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--- publications [2023/03/30 13:52] – cassa
+++ publications [2024/09/15 21:57] (current) – cassa
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 ===== Selected Recent Publications =====
-  - DeMAG predicts the effects of variants in clinically actionable genes by integrating structural and evolutionary epistatic features. Luppino F, Adzhubei I, **Cassa, CA***, Toth-Petroczy A*. Nature Communications (Accepted)
+  - Extracting and calibrating population evidence of variant pathogenicity using biobank data. Bhat V, Yu T, Brown L, Pejaver V, Lebo M, Harrison S, Cassa CA. medRxiv 2024.08.14.24311911; doi: https://doi.org/10.1101/2024.08.14.24311911
-  - Estimating clinical risk in gene regions from population sequencing cohort data. Fife JD, **Cassa CA**. medRxiv 2023 doi: https://doi.org/10.1101/2023.01.06.23284281
+  - FUSE: Improving the estimation and imputation of variant impacts in functional screening. Yu, T, Fife JD, Adzhubey I, Sherwood R*, **Cassa CA***. In Press, Cell Genomics. doi: https://doi.org/10.1101/2023.01.06.23284280
-  - Joint estimation and imputation of variant functional effects using high throughput assay data. Yu, T, Fife JD, Adzhubey I, Sherwood R*, **Cassa CA***. medRxiv 2023 doi: https://doi.org/10.1101/2023.01.06.23284280
+  - Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nat Genet 56, 925–937 (2024) https://doi.org/10.1038/s41588-024-01726-6. Ryu J, Barkal S, Yu T, Jankowiak M, Zhou Y, Francoeur M, Phan QV, Li Z, Tognon M, Brown L, Love MI, Bhat V, Lettre G, Ascher DB, **Cassa CA***, Sherwood RI*, Pinello L*.
-  - Systematic elucidation of genetic mechanisms underlying cholesterol uptake. Hamilton MC, Fife JD, Akinci E, Yu T, Khowpinitchai B, Cha M, Barkal S, Thi TT, Yeo G, Ramos Barroso JP, Francoeur MJ, Velimirovic M, Gifford DK, Lettre G, Yu H, **Cassa CA***, Sherwood RI*. bioRxiv 2023 doi: https://doi.org/10.1101/2023.01.09.500804
+  - Estimating clinical risk in gene regions from population sequencing cohort data. Fife JD, **Cassa CA**. Am J Hum Genet, June 2023. doi: https://doi.org/10.1101/2023.01.06.23284281
-  - The missing link between genetic association and regulatory function. Connally N, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C*, **Cassa CA*, **Sunyaev S*. eLife, Dec. 2022 https://elifesciences.org/articles/74970
+  - DeMAG predicts the effects of variants in clinically actionable genes by integrating structural and evolutionary epistatic features. Luppino, F., Adzhubei, I.A., **Cassa, CA***, Toth-Petroczy A*. Nat Commun 2023 Apr 19;14(1):2230. doi: 10.1038/s41467-023-37661-z. [[https://t.co/mOD0P53Ppn]]
+  - Systematic elucidation of genetic mechanisms underlying cholesterol uptake. Hamilton MC, Fife JD, Akinci E, Yu T, Khowpinitchai B, Cha M, Barkal S, Thi TT, Yeo G, Ramos Barroso JP, Francoeur MJ, Velimirovic M, Gifford DK, Lettre G, Yu H*, **Cassa CA***, Sherwood RI*. Cell Genomics, 2023, 100304. [[https://doi.org/10.1016/j.xgen.2023.100304]]
+  - The missing link between genetic association and regulatory function. Connally N, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C*, **Cassa CA*, **Sunyaev S*. eLife, Dec. 2022 https://elifesciences.org/articles/74970  https://doi.org/10.7554/eLife.74970
   - Informing Variant Assessment using Structured Evidence from Prior Classifications (PS1, PM5, and PVS1 Sequence Variant Interpretation Criteria) Bhat V, Adzhubei IA, Fife JD, Lebo M, **Cassa CA**. Genetics in Medicine, 2022. doi: https://doi.org/10.1101/2022.05.16.22275073
   - A framework for integrated clinical risk assessment using population sequencing data. Fife JD, Tran T, Bernatchez JR, Shepard KE, Koch C, Patel AP, Fahed AC, Krishnamurthy S, Regeneron Genetics Center, DiscovEHR Collaboration, Wang W, Buchanan AH, Carey DJ, Metpally R, Khera AV, Lebo M, **Cassa CA**. Preprint on medRxiv. doi: https://doi.org/10.1101/2021.08.12.21261563