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Results: 1 to 20 of 51

1.

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):250-262. doi: 10.1016/j.cell.2014.06.037. Review.

PMID:
25036628
[PubMed - as supplied by publisher]
2.

Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity.

Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA.

MBio. 2014 Jul 15;5(4). pii: e01371-14. doi: 10.1128/mBio.01371-14.

PMID:
25028427
[PubMed - in process]
Free Article
3.

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch).

Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, Caporaso JG, Svanbäck R.

Ecol Lett. 2014 Aug;17(8):979-87. doi: 10.1111/ele.12301. Epub 2014 May 22.

PMID:
24847735
[PubMed - in process]
4.

The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes.

Sahl JW, Caporaso JG, Rasko DA, Keim P.

PeerJ. 2014 Apr 1;2:e332. doi: 10.7717/peerj.332. eCollection 2014.

PMID:
24749011
[PubMed]
Free PMC Article
5.

The personal human oral microbiome obscures the effects of treatment on periodontal disease.

Schwarzberg K, Le R, Bharti B, Lindsay S, Casaburi G, Salvatore F, Saber MH, Alonaizan F, Slots J, Gottlieb RA, Caporaso JG, Kelley ST.

PLoS One. 2014 Jan 29;9(1):e86708. doi: 10.1371/journal.pone.0086708. eCollection 2014.

PMID:
24489772
[PubMed - in process]
Free PMC Article
6.

Advancing our understanding of the human microbiome using QIIME.

Navas-Molina JA, Peralta-Sánchez JM, González A, McMurdie PJ, Vázquez-Baeza Y, Xu Z, Ursell LK, Lauber C, Zhou H, Song SJ, Huntley J, Ackermann GL, Berg-Lyons D, Holmes S, Caporaso JG, Knight R.

Methods Enzymol. 2013;531:371-444. doi: 10.1016/B978-0-12-407863-5.00019-8.

PMID:
24060131
[PubMed - indexed for MEDLINE]
7.

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C.

Nat Biotechnol. 2013 Sep;31(9):814-21. doi: 10.1038/nbt.2676. Epub 2013 Aug 25.

PMID:
23975157
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Meeting report: fungal its workshop (october 2012).

Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Parfrey LW, Stajich JE.

Stand Genomic Sci. 2013 Apr 15;8(1):118-23. doi: 10.4056/sigs.3737409. eCollection 2013 Apr 15.

PMID:
23961317
[PubMed]
Free PMC Article
9.

The Ecology of Microbial Communities Associated with Macrocystis pyrifera.

Michelou VK, Caporaso JG, Knight R, Palumbi SR.

PLoS One. 2013 Jun 19;8(6):e67480. Print 2013.

PMID:
23840715
[PubMed - as supplied by publisher]
Free PMC Article
10.

Cohabiting family members share microbiota with one another and with their dogs.

Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R.

Elife (Cambridge). 2013 Apr 16;2:e00458. doi: 10.7554/eLife.00458.

PMID:
23599893
[PubMed]
Free PMC Article
11.

A meta-analysis of changes in bacterial and archaeal communities with time.

Shade A, Caporaso JG, Handelsman J, Knight R, Fierer N.

ISME J. 2013 Aug;7(8):1493-506. doi: 10.1038/ismej.2013.54. Epub 2013 Apr 11.

PMID:
23575374
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Evidence for a persistent microbial seed bank throughout the global ocean.

Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, Gilbert JA.

Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4651-5. doi: 10.1073/pnas.1217767110. Epub 2013 Mar 4.

PMID:
23487761
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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
14.

Bacterial diversity in two Neonatal Intensive Care Units (NICUs).

Hewitt KM, Mannino FL, Gonzalez A, Chase JH, Caporaso JG, Knight R, Kelley ST.

PLoS One. 2013;8(1):e54703. doi: 10.1371/journal.pone.0054703. Epub 2013 Jan 23.

PMID:
23372757
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DH, Caporaso JG.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21390-5. doi: 10.1073/pnas.1215210110. Epub 2012 Dec 10.

PMID:
23236140
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.

Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG.

Nat Methods. 2013 Jan;10(1):57-9. doi: 10.1038/nmeth.2276. Epub 2012 Dec 2.

PMID:
23202435
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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]
18.

Diversity, distribution and sources of bacteria in residential kitchens.

Flores GE, Bates ST, Caporaso JG, Lauber CL, Leff JW, Knight R, Fierer N.

Environ Microbiol. 2013 Feb;15(2):588-96. doi: 10.1111/1462-2920.12036. Epub 2012 Nov 22.

PMID:
23171378
[PubMed - indexed for MEDLINE]
19.

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
20.

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

Harris JK, Caporaso JG, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR.

ISME J. 2013 Jan;7(1):50-60. doi: 10.1038/ismej.2012.79. Epub 2012 Jul 26.

PMID:
22832344
[PubMed - indexed for MEDLINE]
Free PMC Article

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