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publications [2022/10/03 20:39] – created - external edit 127.0.0.1publications [2024/09/15 21:57] (current) – cassa
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 ===== Selected Recent Publications ===== ===== Selected Recent Publications =====
  
-  - 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**. Accepted, Genetics in Medicine, 2022. doi: https://doi.org/10.1101/2022.05.16.22275073+  - 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 
 +  - 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 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 
 +  - 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   - 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
-  - The missing link between genetic association and regulatory function. Connally N, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S. Cotsapas C, **Cassa C**, Sunyaev S. Preprint on medRxiv. doi: https://doi.org/10.1101/2021.06.08.21258515 
   - Variants in STXBP3 Are Associated With Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation. Ouahed J, Kelsen JR, Spessott WA, Kooshesh K, Sanmillan ML, Dawany N, Sullivan KE, Hamilton K, Slowik V, Nejentsev S, Neves JF, Flores H, Chung WK, Wilson A, Yeboa KA, Wou K, Jain P, Field M, Tollefson S, Dent MH, Li D, Naito T, McGovern DPB, Kwong AC, Taliaferro F, Ordovas-Montanes J, Horwitz B, Kotlarz D, Klein C, Evans J, Dorsey J, Warner N, Elkadri A, Muise AM, Goldsmith J, Thompson B, Engelhardt KR, Cant AJ, Hambleton S, Barclay A, Toth-Petroczy A, Vuzman D, Carmichael N, Bodea C, **Cassa CA**, Devoto M, Maas RL, Behrens EM, Giraudo CG, Snapper SB. J Crohns Colitis. 2021 Apr 23:jjab077. doi: 10.1093/ecco-jcc/jjab077. PMID: 33891011   - Variants in STXBP3 Are Associated With Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation. Ouahed J, Kelsen JR, Spessott WA, Kooshesh K, Sanmillan ML, Dawany N, Sullivan KE, Hamilton K, Slowik V, Nejentsev S, Neves JF, Flores H, Chung WK, Wilson A, Yeboa KA, Wou K, Jain P, Field M, Tollefson S, Dent MH, Li D, Naito T, McGovern DPB, Kwong AC, Taliaferro F, Ordovas-Montanes J, Horwitz B, Kotlarz D, Klein C, Evans J, Dorsey J, Warner N, Elkadri A, Muise AM, Goldsmith J, Thompson B, Engelhardt KR, Cant AJ, Hambleton S, Barclay A, Toth-Petroczy A, Vuzman D, Carmichael N, Bodea C, **Cassa CA**, Devoto M, Maas RL, Behrens EM, Giraudo CG, Snapper SB. J Crohns Colitis. 2021 Apr 23:jjab077. doi: 10.1093/ecco-jcc/jjab077. PMID: 33891011
   - Louie W, Shen MW, Tahiry Z, Zhang S, Worstell D, **Cassa CA**, Sherwood RI, Gifford DK. Machine learning based CRISPR gRNA design for therapeutic exon skipping. PLoS Comput Biol. 2021 Jan 8;17(1):e1008605. doi: 10.1371/journal.pcbi.1008605. eCollection 2021 Jan. PMID: 33417623    - Louie W, Shen MW, Tahiry Z, Zhang S, Worstell D, **Cassa CA**, Sherwood RI, Gifford DK. Machine learning based CRISPR gRNA design for therapeutic exon skipping. PLoS Comput Biol. 2021 Jan 8;17(1):e1008605. doi: 10.1371/journal.pcbi.1008605. eCollection 2021 Jan. PMID: 33417623