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Reproducible image-based profiling with Pycytominer.
Serrano E, Chandrasekaran SN, Bunten D, Brewer KI, Tomkinson J, Kern R, Bornholdt M, Fleming S, Pei R, Arevalo J, Tsang H, Rubinetti V, Tromans-Coia C, Becker T, Weisbart E, Bunne C, Kalinin AA, Senft R, Taylor SJ, Jamali N, Adeboye A, Abbasi HS, Goodman A, Caicedo JC, Carpenter AE, Cimini BA, Singh S, Way GP. Serrano E, et al. Among authors: bornholdt m. ArXiv [Preprint]. 2023 Nov 22:arXiv:2311.13417v1. ArXiv. 2023. PMID: 38045474 Free PMC article. Preprint.
Morphology and gene expression profiling provide complementary information for mapping cell state.
Way GP, Natoli T, Adeboye A, Litichevskiy L, Yang A, Lu X, Caicedo JC, Cimini BA, Karhohs K, Logan DJ, Rohban MH, Kost-Alimova M, Hartland K, Bornholdt M, Chandrasekaran SN, Haghighi M, Weisbart E, Singh S, Subramanian A, Carpenter AE. Way GP, et al. Among authors: bornholdt m. Cell Syst. 2022 Nov 16;13(11):911-923.e9. doi: 10.1016/j.cels.2022.10.001. Epub 2022 Oct 28. Cell Syst. 2022. PMID: 36395727 Free PMC article.
Learning representations for image-based profiling of perturbations.
Moshkov N, Bornholdt M, Benoit S, Smith M, McQuin C, Goodman A, Senft RA, Han Y, Babadi M, Horvath P, Cimini BA, Carpenter AE, Singh S, Caicedo JC. Moshkov N, et al. Among authors: bornholdt m. Nat Commun. 2024 Feb 21;15(1):1594. doi: 10.1038/s41467-024-45999-1. Nat Commun. 2024. PMID: 38383513 Free PMC article.