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Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer.
Becker WR, Nevins SA, Chen DC, Chiu R, Horning AM, Guha TK, Laquindanum R, Mills M, Chaib H, Ladabaum U, Longacre T, Shen J, Esplin ED, Kundaje A, Ford JM, Curtis C, Snyder MP, Greenleaf WJ. Becker WR, et al. Among authors: greenleaf wj. Nat Genet. 2022 Jul;54(7):985-995. doi: 10.1038/s41588-022-01088-x. Epub 2022 Jun 20. Nat Genet. 2022. PMID: 35726067 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. Among authors: greenleaf wj. 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.
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: greenleaf wj. 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.
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: greenleaf wj. 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.
191 results