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An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.
Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY. Corces MR, et al. Among authors: rubin aj. Nat Methods. 2017 Oct;14(10):959-962. doi: 10.1038/nmeth.4396. Epub 2017 Aug 28. Nat Methods. 2017. PMID: 28846090 Free PMC article.
7SK-BAF axis controls pervasive transcription at enhancers.
Flynn RA, Do BT, Rubin AJ, Calo E, Lee B, Kuchelmeister H, Rale M, Chu C, Kool ET, Wysocka J, Khavari PA, Chang HY. Flynn RA, et al. Among authors: rubin aj. Nat Struct Mol Biol. 2016 Mar;23(3):231-8. doi: 10.1038/nsmb.3176. Epub 2016 Feb 15. Nat Struct Mol Biol. 2016. PMID: 26878240 Free PMC article.
Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.
Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, Snyder M, Chang HY, Fraser P, Khavari PA. Rubin AJ, et al. Nat Genet. 2017 Oct;49(10):1522-1528. doi: 10.1038/ng.3935. Epub 2017 Aug 14. Nat Genet. 2017. PMID: 28805829 Free PMC article.
Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.
Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY. Mumbach MR, et al. Among authors: rubin aj. Nat Genet. 2017 Nov;49(11):1602-1612. doi: 10.1038/ng.3963. Epub 2017 Sep 25. Nat Genet. 2017. PMID: 28945252 Free PMC article.
Transcript-indexed ATAC-seq for precision immune profiling.
Satpathy AT, Saligrama N, Buenrostro JD, Wei Y, Wu B, Rubin AJ, Granja JM, Lareau CA, Li R, Qi Y, Parker KR, Mumbach MR, Serratelli WS, Gennert DG, Schep AN, Corces MR, Khodadoust MS, Kim YH, Khavari PA, Greenleaf WJ, Davis MM, Chang HY. Satpathy AT, et al. Among authors: rubin aj. Nat Med. 2018 May;24(5):580-590. doi: 10.1038/s41591-018-0008-8. Epub 2018 Apr 23. Nat Med. 2018. PMID: 29686426 Free PMC article.
Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment.
Pattison JM, Melo SP, Piekos SN, Torkelson JL, Bashkirova E, Mumbach MR, Rajasingh C, Zhen HH, Li L, Liaw E, Alber D, Rubin AJ, Shankar G, Bao X, Chang HY, Khavari PA, Oro AE. Pattison JM, et al. Among authors: rubin aj. Nat Genet. 2018 Dec;50(12):1658-1665. doi: 10.1038/s41588-018-0263-0. Epub 2018 Nov 5. Nat Genet. 2018. PMID: 30397335 Free PMC article.
HiChIRP reveals RNA-associated chromosome conformation.
Mumbach MR, Granja JM, Flynn RA, Roake CM, Satpathy AT, Rubin AJ, Qi Y, Jiang Z, Shams S, Louie BH, Guo JK, Gennert DG, Corces MR, Khavari PA, Atianand MK, Artandi SE, Fitzgerald KA, Greenleaf WJ, Chang HY. Mumbach MR, et al. Among authors: rubin aj. Nat Methods. 2019 Jun;16(6):489-492. doi: 10.1038/s41592-019-0407-x. Epub 2019 May 27. Nat Methods. 2019. PMID: 31133759 Free PMC article.
34 results