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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.
SenNet recommendations for detecting senescent cells in different tissues.
Suryadevara V, Hudgins AD, Rajesh A, Pappalardo A, Karpova A, Dey AK, Hertzel A, Agudelo A, Rocha A, Soygur B, Schilling B, Carver CM, Aguayo-Mazzucato C, Baker DJ, Bernlohr DA, Jurk D, Mangarova DB, Quardokus EM, Enninga EAL, Schmidt EL, Chen F, Duncan FE, Cambuli F, Kaur G, Kuchel GA, Lee G, Daldrup-Link HE, Martini H, Phatnani H, Al-Naggar IM, Rahman I, Nie J, Passos JF, Silverstein JC, Campisi J, Wang J, Iwasaki K, Barbosa K, Metis K, Nernekli K, Niedernhofer LJ, Ding L, Wang L, Adams LC, Ruiyang L, Doolittle ML, Teneche MG, Schafer MJ, Xu M, Hajipour M, Boroumand M, Basisty N, Sloan N, Slavov N, Kuksenko O, Robson P, Gomez PT, Vasilikos P, Adams PD, Carapeto P, Zhu Q, Ramasamy R, Perez-Lorenzo R, Fan R, Dong R, Montgomery RR, Shaikh S, Vickovic S, Yin S, Kang S, Suvakov S, Khosla S, Garovic VD, Menon V, Xu Y, Song Y, Suh Y, Dou Z, Neretti N. Suryadevara V, et al. Nat Rev Mol Cell Biol. 2024 Jun 3. doi: 10.1038/s41580-024-00738-8. Online ahead of print. Nat Rev Mol Cell Biol. 2024. PMID: 38831121 Review.
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.