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Items: 1 to 20 of 127

1.

Comparison of multiple metagenomes using phylogenetic networks based on ecological indices.

Mitra S, Gilbert JA, Field D, Huson DH.

ISME J. 2010 Oct;4(10):1236-42. doi: 10.1038/ismej.2010.51. Epub 2010 Apr 29.

PMID:
20428222
2.

Exploration of community traits as ecological markers in microbial metagenomes.

Barberán A, Fernández-Guerra A, Bohannan BJ, Casamayor EO.

Mol Ecol. 2012 Apr;21(8):1909-17. doi: 10.1111/j.1365-294X.2011.05383.x. Epub 2011 Nov 28.

PMID:
22121910
3.

Metagenomic signatures of 86 microbial and viral metagenomes.

Willner D, Thurber RV, Rohwer F.

Environ Microbiol. 2009 Jul;11(7):1752-66. doi: 10.1111/j.1462-2920.2009.01901.x. Epub 2009 Mar 18.

PMID:
19302541
4.

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG.

Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, Wilke A, Huson DH.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S21. doi: 10.1186/1471-2105-12-S1-S21.

5.

Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics.

Weber M, Teeling H, Huang S, Waldmann J, Kassabgy M, Fuchs BM, Klindworth A, Klockow C, Wichels A, Gerdts G, Amann R, Glöckner FO.

ISME J. 2011 May;5(5):918-28. doi: 10.1038/ismej.2010.180. Epub 2010 Dec 16.

6.

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
7.

MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions.

Wang TY, Su CH, Tsai HK.

Bioinformatics. 2011 Dec 15;27(24):3341-7. doi: 10.1093/bioinformatics/btr583. Epub 2011 Oct 20.

PMID:
22016405
8.

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
9.

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes.

Kristiansson E, Hugenholtz P, Dalevi D.

Bioinformatics. 2009 Oct 15;25(20):2737-8. doi: 10.1093/bioinformatics/btp508. Epub 2009 Aug 20.

PMID:
19696045
10.

The phylogenetic diversity of metagenomes.

Kembel SW, Eisen JA, Pollard KS, Green JL.

PLoS One. 2011;6(8):e23214. doi: 10.1371/journal.pone.0023214. Epub 2011 Aug 31.

11.

Understanding microbial community diversity metrics derived from metagenomes: performance evaluation using simulated data sets.

Bonilla-Rosso G, Eguiarte LE, Romero D, Travisano M, Souza V.

FEMS Microbiol Ecol. 2012 Oct;82(1):37-49. doi: 10.1111/j.1574-6941.2012.01405.x. Epub 2012 May 25.

12.

Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities.

Suenaga H.

Environ Microbiol. 2012 Jan;14(1):13-22. doi: 10.1111/j.1462-2920.2011.02438.x. Epub 2011 Mar 1. Review.

PMID:
21366818
13.

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.

PMID:
20130030
14.

SmashCommunity: a metagenomic annotation and analysis tool.

Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P.

Bioinformatics. 2010 Dec 1;26(23):2977-8. doi: 10.1093/bioinformatics/btq536. Epub 2010 Oct 19.

PMID:
20959381
15.

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.

16.

Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.

Kröber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehöver P, Pühler A, Schlüter A.

J Biotechnol. 2009 Jun 1;142(1):38-49. doi: 10.1016/j.jbiotec.2009.02.010. Epub 2009 Feb 27.

PMID:
19480946
17.

A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments.

Li M, Hong Y, Klotz MG, Gu JD.

Appl Microbiol Biotechnol. 2010 Mar;86(2):781-90. doi: 10.1007/s00253-009-2361-5. Epub 2010 Jan 27.

PMID:
20107988
18.

Purifying the impure: sequencing metagenomes and metatranscriptomes from complex animal-associated samples.

Lim YW, Haynes M, Furlan M, Robertson CE, Harris JK, Rohwer F.

J Vis Exp. 2014 Dec 22;(94). doi: 10.3791/52117.

19.

Computational challenges of sequence classification in microbiomic data.

Ribeca P, Valiente G.

Brief Bioinform. 2011 Nov;12(6):614-25. doi: 10.1093/bib/bbr019. Epub 2011 Apr 18.

PMID:
21504986
20.

RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes.

Zhang Y, Ji P, Wang J, Zhao F.

Nucleic Acids Res. 2016 Jun 2;44(10):e99. doi: 10.1093/nar/gkw165. Epub 2016 Mar 16.

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