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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: zook jm. 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.
Good laboratory practice for clinical next-generation sequencing informatics pipelines.
Gargis AS, Kalman L, Bick DP, da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni S, Mason CE, Nagarajan R, Voelkerding KV, Worthey EA, Aziz N, Barnes J, Bennett SF, Bisht H, Church DM, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, Hyland FC, Luna RA, MacCannell D, Mann T, McCluskey MR, McDaniel TK, Ganova-Raeva LM, Rehm HL, Reid J, Campo DS, Resnick RB, Ridge PG, Salit ML, Skums P, Wong LJ, Zehnbauer BA, Zook JM, Lubin IM. Gargis AS, et al. Among authors: zook jm. Nat Biotechnol. 2015 Jul;33(7):689-93. doi: 10.1038/nbt.3237. Nat Biotechnol. 2015. PMID: 26154004 Free PMC article. No abstract available.
PEPR: pipelines for evaluating prokaryotic references.
Olson ND, Zook JM, Samarov DV, Jackson SA, Salit ML. Olson ND, et al. Among authors: zook jm. Anal Bioanal Chem. 2016 Apr;408(11):2975-83. doi: 10.1007/s00216-015-9299-5. Epub 2016 Mar 2. Anal Bioanal Chem. 2016. PMID: 26935931 Free PMC article.
International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons.
Olson ND, Lund SP, Zook JM, Rojas-Cornejo F, Beck B, Foy C, Huggett J, Whale AS, Sui Z, Baoutina A, Dobeson M, Partis L, Morrow JB. Olson ND, et al. Among authors: zook jm. Biomol Detect Quantif. 2015 Mar 5;3:17-24. doi: 10.1016/j.bdq.2015.01.004. eCollection 2015 Mar. Biomol Detect Quantif. 2015. PMID: 27077030 Free PMC article.
A research roadmap for next-generation sequencing informatics.
Altman RB, Prabhu S, Sidow A, Zook JM, Goldfeder R, Litwack D, Ashley E, Asimenos G, Bustamante CD, Donigan K, Giacomini KM, Johansen E, Khuri N, Lee E, Liang XS, Salit M, Serang O, Tezak Z, Wall DP, Mansfield E, Kass-Hout T. Altman RB, et al. Among authors: zook jm. Sci Transl Med. 2016 Apr 20;8(335):335ps10. doi: 10.1126/scitranslmed.aaf7314. Sci Transl Med. 2016. PMID: 27099173 Free PMC article. Review.
Genome-wide reconstruction of complex structural variants using read clouds.
Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou S, Sidow A. Spies N, et al. Among authors: zook jm. Nat Methods. 2017 Sep;14(9):915-920. doi: 10.1038/nmeth.4366. Epub 2017 Jul 17. Nat Methods. 2017. PMID: 28714986 Free PMC article.
Tools for annotation and comparison of structural variation.
Sedlazeck FJ, Dhroso A, Bodian DL, Paschall J, Hermes F, Zook JM. Sedlazeck FJ, et al. Among authors: zook jm. F1000Res. 2017 Oct 3;6:1795. doi: 10.12688/f1000research.12516.1. eCollection 2017. F1000Res. 2017. PMID: 29123647 Free PMC article.
96 results