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Items: 1 to 20 of 30

1.

Differentiation of mixed lactic acid bacteria communities in beverage fermentations using targeted terminal restriction fragment length polymorphism.

Bokulich NA, Mills DA.

Food Microbiol. 2012 Aug;31(1):126-32. doi: 10.1016/j.fm.2012.02.007. Epub 2012 Feb 21.

PMID:
22475950
2.

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences.

Soergel DA, Dey N, Knight R, Brenner SE.

ISME J. 2012 Jul;6(7):1440-4. doi: 10.1038/ismej.2011.208. Epub 2012 Jan 12.

3.

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys.

Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT.

ISME J. 2012 Jul;6(7):1273-6. doi: 10.1038/ismej.2011.186. Epub 2011 Dec 15. No abstract available.

4.

Bacterial species associated with sound and Botrytis-infected grapes from a Greek vineyard.

Nisiotou AA, Rantsiou K, Iliopoulos V, Cocolin L, Nychas GJ.

Int J Food Microbiol. 2011 Feb 28;145(2-3):432-6. doi: 10.1016/j.ijfoodmicro.2011.01.017. Epub 2011 Jan 21.

PMID:
21315469
5.

Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects.

Martínez I, Kim J, Duffy PR, Schlegel VL, Walter J.

PLoS One. 2010 Nov 29;5(11):e15046. doi: 10.1371/journal.pone.0015046.

6.

Search and clustering orders of magnitude faster than BLAST.

Edgar RC.

Bioinformatics. 2010 Oct 1;26(19):2460-1. doi: 10.1093/bioinformatics/btq461. Epub 2010 Aug 12.

PMID:
20709691
7.

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4516-22. doi: 10.1073/pnas.1000080107. Epub 2010 Jun 3.

8.

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. Epub 2010 Apr 11. No abstract available.

9.

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.

Kunin V, Engelbrektson A, Ochman H, Hugenholtz P.

Environ Microbiol. 2010 Jan;12(1):118-23. doi: 10.1111/j.1462-2920.2009.02051.x. Epub 2009 Aug 27.

PMID:
19725865
10.

Accurate determination of microbial diversity from 454 pyrosequencing data.

Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT.

Nat Methods. 2009 Sep;6(9):639-41. doi: 10.1038/nmeth.1361. Epub 2009 Aug 9.

PMID:
19668203
11.

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.

Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM.

Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5. doi: 10.1093/nar/gkn879. Epub 2008 Nov 12.

12.

Effect of oenological practices on microbial populations using culture-independent techniques.

Andorrà I, Landi S, Mas A, Guillamón JM, Esteve-Zarzoso B.

Food Microbiol. 2008 Oct;25(7):849-56. doi: 10.1016/j.fm.2008.05.005. Epub 2008 May 23.

PMID:
18721672
13.

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R.

Nat Methods. 2008 Mar;5(3):235-7. doi: 10.1038/nmeth.1184. Epub 2008 Feb 10.

14.

Short pyrosequencing reads suffice for accurate microbial community analysis.

Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R.

Nucleic Acids Res. 2007;35(18):e120. Epub 2007 Sep 18.

15.

Yeast community structures and dynamics in healthy and Botrytis-affected grape must fermentations.

Nisiotou AA, Spiropoulos AE, Nychas GJ.

Appl Environ Microbiol. 2007 Nov;73(21):6705-13. Epub 2007 Aug 31.

16.

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.

Wang Q, Garrity GM, Tiedje JM, Cole JR.

Appl Environ Microbiol. 2007 Aug;73(16):5261-7. Epub 2007 Jun 22.

17.

MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes.

Shyu C, Soule T, Bent SJ, Foster JA, Forney LJ.

Microb Ecol. 2007 May;53(4):562-70. Epub 2007 Apr 4.

PMID:
17406775
18.

Yeast populations residing on healthy or botrytis-infected grapes from a vineyard in Attica, Greece.

Nisiotou AA, Nychas GJ.

Appl Environ Microbiol. 2007 Apr;73(8):2765-8. Epub 2007 Feb 9.

19.

Inventory and monitoring of wine microbial consortia.

Renouf V, Claisse O, Lonvaud-Funel A.

Appl Microbiol Biotechnol. 2007 May;75(1):149-64. Epub 2007 Jan 19.

PMID:
17235561
20.

The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.

Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM.

Nucleic Acids Res. 2007 Jan;35(Database issue):D169-72. Epub 2006 Nov 7.

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