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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: mcdonald d. mSystems. 2022 Apr 26;7(2):e0016722. doi: 10.1128/msystems.00167-22. Epub 2022 Apr 4. mSystems. 2022. PMID: 35369727 Free PMC article.
Collaborative cloud-enabled tools allow rapid, reproducible biological insights.
Ragan-Kelley B, Walters WA, McDonald D, Riley J, Granger BE, Gonzalez A, Knight R, Perez F, Caporaso JG. Ragan-Kelley B, et al. Among authors: mcdonald d. ISME J. 2013 Mar;7(3):461-4. doi: 10.1038/ismej.2012.123. Epub 2012 Oct 25. ISME J. 2013. PMID: 23096404 Free PMC article. No abstract available.
From molecules to dynamic biological communities.
McDonald D, Vázquez-Baeza Y, Walters WA, Caporaso JG, Knight R. McDonald D, et al. Biol Philos. 2013 Mar;28(2):241-259. doi: 10.1007/s10539-013-9364-4. Epub 2013 Feb 5. Biol Philos. 2013. PMID: 23483075 Free PMC article.
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.
Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG. Rideout JR, et al. Among authors: mcdonald d. PeerJ. 2014 Aug 21;2:e545. doi: 10.7717/peerj.545. eCollection 2014. PeerJ. 2014. PMID: 25177538 Free PMC article.
Rethinking "enterotypes".
Knights D, Ward TL, McKinlay CE, Miller H, Gonzalez A, McDonald D, Knight R. Knights D, et al. Among authors: mcdonald d. Cell Host Microbe. 2014 Oct 8;16(4):433-7. doi: 10.1016/j.chom.2014.09.013. Cell Host Microbe. 2014. PMID: 25299329 Free PMC article.
Ribosomal RNA, the lens into life.
McDonald D, Xu Z, Hyde ER, Knight R. McDonald D, et al. RNA. 2015 Apr;21(4):692-4. doi: 10.1261/rna.050799.115. RNA. 2015. PMID: 25780194 Free PMC article. No abstract available.
Context and the human microbiome.
McDonald D, Birmingham A, Knight R. McDonald D, et al. Microbiome. 2015 Nov 4;3:52. doi: 10.1186/s40168-015-0117-2. Microbiome. 2015. PMID: 26530830 Free PMC article. Review.
1,661 results