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Page 1
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.
Fang LT, Zhu B, Zhao Y, Chen W, Yang Z, Kerrigan L, Langenbach K, de Mars M, Lu C, Idler K, Jacob H, Zheng Y, Ren L, Yu Y, Jaeger E, Schroth GP, Abaan OD, Talsania K, Lack J, Shen TW, Chen Z, Stanbouly S, Tran B, Shetty J, Kriga Y, Meerzaman D, Nguyen C, Petitjean V, Sultan M, Cam M, Mehta M, Hung T, Peters E, Kalamegham R, Sahraeian SME, Mohiyuddin M, Guo Y, Yao L, Song L, Lam HYK, Drabek J, Vojta P, Maestro R, Gasparotto D, Kõks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Jensen RV, Pirooznia M, Li Z, Xiao C, Sherry ST, Kusko R, Moos M, Donaldson E, Tezak Z, Ning B, Tong W, Li J, Duerken-Hughes P, Catalanotti C, Maheshwari S, Shuga J, Liang WS, Keats J, Adkins J, Tassone E, Zismann V, McDaniel T, Trent J, Foox J, Butler D, Mason CE, Hong H, Shi L, Wang C, Xiao W; Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium. Fang LT, et al. Among authors: mason ce. Nat Biotechnol. 2021 Sep;39(9):1151-1160. doi: 10.1038/s41587-021-00993-6. Epub 2021 Sep 9. Nat Biotechnol. 2021. PMID: 34504347 Free PMC article.
Extensive sequencing of seven human genomes to characterize benchmark reference materials.
Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M. Zook JM, et al. Among authors: mason ce. Sci Data. 2016 Jun 7;3:160025. doi: 10.1038/sdata.2016.25. Sci Data. 2016. PMID: 27271295 Free PMC article.
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.
McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan NA, Subramanian P, Moffat K, Levy S, Lonardi S, Greenfield N, Colwell RR, Rosen GL, Mason CE. McIntyre ABR, et al. Among authors: mason ce. Genome Biol. 2017 Sep 21;18(1):182. doi: 10.1186/s13059-017-1299-7. Genome Biol. 2017. PMID: 28934964 Free PMC article.
Best practices for benchmarking germline small-variant calls in human genomes.
Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM; Global Alliance for Genomics and Health Benchmarking Team. Krusche P, et al. Among authors: mason ce. Nat Biotechnol. 2019 May;37(5):555-560. doi: 10.1038/s41587-019-0054-x. Epub 2019 Mar 11. Nat Biotechnol. 2019. PMID: 30858580 Free PMC article.
Author Correction: Best practices for benchmarking germline small-variant calls in human genomes.
Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM; Global Alliance for Genomics and Health Benchmarking Team. Krusche P, et al. Among authors: mason ce. Nat Biotechnol. 2019 May;37(5):567. doi: 10.1038/s41587-019-0108-0. Nat Biotechnol. 2019. PMID: 30899106
A robust benchmark for detection of germline large deletions and insertions.
Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AM, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M. Zook JM, et al. Among authors: mason ce. Nat Biotechnol. 2020 Nov;38(11):1347-1355. doi: 10.1038/s41587-020-0538-8. Epub 2020 Jun 15. Nat Biotechnol. 2020. PMID: 32541955 Free PMC article.
Author Correction: A robust benchmark for detection of germline large deletions and insertions.
Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AM, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M. Zook JM, et al. Among authors: mason ce. Nat Biotechnol. 2020 Nov;38(11):1357. doi: 10.1038/s41587-020-0640-y. Nat Biotechnol. 2020. PMID: 32699374
374 results