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OME-Zarr: a cloud-optimized bioimaging file format with international community support.
Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Casas Moreno X, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Küpcü Yoldaş A, Kyoda K, le Tournoulx de la Villegeorges A, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR. Moore J, et al. Among authors: yamauchi ka. Histochem Cell Biol. 2023 Sep;160(3):223-251. doi: 10.1007/s00418-023-02209-1. Epub 2023 Jul 10. Histochem Cell Biol. 2023. PMID: 37428210 Free PMC article.
OME-Zarr: a cloud-optimized bioimaging file format with international community support.
Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Moreno XC, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Yoldaş AK, Kyoda K, de la Villegeorges ALT, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR. Moore J, et al. Among authors: yamauchi ka. bioRxiv [Preprint]. 2023 May 7:2023.02.17.528834. doi: 10.1101/2023.02.17.528834. bioRxiv. 2023. Update in: Histochem Cell Biol. 2023 Sep;160(3):223-251. doi: 10.1007/s00418-023-02209-1 PMID: 36865282 Free PMC article. Updated. Preprint.
SpatialData: an open and universal data framework for spatial omics.
Marconato L, Palla G, Yamauchi KA, Virshup I, Heidari E, Treis T, Vierdag WM, Toth M, Stockhaus S, Shrestha RB, Rombaut B, Pollaris L, Lehner L, Vöhringer H, Kats I, Saeys Y, Saka SK, Huber W, Gerstung M, Moore J, Theis FJ, Stegle O. Marconato L, et al. Among authors: yamauchi ka. Nat Methods. 2024 Mar 20. doi: 10.1038/s41592-024-02212-x. Online ahead of print. Nat Methods. 2024. PMID: 38509327
Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing.
Maynard A, McCoach CE, Rotow JK, Harris L, Haderk F, Kerr DL, Yu EA, Schenk EL, Tan W, Zee A, Tan M, Gui P, Lea T, Wu W, Urisman A, Jones K, Sit R, Kolli PK, Seeley E, Gesthalter Y, Le DD, Yamauchi KA, Naeger DM, Bandyopadhyay S, Shah K, Cech L, Thomas NJ, Gupta A, Gonzalez M, Do H, Tan L, Bacaltos B, Gomez-Sjoberg R, Gubens M, Jahan T, Kratz JR, Jablons D, Neff N, Doebele RC, Weissman J, Blakely CM, Darmanis S, Bivona TG. Maynard A, et al. Among authors: yamauchi ka. Cell. 2020 Sep 3;182(5):1232-1251.e22. doi: 10.1016/j.cell.2020.07.017. Epub 2020 Aug 20. Cell. 2020. PMID: 32822576 Free PMC article.
Molecular hallmarks of heterochronic parabiosis at single-cell resolution.
Pálovics R, Keller A, Schaum N, Tan W, Fehlmann T, Borja M, Kern F, Bonanno L, Calcuttawala K, Webber J, McGeever A; Tabula Muris Consortium; Luo J, Pisco AO, Karkanias J, Neff NF, Darmanis S, Quake SR, Wyss-Coray T. Pálovics R, et al. Nature. 2022 Mar;603(7900):309-314. doi: 10.1038/s41586-022-04461-2. Epub 2022 Mar 2. Nature. 2022. PMID: 35236985 Free PMC article.
ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens.
Zamecnik CR, Rajan JV, Yamauchi KA, Mann SA, Loudermilk RP, Sowa GM, Zorn KC, Alvarenga BD, Gaebler C, Caskey M, Stone M, Norris PJ, Gu W, Chiu CY, Ng D, Byrnes JR, Zhou XX, Wells JA, Robbiani DF, Nussenzweig MC, DeRisi JL, Wilson MR. Zamecnik CR, et al. Among authors: yamauchi ka. Cell Rep Med. 2020 Oct 20;1(7):100123. doi: 10.1016/j.xcrm.2020.100123. Epub 2020 Sep 24. Cell Rep Med. 2020. PMID: 32995758 Free PMC article.
Ageing hallmarks exhibit organ-specific temporal signatures.
Schaum N, Lehallier B, Hahn O, Pálovics R, Hosseinzadeh S, Lee SE, Sit R, Lee DP, Losada PM, Zardeneta ME, Fehlmann T, Webber JT, McGeever A, Calcuttawala K, Zhang H, Berdnik D, Mathur V, Tan W, Zee A, Tan M; Tabula Muris Consortium; Pisco AO, Karkanias J, Neff NF, Keller A, Darmanis S, Quake SR, Wyss-Coray T. Schaum N, et al. Nature. 2020 Jul;583(7817):596-602. doi: 10.1038/s41586-020-2499-y. Epub 2020 Jul 15. Nature. 2020. PMID: 32669715 Free PMC article.
20 results