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Results: 1 to 20 of 104

1.

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data.

Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF.

Genome Biol. 2011;12(5):R44. doi: 10.1186/gb-2011-12-5-r44. Epub 2011 May 19.

PMID:
21595876
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Assembling full-length rRNA genes from short-read metagenomic sequence datasets using EMIRGE.

Miller CS.

Methods Enzymol. 2013;531:333-52. doi: 10.1016/B978-0-12-407863-5.00017-4.

PMID:
24060129
[PubMed - indexed for MEDLINE]
3.

Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs.

Mizrahi-Man O, Davenport ER, Gilad Y.

PLoS One. 2013;8(1):e53608. doi: 10.1371/journal.pone.0053608. Epub 2013 Jan 7.

PMID:
23308262
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.

Kembel SW, Wu M, Eisen JA, Green JL.

PLoS Comput Biol. 2012;8(10):e1002743. doi: 10.1371/journal.pcbi.1002743. Epub 2012 Oct 25.

PMID:
23133348
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain.

Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MC.

Microbiology. 2012 Apr;158(Pt 4):1005-15. doi: 10.1099/mic.0.055459-0. Epub 2012 Jan 27.

PMID:
22282518
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

CLUSTOM: a novel method for clustering 16S rRNA next generation sequences by overlap minimization.

Hwang K, Oh J, Kim TK, Kim BK, Yu DS, Hou BK, Caetano-Anollés G, Hong SG, Kim KM.

PLoS One. 2013 May 1;8(5):e62623. doi: 10.1371/journal.pone.0062623. Print 2013. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/bb3baaad-6b58-41a0-96cc-7bdc819de411.

PMID:
23650520
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers.

Liu Z, DeSantis TZ, Andersen GL, Knight R.

Nucleic Acids Res. 2008 Oct;36(18):e120. doi: 10.1093/nar/gkn491. Epub 2008 Aug 22.

PMID:
18723574
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies.

Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF, Kjelleberg S.

Appl Environ Microbiol. 2007 Jan;73(1):278-88. Epub 2006 Oct 27.

PMID:
17071787
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Novel archaea and bacteria dominate stable microbial communities in North America's Largest Hot Spring.

Wilson MS, Siering PL, White CL, Hauser ME, Bartles AN.

Microb Ecol. 2008 Aug;56(2):292-305. Epub 2007 Dec 13.

PMID:
18080156
[PubMed - indexed for MEDLINE]
10.

VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences.

Mori H, Maruyama F, Kurokawa K.

BMC Bioinformatics. 2010 Jun 18;11:332. doi: 10.1186/1471-2105-11-332.

PMID:
20565810
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Peptide markers of aminoacyl tRNA synthetases facilitate taxa counting in metagenomic data.

Persi E, Weingart U, Freilich S, Horn D.

BMC Genomics. 2012 Feb 10;13:65. doi: 10.1186/1471-2164-13-65.

PMID:
22325056
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Diversity of bacteria and fungi in aerosols during screening in a green waste composting plant.

Bru-Adan V, Wéry N, Moletta-Denat M, Boiron P, Delgènes JP, Godon JJ.

Curr Microbiol. 2009 Sep;59(3):326-35. doi: 10.1007/s00284-009-9438-3. Epub 2009 Jun 16.

PMID:
19533230
[PubMed - indexed for MEDLINE]
13.

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.

Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, McDonald IR, Cary SC.

PLoS One. 2012;7(9):e44224. doi: 10.1371/journal.pone.0044224. Epub 2012 Sep 6.

PMID:
22970184
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

In-depth characterization via complementing culture-independent approaches of the microbial community in an acidic hot spring of the Colombian Andes.

Bohorquez LC, Delgado-Serrano L, López G, Osorio-Forero C, Klepac-Ceraj V, Kolter R, Junca H, Baena S, Zambrano MM.

Microb Ecol. 2012 Jan;63(1):103-15. doi: 10.1007/s00248-011-9943-3. Epub 2011 Sep 27. Erratum in: Microb Ecol. 2012 Jan;63(1):238.

PMID:
21947461
[PubMed - indexed for MEDLINE]
15.

Novel high-rank phylogenetic lineages within a sulfur spring (Zodletone Spring, Oklahoma), revealed using a combined pyrosequencing-sanger approach.

Youssef N, Steidley BL, Elshahed MS.

Appl Environ Microbiol. 2012 Apr;78(8):2677-88. doi: 10.1128/AEM.00002-12. Epub 2012 Feb 3.

PMID:
22307312
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Comparative microbial diversity analyses of modern marine thrombolitic mats by barcoded pyrosequencing.

Mobberley JM, Ortega MC, Foster JS.

Environ Microbiol. 2012 Jan;14(1):82-100. doi: 10.1111/j.1462-2920.2011.02509.x. Epub 2011 Jun 10.

PMID:
21658172
[PubMed - indexed for MEDLINE]
17.

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.

PMID:
17881377
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.

Ghyselinck J, Pfeiffer S, Heylen K, Sessitsch A, De Vos P.

PLoS One. 2013 Aug 19;8(8):e71360. doi: 10.1371/journal.pone.0071360. eCollection 2013.

PMID:
23977026
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys.

Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, Elshahed MS.

Appl Environ Microbiol. 2009 Aug;75(16):5227-36. doi: 10.1128/AEM.00592-09. Epub 2009 Jun 26.

PMID:
19561178
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

OTU analysis using metagenomic shotgun sequencing data.

Hao X, Chen T.

PLoS One. 2012;7(11):e49785. doi: 10.1371/journal.pone.0049785. Epub 2012 Nov 26.

PMID:
23189163
[PubMed - indexed for MEDLINE]
Free PMC Article

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