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Items: 1 to 20 of 256

1.

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.

Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG.

Environ Microbiol. 2014 Sep;16(9):2659-71. doi: 10.1111/1462-2920.12250. Epub 2013 Sep 18.

PMID:
24102695
2.

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.

3.

Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform.

Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, Allcock R, O'Donnell A.

J Microbiol Methods. 2012 Oct;91(1):80-8. doi: 10.1016/j.mimet.2012.07.008. Epub 2012 Jul 29.

PMID:
22849830
4.

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
5.

Design and experimental application of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify eukaryotic rRNA genes.

Mori H, Maruyama F, Kato H, Toyoda A, Dozono A, Ohtsubo Y, Nagata Y, Fujiyama A, Tsuda M, Kurokawa K.

DNA Res. 2014;21(2):217-27. doi: 10.1093/dnares/dst052. Epub 2013 Nov 25.

6.

PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets.

Pinto AJ, Raskin L.

PLoS One. 2012;7(8):e43093. doi: 10.1371/journal.pone.0043093. Epub 2012 Aug 15.

7.

The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation.

Gilbert JA, Field D, Swift P, Thomas S, Cummings D, Temperton B, Weynberg K, Huse S, Hughes M, Joint I, Somerfield PJ, Mühling M.

PLoS One. 2010 Nov 29;5(11):e15545. doi: 10.1371/journal.pone.0015545.

8.

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.

9.

Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.

Kröber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehöver P, Pühler A, Schlüter A.

J Biotechnol. 2009 Jun 1;142(1):38-49. doi: 10.1016/j.jbiotec.2009.02.010. Epub 2009 Feb 27.

PMID:
19480946
10.

Illumina-based analysis of microbial community diversity.

Degnan PH, Ochman H.

ISME J. 2012 Jan;6(1):183-94. doi: 10.1038/ismej.2011.74. Epub 2011 Jun 16.

11.

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.

12.
13.

Analysis of microbial diversity by pyrosequencing the small-subunit ribosomal RNA without PCR amplification.

Li XR, Lv Y, Meng H, Gu JD, Quan ZX.

Appl Microbiol Biotechnol. 2014 Apr;98(8):3777-89. doi: 10.1007/s00253-014-5583-0. Epub 2014 Feb 16.

PMID:
24531274
14.

Experimental factors affecting PCR-based estimates of microbial species richness and evenness.

Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, Hugenholtz P.

ISME J. 2010 May;4(5):642-7. doi: 10.1038/ismej.2009.153. Epub 2010 Jan 21.

PMID:
20090784
15.

Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets.

Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH.

Res Microbiol. 2012 Jul;163(6-7):407-12. doi: 10.1016/j.resmic.2012.07.001. Epub 2012 Jul 21.

PMID:
22824070
16.

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data.

Aßhauer KP, Wemheuer B, Daniel R, Meinicke P.

Bioinformatics. 2015 Sep 1;31(17):2882-4. doi: 10.1093/bioinformatics/btv287. Epub 2015 May 7.

17.
18.

Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing.

Takahashi S, Tomita J, Nishioka K, Hisada T, Nishijima M.

PLoS One. 2014 Aug 21;9(8):e105592. doi: 10.1371/journal.pone.0105592. eCollection 2014.

19.

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.

Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M.

Environ Microbiol. 2013 Jun;15(6):1882-99. doi: 10.1111/1462-2920.12086. Epub 2013 Feb 6.

20.

Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem.

Oh S, Caro-Quintero A, Tsementzi D, DeLeon-Rodriguez N, Luo C, Poretsky R, Konstantinidis KT.

Appl Environ Microbiol. 2011 Sep;77(17):6000-11. doi: 10.1128/AEM.00107-11. Epub 2011 Jul 15.

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