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Sources of bacteria in outdoor air across cities in the midwestern United States.

Bowers RM, Sullivan AP, Costello EK, Collett JL Jr, Knight R, Fierer N.

Appl Environ Microbiol. 2011 Sep;77(18):6350-6. doi: 10.1128/AEM.05498-11.


Bayesian community-wide culture-independent microbial source tracking.

Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST.

Nat Methods. 2011 Jul 17;8(9):761-3. doi: 10.1038/nmeth.1650.


The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens.

Dong Q, Nelson DE, Toh E, Diao L, Gao X, Fortenberry JD, Van der Pol B.

PLoS One. 2011;6(5):e19709. doi: 10.1371/journal.pone.0019709.


The skin microbiome.

Grice EA, Segre JA.

Nat Rev Microbiol. 2011 Apr;9(4):244-53. doi: 10.1038/nrmicro2537. Review. Erratum in: Nat Rev Microbiol. 2011 Aug;9(8):626.


The vaginal microbiome: new information about genital tract flora using molecular based techniques.

Lamont RF, Sobel JD, Akins RA, Hassan SS, Chaiworapongsa T, Kusanovic JP, Romero R.

BJOG. 2011 Apr;118(5):533-49. doi: 10.1111/j.1471-0528.2010.02840.x. Review.


Microbial contamination in kitchens and bathrooms of rural Cambodian village households.

Sinclair RG, Gerba CP.

Lett Appl Microbiol. 2011 Feb;52(2):144-9. doi: 10.1111/j.1472-765X.2010.02978.x.


Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth.

Zhou X, Brotman RM, Gajer P, Abdo Z, Schüette U, Ma S, Ravel J, Forney LJ.

Infect Dis Obstet Gynecol. 2010;2010:737425. doi: 10.1155/2010/737425. Review.


Impact of prescribed cleaning and disinfectant use on microbial contamination in the home.

Medrano-Félix A, Martínez C, Castro-del Campo N, León-Félix J, Peraza-Garay F, Gerba CP, Chaidez C.

J Appl Microbiol. 2011 Feb;110(2):463-71. doi: 10.1111/j.1365-2672.2010.04901.x.


Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection.

Nelson DE, Van Der Pol B, Dong Q, Revanna KV, Fan B, Easwaran S, Sodergren E, Weinstock GM, Diao L, Fortenberry JD.

PLoS One. 2010 Nov 24;5(11):e14116. doi: 10.1371/journal.pone.0014116.


Search and clustering orders of magnitude faster than BLAST.

Edgar RC.

Bioinformatics. 2010 Oct 1;26(19):2460-1. doi: 10.1093/bioinformatics/btq461.


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.

Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. No abstract available.


Forensic identification using skin bacterial communities.

Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R.

Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6477-81. doi: 10.1073/pnas.1000162107.


PyNAST: a flexible tool for aligning sequences to a template alignment.

Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R.

Bioinformatics. 2010 Jan 15;26(2):266-7. doi: 10.1093/bioinformatics/btp636.


Bacterial community variation in human body habitats across space and time.

Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R.

Science. 2009 Dec 18;326(5960):1694-7. doi: 10.1126/science.1177486.


Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine.

Claesson MJ, O'Sullivan O, Wang Q, Nikkilä J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O'Toole PW.

PLoS One. 2009 Aug 20;4(8):e6669. doi: 10.1371/journal.pone.0006669.


Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale.

Lauber CL, Hamady M, Knight R, Fierer N.

Appl Environ Microbiol. 2009 Aug;75(15):5111-20. doi: 10.1128/AEM.00335-09.


FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.

Price MN, Dehal PS, Arkin AP.

Mol Biol Evol. 2009 Jul;26(7):1641-50. doi: 10.1093/molbev/msp077.


Investigation of bacterial pathogens on 70 frequently used environmental surfaces in a large urban U.S. university.

Brooke JS, Annand JW, Hammer A, Dembkowski K, Shulman ST.

J Environ Health. 2009 Jan-Feb;71(6):17-22.


A core gut microbiome in obese and lean twins.

Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI.

Nature. 2009 Jan 22;457(7228):480-4. doi: 10.1038/nature07540.

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