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Community assessment of methods to deconvolve cellular composition from bulk gene expression.
White BS, de Reyniès A, Newman AM, Waterfall JJ, Lamb A, Petitprez F, Lin Y, Yu R, Guerrero-Gimenez ME, Domanskyi S, Monaco G, Chung V, Banerjee J, Derrick D, Valdeolivas A, Li H, Xiao X, Wang S, Zheng F, Yang W, Catania CA, Lang BJ, Bertus TJ, Piermarocchi C, Caruso FP, Ceccarelli M, Yu T, Guo X, Bletz J, Coller J, Maecker H, Duault C, Shokoohi V, Patel S, Liliental JE, Simon S; Tumor Deconvolution DREAM Challenge consortium; Saez-Rodriguez J, Heiser LM, Guinney J, Gentles AJ. White BS, et al. Among authors: gentles aj. Nat Commun. 2024 Aug 27;15(1):7362. doi: 10.1038/s41467-024-50618-0. Nat Commun. 2024. PMID: 39191725 Free PMC article.
Robust enumeration of cell subsets from tissue expression profiles.
Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA. Newman AM, et al. Among authors: gentles aj. Nat Methods. 2015 May;12(5):453-7. doi: 10.1038/nmeth.3337. Epub 2015 Mar 30. Nat Methods. 2015. PMID: 25822800 Free PMC article.
Determining cell type abundance and expression from bulk tissues with digital cytometry.
Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, Khodadoust MS, Esfahani MS, Luca BA, Steiner D, Diehn M, Alizadeh AA. Newman AM, et al. Among authors: gentles aj. Nat Biotechnol. 2019 Jul;37(7):773-782. doi: 10.1038/s41587-019-0114-2. Epub 2019 May 6. Nat Biotechnol. 2019. PMID: 31061481 Free PMC article.
Atlas of clinically distinct cell states and ecosystems across human solid tumors.
Luca BA, Steen CB, Matusiak M, Azizi A, Varma S, Zhu C, Przybyl J, Espín-Pérez A, Diehn M, Alizadeh AA, van de Rijn M, Gentles AJ, Newman AM. Luca BA, et al. Among authors: gentles aj. Cell. 2021 Oct 14;184(21):5482-5496.e28. doi: 10.1016/j.cell.2021.09.014. Epub 2021 Sep 30. Cell. 2021. PMID: 34597583 Free PMC article.
110 results