How to Cite Our Work

Figures generated in this website can be directly used in your publication. If you do, please cite our work, "The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions." http://biorxiv.org/content/early/2017/02/27/112268, Biorxiv, 2017.

Sources of Data

We are hosting all the Hi-C and ChIA-PET datasets produced by the ENCODE Consortium. You can also visualize and explore the chromatin interaction data from the following publications. If you have suggestions of datasets to be added to the browser, please contact us.

1.  Lieberman-Aiden, E., Nynke L. van Berkum, Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O., Sandstrom, R., Bernstein, B., Bender, M.A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L.A., Lander, E.S. & Dekker, J. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science. 2009. 326(5950):289-293. Pubmed Paper Dataset

2.  Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376-380. Pubmed Paper Dataset

3.  Shen, Y., Yue, F., McCleary, D., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. & Ren, B. A map of the cis-regulatory sequences in the mouse genome". Nature. 2012;488(7409):116-120. Paper Dataset

4.  Rao, S.S.P., Huntley, M.H., Durand, N.C., Stamenova, E.K., Bochkov, I.D., Robinson, J.T., Sanborn, A.L., Machol, I., Omer, A.D., Lander, E.S. & Aiden-Lieberman, E. 2014,. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell. 2014;159(7):1665-1680. Pubmed Paper Dataset

5.  Heidari, N., Phanstiel, D.H., He, C., Grubert, F., Jahanbani, F., Kasowski, M., Zhang, M., Snyder, M.P. Genome-wide map of regulatory interactions in the human genome. Genome Research. 2014 Dec; 24(12): 1905-1917. Pubmed

6.  Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, Thomson JA, Ren B. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015;518(7539):331-336. Pubmed Paper Dataset

7.  Leung, D., Jung, I., Rajagopal, N., Schmitt, A., Selvaraj, S., Lee, A. Y. & Ren, B. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 2015;518(7539):350-354. Pubmed Paper Dataset

8.  Nagano, T., Lubling, Y., Yaffe, E., Wingett, S. W., Dean, W., Tanay, A., & Fraser, P. Single-cell hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell. Nature Protocols. 2015;10(12):1986-2003.

9.   Mifsud, B., Tavares-Cadete, F., Young, A., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S., Andrews, S., Grey, W., Ewels, P., Herman, B., Happe, S., Higgs, A., LeProust, E., Follows, G., Fraser, P., Luscombe, N. & Osborne, C. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nature Genetics. 2015;47(6):598-606. Pubmed Paper Dataset

10.   Tang, Z., Luo, O., Li, G., Li, X., Zheng, M., Zhu, J., Szalaj, P., Trzaskoma, P., Magalska, A., Wlodarczyk, J., Ruszczycki, B., Michalski, P., Piecuch, E., Wang, P., Wang, D., Tian, S., Penrad-Mobayed, M., Sachs, L., Ruan, Y., Ruan, X., Wei, C., Liu, E., Wilczynski, G. & Plewczynski, D. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell. 2015, 163(7), p1611-1627. Paper

11.  Schmitt, A., Hu, M., Jung, I., Xu, Z., Qiu, Y., Tan, C., Li, Y., Lin, S., Lin, Y., Barr, C. & Ren, B. A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Cell Reports. 2016;17(8):2042-2059. Pubmed Paper Dataset

12.  Javierre, B., Burren, O., Wilder, S., Kreuzhuber, R., Hill, S., Sewitz, S., Cairns, J., Wingett, S., Várnai, C., Thiecke, M., Burden, F., Farrow, S., Cutler, A., Rehnström, K., Downes, K., Grassi, L., Kostadima, M., Freire-Pritchett, P., Wang, F., Stunnenberg, H.G., Todd, J.A., Zerbino, D.R., Stegle, O., Ouwehand, W.H., Frontini, M., Wallace, C., Spivakov, M. & Fraser, P., Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters. Cell. 2016;167(5):1369-1384.e19. Pubmed Paper

13.  Fang, R., Yu, M., Li, G., Chee, S., Liu, T., Schmitt, A.D., and Ren, B. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res. 2016 Dec;26(12):1345-1348. Paper Dataset

14.  Mumbach, M.R., Rubin, A.J., Flynn, R.A., Dai, C., Khavari, P.A., Greenleaf, W.J. & Chang, H.Y. 2016, HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nature Methods.2016;13(11):919-922. Paper

15.  Won, H., Torre-Ubieta, L., Stein, J.L., Parkshak, N.N., Huang, J., Opland, C.K., Gandal, M.J., Sutton, G.J., Hormozdiari, F., Lu, D., Lee, C., Eskin, E., Voineagu, I., Ernst, J., & Geschwind, D.H., Chromosome conformation elucidates regulatory relationships in developing human brain. Nature. 2016,538, 523-527. Paper Dataset

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