Salk Institute

Dixon Lab
Dixon Lab

Dixon Lab - Publications

  • Dixon JR, Gorkin DU, Ren B. (2016). Chromatin domains: the unit of chromosome organization. Molecular Cell 62 (5) 668-680.
  • Diao Y, Li B, Meng Z, Jung I, Lee AY, Dixon JR, Maliskova L, Guan KL, Shen Y, Ren B. (2016). A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. Genome Research 26 (3) 397-405.
  • Selvaraj S, Schmidtt AD, Dixon JR, Ren B. (2015). Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq. BMC genomics 16 (1), 900.
  • Ren B and Dixon JR. (2015) A CRISPR connection between chromatin topology and genetic disorders. Cell, 161 (5) 955-957.
  • Dixon JR*, Jung I*, Selvaraj S*, Shen, Y, Antosiewica-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanekov V, Ecker J, Thomson J, Ren B. (2015). Chromatin architecture reorganization during stem cell differentiation. Nature 518 331-336.
  • Roadmaps Epigenomics Consortium. Integrative analysis of 111 reference human epigenomes. Nature 518 317-330.
  • Li Y, Rivera CM, Ishii H, Jin F, Selvaraj S, Lee AY, Dixon JR, Ren, Bing. (2014) CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells. PLoS ONE 9 (12): e114485.
  • Attanasio, C, Nord, AS, Zhu, Y, Blow, MJ, Biddie, SC, Mendenhall EM, Dixon, JR, Wright, C, Hosseini, R, Akiyama, JA, Holt, A, Plajzer-Frick, I, Shoukry, M, Afzal, V, Ren, B, Berstein, BE, Rubin, EM, Visel, A, Pennachio, LA. (2014) Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Research, 24 (6): 920-929.
  • Zuin J*, Dixon JR*, van der Reijden M, Ye Z, Kolovos P, Brouwer R, van de Corput M, van de Werken H, Knoch T, van Ijcken W, Grosveld F, Ren B, Wendt K. (2014) Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proceeding of the National Academy of Sciences, 111 (3), 996-1001.
  • Selvaraj S*, Dixon JR*, Bansal V, Ren B. (2013) Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nature Biotechnology, 31 (12), 1111-1118.
  • Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B. (2013) A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature, 503 (7475), 290-294.
  • Hu, M, Deng, K, Qin, Z, Dixon, J, Selvaraj, S, Fang, J, Ren, B, Liu, JS. (2013) Bayesian inference of spatial organizations of chromosomes. PLoS Computational Biology 9 (1), e1002893.
  • Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. (2012) A map of cis-regulatory sequences in the mouse genome. Nature 488 (7409):116-20.
  • Dixon, JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485 (7398) 376-80.
  • Barish, GD, Yu, RT, Karunasiri, M, Ocampo, CB, Dixon, J, Benner, C, Dent, AL, Tangirala, RK, Evans, RM (2010) Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. Genes Dev. 24 (24), 2760-2765.
  • Pagliarini DJ, Wiley SE, Kimple ME, Dixon JR, Kelly P, Worby CA, Casey PJ, and Dixon JE (2005) Involvement of a mitochondrial phosphatase in the regulation of ATP production and insulin secretion in pancreatic beta cells. Mol. Cell 19 (2), 197-207.

*These authors contributed equally to this work

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