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2022 5
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Spatial epigenome-transcriptome co-profiling of mammalian tissues.
Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G, Fan R. Zhang D, et al. Nature. 2023 Apr;616(7955):113-122. doi: 10.1038/s41586-023-05795-1. Epub 2023 Mar 15. Nature. 2023. PMID: 36922587 Free PMC article.
Spatial profiling of chromatin accessibility in mouse and human tissues.
Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R. Deng Y, et al. Nature. 2022 Sep;609(7926):375-383. doi: 10.1038/s41586-022-05094-1. Epub 2022 Aug 17. Nature. 2022. PMID: 35978191 Free PMC article.
Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues.
Bai Z, Zhang D, Gao Y, Tao B, Bao S, Enninful A, Zhang D, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R. Bai Z, et al. bioRxiv [Preprint]. 2024 Feb 8:2024.02.06.579143. doi: 10.1101/2024.02.06.579143. bioRxiv. 2024. Update in: Cell. 2024 Nov 14;187(23):6760-6779.e24. doi: 10.1016/j.cell.2024.09.001. PMID: 38370833 Free PMC article. Updated. Preprint.
Gene trajectory inference for single-cell data by optimal transport metrics.
Qu R, Cheng X, Sefik E, Stanley Iii JS, Landa B, Strino F, Platt S, Garritano J, Odell ID, Coifman R, Flavell RA, Myung P, Kluger Y. Qu R, et al. Nat Biotechnol. 2024 Apr 5:10.1038/s41587-024-02186-3. doi: 10.1038/s41587-024-02186-3. Online ahead of print. Nat Biotechnol. 2024. PMID: 38580861
Biwhitening Reveals the Rank of a Count Matrix.
Landa B, Zhang TTCK, Kluger Y. Landa B, et al. SIAM J Math Data Sci. 2022;4(4):1420-1446. doi: 10.1137/21m1456807. SIAM J Math Data Sci. 2022. PMID: 37576699 Free PMC article.
Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping.
Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft JE, Hafler D, Fan R. Liu Y, et al. Res Sq [Preprint]. 2022 Mar 30:rs.3.rs-1499315. doi: 10.21203/rs.3.rs-1499315/v1. Res Sq. 2022. Update in: Nat Biotechnol. 2023 Oct;41(10):1405-1409. doi: 10.1038/s41587-023-01676-0. PMID: 35378748 Free PMC article. Updated. Preprint.
15 results