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GABA-modulating bacteria of the human gut microbiota.
Strandwitz P, Kim KH, Terekhova D, Liu JK, Sharma A, Levering J, McDonald D, Dietrich D, Ramadhar TR, Lekbua A, Mroue N, Liston C, Stewart EJ, Dubin MJ, Zengler K, Knight R, Gilbert JA, Clardy J, Lewis K. Strandwitz P, et al. Among authors: mcdonald d. Nat Microbiol. 2019 Mar;4(3):396-403. doi: 10.1038/s41564-018-0307-3. Epub 2018 Dec 10. Nat Microbiol. 2019. PMID: 30531975 Free PMC article.
Boulder ALignment Editor (ALE): a web-based RNA alignment tool.
Stombaugh J, Widmann J, McDonald D, Knight R. Stombaugh J, et al. Among authors: mcdonald d. Bioinformatics. 2011 Jun 15;27(12):1706-7. doi: 10.1093/bioinformatics/btr258. Epub 2011 May 5. Bioinformatics. 2011. PMID: 21546392 Free PMC article.
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.
The treatment-naive microbiome in new-onset Crohn's disease.
Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ. Gevers D, et al. Among authors: mcdonald d. Cell Host Microbe. 2014 Mar 12;15(3):382-392. doi: 10.1016/j.chom.2014.02.005. Cell Host Microbe. 2014. PMID: 24629344 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.
1,663 results