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Results: 1 to 20 of 80

1.

The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments.

Saeed I, Halgamuge SK.

BMC Genomics. 2009 Dec 3;10 Suppl 3:S10. doi: 10.1186/1471-2164-10-S3-S10.

PMID:
19958473
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Binning sequences using very sparse labels within a metagenome.

Chan CK, Hsu AL, Halgamuge SK, Tang SL.

BMC Bioinformatics. 2008 Apr 28;9:215. doi: 10.1186/1471-2105-9-215.

PMID:
18442374
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

Alsop EB, Raymond J.

PLoS One. 2013 Jul 1;8(7):e67337. doi: 10.1371/journal.pone.0067337. Print 2013.

PMID:
23840870
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition.

Saeed I, Tang SL, Halgamuge SK.

Nucleic Acids Res. 2012 Mar;40(5):e34. doi: 10.1093/nar/gkr1204. Epub 2011 Dec 17.

PMID:
22180538
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Short prokaryotic DNA fragment binning using a hierarchical classifier based on linear discriminant analysis and principal component analysis.

Zheng H, Wu H.

J Bioinform Comput Biol. 2010 Dec;8(6):995-1011.

PMID:
21121023
[PubMed - indexed for MEDLINE]
6.

A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio.

Leung HC, Yiu SM, Yang B, Peng Y, Wang Y, Liu Z, Chen J, Qin J, Li R, Chin FY.

Bioinformatics. 2011 Jun 1;27(11):1489-95. doi: 10.1093/bioinformatics/btr186. Epub 2011 Apr 14.

PMID:
21493653
[PubMed - indexed for MEDLINE]
Free Article
7.

Unsupervised statistical clustering of environmental shotgun sequences.

Kislyuk A, Bhatnagar S, Dushoff J, Weitz JS.

BMC Bioinformatics. 2009 Oct 2;10:316. doi: 10.1186/1471-2105-10-316.

PMID:
19799776
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

The binning of metagenomic contigs for microbial physiology of mixed cultures.

Strous M, Kraft B, Bisdorf R, Tegetmeyer HE.

Front Microbiol. 2012 Dec 5;3:410. doi: 10.3389/fmicb.2012.00410. eCollection 2012.

PMID:
23227024
[PubMed]
Free PMC Article
9.

Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers.

Yang B, Peng Y, Leung HC, Yiu SM, Chen JC, Chin FY.

BMC Bioinformatics. 2010 Apr 16;11 Suppl 2:S5. doi: 10.1186/1471-2105-11-S2-S5.

PMID:
20406503
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Alignment-free supervised classification of metagenomes by recursive SVM.

Cui H, Zhang X.

BMC Genomics. 2013 Sep 22;14:641. doi: 10.1186/1471-2164-14-641.

PMID:
24053649
[PubMed - in process]
Free PMC Article
11.

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences.

Teeling H, Waldmann J, Lombardot T, Bauer M, Glöckner FO.

BMC Bioinformatics. 2004 Oct 26;5:163.

PMID:
15507136
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A base composition analysis of natural patterns for the preprocessing of metagenome sequences.

Bonham-Carter O, Ali H, Bastola D.

BMC Bioinformatics. 2013;14 Suppl 11:S5. doi: 10.1186/1471-2105-14-S11-S5. Epub 2013 Nov 4.

PMID:
24564274
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Intrinsic correlation of oligonucleotides: a novel genomic signature for metagenome analysis.

Ding X, Cao CC, Sun X.

J Theor Biol. 2014 Jul 21;353:9-18. doi: 10.1016/j.jtbi.2014.02.039. Epub 2014 Mar 11.

PMID:
24631045
[PubMed - in process]
14.

Multilocus sequence typing breathes life into a microbial metagenome.

Mahenthiralingam E, Baldwin A, Drevinek P, Vanlaere E, Vandamme P, LiPuma JJ, Dowson CG.

PLoS One. 2006 Dec 20;1:e17.

PMID:
17183643
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
[PubMed - indexed for MEDLINE]
16.

MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning.

Wang Y, Leung H, Yiu S, Chin F.

BMC Genomics. 2014;15 Suppl 1:S12. doi: 10.1186/1471-2164-15-S1-S12. Epub 2014 Jan 24.

PMID:
24564377
[PubMed - in process]
Free PMC Article
17.

Taxonomic binning of metagenome samples generated by next-generation sequencing technologies.

Dröge J, McHardy AC.

Brief Bioinform. 2012 Nov;13(6):646-55. doi: 10.1093/bib/bbs031. Epub 2012 Jul 31.

PMID:
22851513
[PubMed - indexed for MEDLINE]
18.

MetaCluster 4.0: a novel binning algorithm for NGS reads and huge number of species.

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

J Comput Biol. 2012 Feb;19(2):241-9. doi: 10.1089/cmb.2011.0276.

PMID:
22300323
[PubMed - indexed for MEDLINE]
19.

What's in the mix: phylogenetic classification of metagenome sequence samples.

McHardy AC, Rigoutsos I.

Curr Opin Microbiol. 2007 Oct;10(5):499-503. Epub 2007 Oct 22. Review.

PMID:
17933580
[PubMed - indexed for MEDLINE]
20.

TWARIT: an extremely rapid and efficient approach for phylogenetic classification of metagenomic sequences.

Reddy RM, Mohammed MH, Mande SS.

Gene. 2012 Sep 1;505(2):259-65. doi: 10.1016/j.gene.2012.06.014. Epub 2012 Jun 15.

PMID:
22710135
[PubMed - indexed for MEDLINE]

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