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PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.
Olson ND, Wagner J, McDaniel J, Stephens SH, Westreich ST, Prasanna AG, Johanson E, Boja E, Maier EJ, Serang O, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, Kyriakidis K, Malousi A, Shafin K, Pesout T, Jain M, Paten B, Chang PC, Kolesnikov A, Nattestad M, Baid G, Goel S, Yang H, Carroll A, Eveleigh R, Bourgey M, Bourque G, Li G, Ma C, Tang L, Du Y, Zhang S, Morata J, Tonda R, Parra G, Trotta JR, Brueffer C, Demirkaya-Budak S, Kabakci-Zorlu D, Turgut D, Kalay Ö, Budak G, Narcı K, Arslan E, Brown R, Johnson IJ, Dolgoborodov A, Semenyuk V, Jain A, Tetikol HS, Jain V, Ruehle M, Lajoie B, Roddey C, Catreux S, Mehio R, Ahsan MU, Liu Q, Wang K, Sahraeian SME, Fang LT, Mohiyuddin M, Hung C, Jain C, Feng H, Li Z, Chen L, Sedlazeck FJ, Zook JM. Olson ND, et al. Among authors: carroll a. Cell Genom. 2022 May 11;2(5):100129. doi: 10.1016/j.xgen.2022.100129. Epub 2022 Apr 27. Cell Genom. 2022. PMID: 35720974 Free PMC article.
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW. Wenger AM, et al. Among authors: carroll a. Nat Biotechnol. 2019 Oct;37(10):1155-1162. doi: 10.1038/s41587-019-0217-9. Epub 2019 Aug 12. Nat Biotechnol. 2019. PMID: 31406327 Free PMC article.
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: carroll a. 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.
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: carroll a. 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.
A diploid assembly-based benchmark for variants in the major histocompatibility complex.
Chin CS, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A, Rautiainen M, Aganezov S, Kirsche M, Zarate S, Schatz MC, Xiao C, Rowell WJ, Markello C, Farek J, Sedlazeck FJ, Bansal V, Yoo B, Miller N, Zhou X, Carroll A, Barrio AM, Salit M, Marschall T, Dilthey AT, Zook JM. Chin CS, et al. Among authors: carroll a. Nat Commun. 2020 Sep 22;11(1):4794. doi: 10.1038/s41467-020-18564-9. Nat Commun. 2020. PMID: 32963235 Free PMC article.
Chromosome-scale, haplotype-resolved assembly of human genomes.
Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin CS, Church GM, Li H. Garg S, et al. Among authors: carroll a. Nat Biotechnol. 2021 Mar;39(3):309-312. doi: 10.1038/s41587-020-0711-0. Epub 2020 Dec 7. Nat Biotechnol. 2021. PMID: 33288905 Free PMC article.
Parliament2: Accurate structural variant calling at scale.
Zarate S, Carroll A, Mahmoud M, Krasheninina O, Jun G, Salerno WJ, Schatz MC, Boerwinkle E, Gibbs RA, Sedlazeck FJ. Zarate S, et al. Among authors: carroll a. Gigascience. 2020 Dec 21;9(12):giaa145. doi: 10.1093/gigascience/giaa145. Gigascience. 2020. PMID: 33347570 Free PMC article.
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes.
Sirén J, Monlong J, Chang X, Novak AM, Eizenga JM, Markello C, Sibbesen JA, Hickey G, Chang PC, Carroll A, Gupta N, Gabriel S, Blackwell TW, Ratan A, Taylor KD, Rich SS, Rotter JI, Haussler D, Garrison E, Paten B. Sirén J, et al. Among authors: carroll a. Science. 2021 Dec 17;374(6574):abg8871. doi: 10.1126/science.abg8871. Epub 2021 Dec 17. Science. 2021. PMID: 34914532 Free PMC article.
1,631 results