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Items: 1 to 20 of 111

1.

The PhyloPythiaS web server for taxonomic assignment of metagenome sequences.

Patil KR, Roune L, McHardy AC.

PLoS One. 2012;7(6):e38581. doi: 10.1371/journal.pone.0038581. Epub 2012 Jun 20.

2.

Rapid identification of high-confidence taxonomic assignments for metagenomic data.

MacDonald NJ, Parks DH, Beiko RG.

Nucleic Acids Res. 2012 Aug;40(14):e111. doi: 10.1093/nar/gks335. Epub 2012 Apr 24.

3.

High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing.

Ross EM, Moate PJ, Bath CR, Davidson SE, Sawbridge TI, Guthridge KM, Cocks BG, Hayes BJ.

BMC Genet. 2012 Jul 2;13:53. doi: 10.1186/1471-2156-13-53.

4.

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.

5.

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms.

Liu J, Wang H, Yang H, Zhang Y, Wang J, Zhao F, Qi J.

Nucleic Acids Res. 2013 Jan 7;41(1):e3. doi: 10.1093/nar/gks828. Epub 2012 Aug 31.

6.

AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization.

Langenkämper D, Goesmann A, Nattkemper TW.

BMC Bioinformatics. 2014 Dec 13;15:384. doi: 10.1186/s12859-014-0384-0.

7.

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.

8.

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
9.

Classifying short genomic fragments from novel lineages using composition and homology.

Parks DH, MacDonald NJ, Beiko RG.

BMC Bioinformatics. 2011 Aug 9;12:328. doi: 10.1186/1471-2105-12-328.

10.

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences.

Mohammed MH, Ghosh TS, Reddy RM, Reddy CV, Singh NK, Mande SS.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S4. doi: 10.1186/1471-2164-12-S3-S4. Epub 2011 Nov 30.

11.

Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences.

Kapitonov VV, Tempel S, Jurka J.

Gene. 2009 Dec 15;448(2):207-13. doi: 10.1016/j.gene.2009.07.019. Epub 2009 Aug 3.

12.

Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen: a preliminary study.

Singh KM, Ahir VB, Tripathi AK, Ramani UV, Sajnani M, Koringa PG, Jakhesara S, Pandya PR, Rank DN, Murty DS, Kothari RK, Joshi CG.

Mol Biol Rep. 2012 Apr;39(4):4841-8. doi: 10.1007/s11033-011-1278-0. Epub 2011 Sep 27.

PMID:
21947953
13.

Analysis of composition-based metagenomic classification.

Higashi S, Barreto Ada M, Cantão ME, de Vasconcelos AT.

BMC Genomics. 2012;13 Suppl 5:S1. doi: 10.1186/1471-2164-13-S5-S1. Epub 2012 Oct 19.

14.

Taxonomic binning of metagenome samples generated by next-generation sequencing technologies.

Dröge J, McHardy AC.

Brief Bioinform. 2012 Nov;13(6):646-55. doi: 10.1093/bib/bbs031. Epub 2012 Jul 31.

15.

Census-based rapid and accurate metagenome taxonomic profiling.

Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R.

BMC Genomics. 2014 Oct 21;15:918. doi: 10.1186/1471-2164-15-918.

16.

Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome.

Montaña JS, Jiménez DJ, Hernández M, Angel T, Baena S.

Antonie Van Leeuwenhoek. 2012 Feb;101(2):205-15. doi: 10.1007/s10482-011-9624-8. Epub 2011 Jul 27.

PMID:
21792685
17.

Signature, a web server for taxonomic characterization of sequence samples using signature genes.

Dutilh BE, He Y, Hekkelman ML, Huynen MA.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W470-4. doi: 10.1093/nar/gkn277. Epub 2008 May 17.

18.

Mixture models for analysis of the taxonomic composition of metagenomes.

Meinicke P, Asshauer KP, Lingner T.

Bioinformatics. 2011 Jun 15;27(12):1618-24. doi: 10.1093/bioinformatics/btr266. Epub 2011 May 5.

19.

CoMet--a web server for comparative functional profiling of metagenomes.

Lingner T, Asshauer KP, Schreiber F, Meinicke P.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W518-23. doi: 10.1093/nar/gkr388. Epub 2011 May 26.

20.

RAIphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles.

Nalbantoglu OU, Way SF, Hinrichs SH, Sayood K.

BMC Bioinformatics. 2011 Jan 31;12:41. doi: 10.1186/1471-2105-12-41.

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