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Bacterial, fungal, and interkingdom microbiome features of exclusively breastfeeding dyads are associated with infant age, antibiotic exposure, and birth mode.
Heisel T, Johnson AJ, Gonia S, Dillon A, Skalla E, Haapala J, Jacobs KM, Nagel E, Pierce S, Fields D, Demerath E, Knights D, Gale CA. Heisel T, et al. Among authors: knights d. Front Microbiol. 2022 Nov 17;13:1050574. doi: 10.3389/fmicb.2022.1050574. eCollection 2022. Front Microbiol. 2022. PMID: 36466688 Free PMC article.
Moving pictures of the human microbiome.
Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, Knight R. Caporaso JG, et al. Among authors: knights d. Genome Biol. 2011;12(5):R50. doi: 10.1186/gb-2011-12-5-r50. Genome Biol. 2011. PMID: 21624126 Free PMC article.
Bacterial community structures are unique and resilient in full-scale bioenergy systems.
Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, Cummings TA, Beers AR, Knight R, Angenent LT. Werner JJ, et al. Among authors: knights d. Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4158-63. doi: 10.1073/pnas.1015676108. Epub 2011 Feb 22. Proc Natl Acad Sci U S A. 2011. PMID: 21368115 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: knights d. Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823. Nat Biotechnol. 2011. PMID: 21552244 Free PMC article.
Direct sequencing of the human microbiome readily reveals community differences.
Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley ST, Ley RE, Gordon JI, Knight R. Kuczynski J, et al. Among authors: knights d. Genome Biol. 2010;11(5):210. doi: 10.1186/gb-2010-11-5-210. Epub 2010 May 5. Genome Biol. 2010. PMID: 20441597 Free PMC article. Review.
Linking long-term dietary patterns with gut microbial enterotypes.
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. Wu GD, et al. Among authors: knights d. Science. 2011 Oct 7;334(6052):105-8. doi: 10.1126/science.1208344. Epub 2011 Sep 1. Science. 2011. PMID: 21885731 Free PMC article. Clinical Trial.
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. 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.
QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. Caporaso JG, et al. Among authors: knights d. Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11. Nat Methods. 2010. PMID: 20383131 Free PMC article. No abstract available.
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