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Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2.
Zhou B, Ho SS, Greer SU, Spies N, Bell JM, Zhang X, Zhu X, Arthur JG, Byeon S, Pattni R, Saha I, Huang Y, Song G, Perrin D, Wong WH, Ji HP, Abyzov A, Urban AE. Zhou B, et al. Among authors: spies n. Nucleic Acids Res. 2019 May 7;47(8):3846-3861. doi: 10.1093/nar/gkz169. Nucleic Acids Res. 2019. PMID: 30864654 Free PMC article.
svclassify: a method to establish benchmark structural variant calls.
Parikh H, Mohiyuddin M, Lam HY, Iyer H, Chen D, Pratt M, Bartha G, Spies N, Losert W, Zook JM, Salit M. Parikh H, et al. Among authors: spies n. BMC Genomics. 2016 Jan 16;17:64. doi: 10.1186/s12864-016-2366-2. BMC Genomics. 2016. PMID: 26772178 Free PMC article.
A crowdsourced set of curated structural variants for the human genome.
Chapman LM, Spies N, Pai P, Lim CS, Carroll A, Narzisi G, Watson CM, Proukakis C, Clarke WE, Nariai N, Dawson E, Jones G, Blankenberg D, Brueffer C, Xiao C, Kolora SRR, Alexander N, Wolujewicz P, Ahmed AE, Smith G, Shehreen S, Wenger AM, Salit M, Zook JM. Chapman LM, et al. Among authors: spies n. PLoS Comput Biol. 2020 Jun 19;16(6):e1007933. doi: 10.1371/journal.pcbi.1007933. eCollection 2020 Jun. PLoS Comput Biol. 2020. PMID: 32559231 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: spies n. Sci Data. 2016 Jun 7;3:160025. doi: 10.1038/sdata.2016.25. Sci Data. 2016. PMID: 27271295 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: spies n. Nat Biotechnol. 2020 Nov;38(11):1357. doi: 10.1038/s41587-020-0640-y. Nat Biotechnol. 2020. PMID: 32699374
51 results