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—publications [2025/06/19 21:24] (current) – cassa
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 +===== Selected Recent Publications =====
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 +  - 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
 +  - 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) American Journal of Human Genetics; 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***. Cell Genomics, Volume 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*.
 +  - 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
 +  - 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 
 +  - Kousi M, Soylemez O, Ozanturk A, Mourtzi N, Akle S, Jungreis I, Jungreis I, Muller J, **Cassa  CA**, Brand H, Mokry JA, Wolf MY, Sadeghpour A, McFadden K,  Lewis RA, Talkowski ME, Dollfus H, Kellis M, Davis EE, Sunyaev SR, Katsanis N. Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy. //Nat. Gen.// 2020 Oct 12. PMID: 33046855 DOI: 10.1038/s41588-020-0707-1
 +  - Akinci E, Cha M, Lin L, Yeo G, Hamilton MC, Donahue CJ, Bermudez-Cabrera HC, Zanetti LC, Chen M, Barkal SA, Khowpinitchai B, Chu N, Velimirovic M, Jodhani R, Fife JD, Sovrovic M, Cole PA, Davey RA, **Cassa CA**, Sherwood RI. Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics. //bioRxiv// 2020 Aug 28:2020.08.27.270819. doi: 10.1101/2020.08.27.270819. (Preprint.) PMID: 32869031 
 +  - Fahed AC, Wang M, Homburger JR, Patel AP, Bick AG, Neben CL, Lai C, Brockman D, Philippakis A, Ellinor PT, **Cassa CA**, Lebo M, Ng K, Lander ES, Zhou AY, Kathiresan S, Khera AV. Polygenic background modifies penetrance of monogenic variants for tier 1 genomic conditions. //Nat. Commun.// 2020 Aug 20;11(1):3635. doi: 10.1038/s41467-020-17374-3. PMID: 32820175 
 +  - Arbab M, Shen MW, Mok B, Wilson C, Matusek Z, **Cassa CA**, Lui DR. Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning. //Cell// 2020 https://doi.org/10.1016/j.cell.2020.05.037
 +  - Patel AP, Wang M, Fahed AC, Mason-Suares H, Brockman D, Pelletier R, Amr S, Machini K, Hawley M, Witkowski L, Koch C, Philippakis A, **Cassa CA**, Ellinor PT, Kathiresan S, Ng K, Lebo M, Khera AV. Association of Rare Pathogenic DNA Variants for Familial Hypercholesterolemia, Hereditary Breast and Ovarian Cancer Syndrome, and Lynch Syndrome With Disease Risk in Adults According to Family History. //JAMA Netw Open// 2020 Apr 1;3(4):e203959. doi: 10.1001/jamanetworkopen.2020.3959. 
 +  - Nissim S, Leshchiner I, Mancias JD, Greenblatt MB, Maertens O, **Cassa CA**, Rosenfeld JA, Cox AG, Hedgepeth J, Wucherpfennig JI, Kim AJ, Henderson JE, Gonyo P, Brandt A, Lorimer E, Unger B, Prokop JW, Heidel JR, Wang XX, Ukaegbu CI, Jennings BC, Paulo JA, Gableske S, Fierke CA, Getz G, Sunyaev SR, Wade Harper J, Cichowski K, Kimmelman AC, Houvras Y, Syngal S, Williams C, Goessling W. Mutations in RABL3 alter KRAS prenylation and are associated with hereditary pancreatic cancer. //Nat Genet.// 2019 Sep;51(9):1308-1314. PMID: 31406347 https://www.nature.com/articles/s41588-019-0475-y
 +  - Weghorn D, Balick DJ, **Cassa C**, Kosmicki JA, Daly MJ, Beier DR, Sunyaev SR. Applicability of the Mutation-Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans. //Mol Biol Evol.// 2019 Aug 1;36(8):1701-1710. doi: 10.1093/molbev/msz092. PMID: 31004148
 +  - **Cassa CA**, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O'Donnell-Luria A, MacArthur DG, Daly MJ, Beier DR, Sunyaev SR. Reply to 'Selective effects of heterozygous protein-truncating variants'. Nat Genet. 2019 Jan; 51(1):3-4. PMID: 30478437.
 +  - Kumar Mohanty A, Vuzman D, Francioli L, **Cassa C**, Toth-Petroczy A, Sunyaev S. novoCaller: A Bayesian network approach for de novo variant calling from pedigree and population sequence data. //Bioinformatics.// 2018 Aug 30. PMID: 30169785.
 +  - Shen MW, Arbab M, Hsu JY, Worstell D, Culbertson SJ, Krabbe O, **Cassa CA**, Liu DR, Gifford DK, Sherwood RI. Predictable and precise template-free CRISPR editing of pathogenic variants. //Nature// 2018. https://www.nature.com/articles/s41586-018-0686-x
 +  - **Cassa CA**, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O'Donnell-Luria A, MacArthur DG, Daly MJ, Beier DR, Sunyaev, SR. Response to comment on “Estimating the selective effects of heterozygous protein-truncating variants from human exome data”, Cassa et al. //Nat Genet.// 2018 
 +  - Haghighi A, Krier JB, Toth-Petroczy A, **Cassa CA**, Frank NY, Carmichael N, Fieg E, Bjonnes A, Mohanty A, Briere LC, Lincoln S, Lucia S, Gupta VA, Söylemez O, Sutti S, Kooshesh K, Qiu H, Fay CJ, Perroni V, Valerius J, Hanna M, Frank A, Ouahed J, Snapper SB, Pantazi A, Chopra SS, Leshchiner I, Stitziel NO, Feldweg A, Mannstadt M, Loscalzo J, Sweetser DA, Liao E, Stoler JM, Nowak CB, Sanchez-Lara PA, Klein OD, Perry H, Patsopoulos NA, Raychaudhuri S, Goessling W, Green RC, Seidman CE, MacRae CA, Sunyaev SR, Maas RL, Vuzman D; Undiagnosed Diseases Network, Brigham and Women’s Hospital FaceBase Project, Brigham Genomic Medicine (BGM). An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery. //NPJ Genom Med.// 2018 Aug 13;3:21. doi: 10.1038/s41525-018-0060-9.
 +  - **Cassa CA**, Jordan DM, Adzhubei I, Sunyaev SR. A literature review at genome scale: improving clinical variant assessment. //Genet. Med.// 2018 Feb 1. doi: 10.1038/gim.2017.230. PMID: 29388949 PDF: http://rdcu.be/F3q3
 +  - **Cassa CA**, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O'Donnell-Luria A, MacArthur DG, Daly MJ, Beier DR, Sunyaev, SR. Estimating the Selective Effects of Heterozygous Protein Truncating Variants from Human Exome Data. //Nat Genet.// 2017 May;49(5):806-810. doi: 10.1038/ng.3831. PMID: 28369035 PMC: https://www.ncbi.nlm.nih.gov/pubmed/28369035
 +  - **Cassa CA**, Akle S, Jordan DM, Rosenfeld JA. When “N of 2” is not enough: Integrating statistical and functional data in gene discovery. C//old Spring Harb Mol Case Stud.// 2017 May;3(3):a001099. doi: 10.1101/mcs.a001099. PMID: 28487880
 +  - Akle S, Chun S, Jordan DM, **Cassa CA**. Mitigating false-positive associations in rare disease gene discovery. //Hum Mutat.// 2015 Oct;36(10):998-1003. doi: 10.1002/humu.22847. PMID: 26378430
 +  - **Cassa CA**, Smith SE, Docken W, Hoffman E, McLaughlin H, Chun S, Leshchiner I, Miraoui H, Raychaudhuri S, Frank NY, Wilson BJ, Sunyaev SR, Maas RL; Brigham Genomic Medicine, Vuzman D. An argument for early genomic sequencing in atypical cases: a WISP3 variant leads to diagnosis of progressive pseudorheumatoid arthropathy of childhood. //Rheumatology// (Oxford). 2015 Oct 22. pii: kev367. PMID: 26493744
 +  - Chopra SS, Leshchiner I, Duzkale H, McLaughlin H, Giovanni M, Zhang C, Stitziel N, Fingeroth J, Joyce RM, Lebo M, Rehm H, Vuzman D, Maas R, Sunyaev SR, Murray M, **Cassa CA**. Inherited CHST11/MIR3922 deletion is associated with a novel recessive syndrome presenting with skeletal malformation and malignant lymphoproliferative disease. //Mol Genet Genomic Med.// 2015 Sep;3(5):413-23. PMID: 26436107
 +  - Balick DJ, Do R, **Cassa CA**, Reich D, Sunyaev SR. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck. //PLoS Genet.// 2015 Aug 28;11(8):e1005436. PMID: 26317225
 +  - Jordan DM, Frangakis SG, Golzio C, **Cassa CA**, Kurtzberg J; Task Force for Neonatal Genomics, Davis EE, Sunyaev SR, Katsanis N. Identification of cis-suppression of human disease mutations by comparative genomics. //Nature.// 2015 Aug 13;524(7564):225-9. doi: 10.1038/nature14497. Epub 2015 Jun 29. PMID: 26123021
 +  - Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, **Cassa CA**, ... Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.\\ Genome Biol. 15(3):R53 (2014) PubMed [[http://www.ncbi.nlm.nih.gov/pubmed/24667040|PMID:24667040]].
 +  - **Cassa CA**, Tong MY, Jordan DM. Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals. Hum Mutat 34(9):1216-20 (2013). PubMed [[http://www.ncbi.nlm.nih.gov/pubmed/23818451|PMID:23818451
 +  - **Cassa, CA**, Chunara R, Mandl K, Brownstein JS. Twitter as a sentinel in emergency situations: lessons from the Boston marathon explosions. PLoS Curr. 2013; 5. PMID: 23852273; PMCID: PMC3706072.1.
 +  - **Cassa, CA**, Miller RA, Mandl KD. A novel, privacy-preserving cryptographic approach for sharing sequencing data. J Am Med Inform Assoc. 2013 Jan 1; 20(1):69-76. PMID: 23125421; PMCID: PMC3555340.
 +  - **Cassa, CA**, Savage SK, Taylor PL, Green RC, McGuire AL, Mandl KD. Disclosing pathogenic genetic variants to research participants: quantifying an emerging ethical responsibility. Genome Res. 2012 Mar; 22(3):421-8. PMID: 22147367; PMCID: PMC3290777.
 +  - Tong MY, **Cassa, CA**, Kohane IS. Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations. Bioinformatics. 2011 Mar 15; 27(6):891-3. PMID: 21258063; PMCID: PMC3051330.
 +  - Malin, B, **Cassa, C**, Kantarcioglu M . Privacy-Aware Knowledge Discovery: Novel Applications and New Techniques, Chapman Hall / CRC Press. A Survey of Challenges and Solutions for Privacy in Clinical Genomics Data Mining. 2010.
 +  - **Cassa, CA**, Mandl KD. AMIA Annu Symp Proc. 2009. Risk of Re-Identification: Privacy Implications for Rare Mutation. 2009.
 +  - Stoto, M. A., Dempsey, J. X., Baer, A., **Cassa, C**, Gibson, P. J., & Buehler, J. W. . Advances in Disease Surveillance. Expert Meeting on Privacy, Confidentiality, and Other Legal and Ethical Issues in Syndromic Surveillance. 2009; 7(2).
 +  - Wieland SC, **Cassa, CA**, Mandl KD, Berger B. Revealing the spatial distribution of a disease while preserving privacy. Proc Natl Acad Sci U S A. 2008 Nov 18; 105(46):17608-13. PMID: 19015533; PMCID: PMC2584758.
 +  - **Cassa, CA**, Kenfield S, Daniel J, Mandl KD. The Massachusetts Health and Homeland Alert Network: a scalable and secure public health knowledge management and notification system. AMIA Annu Symp Proc. 2008; 893. PMID: 18999074.
 +  - **Cassa, CA**, Wieland SC, Mandl KD. Re-identification of home addresses from spatial locations anonymized by Gaussian skew. Int J Health Geogr. 2008; 7:45. PMID: 18700031; PMCID: PMC2526988.
 +  - **Cassa, CA**, Schmidt B, Kohane IS, Mandl KD. My sister's keeper?: genomic research and the identifiability of siblings. BMC Med Genomics. 2008; 1:32. PMID: 18655711; PMCID: PMC2503988.
 +  - **Cassa, CA**. Privacy and identifiability in clinical research, personalized medicine, and public health surveillance. 2008.
 +  - **Cassa, CA**, Mandl KD. Multi-factor authentication using contents from disparate EHRs. AMIA Annu Symp Proc. 2007; 891. PMID: 18693992.
 +  - Brownstein JS, **Cassa, CA**, Kohane IS, Mandl KD. An unsupervised classification method for inferring original case locations from low-resolution disease maps. Int J Health Geogr. 2006; 5:56. PMID: 17156451; PMCID: PMC1702538.
 +  - Brownstein JS, **Cassa, CA**, Mandl KD. No place to hide--reverse identification of patients from published maps. N Engl J Med. 2006 Oct 19; 355(16):1741-2. PMID: 17050904.
 +  - Grannis S, Egg J, **Cassa, C**, Olson K, Mandl K, Overhage J . Proc Symp 2006 Syndromic Surveillance Conf, Baltimore, MD. Evaluating the Performance of a Spatial Scan Statistic Using Simulated Outbreak Characteristics. 2006.
 +  - **Cassa, CA**, Grannis SJ, Overhage JM, Mandl KD. A context-sensitive approach to anonymizing spatial surveillance data: impact on outbreak detection. J Am Med Inform Assoc. 2006 Mar-Apr; 13(2):160-5. PMID: 16357353; PMCID: PMC1447544.
 +  - **Cassa, CA**, Iancu K, Olson KL, Mandl KD. A software tool for creating simulated outbreaks to benchmark surveillance systems. BMC Med Inform Decis Mak. 2005; 5:22. PMID: 16018815; PMCID: PMC1182374.
 +  - Brownstein JS, **Cassa, CA**, Kohane IS, Mandl KD. Reverse geocoding: concerns about patient confidentiality in the display of geospatial health data. AMIA Annu Symp Proc. 2005; 905. PMID: 16779192; PMCID: PMC1560748.
 +  - Grannis S, Mandl K, Olson K, **Cassa, CA**, Overhage JM . International Society of Disease Surveillance Annu Symp Proc. Boston, MA. Geographic Coordinate Transformation Methods to Reduce Privacy Risks Associated with Surveillance. 2004.
 +  - Mandl KD, Reis B, **Cassa, C**. Measuring outbreak-detection performance by using controlled feature set simulations. MMWR Morb Mortal Wkly Rep. 2004 Sep 24; 53 Suppl:130-6. PMID: 15714642.
 +  - **Cassa, CA**. Spatial outbreak detection analysis tool : a system to create sets of semi-synthetic geo-spatial clusters. 2004.
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