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Items: 1 to 20 of 130

1.

Practical innovations for high-throughput amplicon sequencing.

Lundberg DS, Yourstone S, Mieczkowski P, Jones CD, Dangl JL.

Nat Methods. 2013 Oct;10(10):999-1002. doi: 10.1038/nmeth.2634. Epub 2013 Sep 1.

PMID:
23995388
2.

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.

3.

Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences.

Wang X, Cai Y, Sun Y, Knight R, Mai V.

ISME J. 2012 Jul;6(7):1277-80. doi: 10.1038/ismej.2011.187. Epub 2011 Dec 15. No abstract available.

4.

Evaluating bias of illumina-based bacterial 16S rRNA gene profiles.

Kennedy K, Hall MW, Lynch MD, Moreno-Hagelsieb G, Neufeld JD.

Appl Environ Microbiol. 2014 Sep;80(18):5717-22. doi: 10.1128/AEM.01451-14. Epub 2014 Jul 7.

5.

Secondary structure improves OTU assignments of 16S rRNA gene sequences.

Schloss PD.

ISME J. 2013 Mar;7(3):457-60. doi: 10.1038/ismej.2012.102. Epub 2012 Sep 27. No abstract available.

6.

Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing.

Zakrzewski M, Goesmann A, Jaenicke S, Jünemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sørensen S, Pühler A, Schlüter A.

J Biotechnol. 2012 Apr 30;158(4):248-58. doi: 10.1016/j.jbiotec.2012.01.020. Epub 2012 Feb 8.

PMID:
22342600
7.

High throughput sequencing methods for microbiome profiling: application to food animal systems.

Highlander SK.

Anim Health Res Rev. 2012 Jun;13(1):40-53. doi: 10.1017/S1466252312000126. Review.

PMID:
22853944
8.

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.

9.

Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.

Salipante SJ, Sengupta DJ, Rosenthal C, Costa G, Spangler J, Sims EH, Jacobs MA, Miller SI, Hoogestraat DR, Cookson BT, McCoy C, Matsen FA, Shendure J, Lee CC, Harkins TT, Hoffman NG.

PLoS One. 2013 May 29;8(5):e65226. doi: 10.1371/journal.pone.0065226. Print 2013.

10.

Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2.

Zhou J, Deng Y, Luo F, He Z, Yang Y.

MBio. 2011 Jul 26;2(4). pii: e00122-11. doi: 10.1128/mBio.00122-11. Print 2011.

11.

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.

Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO.

Nucleic Acids Res. 2013 Jan 7;41(1):e1. doi: 10.1093/nar/gks808. Epub 2012 Aug 28.

12.

Data analysis for 16S microbial profiling from different benchtop sequencing platforms.

Pylro VS, Roesch LF, Morais DK, Clark IM, Hirsch PR, Tótola MR.

J Microbiol Methods. 2014 Dec;107:30-7. doi: 10.1016/j.mimet.2014.08.018. Epub 2014 Sep 3.

13.

A framework for analysis of metagenomic sequencing data.

Murat Eren A, Ferris MJ, Taylor CM.

Pac Symp Biocomput. 2011:131-41.

14.

SPINGO: a rapid species-classifier for microbial amplicon sequences.

Allard G, Ryan FJ, Jeffery IB, Claesson MJ.

BMC Bioinformatics. 2015 Oct 8;16:324. doi: 10.1186/s12859-015-0747-1.

15.

Bacterial metabarcoding by 16S rRNA gene ion torrent amplicon sequencing.

Fantini E, Gianese G, Giuliano G, Fiore A.

Methods Mol Biol. 2015;1231:77-90. doi: 10.1007/978-1-4939-1720-4_5.

PMID:
25343859
16.

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.

17.

Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons.

Siddiqui H, Nederbragt AJ, Lagesen K, Jeansson SL, Jakobsen KS.

BMC Microbiol. 2011 Nov 2;11:244. doi: 10.1186/1471-2180-11-244.

18.

V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences.

Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH.

J Microbiol Methods. 2010 Nov;83(2):250-3. doi: 10.1016/j.mimet.2010.08.008. Epub 2010 Aug 27.

PMID:
20804791
19.

Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples.

Mosher JJ, Bernberg EL, Shevchenko O, Kan J, Kaplan LA.

J Microbiol Methods. 2013 Nov;95(2):175-81. doi: 10.1016/j.mimet.2013.08.009. Epub 2013 Aug 30.

PMID:
23999276
20.

Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics.

Poretsky R, Rodriguez-R LM, Luo C, Tsementzi D, Konstantinidis KT.

PLoS One. 2014 Apr 8;9(4):e93827. doi: 10.1371/journal.pone.0093827. eCollection 2014.

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