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Results: 1 to 20 of 108

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.

PMID:
22745671
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
22532608
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
22747657
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
18723574
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
22941634
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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
[PubMed - indexed for MEDLINE]
7.

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.

PMID:
21827705
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22369237
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
19651192
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
[PubMed - indexed for MEDLINE]
11.

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.

PMID:
23095761
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
22851513
[PubMed - indexed for MEDLINE]
13.

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
[PubMed - indexed for MEDLINE]
14.

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.

PMID:
18487625
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
21546400
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
21622656
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
21281493
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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
[PubMed - indexed for MEDLINE]
19.

Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.

Sharma VK, Kumar N, Prakash T, Taylor TD.

PLoS One. 2012;7(4):e34030. doi: 10.1371/journal.pone.0034030. Epub 2012 Apr 4.

PMID:
22496776
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
21989143
[PubMed - indexed for MEDLINE]
Free PMC Article

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