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CherryML: scalable maximum likelihood estimation of phylogenetic models.
Nat Methods. 2023 Aug;20(8):1232-1236. doi: 10.1038/s41592-023-01917-9. Epub 2023 Jun 29.
Nat Methods. 2023.
PMID: 37386188
Free PMC article.
An empirical Bayes method for differential expression analysis of single cells with deep generative models.
Boyeau P, Regier J, Gayoso A, Jordan MI, Lopez R, Yosef N.
Boyeau P, et al.
Proc Natl Acad Sci U S A. 2023 May 23;120(21):e2209124120. doi: 10.1073/pnas.2209124120. Epub 2023 May 16.
Proc Natl Acad Sci U S A. 2023.
PMID: 37192164
Free PMC article.
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Predicting cellular responses to complex perturbations in high-throughput screens.
Lotfollahi M, Klimovskaia Susmelj A, De Donno C, Hetzel L, Ji Y, Ibarra IL, Srivatsan SR, Naghipourfar M, Daza RM, Martin B, Shendure J, McFaline-Figueroa JL, Boyeau P, Wolf FA, Yakubova N, Günnemann S, Trapnell C, Lopez-Paz D, Theis FJ.
Lotfollahi M, et al. Among authors: boyeau p.
Mol Syst Biol. 2023 Jun 12;19(6):e11517. doi: 10.15252/msb.202211517. Epub 2023 May 8.
Mol Syst Biol. 2023.
PMID: 37154091
Free PMC article.
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The scverse project provides a computational ecosystem for single-cell omics data analysis.
Virshup I, Bredikhin D, Heumos L, Palla G, Sturm G, Gayoso A, Kats I, Koutrouli M; Scverse Community; Berger B, Pe'er D, Regev A, Teichmann SA, Finotello F, Wolf FA, Yosef N, Stegle O, Theis FJ.
Virshup I, et al.
Nat Biotechnol. 2023 May;41(5):604-606. doi: 10.1038/s41587-023-01733-8.
Nat Biotechnol. 2023.
PMID: 37037904
No abstract available.
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DestVI identifies continuums of cell types in spatial transcriptomics data.
Lopez R, Li B, Keren-Shaul H, Boyeau P, Kedmi M, Pilzer D, Jelinski A, Yofe I, David E, Wagner A, Ergen C, Addadi Y, Golani O, Ronchese F, Jordan MI, Amit I, Yosef N.
Lopez R, et al. Among authors: boyeau p.
Nat Biotechnol. 2022 Sep;40(9):1360-1369. doi: 10.1038/s41587-022-01272-8. Epub 2022 Apr 21.
Nat Biotechnol. 2022.
PMID: 35449415
Free PMC article.
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A Python library for probabilistic analysis of single-cell omics data.
Gayoso A, Lopez R, Xing G, Boyeau P, Valiollah Pour Amiri V, Hong J, Wu K, Jayasuriya M, Mehlman E, Langevin M, Liu Y, Samaran J, Misrachi G, Nazaret A, Clivio O, Xu C, Ashuach T, Gabitto M, Lotfollahi M, Svensson V, da Veiga Beltrame E, Kleshchevnikov V, Talavera-López C, Pachter L, Theis FJ, Streets A, Jordan MI, Regier J, Yosef N.
Gayoso A, et al. Among authors: boyeau p.
Nat Biotechnol. 2022 Feb;40(2):163-166. doi: 10.1038/s41587-021-01206-w.
Nat Biotechnol. 2022.
PMID: 35132262
No abstract available.
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