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Items: 1 to 20 of 32

1.

Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems.

Roux S, Enault F, Bronner G, Debroas D.

FEMS Microbiol Ecol. 2011 Dec;78(3):617-28. doi: 10.1111/j.1574-6941.2011.01190.x. Epub 2011 Sep 19.

2.

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.

3.

Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads.

Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD.

Appl Environ Microbiol. 2011 Jun;77(11):3846-52. doi: 10.1128/AEM.02772-10. Epub 2011 Apr 1. Erratum in: Appl Environ Microbiol. 2011 Aug;77(15):5569.

4.

Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils.

Nacke H, Thürmer A, Wollherr A, Will C, Hodac L, Herold N, Schöning I, Schrumpf M, Daniel R.

PLoS One. 2011 Feb 16;6(2):e17000. doi: 10.1371/journal.pone.0017000.

5.

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method.

Wu JY, Jiang XT, Jiang YX, Lu SY, Zou F, Zhou HW.

BMC Microbiol. 2010 Oct 12;10:255. doi: 10.1186/1471-2180-10-255.

6.

Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes.

Will C, Thürmer A, Wollherr A, Nacke H, Herold N, Schrumpf M, Gutknecht J, Wubet T, Buscot F, Daniel R.

Appl Environ Microbiol. 2010 Oct;76(20):6751-9. doi: 10.1128/AEM.01063-10. Epub 2010 Aug 20.

7.

Illumina sequencing library preparation for highly multiplexed target capture and sequencing.

Meyer M, Kircher M.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5448. doi: 10.1101/pdb.prot5448.

PMID:
20516186
8.

Replicate or lie.

Prosser JI.

Environ Microbiol. 2010 Jul;12(7):1806-10. doi: 10.1111/j.1462-2920.2010.02201.x. Epub 2010 Apr 28. Review. No abstract available.

PMID:
20438583
9.

A high-throughput DNA sequence aligner for microbial ecology studies.

Schloss PD.

PLoS One. 2009 Dec 14;4(12):e8230. doi: 10.1371/journal.pone.0008230.

10.
11.

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF.

Appl Environ Microbiol. 2009 Dec;75(23):7537-41. doi: 10.1128/AEM.01541-09. Epub 2009 Oct 2.

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.

Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.

Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, Sogin ML.

PLoS Genet. 2008 Nov;4(11):e1000255. doi: 10.1371/journal.pgen.1000255. Epub 2008 Nov 21. Erratum in: PLoS Genet. 2008 Dec;4(12). doi: 10.1371/annotation/3d8a6578-ce56-45aa-bc71-05078355b851. Welch, David Mark [corrected to Mark Welch, David].

14.

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.

15.

Pyrosequencing enumerates and contrasts soil microbial diversity.

Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD, Daroub SH, Camargo FA, Farmerie WG, Triplett EW.

ISME J. 2007 Aug;1(4):283-90. Epub 2007 Jul 5.

16.

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.

Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO.

Nucleic Acids Res. 2007;35(21):7188-96. Epub 2007 Oct 18.

17.

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.

18.

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities.

Lozupone CA, Hamady M, Kelley ST, Knight R.

Appl Environ Microbiol. 2007 Mar;73(5):1576-85. Epub 2007 Jan 12.

19.

Clearcut: a fast implementation of relaxed neighbor joining.

Sheneman L, Evans J, Foster JA.

Bioinformatics. 2006 Nov 15;22(22):2823-4. Epub 2006 Sep 18.

PMID:
16982706
20.

Bio3d: an R package for the comparative analysis of protein structures.

Grant BJ, Rodrigues AP, ElSawy KM, McCammon JA, Caves LS.

Bioinformatics. 2006 Nov 1;22(21):2695-6. Epub 2006 Aug 29.

PMID:
16940322

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