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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy.
Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R. Zhu Q, et al. Among authors: kuczynski j. mSystems. 2022 Apr 26;7(2):e0016722. doi: 10.1128/msystems.00167-22. Epub 2022 Apr 4. mSystems. 2022. PMID: 35369727 Free PMC article.
Bayesian community-wide culture-independent microbial source tracking.
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. Knights D, et al. Among authors: kuczynski j. Nat Methods. 2011 Jul 17;8(9):761-3. doi: 10.1038/nmeth.1650. Nat Methods. 2011. PMID: 21765408 Free PMC article.
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO. Yilmaz P, et al. Among authors: kuczynski j. Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823. Nat Biotechnol. 2011. PMID: 21552244 Free PMC article.
Supervised classification of microbiota mitigates mislabeling errors.
Knights D, Kuczynski J, Koren O, Ley RE, Field D, Knight R, DeSantis TZ, Kelley ST. Knights D, et al. Among authors: kuczynski j. ISME J. 2011 Apr;5(4):570-3. doi: 10.1038/ismej.2010.148. Epub 2010 Oct 7. ISME J. 2011. PMID: 20927137 Free PMC article. No abstract available.
82 results