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Items: 1 to 20 of 169

1.

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P.

ISME J. 2012 Mar;6(3):610-8. doi: 10.1038/ismej.2011.139. Epub 2011 Dec 1.

2.

The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.

Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R.

Syst Appl Microbiol. 2008 Sep;31(4):241-50. doi: 10.1016/j.syapm.2008.07.001. Epub 2008 Aug 9.

PMID:
18692976
3.

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL.

Appl Environ Microbiol. 2006 Jul;72(7):5069-72.

4.

Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses.

Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH, Glöckner FO, Rosselló-Móra R.

Syst Appl Microbiol. 2010 Oct;33(6):291-9. doi: 10.1016/j.syapm.2010.08.001.

PMID:
20817437
5.

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO.

Nucleic Acids Res. 2014 Jan;42(Database issue):D643-8. doi: 10.1093/nar/gkt1209. Epub 2013 Nov 28.

6.

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.

Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE.

ISME J. 2012 Jan;6(1):94-103. doi: 10.1038/ismej.2011.82. Epub 2011 Jun 30.

7.

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.

Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M.

BMC Genomics. 2011;12 Suppl 2:S4. doi: 10.1186/1471-2164-12-S2-S4. Epub 2011 Jul 27.

8.

CREST--classification resources for environmental sequence tags.

Lanzén A, Jørgensen SL, Huson DH, Gorfer M, Grindhaug SH, Jonassen I, Øvreås L, Urich T.

PLoS One. 2012;7(11):e49334. doi: 10.1371/journal.pone.0049334. Epub 2012 Nov 8.

9.

The ecological coherence of high bacterial taxonomic ranks.

Philippot L, Andersson SG, Battin TJ, Prosser JI, Schimel JP, Whitman WB, Hallin S.

Nat Rev Microbiol. 2010 Jul;8(7):523-9. doi: 10.1038/nrmicro2367.

PMID:
20531276
10.

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.

Zuo G, Hao B.

Genomics Proteomics Bioinformatics. 2015 Oct;13(5):321-31. doi: 10.1016/j.gpb.2015.08.004. Epub 2015 Nov 10.

11.

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea.

Chun J, Rainey FA.

Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):316-24. doi: 10.1099/ijs.0.054171-0. Review.

PMID:
24505069
12.

The bacterial species dilemma and the genomic-phylogenetic species concept.

Staley JT.

Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):1899-909. Review.

13.

En route to a genome-based classification of Archaea and Bacteria?

Klenk HP, Göker M.

Syst Appl Microbiol. 2010 Jun;33(4):175-82. doi: 10.1016/j.syapm.2010.03.003. Epub 2010 Apr 20. Review.

PMID:
20409658
14.

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.

Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE.

Database (Oxford). 2010 Jul 6;2010:baq013. doi: 10.1093/database/baq013.

15.

From learning taxonomies to phylogenetic learning: integration of 16S rRNA gene data into FAME-based bacterial classification.

Slabbinck B, Waegeman W, Dawyndt P, De Vos P, De Baets B.

BMC Bioinformatics. 2010 Jan 30;11:69. doi: 10.1186/1471-2105-11-69.

16.

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.

17.

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers.

Liu Z, DeSantis TZ, Andersen GL, Knight R.

Nucleic Acids Res. 2008 Oct;36(18):e120. doi: 10.1093/nar/gkn491. Epub 2008 Aug 22.

18.

Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories.

Rosselló-Móra R.

Environ Microbiol. 2012 Feb;14(2):318-34. doi: 10.1111/j.1462-2920.2011.02599.x. Epub 2011 Sep 29. Review.

PMID:
21958017
19.

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T; Quest for Orthologs Species Tree Working Group.

Genome Biol Evol. 2015 Jul 1;7(7):1988-99. doi: 10.1093/gbe/evv121.

20.

Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

Alsop EB, Raymond J.

PLoS One. 2013 Jul 1;8(7):e67337. doi: 10.1371/journal.pone.0067337. Print 2013.

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