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Results: 1 to 20 of 137

1.

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.

PeerJ. 2014 Aug 21;2:e545. doi: 10.7717/peerj.545. eCollection 2014.

PMID:
25177538
[PubMed]
Free PMC Article
2.

Conducting a microbiome study.

Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE.

Cell. 2014 Jul 17;158(2):250-62. doi: 10.1016/j.cell.2014.06.037.

PMID:
25036628
[PubMed - in process]
3.

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.

Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R.

Front Microbiol. 2014 Jun 19;5:298. doi: 10.3389/fmicb.2014.00298. eCollection 2014.

PMID:
24995004
[PubMed]
Free PMC Article
4.

Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples.

Green HC, Haugland RA, Varma M, Millen HT, Borchardt MA, Field KG, Walters WA, Knight R, Sivaganesan M, Kelty CA, Shanks OC.

Appl Environ Microbiol. 2014 May;80(10):3086-94. doi: 10.1128/AEM.04137-13. Epub 2014 Mar 7.

PMID:
24610857
[PubMed - in process]
5.

Technology and techniques for microbial ecology via DNA sequencing.

Walters WA, Knight R.

Ann Am Thorac Soc. 2014 Jan;11 Suppl 1:S16-20. doi: 10.1513/AnnalsATS.201306-160MG.

PMID:
24437399
[PubMed - in process]
6.

Gut microbiota from twins discordant for obesity modulate metabolism in mice.

Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI.

Science. 2013 Sep 6;341(6150):1241214. doi: 10.1126/science.1241214.

PMID:
24009397
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

From molecules to dynamic biological communities.

McDonald D, Vázquez-Baeza Y, Walters WA, Caporaso JG, Knight R.

Biol Philos. 2013 Mar;28(2):241-259. Epub 2013 Feb 5.

PMID:
23483075
[PubMed]
Free PMC Article
8.

Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.

Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, Janssen PH.

PLoS One. 2013;8(2):e47879. doi: 10.1371/journal.pone.0047879. Epub 2013 Feb 8.

PMID:
23408926
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Global biogeography of highly diverse protistan communities in soil.

Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW, Knight R, Fierer N.

ISME J. 2013 Mar;7(3):652-9. doi: 10.1038/ismej.2012.147. Epub 2012 Dec 13.

PMID:
23235291
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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]
11.

Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle.

Carey HV, Walters WA, Knight R.

Am J Physiol Regul Integr Comp Physiol. 2013 Jan 1;304(1):R33-42. doi: 10.1152/ajpregu.00387.2012. Epub 2012 Nov 14.

PMID:
23152108
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

ISME J. 2013 Mar;7(3):461-4. doi: 10.1038/ismej.2012.123. Epub 2012 Oct 25. No abstract available.

PMID:
23096404
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood.

Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, Knight R, Krauter KS.

Genome Res. 2012 Nov;22(11):2146-52. doi: 10.1101/gr.140608.112. Epub 2012 Oct 12.

PMID:
23064750
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome.

Zupancic ML, Cantarel BL, Liu Z, Drabek EF, Ryan KA, Cirimotich S, Jones C, Knight R, Walters WA, Knights D, Mongodin EF, Horenstein RB, Mitchell BD, Steinle N, Snitker S, Shuldiner AR, Fraser CM.

PLoS One. 2012;7(8):e43052. doi: 10.1371/journal.pone.0043052. Epub 2012 Aug 15.

PMID:
22905200
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice.

Carvalho FA, Koren O, Goodrich JK, Johansson ME, Nalbantoglu I, Aitken JD, Su Y, Chassaing B, Walters WA, González A, Clemente JC, Cullender TC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, Knight R, Ley RE, Gewirtz AT.

Cell Host Microbe. 2012 Aug 16;12(2):139-52. doi: 10.1016/j.chom.2012.07.004. Epub 2012 Aug 2.

PMID:
22863420
[PubMed - indexed for MEDLINE]
Free Article
16.

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R.

ISME J. 2012 Aug;6(8):1621-4. doi: 10.1038/ismej.2012.8. Epub 2012 Mar 8.

PMID:
22402401
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The under-recognized dominance of Verrucomicrobia in soil bacterial communities.

Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, Knight R, Fierer N.

Soil Biol Biochem. 2011 Jul;43(7):1450-1455.

PMID:
22267877
[PubMed]
Free PMC Article
18.

Experimental and analytical tools for studying the human microbiome.

Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R.

Nat Rev Genet. 2011 Dec 16;13(1):47-58. doi: 10.1038/nrg3129. Review.

PMID:
22179717
[PubMed - indexed for MEDLINE]
19.

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
20.

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.

Science. 2011 Oct 7;334(6052):105-8. doi: 10.1126/science.1208344. Epub 2011 Sep 1.

PMID:
21885731
[PubMed - indexed for MEDLINE]
Free PMC Article

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