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Items: 1 to 20 of 160

1.

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.

2.

Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing.

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

J Biomed Biotechnol. 2008;2008:513701. doi: 10.1155/2008/513701.

3.

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.

4.

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences.

Monzoorul Haque M, Ghosh TS, Komanduri D, Mande SS.

Bioinformatics. 2009 Jul 15;25(14):1722-30. doi: 10.1093/bioinformatics/btp317. Epub 2009 May 13.

PMID:
19439565
5.

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.

6.

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.

7.

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.

Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC.

Nat Methods. 2007 Jun;4(6):495-500. Epub 2007 Apr 29.

PMID:
17468765
8.

A New Unsupervised Binning Approach for Metagenomic Sequences Based on N-grams and Automatic Feature Weighting.

Liao R, Zhang R, Guan J, Zhou S.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):42-54. doi: 10.1109/TCBB.2013.137.

PMID:
26355506
10.

RAIphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles.

Nalbantoglu OU, Way SF, Hinrichs SH, Sayood K.

BMC Bioinformatics. 2011 Jan 31;12:41. doi: 10.1186/1471-2105-12-41.

11.

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
12.

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.

13.

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.

14.

Improving contig binning of metagenomic data using [Formula: see text] oligonucleotide frequency dissimilarity.

Wang Y, Wang K, Lu YY, Sun F.

BMC Bioinformatics. 2017 Sep 20;18(1):425. doi: 10.1186/s12859-017-1835-1.

15.

A two-phase binning algorithm using l-mer frequency on groups of non-overlapping reads.

Vinh le V, Lang TV, Binh le T, Hoai TV.

Algorithms Mol Biol. 2015 Jan 16;10(1):2. doi: 10.1186/s13015-014-0030-4. eCollection 2015.

16.

Classifying short genomic fragments from novel lineages using composition and homology.

Parks DH, MacDonald NJ, Beiko RG.

BMC Bioinformatics. 2011 Aug 9;12:328. doi: 10.1186/1471-2105-12-328.

17.

A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes.

Gkanogiannis A, Gazut S, Salanoubat M, Kanj S, Brüls T.

BMC Bioinformatics. 2016 Aug 19;17(1):311. doi: 10.1186/s12859-016-1186-3.

18.

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database.

Ritari J, Salojärvi J, Lahti L, de Vos WM.

BMC Genomics. 2015 Dec 12;16:1056. doi: 10.1186/s12864-015-2265-y.

19.

MBBC: an efficient approach for metagenomic binning based on clustering.

Wang Y, Hu H, Li X.

BMC Bioinformatics. 2015 Feb 5;16:36. doi: 10.1186/s12859-015-0473-8.

20.

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

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