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Functional inference of gene regulation using single-cell multi-omics.
Kartha VK, Duarte FM, Hu Y, Ma S, Chew JG, Lareau CA, Earl A, Burkett ZD, Kohlway AS, Lebofsky R, Buenrostro JD. Kartha VK, et al. Among authors: earl a. Cell Genom. 2022 Sep 14;2(9):100166. doi: 10.1016/j.xgen.2022.100166. Epub 2022 Aug 4. Cell Genom. 2022. PMID: 36204155 Free PMC article.
Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin.
Ma S, Zhang B, LaFave LM, Earl AS, Chiang Z, Hu Y, Ding J, Brack A, Kartha VK, Tay T, Law T, Lareau C, Hsu YC, Regev A, Buenrostro JD. Ma S, et al. Among authors: earl as. Cell. 2020 Nov 12;183(4):1103-1116.e20. doi: 10.1016/j.cell.2020.09.056. Epub 2020 Oct 23. Cell. 2020. PMID: 33098772 Free PMC article.
Spatial genomics enables multi-modal study of clonal heterogeneity in tissues.
Zhao T, Chiang ZD, Morriss JW, LaFave LM, Murray EM, Del Priore I, Meli K, Lareau CA, Nadaf NM, Li J, Earl AS, Macosko EZ, Jacks T, Buenrostro JD, Chen F. Zhao T, et al. Among authors: earl as. Nature. 2022 Jan;601(7891):85-91. doi: 10.1038/s41586-021-04217-4. Epub 2021 Dec 15. Nature. 2022. PMID: 34912115 Free PMC article.
Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements.
Hu Y, Ma S, Kartha VK, Duarte FM, Horlbeck M, Zhang R, Shrestha R, Labade A, Kletzien H, Meliki A, Castillo A, Durand N, Mattei E, Anderson LJ, Tay T, Earl AS, Shoresh N, Epstein CB, Wagers A, Buenrostro JD. Hu Y, et al. Among authors: earl as. bioRxiv [Preprint]. 2023 Mar 29:2023.03.28.533945. doi: 10.1101/2023.03.28.533945. bioRxiv. 2023. PMID: 37034577 Free PMC article. Preprint.
Epigenetic memory of coronavirus infection in innate immune cells and their progenitors.
Cheong JG, Ravishankar A, Sharma S, Parkhurst CN, Grassmann SA, Wingert CK, Laurent P, Ma S, Paddock L, Miranda IC, Karakaslar EO, Nehar-Belaid D, Thibodeau A, Bale MJ, Kartha VK, Yee JK, Mays MY, Jiang C, Daman AW, Martinez de Paz A, Ahimovic D, Ramos V, Lercher A, Nielsen E, Alvarez-Mulett S, Zheng L, Earl A, Yallowitz A, Robbins L, LaFond E, Weidman KL, Racine-Brzostek S, Yang HS, Price DR, Leyre L, Rendeiro AF, Ravichandran H, Kim J, Borczuk AC, Rice CM, Jones RB, Schenck EJ, Kaner RJ, Chadburn A, Zhao Z, Pascual V, Elemento O, Schwartz RE, Buenrostro JD, Niec RE, Barrat FJ, Lief L, Sun JC, Ucar D, Josefowicz SZ. Cheong JG, et al. Among authors: earl a. Cell. 2023 Aug 31;186(18):3882-3902.e24. doi: 10.1016/j.cell.2023.07.019. Epub 2023 Aug 18. Cell. 2023. PMID: 37597510
Cell of origin epigenetic priming determines susceptibility to Tet2 mutation.
Schiroli G, Kartha V, Duarte FM, Kristiansen TA, Mayerhofer C, Shrestha R, Earl A, Hu Y, Tay T, Rhee C, Buenrostro JD, Scadden DT. Schiroli G, et al. Among authors: earl a. Nat Commun. 2024 May 21;15(1):4325. doi: 10.1038/s41467-024-48508-6. Nat Commun. 2024. PMID: 38773071 Free PMC article.
Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection.
Young MG, Straub TJ, Worby CJ, Metsky HC, Gnirke A, Bronson RA, van Dijk LR, Desjardins CA, Matranga C, Qu J, Villicana JB, Azimzadeh P, Kau AL, Dodson KW, Schreiber HL, Manson AL, Hultgren SJ, Earl AM. Young MG, et al. Among authors: earl am. bioRxiv [Preprint]. 2024 Jun 1:2024.02.29.582780. doi: 10.1101/2024.02.29.582780. bioRxiv. 2024. PMID: 38463963 Free PMC article. Preprint.
198 results