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publications [2025/05/21 02:26] – cassapublications [2026/04/19 18:38] (current) – cassa
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-===== Selected Recent Publications =====+===== Selected Recent Publications and Preprints =====
  
-  - From Text to Translation: Using Language Models to Prioritize Variants for Clinical Review. Li W, Li X, Lavallee E, Saparov A, Zitnik M, **Cassa C**. medRxiv 2024.12.31.24319792; doi: https://doi.org/10.1101/2024.12.31.24319792 +  - LDLR variant classification through activity-normalized prime editing screening. Zhou PJ, Velimirovic M, Yu T, Gligorovski V, Mathis N, Zhao J, Phan QV, Vogd F, Ryu J, Pan Q, Tyagi A, Ascher DB, Schwank G, Pinello L, **Cassa CA***, Sherwood RI*. bioRxiv 2025.12.16.694467; doi: https://doi.org/10.64898/2025.12.16.694467  
-  - 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**. Accepted to American Journal of Human Genetics; doi: https://doi.org/10.1101/2024.08.14.24311911 +  - Language models reveal evidence gaps in variants of uncertain significance. Li W, Bhat V, Yu T, Lebo M, Zitnik M, **Cassa CA**. medRxiv 2026.02.28.26347206; doi: https://doi.org/10.64898/2026.02.28.26347206 
-  - 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+  - From Text to Translation: Using Language Models to Prioritize Variants for Clinical Review. Li W, Li X, Lavallee E, Saparov A, Zitnik M, **Cassa C**. Accepted April 2026, //Genome Medicine//; doi: https://doi.org/10.1101/2024.12.31.24319792 
 +  - 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**. American Journal of Human Genetics, Vol 112, Issue 8, 1805-1817; doi: 10.1016/j.ajhg.2025.06.012 
 +   - FUSE: Improving the estimation and imputation of variant impacts in functional screening. Yu, T, Fife JD, Adzhubey I, Sherwood R*, **Cassa CA***. Cell Genomics, Vol 4, Issue 10, 100667 doi: https://doi.org/10.1016/j.xgen.2024.100667
   - 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*.   - 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*.
   - 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   - 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