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Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction.

Yun T, Cosentino J, Behsaz B, McCaw ZR, Hill D, Luben R, Lai D, Bates J, Yang H, Schwantes-An TH, Zhou Y, Khawaja AP, Carroll A, Hobbs BD, Cho MH, McLean CY, Hormozdiari F. Yun T, et al. Among authors: mclean cy. Nat Genet. 2024 Aug;56(8):1604-1613. doi: 10.1038/s41588-024-01831-6. Epub 2024 Jul 8. Nat Genet. 2024. PMID: 38977853 Free PMC article.

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GenomeWarp: an alignment-based variant coordinate transformation.

McLean CY, Hwang Y, Poplin R, DePristo MA. McLean CY, et al. Bioinformatics. 2019 Nov 1;35(21):4389-4391. doi: 10.1093/bioinformatics/btz218. Bioinformatics. 2019. PMID: 30916319 Free PMC article.

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A personal health large language model for sleep and fitness coaching.

Khasentino J, Belyaeva A, Liu X, Yang Z, Furlotte NA, Lee C, Schenck E, Patel Y, Cui J, Schneider LD, Bryant R, Gomes RG, Jiang A, Lee R, Liu Y, Perez J, Rogers JK, Speed C, Tailor S, Walker M, Yu J, Althoff T, Heneghan C, Hernandez J, Malhotra M, Stern L, Matias Y, Corrado GS, Patel S, Shetty S, Zhan J, Prabhakara S, McDuff D, McLean CY. Khasentino J, et al. Among authors: mclean cy. Nat Med. 2025 Aug 14. doi: 10.1038/s41591-025-03888-0. Online ahead of print. Nat Med. 2025. PMID: 40813712

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A population-specific reference panel for improved genotype imputation in African Americans.

O'Connell J, Yun T, Moreno M, Li H, Litterman N, Kolesnikov A, Noblin E, Chang PC, Shastri A, Dorfman EH, Shringarpure S; 23andMe Research Team; Auton A, Carroll A, McLean CY. O'Connell J, et al. Among authors: mclean cy. Commun Biol. 2021 Nov 5;4(1):1269. doi: 10.1038/s42003-021-02777-9. Commun Biol. 2021. PMID: 34741098 Free PMC article.

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Genomewide Association Studies of LRRK2 Modifiers of Parkinson's Disease.

Lai D, Alipanahi B, Fontanillas P, Schwantes-An TH, Aasly J, Alcalay RN, Beecham GW, Berg D, Bressman S, Brice A, Brockman K, Clark L, Cookson M, Das S, Van Deerlin V, Follett J, Farrer MJ, Trinh J, Gasser T, Goldwurm S, Gustavsson E, Klein C, Lang AE, Langston JW, Latourelle J, Lynch T, Marder K, Marras C, Martin ER, McLean CY, Mejia-Santana H, Molho E, Myers RH, Nuytemans K, Ozelius L, Payami H, Raymond D, Rogaeva E, Rogers MP, Ross OA, Samii A, Saunders-Pullman R, Schüle B, Schulte C, Scott WK, Tanner C, Tolosa E, Tomkins JE, Vilas D, Trojanowski JQ; 23andMe Research Team; Uitti R, Vance JM, Visanji NP, Wszolek ZK, Zabetian CP, Mirelman A, Giladi N, Orr Urtreger A, Cannon P, Fiske B, Foroud T. Lai D, et al. Among authors: mclean cy. Ann Neurol. 2021 Jul;90(1):76-88. doi: 10.1002/ana.26094. Epub 2021 May 17. Ann Neurol. 2021. PMID: 33938021 Free PMC article.

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DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer.

Baid G, Cook DE, Shafin K, Yun T, Llinares-López F, Berthet Q, Belyaeva A, Töpfer A, Wenger AM, Rowell WJ, Yang H, Kolesnikov A, Ammar W, Vert JP, Vaswani A, McLean CY, Nattestad M, Chang PC, Carroll A. Baid G, et al. Among authors: mclean cy. Nat Biotechnol. 2023 Feb;41(2):232-238. doi: 10.1038/s41587-022-01435-7. Epub 2022 Sep 1. Nat Biotechnol. 2023. PMID: 36050551

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Longitudinal fundus imaging and its genome-wide association analysis provide evidence for a human retinal aging clock.

Ahadi S, Wilson KA, Babenko B, McLean CY, Bryant D, Pritchard O, Kumar A, Carrera EM, Lamy R, Stewart JM, Varadarajan A, Berndl M, Kapahi P, Bashir A. Ahadi S, et al. Among authors: mclean cy. Elife. 2023 Apr 17;12:e82364. doi: 10.7554/eLife.82364. Elife. 2023. PMID: 36975205 Free PMC article.

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Accurate, scalable cohort variant calls using DeepVariant and GLnexus.

Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY. Yun T, et al. Among authors: mclean cy. Bioinformatics. 2021 Apr 5;36(24):5582-5589. doi: 10.1093/bioinformatics/btaa1081. Bioinformatics. 2021. PMID: 33399819 Free PMC article.

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Large-scale machine-learning-based phenotyping significantly improves genomic discovery for optic nerve head morphology.

Alipanahi B, Hormozdiari F, Behsaz B, Cosentino J, McCaw ZR, Schorsch E, Sculley D, Dorfman EH, Foster PJ, Peng LH, Phene S, Hammel N, Carroll A, Khawaja AP, McLean CY. Alipanahi B, et al. Among authors: mclean cy. Am J Hum Genet. 2021 Jul 1;108(7):1217-1230. doi: 10.1016/j.ajhg.2021.05.004. Epub 2021 Jun 1. Am J Hum Genet. 2021. PMID: 34077760 Free PMC article.

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DeepNull models non-linear covariate effects to improve phenotypic prediction and association power.

McCaw ZR, Colthurst T, Yun T, Furlotte NA, Carroll A, Alipanahi B, McLean CY, Hormozdiari F. McCaw ZR, et al. Among authors: mclean cy. Nat Commun. 2022 Jan 11;13(1):241. doi: 10.1038/s41467-021-27930-0. Nat Commun. 2022. PMID: 35017556 Free PMC article.

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