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Items: 1 to 20 of 143

1.

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.

2.

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
3.

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.

4.

Molecular ecological network analyses.

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

BMC Bioinformatics. 2012 May 30;13:113. doi: 10.1186/1471-2105-13-113.

5.

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity.

He Z, Deng Y, Van Nostrand JD, Tu Q, Xu M, Hemme CL, Li X, Wu L, Gentry TJ, Yin Y, Liebich J, Hazen TC, Zhou J.

ISME J. 2010 Sep;4(9):1167-79. doi: 10.1038/ismej.2010.46. Epub 2010 Apr 29.

PMID:
20428223
6.

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences.

Sun Y, Cai Y, Liu L, Yu F, Farrell ML, McKendree W, Farmerie W.

Nucleic Acids Res. 2009 Jun;37(10):e76. doi: 10.1093/nar/gkp285. Epub 2009 May 5.

7.

Introduction to the analysis of environmental sequences: metagenomics with MEGAN.

Huson DH, Mitra S.

Methods Mol Biol. 2012;856:415-29. doi: 10.1007/978-1-61779-585-5_17.

PMID:
22399469
8.

Phoenix 2: a locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface.

Soh J, Dong X, Caffrey SM, Voordouw G, Sensen CW.

J Biotechnol. 2013 Sep 20;167(4):393-403. doi: 10.1016/j.jbiotec.2013.07.004. Epub 2013 Jul 16.

9.
10.

Identifying biologically relevant differences between metagenomic communities.

Parks DH, Beiko RG.

Bioinformatics. 2010 Mar 15;26(6):715-21. doi: 10.1093/bioinformatics/btq041. Epub 2010 Feb 3.

11.

Ironing out the wrinkles in the rare biosphere through improved OTU clustering.

Huse SM, Welch DM, Morrison HG, Sogin ML.

Environ Microbiol. 2010 Jul;12(7):1889-98. doi: 10.1111/j.1462-2920.2010.02193.x. Epub 2010 Mar 11.

12.

High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment.

DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL.

Microb Ecol. 2007 Apr;53(3):371-83. Epub 2007 Mar 2.

PMID:
17334858
13.

Get the most out of your metagenome: computational analysis of environmental sequence data.

Raes J, Foerstner KU, Bork P.

Curr Opin Microbiol. 2007 Oct;10(5):490-8. Epub 2007 Oct 23. Review.

PMID:
17936679
14.

Assessment of microbial communities by graph partitioning in a study of soil fungi in two Alpine meadows.

Zinger L, Coissac E, Choler P, Geremia RA.

Appl Environ Microbiol. 2009 Sep;75(18):5863-70. doi: 10.1128/AEM.00748-09. Epub 2009 Jul 17.

15.

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.

16.

iBarcode.org: web-based molecular biodiversity analysis.

Singer GA, Hajibabaei M.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S14. doi: 10.1186/1471-2105-10-S6-S14.

17.
18.

Pyrosequencing of chaperonin-60 (cpn60) amplicons as a means of determining microbial community composition.

Schellenberg J, Links MG, Hill JE, Hemmingsen SM, Peters GA, Dumonceaux TJ.

Methods Mol Biol. 2011;733:143-58. doi: 10.1007/978-1-61779-089-8_10.

PMID:
21431768
19.

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.

20.

Molecular methods to study complex microbial communities.

Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M.

Methods Mol Biol. 2010;668:1-37. doi: 10.1007/978-1-60761-823-2_1.

PMID:
20830553
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