/nmeth.3922. Epub 2016 Jul 4.

PMID:
27376768
13.

Determining spatial chromatin organization of large genomic regions using 5C technology.

van Berkum NL, Dekker J.

Methods Mol Biol. 2009;567:189-213. doi: 10.1007/978-1-60327-414-2_13. Review.

14.

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.

Belaghzal H, Dekker J, Gibcus JH.

Methods. 2017 Jul 1;123:56-65. doi: 10.1016/j.ymeth.2017.04.004. Epub 2017 Apr 18.

PMID:
28435001
15.

Circular Chromosome Conformation Capture in Plants.

Grob S.

Methods Mol Biol. 2017;1610:73-92. doi: 10.1007/978-1-4939-7003-2_6.

PMID:
28439858
16.

Chromatin Conformation Capture-Based Analysis of Nuclear Architecture.

Grob S, Grossniklaus U.

Methods Mol Biol. 2017;1456:15-32.

PMID:
27770354
17.

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.

Methods Enzymol. 2012;513:89-112. doi: 10.1016/B978-0-12-391938-0.00004-5.

PMID:
22929766
18.

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.

19.

Chromatin conformation signatures: ideal human disease biomarkers?

Crutchley JL, Wang XQ, Ferraiuolo MA, Dostie J.

Biomark Med. 2010 Aug;4(4):611-29. doi: 10.2217/bmm.10.68. Review.

20.

Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.

Li W, Gong K, Li Q, Alber F, Zhou XJ.

Bioinformatics. 2015 Mar 15;31(6):960-2. doi: 10.1093/bioinformatics/btu747. Epub 2014 Nov 12.

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