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Items: 1 to 20 of 389

1.

A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.

Jiang H, An L, Lin SM, Feng G, Qiu Y.

PLoS One. 2012;7(10):e46450. doi: 10.1371/journal.pone.0046450. Epub 2012 Oct 1. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/c08da7e7-60fe-4f7d-a457-299bf9f24148.

2.

Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.

Qiu YQ, Tian X, Zhang S.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct;12(5):1112-22. doi: 10.1109/TCBB.2015.2415814.

PMID:
26451823
3.

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets.

Scheuch M, Höper D, Beer M.

BMC Bioinformatics. 2015 Mar 3;16:69. doi: 10.1186/s12859-015-0503-6.

4.

MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing.

Pan W, Chen B, Xu Y.

Interdiscip Sci. 2015 Dec;7(4):405-13. doi: 10.1007/s12539-015-0281-x. Epub 2015 Aug 21.

PMID:
26293485
5.

MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks.

Gori F, Folino G, Jetten MS, Marchiori E.

Bioinformatics. 2011 Jan 15;27(2):196-203. doi: 10.1093/bioinformatics/btq649. Epub 2010 Dec 1.

6.

MetaID: a novel method for identification and quantification of metagenomic samples.

Srinivasan SM, Guda C.

BMC Genomics. 2013;14 Suppl 8:S4. doi: 10.1186/1471-2164-14-S8-S4. Epub 2013 Dec 9.

7.

Scalable metagenomic taxonomy classification using a reference genome database.

Ames SK, Hysom DA, Gardner SN, Lloyd GS, Gokhale MB, Allen JE.

Bioinformatics. 2013 Sep 15;29(18):2253-60. doi: 10.1093/bioinformatics/btt389. Epub 2013 Jul 4.

8.

Accurate genome relative abundance estimation based on shotgun metagenomic reads.

Xia LC, Cram JA, Chen T, Fuhrman JA, Sun F.

PLoS One. 2011;6(12):e27992. doi: 10.1371/journal.pone.0027992. Epub 2011 Dec 6.

9.

Investigating microbial co-occurrence patterns based on metagenomic compositional data.

Ban Y, An L, Jiang H.

Bioinformatics. 2015 Oct 15;31(20):3322-9. doi: 10.1093/bioinformatics/btv364. Epub 2015 Jun 16.

10.

Accurate genome relative abundance estimation for closely related species in a metagenomic sample.

Sohn MB, An L, Pookhao N, Li Q.

BMC Bioinformatics. 2014 Jul 16;15:242. doi: 10.1186/1471-2105-15-242.

11.

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads.

Rosen GL, Reichenberger ER, Rosenfeld AM.

Bioinformatics. 2011 Jan 1;27(1):127-9. doi: 10.1093/bioinformatics/btq619. Epub 2010 Nov 8.

12.

DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences.

Ghosh TS, Monzoorul Haque M, Mande SS.

BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S14. doi: 10.1186/1471-2105-11-S7-S14.

13.

Accurate taxonomic assignment of short pyrosequencing reads.

Clemente JC, Jansson J, Valiente G.

Pac Symp Biocomput. 2010:3-9.

14.

Flexible taxonomic assignment of ambiguous sequencing reads.

Clemente JC, Jansson J, Valiente G.

BMC Bioinformatics. 2011 Jan 7;12:8. doi: 10.1186/1471-2105-12-8.

15.

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.

17.

MetaSpark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes.

Zhou W, Li R, Yuan S, Liu C, Yao S, Luo J, Niu B.

Bioinformatics. 2017 Apr 1;33(7):1090-1092. doi: 10.1093/bioinformatics/btw750.

PMID:
28065898
18.

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

Albanese D, Fontana P, De Filippo C, Cavalieri D, Donati C.

Sci Rep. 2015 May 19;5:9743. doi: 10.1038/srep09743.

19.

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.

Brown BL, Watson M, Minot SS, Rivera MC, Franklin RB.

Gigascience. 2017 Feb 24. doi: 10.1093/gigascience/gix007. [Epub ahead of print]

20.

Phylogeny-based classification of microbial communities.

Tanaseichuk O, Borneman J, Jiang T.

Bioinformatics. 2014 Feb 15;30(4):449-56. doi: 10.1093/bioinformatics/btt700. Epub 2013 Dec 24.

PMID:
24369151

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