Publications
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Biphasic assembly of the murine intestinal microbiota during early development.
Pantoja-Feliciano IG,
Clemente JC, Costello EK, Perez ME, Blaser MJ, Knight R, Dominguez-Bello MG.
ISME J.
2013
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Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents.
Blaser MJ,
Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R.
ISME J.
2013;
7
(1):
85-95
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Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States.
Lin A,
Bik EM, Costello EK, Dethlefsen L, Haque R, Relman DA, Singh U.
PLoS One.
2013;
8
(1):
e53838
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Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization.
Sharon I,
Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF.
Genome Res.
2013;
23
(1):
111-20
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The application of ecological theory toward an understanding of the human microbiome.
Costello EK,
Stagaman K, Dethlefsen L, Bohannan BJ, Relman DA.
Science.
2012;
336
(6086):
1255-62
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Global patterns in the biogeography of bacterial taxa.
Nemergut DR,
Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK, Fierer N, Townsend AR, Cleveland CC, Stanish L, Knight R.
Environ Microbiol.
2011;
13
(1):
135-44
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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;
29
(5):
415-20
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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
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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, Knight R, Fierer N.
Appl Environ Microbiol.
2011;
77
(18):
6350-6
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Strain-resolved community genomic analysis of gut microbial colonization in a premature infant.
Morowitz MJ,
Denef VJ, Costello EK, Thomas BC, Poroyko V, Relman DA, Banfield JF.
Proc Natl Acad Sci U S A.
2011;
108
(3):
1128-33
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Supervised classification of human microbiota.
Knights D,
Costello EK, Knight R.
FEMS Microbiol Rev.
2011;
35
(2):
343-59
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Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.
Dominguez-Bello MG,
Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R.
Proc Natl Acad Sci U S A.
2010;
107
(26):
11971-5
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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.
Genome Biol.
2010;
11
(5):
210
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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;
107
(14):
6477-81
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Postprandial remodeling of the gut microbiota in Burmese pythons.
Costello EK,
Gordon JI, Secor SM, Knight R.
ISME J.
2010;
4
(11):
1375-85
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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;
7
(5):
335-6
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The bacterial microbiota in the oral mucosa of rural Amerindians.
Contreras M,
Costello EK, Hidalgo G, Magris M, Knight R, Dominguez-Bello MG.
Microbiology.
2010;
156
(Pt 11):
3282-7
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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;
326
(5960):
1694-7
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Environmental DNA sequencing primers for eutardigrades and bdelloid rotifers.
Robeson MS,
Costello EK, Freeman KR, Whiting J, Adams B, Martin AP, Schmidt SK.
BMC Ecol.
2009:
9
25
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Fumarole-supported islands of biodiversity within a hyperarid, high-elevation landscape on Socompa Volcano, Puna de Atacama, Andes.
Costello EK,
Halloy SR, Reed SC, Sowell P, Schmidt SK.
Appl Environ Microbiol.
2009;
75
(3):
735-47
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Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation.
Crawford PA,
Crowley JR, Sambandam N, Muegge BD, Costello EK, Hamady M, Knight R, Gordon JI.
Proc Natl Acad Sci U S A.
2009;
106
(27):
11276-81
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Soil CO2 flux and photoautotrophic community composition in high-elevation, 'barren' soil.
Freeman KR,
Pescador MY, Reed SC, Costello EK, Robeson MS, Schmidt SK.
Environ Microbiol.
2009;
11
(3):
674-86
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The earliest stages of ecosystem succession in high-elevation (5000 metres above sea level), recently deglaciated soils.
Schmidt SK,
Reed SC, Nemergut DR, Grandy AS, Cleveland CC, Weintraub MN, Hill AW, Costello EK, Meyer AF, Neff JC, Martin AM.
Proc Biol Sci.
2008;
275
(1653):
2793-802
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Biogeochemical consequences of rapid microbial turnover and seasonal succession in soil.
Schmidt SK,
Costello EK, Nemergut DR, Cleveland CC, Reed SC, Weintraub MN, Meyer AF, Martin AM.
Ecology.
2007;
88
(6):
1379-85
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Microbial diversity in alpine tundra wet meadow soil: novel Chloroflexi from a cold, water-saturated environment.
Costello EK,
Schmidt SK.
Environ Microbiol.
2006;
8
(8):
1471-86
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Structure and function of alpine and arctic soil microbial communities.
Nemergut DR,
Costello EK, Meyer AF, Pescador MY, Weintraub MN, Schmidt SK.
Res Microbiol.
2005;
156
(7):
775-84
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The rate and pattern of cladogenesis in microbes.
Martin AP,
Costello EK, Meyer AF, Nemergut DR, Schmidt SK.
Evolution.
2004;
58
(5):
946-55
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