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Items: 1 to 20 of 148

1.

High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.

Amir A, Zeisel A, Zuk O, Elgart M, Stern S, Shamir O, Turnbaugh PJ, Soen Y, Shental N.

Nucleic Acids Res. 2013 Dec;41(22):e205. doi: 10.1093/nar/gkt1070. Epub 2013 Nov 7.

2.

Rethinking microbial diversity analysis in the high throughput sequencing era.

Lemos LN, Fulthorpe RR, Triplett EW, Roesch LF.

J Microbiol Methods. 2011 Jul;86(1):42-51. doi: 10.1016/j.mimet.2011.03.014. Epub 2011 Mar 30.

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.

Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions.

Maughan H, Wang PW, Diaz Caballero J, Fung P, Gong Y, Donaldson SL, Yuan L, Keshavjee S, Zhang Y, Yau YC, Waters VJ, Tullis DE, Hwang DM, Guttman DS.

PLoS One. 2012;7(10):e45791. doi: 10.1371/journal.pone.0045791. Epub 2012 Oct 2.

5.

Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.

Ong SH, Kukkillaya VU, Wilm A, Lay C, Ho EX, Low L, Hibberd ML, Nagarajan N.

PLoS One. 2013 Apr 8;8(4):e60811. doi: 10.1371/journal.pone.0060811. Print 2013.

6.

Enhanced microbial diversity in the saliva microbiome induced by short-term probiotic intake revealed by 16S rRNA sequencing on the IonTorrent PGM platform.

Dassi E, Ballarini A, Covello G; HTM-CMB2013, Quattrone A, Jousson O, De Sanctis V, Bertorelli R, Denti MA, Segata N.

J Biotechnol. 2014 Nov 20;190:30-9. doi: 10.1016/j.jbiotec.2014.03.024. Epub 2014 Mar 23.

PMID:
24670254
7.

Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis.

Wu L, Wen C, Qin Y, Yin H, Tu Q, Van Nostrand JD, Yuan T, Yuan M, Deng Y, Zhou J.

BMC Microbiol. 2015 Jun 19;15:125. doi: 10.1186/s12866-015-0450-4.

8.

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.

9.

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.

10.

Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys.

Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J.

PLoS One. 2014 Apr 10;9(4):e94249. doi: 10.1371/journal.pone.0094249. eCollection 2014.

11.

Low sequencing efforts bias analyses of shared taxa in microbial communities.

Lemos LN, Fulthorpe RR, Roesch LF.

Folia Microbiol (Praha). 2012 Sep;57(5):409-13. doi: 10.1007/s12223-012-0155-0. Epub 2012 May 5.

PMID:
22562492
12.

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.

13.

[Strategy of selecting 16S rRNA hypervariable regions for metagenome-phylogenetic marker genes based analysis].

Zhang JY, Zhu BC, Xu C, Ding X, Li JF, Zhang XG, Lu ZH.

Ying Yong Sheng Tai Xue Bao. 2015 Nov;26(11):3545-53. Chinese.

PMID:
26915214
14.

A novel method for determining microflora composition using dynamic phylogenetic analysis of 16S ribosomal RNA deep sequencing data.

Chan ER, Hester J, Kalady M, Xiao H, Li X, Serre D.

Genomics. 2011 Oct;98(4):253-9. doi: 10.1016/j.ygeno.2011.04.002. Epub 2011 Apr 15.

15.

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C.

Nat Biotechnol. 2013 Sep;31(9):814-21. doi: 10.1038/nbt.2676. Epub 2013 Aug 25.

16.

Integrating high-throughput pyrosequencing and quantitative real-time PCR to analyze complex microbial communities.

Zhang H, Parameswaran P, Badalamenti J, Rittmann BE, Krajmalnik-Brown R.

Methods Mol Biol. 2011;733:107-28. doi: 10.1007/978-1-61779-089-8_8.

PMID:
21431766
17.

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering.

Franzén O, Hu J, Bao X, Itzkowitz SH, Peter I, Bashir A.

Microbiome. 2015 Oct 5;3:43. doi: 10.1186/s40168-015-0105-6. Erratum in: Microbiome. 2015;3:57.

18.

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers.

Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, A Weitz D, Pitkänen LK, Vigneault F, Juhani Virta MP, Alm EJ.

ISME J. 2016 Feb;10(2):427-36. doi: 10.1038/ismej.2015.124. Epub 2015 Sep 22.

19.

Bacterial flora-typing with targeted, chip-based Pyrosequencing.

Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, Pullen KM, El-Sayed YY, Taslimi MM, Batzoglou S, Ronaghi M.

BMC Microbiol. 2007 Nov 30;7:108.

20.

Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer.

Benítez-Páez A, Portune KJ, Sanz Y.

Gigascience. 2016 Jan 28;5:4. doi: 10.1186/s13742-016-0111-z. eCollection 2016.

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