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Items: 1 to 20 of 65

1.

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation.

Fuentes S, Barra B, Caporaso JG, Seeger M.

Appl Environ Microbiol. 2015 Nov 20;82(3):888-96. doi: 10.1128/AEM.02625-15.

PMID:
26590285
2.

Quantitative microbial ecology through stable isotope probing.

Hungate BA, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, Koch BJ, Liu CM, McHugh TA, Marks JC, Morrissey EM, Price LB.

Appl Environ Microbiol. 2015 Nov;81(21):7570-81. doi: 10.1128/AEM.02280-15. Epub 2015 Aug 21.

PMID:
26296731
3.

Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW.

Microbiome. 2015 Jul 31;3:34. doi: 10.1186/s40168-015-0098-1. eCollection 2015.

4.

The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention.

McFadden RM, Larmonier CB, Shehab KW, Midura-Kiela M, Ramalingam R, Harrison CA, Besselsen DG, Chase JH, Caporaso JG, Jobin C, Ghishan FK, Kiela PR.

Inflamm Bowel Dis. 2015 Nov;21(11):2483-94. doi: 10.1097/MIB.0000000000000522.

PMID:
26218141
5.

Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography.

Marzinelli EM, Campbell AH, Zozaya Valdes E, Vergés A, Nielsen S, Wernberg T, de Bettignies T, Bennett S, Caporaso JG, Thomas T, Steinberg PD.

Environ Microbiol. 2015 Oct;17(10):4078-88. doi: 10.1111/1462-2920.12972. Epub 2015 Aug 4.

PMID:
26148974
6.

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW.

Microbiome. 2015 May 20;3:20. doi: 10.1186/s40168-015-0081-x. eCollection 2015. Erratum in: Microbiome. 2015;3:34.

7.

Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone.

Kang DW, DiBaise JK, Ilhan ZE, Crowell MD, Rideout JR, Caporaso JG, Rittmann BE, Krajmalnik-Brown R.

Anaerobe. 2015 Jun;33:33-41. doi: 10.1016/j.anaerobe.2015.01.005. Epub 2015 Jan 21.

PMID:
25617726
8.

A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples.

Rothrock MJ Jr, Hiett KL, Gamble J, Caudill AC, Cicconi-Hogan KM, Caporaso JG.

J Vis Exp. 2014 Dec 10;(94). doi: 10.3791/52161.

PMID:
25548939
9.

Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial.

Holscher HD, Caporaso JG, Hooda S, Brulc JM, Fahey GC Jr, Swanson KS.

Am J Clin Nutr. 2015 Jan;101(1):55-64. doi: 10.3945/ajcn.114.092064. Epub 2014 Nov 12.

10.

Temporal variability is a personalized feature of the human microbiome.

Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, Leff JW, Vázquez-Baeza Y, Gonzalez A, Knight R, Dunn RR, Fierer N.

Genome Biol. 2014 Dec 3;15(12):531. doi: 10.1186/s13059-014-0531-y.

11.

Advancing the microbiome research community.

Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J; Scientists for Advancement of Microbiome Research, White O.

Cell. 2014 Oct 9;159(2):227-30. doi: 10.1016/j.cell.2014.09.022.

12.

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.

13.

Individual diet has sex-dependent effects on vertebrate gut microbiota.

Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Org E, Parks B, Lusis AJ, Knight R, Caporaso JG, Svanbäck R.

Nat Commun. 2014 Jul 29;5:4500. doi: 10.1038/ncomms5500.

14.

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
15.

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):e01371-14. doi: 10.1128/mBio.01371-14.

16.

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity.

Bolnick DI, Snowberg LK, Caporaso JG, Lauber C, Knight R, Stutz WE.

Mol Ecol. 2014 Oct;23(19):4831-45. doi: 10.1111/mec.12846. Epub 2014 Jul 31.

17.

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.

18.

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.

19.

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.

20.

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.

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