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Items: 1 to 20 of 70

1.

Metagenomic analysis: the challenge of the data bonanza.

Hunter CI, Mitchell A, Jones P, McAnulla C, Pesseat S, Scheremetjew M, Hunter S.

Brief Bioinform. 2012 Nov;13(6):743-6. doi: 10.1093/bib/bbs020. Epub 2012 Sep 8. Review.

2.

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.

3.

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
4.

Advances in computational analysis of metagenome sequences.

Davenport CF, T├╝mmler B.

Environ Microbiol. 2013 Jan;15(1):1-5. doi: 10.1111/j.1462-2920.2012.02843.x. Epub 2012 Aug 8.

PMID:
22882611
5.

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.

6.

Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes.

Gori F, Tringe SG, Folino G, van Hijum SA, Op den Camp HJ, Jetten MS, Marchiori E.

BMC Genomics. 2013 Jan 16;14:7. doi: 10.1186/1471-2164-14-7.

7.

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.

8.

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
9.

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.

Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA.

BMC Bioinformatics. 2008 Sep 19;9:386. doi: 10.1186/1471-2105-9-386.

10.

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.

Scholz MB, Lo CC, Chain PS.

Curr Opin Biotechnol. 2012 Feb;23(1):9-15. doi: 10.1016/j.copbio.2011.11.013. Epub 2011 Dec 9. Review.

PMID:
22154470
11.

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.

12.

Classification of metagenomic sequences: methods and challenges.

Mande SS, Mohammed MH, Ghosh TS.

Brief Bioinform. 2012 Nov;13(6):669-81. doi: 10.1093/bib/bbs054. Epub 2012 Sep 8. Review.

PMID:
22962338
13.

Ultrafast clustering algorithms for metagenomic sequence analysis.

Li W, Fu L, Niu B, Wu S, Wooley J.

Brief Bioinform. 2012 Nov;13(6):656-68. doi: 10.1093/bib/bbs035. Epub 2012 Jul 6.

14.

Real time metagenomics: using k-mers to annotate metagenomes.

Edwards RA, Olson R, Disz T, Pusch GD, Vonstein V, Stevens R, Overbeek R.

Bioinformatics. 2012 Dec 15;28(24):3316-7. doi: 10.1093/bioinformatics/bts599. Epub 2012 Oct 9.

15.

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
16.

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
17.

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.

18.

FANTOM: Functional and taxonomic analysis of metagenomes.

Sanli K, Karlsson FH, Nookaew I, Nielsen J.

BMC Bioinformatics. 2013 Feb 1;14:38. doi: 10.1186/1471-2105-14-38.

19.

Short clones or long clones? A simulation study on the use of paired reads in metagenomics.

Mitra S, Schubach M, Huson DH.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S12. doi: 10.1186/1471-2105-11-S1-S12.

20.

MetaBinG: using GPUs to accelerate metagenomic sequence classification.

Jia P, Xuan L, Liu L, Wei C.

PLoS One. 2011;6(11):e25353. doi: 10.1371/journal.pone.0025353. Epub 2011 Nov 23.

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