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Items: 1 to 20 of 99

1.

Advancing analytical algorithms and pipelines for billions of microbial sequences.

Gonzalez A, Knight R.

Curr Opin Biotechnol. 2012 Feb;23(1):64-71. doi: 10.1016/j.copbio.2011.11.028. Epub 2011 Dec 13. Review.

2.

MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.

Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A.

J Biotechnol. 2013 Aug 20;167(2):156-65. doi: 10.1016/j.jbiotec.2012.09.013. Epub 2012 Sep 29.

PMID:
23026555
3.

Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data.

Sun Y, Cai Y, Mai V, Farmerie W, Yu F, Li J, Goodison S.

Nucleic Acids Res. 2010 Dec;38(22):e205. doi: 10.1093/nar/gkq872. Epub 2010 Oct 6.

4.

Computational meta'omics for microbial community studies.

Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C.

Mol Syst Biol. 2013 May 14;9:666. doi: 10.1038/msb.2013.22. Review.

5.

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods.

Dröge J, Gregor I, McHardy AC.

Bioinformatics. 2015 Mar 15;31(6):817-24. doi: 10.1093/bioinformatics/btu745. Epub 2014 Nov 10.

6.

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.

7.

A survey of the methods for the characterization of microbial consortia and communities.

Spiegelman D, Whissell G, Greer CW.

Can J Microbiol. 2005 May;51(5):355-86. Review.

PMID:
16088332
8.

Technology and techniques for microbial ecology via DNA sequencing.

Walters WA, Knight R.

Ann Am Thorac Soc. 2014 Jan;11 Suppl 1:S16-20. doi: 10.1513/AnnalsATS.201306-160MG. Review.

PMID:
24437399
9.

Oligonucleotide microarrays for identification of microbial pathogens and detection of their virulence-associated or drug-resistance determinants.

Volokhov DV, Kong H, Herold K, Chizhikov VE, Rasooly A.

Methods Mol Biol. 2011;671:55-94. doi: 10.1007/978-1-59745-551-0_3.

PMID:
20967623
10.

Advances in computational analysis of metagenome sequences.

Davenport CF, Tümmler B.

Environ Microbiol. 2013 Jan;15(1):1-5. doi: 10.1111/j.1462-2920.2012.02843.x. Epub 2012 Aug 8.

PMID:
22882611
11.

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.

Wu M, Scott AJ.

Bioinformatics. 2012 Apr 1;28(7):1033-4. doi: 10.1093/bioinformatics/bts079. Epub 2012 Feb 12.

12.

DNACLUST: accurate and efficient clustering of phylogenetic marker genes.

Ghodsi M, Liu B, Pop M.

BMC Bioinformatics. 2011 Jun 30;12:271. doi: 10.1186/1471-2105-12-271.

13.

Microbial community analysis using MEGAN.

Huson DH, Weber N.

Methods Enzymol. 2013;531:465-85. doi: 10.1016/B978-0-12-407863-5.00021-6.

PMID:
24060133
14.

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns.

Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, Knight R.

Nat Methods. 2010 Oct;7(10):813-9. doi: 10.1038/nmeth.1499. Epub 2010 Sep 5.

15.

Application of 'next-generation' sequencing technologies to microbial genetics.

MacLean D, Jones JD, Studholme DJ.

Nat Rev Microbiol. 2009 Apr;7(4):287-96. doi: 10.1038/nrmicro2122. Review.

PMID:
19287448
16.

A framework for analysis of metagenomic sequencing data.

Murat Eren A, Ferris MJ, Taylor CM.

Pac Symp Biocomput. 2011:131-41.

17.

PANGEA: pipeline for analysis of next generation amplicons.

Giongo A, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, Casella G, Roesch LF, Walts B, Riva A, King G, Triplett EW.

ISME J. 2010 Jul;4(7):852-61. doi: 10.1038/ismej.2010.16. Epub 2010 Feb 25.

18.

Genomic sequencing of uncultured microorganisms from single cells.

Lasken RS.

Nat Rev Microbiol. 2012 Sep;10(9):631-40. doi: 10.1038/nrmicro2857. Review.

PMID:
22890147
19.

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics.

Lombard N, Prestat E, van Elsas JD, Simonet P.

FEMS Microbiol Ecol. 2011 Oct;78(1):31-49. doi: 10.1111/j.1574-6941.2011.01140.x. Epub 2011 Jun 28. Review.

20.

Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes.

Kuntal BK, Ghosh TS, Mande SS.

Genomics. 2013 Oct;102(4):409-18. doi: 10.1016/j.ygeno.2013.08.004. Epub 2013 Aug 24.

PMID:
23978768
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