Publications

all Publications


Gatchalian, J., Malik, S., Ho, J., Lee, D.S., Kelso, T.W.R., Shokhirev, M.N., Dixon, J.R., Hargreaves, D.C. A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells (2018) Nature Communications. 9:Article number: 5139. DOI: DOI: 10.1038/s41467-018-07528-9

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Dixon, J.R., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V.T., Yardımcı, G.G., Chakraborty, A., Bann, D.V., Wang, Y., Clark, R., Zhang, L., Yang, H., Liu, T., Iyyanki, S., An, L., Pool, C., Sasaki, T., Rivera-Mulia, J.C., Ozadam, H., Lajoie, B.R., Kaul, R., Buckley, M., Lee, K., Diegel, M., Pezic, D., Ernst, C., Hadjur, S., Odom, D.T., Stamatoyannopoulos, J.A., Broach, J.R., Hardison, R.C., Ay, F., Noble, W.S., Dekker, J., Gilbert, D.M., Yue, F. Integrative detection and analysis of structural variation in cancer genomes. (2018) Nat. Genet. DOI: 10.1038/s41588-018-0195-8

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Du, Z., Zheng, H., Huang, B., Ma, R., Wu, J., Zhang, X., He, J., Xiang, Y., Wang, Q., Li, Y., Ma, J., Zhang, X., Zhang, K., Wang, Y., Zhang, M.Q., Gao, J., Dixon, J.R., Wang, X., Zeng, J., Xie, W. Allelic reprogramming of 3D chromatin architecture during early mammalian development. (2017) Nature. 547(7662):232-235. DOI: 10.1038/nature23263

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Dixon, J.R., Gorkin, D.U., Ren, B. Chromatin Domains: The Unit of Chromosome Organization. (2016) Mol. Cell. 62(5):668-80. DOI: 10.1016/j.molcel.2016.05.018

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Diao, Y., Li, B., Meng, Z., Jung, I., Lee, A.Y., Dixon, J., Maliskova, L., Guan, K.L., Shen, Y., Ren, B. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. (2016) Genome Res. 26(3):397-405. DOI: 10.1101/gr.197152.115

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Selvaraj, S., Schmitt, A.D., Dixon, J.R., Ren, B. Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq. (2015) BMC Genomics. 16:900. DOI: 10.1186/s12864-015-1949-7

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Ren, B., Dixon, J.R. A CRISPR Connection between Chromatin Topology and Genetic Disorders. (2015) Cell. 161(5):955-957. DOI: 10.1016/j.cell.2015.04.047

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Dixon, J.R.*, Jung, I.*, Selvaraj, S.*, Shen, Y., Antosiewicz-Bourget, J.E., Lee, A.Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., Diao, Y., Liang, J., Zhao, H., Lobanenkov, V.V., Ecker, J.R., Thomson, J.A., Ren, B. Chromatin architecture reorganization during stem cell differentiation. (2015) Nature. 518(7539):331-6. DOI: 10.1038/nature14222

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Li, Y., Rivera, C.M., Ishii, H., Jin, F., Selvaraj, S., Lee, A.Y., Dixon, J.R., Ren, B. CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. (2014) PLoS ONE. 9(12):e114485. DOI: 10.1371/journal.pone.0114485

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Attanasio, C., Nord, A.S., Zhu, Y., Blow, M.J., Biddie, S.C., Mendenhall, E.M., Dixon, J., Wright, C., Hosseini, R., Akiyama, J.A., Holt, A., Plajzer-Frick, I., Shoukry, M., Afzal, V., Ren, B., Bernstein, B.E., Rubin, E.M., Visel, A., Pennacchio, L.A. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. (2014) Genome Res. 24(6):920-9. DOI: 10.1101/gr.168930.113

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Zuin, J.*, Dixon, J.R.*, van der Reijden, M.I., Ye, Z., Kolovos, P., Brouwer, R.W., van de Corput, M.P., van de Werken, H.J., Knoch, T.A., van IJcken, W.F., Grosveld, F.G., Ren, B., Wendt, K.S. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. (2014) Proc. Natl. Acad. Sci. U.S.A. 111(3):996-1001. DOI: 10.1073/pnas.1317788111

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Selvaraj, S.*, Dixon, J.R.*, Bansal, V., Ren, B. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. (2013) Nat. Biotechnol. 31(12):1111-8. DOI: 10.1038/nbt.2728

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Jin, F., Li, Y., Dixon, J.R., Selvaraj, S., Ye, Z., Lee, A.Y., Yen, C.A., Schmitt, A.D., Espinoza, C.A., Ren, B. A high-resolution map of the three-dimensional chromatin interactome in human cells. (2013) Nature. 503(7475):290-4. DOI: 10.1038/nature12644

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Hu, M., Deng, K., Qin, Z., Dixon, J., Selvaraj, S., Fang, J., Ren, B., Liu, J.S. Bayesian inference of spatial organizations of chromosomes. (2013) PLoS Comput. Biol. 9(1):e1002893. DOI: 10.1371/journal.pcbi.1002893

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Shen, Y., Yue, F., McCleary, D.F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V.V., Ren, B. A map of the cis-regulatory sequences in the mouse genome. (2012) Nature. 488(7409):116-20. DOI: 10.1038/nature11243

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Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S., Ren, B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. (2012) Nature. 485(7398):376-80. DOI: 10.1038/nature11082

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Barish, G.D., Yu, R.T., Karunasiri, M., Ocampo, C.B., Dixon, J., Benner, C., Dent, A.L., Tangirala, R.K., Evans, R.M. Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. (2010) Genes Dev. 24(24):2760-5. DOI: 10.1101/gad.1998010

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Pagliarini, D.J., Wiley, S.E., Kimple, M.E., Dixon, J.R., Kelly, P., Worby, C.A., Casey, P.J., Dixon, J.E. Involvement of a mitochondrial phosphatase in the regulation of ATP production and insulin secretion in pancreatic beta cells. (2005) Mol. Cell. 19(2):197-207. DOI: 10.1016/j.molcel.2005.06.008

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