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Results: 1 to 20 of 33

1.

Meta-analyses of studies of the human microbiota.

Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, Jansson JK, Gordon JI, Knight R.

Genome Res. 2013 Oct;23(10):1704-14. doi: 10.1101/gr.151803.112. Epub 2013 Jul 16.

PMID:
23861384
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Widespread colonization of the lung by Tropheryma whipplei in HIV infection.

Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP; Lung HIV Microbiome Project.

Am J Respir Crit Care Med. 2013 May 15;187(10):1110-7. doi: 10.1164/rccm.201211-2145OC.

PMID:
23392441
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R.

Curr Protoc Microbiol. 2012 Nov;Chapter 1:Unit 1E.5.. doi: 10.1002/9780471729259.mc01e05s27.

PMID:
23184592
[PubMed - indexed for MEDLINE]
4.

Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish.

Semova I, Carten JD, Stombaugh J, Mackey LC, Knight R, Farber SA, Rawls JF.

Cell Host Microbe. 2012 Sep 13;12(3):277-88. doi: 10.1016/j.chom.2012.08.003.

PMID:
22980325
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Lake microbial communities are resilient after a whole-ecosystem disturbance.

Shade A, Read JS, Youngblut ND, Fierer N, Knight R, Kratz TK, Lottig NR, Roden EE, Stanley EH, Stombaugh J, Whitaker RJ, Wu CH, McMahon KD.

ISME J. 2012 Dec;6(12):2153-67. doi: 10.1038/ismej.2012.56. Epub 2012 Jun 28.

PMID:
22739495
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs.

Widmann J, Stombaugh J, McDonald D, Chocholousova J, Gardner P, Iyer MK, Liu Z, Lozupone CA, Quinn J, Smit S, Wikman S, Zaneveld JR, Knight R.

RNA. 2012 Jul;18(7):1319-27. doi: 10.1261/rna.032052.111. Epub 2012 May 29.

PMID:
22645380
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.

McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG.

Gigascience. 2012 Jul 12;1(1):7. doi: 10.1186/2047-217X-1-7.

PMID:
23587224
[PubMed]
Free PMC Article
8.

SitePainter: a tool for exploring biogeographical patterns.

Gonzalez A, Stombaugh J, Lauber CL, Fierer N, Knight R.

Bioinformatics. 2012 Feb 1;28(3):436-8. doi: 10.1093/bioinformatics/btr685. Epub 2011 Dec 9.

PMID:
22171330
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R.

Curr Protoc Bioinformatics. 2011 Dec;Chapter 10:Unit 10.7.. doi: 10.1002/0471250953.bi1007s36.

PMID:
22161565
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Microbial biogeography of public restroom surfaces.

Flores GE, Bates ST, Knights D, Lauber CL, Stombaugh J, Knight R, Fierer N.

PLoS One. 2011;6(11):e28132. doi: 10.1371/journal.pone.0028132. Epub 2011 Nov 23.

PMID:
22132229
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Comprehensive survey and geometric classification of base triples in RNA structures.

Abu Almakarem AS, Petrov AI, Stombaugh J, Zirbel CL, Leontis NB.

Nucleic Acids Res. 2012 Feb;40(4):1407-23. doi: 10.1093/nar/gkr810. Epub 2011 Nov 3.

PMID:
22053086
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.

Pirrung M, Kennedy R, Caporaso JG, Stombaugh J, Wendel D, Knight R.

Bioinformatics. 2011 Nov 1;27(21):3067-9. doi: 10.1093/bioinformatics/btr517. Epub 2011 Sep 8.

PMID:
21903626
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation.

Zaneveld JR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R.

Trends Microbiol. 2011 Oct;19(10):472-82. doi: 10.1016/j.tim.2011.07.006. Epub 2011 Aug 25. Review.

PMID:
21872475
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Meeting report of the RNA Ontology Consortium January 8-9, 2011.

Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, Laederach A.

Stand Genomic Sci. 2011 Apr 29;4(2):252-6. doi: 10.4056/sigs.1724282.

PMID:
21677862
[PubMed]
Free PMC Article
15.

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.

Genome Biol. 2011;12(5):R50. doi: 10.1186/gb-2011-12-5-r50.

PMID:
21624126
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Sharing and archiving nucleic acid structure mapping data.

Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, Zirbel CL, Laederach A.

RNA. 2011 Jul;17(7):1204-12. doi: 10.1261/rna.2753211. Epub 2011 May 24.

PMID:
21610212
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Responses of gut microbiota to diet composition and weight loss in lean and obese mice.

Ravussin Y, Koren O, Spor A, LeDuc C, Gutman R, Stombaugh J, Knight R, Ley RE, Leibel RL.

Obesity (Silver Spring). 2012 Apr;20(4):738-47. doi: 10.1038/oby.2011.111. Epub 2011 May 19.

PMID:
21593810
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823.

PMID:
21552244
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Boulder ALignment Editor (ALE): a web-based RNA alignment tool.

Stombaugh J, Widmann J, McDonald D, Knight R.

Bioinformatics. 2011 Jun 15;27(12):1706-7. doi: 10.1093/bioinformatics/btr258. Epub 2011 May 5.

PMID:
21546392
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

The mind-body-microbial continuum.

Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R.

Dialogues Clin Neurosci. 2011;13(1):55-62.

PMID:
21485746
[PubMed - indexed for MEDLINE]
Free PMC Article

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