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Items: 1 to 20 of 135

1.

MetaSee: an interactive and extendable visualization toolbox for metagenomic sample analysis and comparison.

Song B, Su X, Xu J, Ning K.

PLoS One. 2012;7(11):e48998. doi: 10.1371/journal.pone.0048998. Epub 2012 Nov 8.

2.

Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization.

Su X, Pan W, Song B, Xu J, Ning K.

PLoS One. 2014 Mar 3;9(3):e89323. doi: 10.1371/journal.pone.0089323. eCollection 2014 Mar 3.

3.
4.

Parallel-META: efficient metagenomic data analysis based on high-performance computation.

Su X, Xu J, Ning K.

BMC Syst Biol. 2012;6 Suppl 1:S16. doi: 10.1186/1752-0509-6-S1-S16. Epub 2012 Jul 16.

5.

Joint analysis of multiple metagenomic samples.

Baran Y, Halperin E.

PLoS Comput Biol. 2012;8(2):e1002373. doi: 10.1371/journal.pcbi.1002373. Epub 2012 Feb 16.

6.

Interactive metagenomic visualization in a Web browser.

Ondov BD, Bergman NH, Phillippy AM.

BMC Bioinformatics. 2011 Sep 30;12:385. doi: 10.1186/1471-2105-12-385.

7.

From bacterial to microbial ecosystems (metagenomics).

Williamson SJ, Yooseph S.

Methods Mol Biol. 2012;804:35-55. doi: 10.1007/978-1-61779-361-5_3. Review.

PMID:
22144147
8.

[Meta-Mesh: metagenomic data analysis system].

Su X, Song B, Wang X, Ma X, Xu J, Ning K.

Sheng Wu Gong Cheng Xue Bao. 2014 Jan;30(1):6-17. Chinese.

PMID:
24818475
9.

From genomics to metagenomics.

Desai N, Antonopoulos D, Gilbert JA, Glass EM, Meyer F.

Curr Opin Biotechnol. 2012 Feb;23(1):72-6. doi: 10.1016/j.copbio.2011.12.017. Epub 2012 Jan 5. Review.

PMID:
22227326
10.

MEGAN analysis of metagenomic data.

Huson DH, Auch AF, Qi J, Schuster SC.

Genome Res. 2007 Mar;17(3):377-86. Epub 2007 Jan 25.

11.

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.

12.

Metagenomics using next-generation sequencing.

Bragg L, Tyson GW.

Methods Mol Biol. 2014;1096:183-201. doi: 10.1007/978-1-62703-712-9_15.

PMID:
24515370
13.

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.

14.

Alignment-free visualization of metagenomic data by nonlinear dimension reduction.

Laczny CC, Pinel N, Vlassis N, Wilmes P.

Sci Rep. 2014 Mar 31;4:4516. doi: 10.1038/srep04516.

15.

Meta-IDBA: a de Novo assembler for metagenomic data.

Peng Y, Leung HC, Yiu SM, Chin FY.

Bioinformatics. 2011 Jul 1;27(13):i94-101. doi: 10.1093/bioinformatics/btr216.

16.

Functional assignment of metagenomic data: challenges and applications.

Prakash T, Taylor TD.

Brief Bioinform. 2012 Nov;13(6):711-27. doi: 10.1093/bib/bbs033. Epub 2012 Jul 6. Review.

17.

Estimating DNA coverage and abundance in metagenomes using a gamma approximation.

Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN, Kyrpides NC.

Bioinformatics. 2010 Feb 1;26(3):295-301. doi: 10.1093/bioinformatics/btp687. Epub 2009 Dec 14.

18.
19.

Comparison of metagenomic samples using sequence signatures.

Jiang B, Song K, Ren J, Deng M, Sun F, Zhang X.

BMC Genomics. 2012 Dec 27;13:730. doi: 10.1186/1471-2164-13-730.

20.

Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.

Carr R, Shen-Orr SS, Borenstein E.

PLoS Comput Biol. 2013;9(10):e1003292. doi: 10.1371/journal.pcbi.1003292. Epub 2013 Oct 17.

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