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Items: 1 to 20 of 74

1.

Metagenomic biomarker discovery and explanation.

Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C.

Genome Biol. 2011 Jun 24;12(6):R60. doi: 10.1186/gb-2011-12-6-r60.

2.

Reliable Biomarker discovery from Metagenomic data via RegLRSD algorithm.

Alshawaqfeh M, Bashaireh A, Serpedin E, Suchodolski J.

BMC Bioinformatics. 2017 Jul 10;18(1):328. doi: 10.1186/s12859-017-1738-1.

3.

Kraken: ultrafast metagenomic sequence classification using exact alignments.

Wood DE, Salzberg SL.

Genome Biol. 2014 Mar 3;15(3):R46. doi: 10.1186/gb-2014-15-3-r46.

4.

Ray Meta: scalable de novo metagenome assembly and profiling.

Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J.

Genome Biol. 2012 Dec 22;13(12):R122. doi: 10.1186/gb-2012-13-12-r122.

5.

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
6.

Metagenomic microbial community profiling using unique clade-specific marker genes.

Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C.

Nat Methods. 2012 Jun 10;9(8):811-4. doi: 10.1038/nmeth.2066.

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.

Bambus 2: scaffolding metagenomes.

Koren S, Treangen TJ, Pop M.

Bioinformatics. 2011 Nov 1;27(21):2964-71. doi: 10.1093/bioinformatics/btr520. Epub 2011 Sep 16.

9.

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
10.

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data.

Aßhauer KP, Wemheuer B, Daniel R, Meinicke P.

Bioinformatics. 2015 Sep 1;31(17):2882-4. doi: 10.1093/bioinformatics/btv287. Epub 2015 May 7.

11.

cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data.

Zhou F, Xu Y.

Bioinformatics. 2010 Aug 15;26(16):2051-2. doi: 10.1093/bioinformatics/btq299. Epub 2010 Jun 10.

12.

SitePainter: a tool for exploring biogeographical patterns.

Gonzalez A, Stombaugh J, Lauber CL, Fierer N, Knight R.

Bioinformatics. 2012 Feb 1;28(3):436-8. doi: 10.1093/bioinformatics/btr685. Epub 2011 Dec 9.

13.

[A review on the bioinformatics pipelines for metagenomic research].

Ye DD, Fan MM, Guan Q, Chen HJ, Ma ZS.

Dongwuxue Yanjiu. 2012 Dec;33(6):574-85. doi: 10.3724/SP.J.1141.2012.06574. Review. Chinese.

14.

Adapting functional genomic tools to metagenomic analyses: investigating the role of gut bacteria in relation to obesity.

Liu Y, Zhang C, Zhao L, Nardini C.

Brief Funct Genomics. 2010 Dec;9(5-6):355-61. doi: 10.1093/bfgp/elq011. Epub 2010 May 6.

15.

Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data.

Liu Z, Hsiao W, Cantarel BL, Drábek EF, Fraser-Liggett C.

Bioinformatics. 2011 Dec 1;27(23):3242-9. doi: 10.1093/bioinformatics/btr547. Epub 2011 Oct 7.

16.

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.

Kushwaha SK, Manoharan L, Meerupati T, Hedlund K, Ahrén D.

BMC Bioinformatics. 2015 Feb 28;16:65. doi: 10.1186/s12859-015-0501-8. Erratum in: BMC Bioinformatics. 2016;17:39.

17.

Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline.

Duhaime MB, Sullivan MB.

Virology. 2012 Dec 20;434(2):181-6. doi: 10.1016/j.virol.2012.09.036. Epub 2012 Oct 16. Review.

18.

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
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.

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures.

Freitas TA, Li PE, Scholz MB, Chain PS.

Nucleic Acids Res. 2015 May 26;43(10):e69. doi: 10.1093/nar/gkv180. Epub 2015 Mar 12.

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