My NCBI Collection - 4DN analysis library View in My NCBI

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HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.

Hwang YC, Lin CF, Valladares O, Malamon J, Kuksa PP, Zheng Q, Gregory BD, Wang LS. Hwang YC, et al. Bioinformatics. 2015 Apr 15;31(8):1290-2. doi: 10.1093/bioinformatics/btu801. Epub 2014 Dec 4. Bioinformatics. 2015. PMID: 25480377 Free PMC article.

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Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data.

Fortin JP, Hansen KD. Fortin JP, et al. Genome Biol. 2015 Aug 28;16(1):180. doi: 10.1186/s13059-015-0741-y. Genome Biol. 2015. PMID: 26316348 Free PMC article.

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GeNemo: a search engine for web-based functional genomic data.

Zhang Y, Cao X, Zhong S. Zhang Y, et al. Nucleic Acids Res. 2016 Jul 8;44(W1):W122-7. doi: 10.1093/nar/gkw299. Epub 2016 Apr 20. Nucleic Acids Res. 2016. PMID: 27098038 Free PMC article.

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CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks.

Shavit Y, Lio' P. Shavit Y, et al. Bioinformatics. 2013 May 1;29(9):1206-7. doi: 10.1093/bioinformatics/btt120. Epub 2013 Mar 18. Bioinformatics. 2013. PMID: 23508968 Free article.

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Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.

Lan X, Witt H, Katsumura K, Ye Z, Wang Q, Bresnick EH, Farnham PJ, Jin VX. Lan X, et al. Nucleic Acids Res. 2012 Sep;40(16):7690-704. doi: 10.1093/nar/gks501. Epub 2012 Jun 6. Nucleic Acids Res. 2012. PMID: 22675074 Free PMC article.

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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.

Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, Heard E, Dekker J, Barillot E. Servant N, et al. Genome Biol. 2015 Dec 1;16:259. doi: 10.1186/s13059-015-0831-x. Genome Biol. 2015. PMID: 26619908 Free PMC article.

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ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data.

Sato T, Suyama M. Sato T, et al. BMC Genomics. 2015 Dec 15;16:1060. doi: 10.1186/s12864-015-2282-x. BMC Genomics. 2015. PMID: 26666652 Free PMC article.

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HiCPlotter integrates genomic data with interaction matrices.

Akdemir KC, Chin L. Akdemir KC, et al. Genome Biol. 2015 Sep 21;16(1):198. doi: 10.1186/s13059-015-0767-1. Genome Biol. 2015. PMID: 26392354 Free PMC article.

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HiCdat: a fast and easy-to-use Hi-C data analysis tool.

Schmid MW, Grob S, Grossniklaus U. Schmid MW, et al. BMC Bioinformatics. 2015 Sep 3;16(1):277. doi: 10.1186/s12859-015-0678-x. BMC Bioinformatics. 2015. PMID: 26334796 Free PMC article.

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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. Rousseau M, et al. BMC Bioinformatics. 2011 Oct 25;12:414. doi: 10.1186/1471-2105-12-414. BMC Bioinformatics. 2011. PMID: 22026390 Free PMC article.

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