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Results: 1 to 20 of 63

1.

ProViDE: A software tool for accurate estimation of viral diversity in metagenomic samples.

Ghosh TS, Mohammed MH, Komanduri D, Mande SS.

Bioinformation. 2011 Mar 26;6(2):91-4.

PMID:
21544173
[PubMed]
Free PMC Article
2.

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
[PubMed - indexed for MEDLINE]
Free Article
3.

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.

PMID:
21106121
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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]
5.

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences.

Mohammed MH, Ghosh TS, Reddy RM, Reddy CV, Singh NK, Mande SS.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S4. doi: 10.1186/1471-2164-12-S3-S4. Epub 2011 Nov 30.

PMID:
22369237
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
21989143
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Eu-Detect: an algorithm for detecting eukaryotic sequences in metagenomic data sets.

Mohammed MH, Chadaram S, Komanduri D, Ghosh TS, Mande SS.

J Biosci. 2011 Sep;36(4):709-17.

PMID:
21857117
[PubMed - indexed for MEDLINE]
Free Article
8.

C16S - a Hidden Markov Model based algorithm for taxonomic classification of 16S rRNA gene sequences.

Ghosh TS, Gajjalla P, Mohammed MH, Mande SS.

Genomics. 2012 Apr;99(4):195-201. doi: 10.1016/j.ygeno.2012.01.008. Epub 2012 Feb 3.

PMID:
22326741
[PubMed - indexed for MEDLINE]
Free Article
9.

Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.

Sharma VK, Kumar N, Prakash T, Taylor TD.

PLoS One. 2012;7(4):e34030. doi: 10.1371/journal.pone.0034030. Epub 2012 Apr 4.

PMID:
22496776
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
11.

Artificial and natural duplicates in pyrosequencing reads of metagenomic data.

Niu B, Fu L, Sun S, Li W.

BMC Bioinformatics. 2010 Apr 13;11:187. doi: 10.1186/1471-2105-11-187.

PMID:
20388221
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Stratification of co-evolving genomic groups using ranked phylogenetic profiles.

Freilich S, Goldovsky L, Gottlieb A, Blanc E, Tsoka S, Ouzounis CA.

BMC Bioinformatics. 2009 Oct 27;10:355. doi: 10.1186/1471-2105-10-355.

PMID:
19860884
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

SPHINX--an algorithm for taxonomic binning of metagenomic sequences.

Mohammed MH, Ghosh TS, Singh NK, Mande SS.

Bioinformatics. 2011 Jan 1;27(1):22-30. doi: 10.1093/bioinformatics/btq608. Epub 2010 Oct 28.

PMID:
21030462
[PubMed - indexed for MEDLINE]
Free Article
14.

ProClust: improved clustering of protein sequences with an extended graph-based approach.

Pipenbacher P, Schliep A, Schneckener S, Schönhuth A, Schomburg D, Schrader R.

Bioinformatics. 2002;18 Suppl 2:S182-91.

PMID:
12386002
[PubMed - indexed for MEDLINE]
Free Article
15.

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.

PMID:
21211059
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
21827705
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Taxonomic classification of metagenomic shotgun sequences with CARMA3.

Gerlach W, Stoye J.

Nucleic Acids Res. 2011 Aug;39(14):e91. doi: 10.1093/nar/gkr225. Epub 2011 May 17.

PMID:
21586583
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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]
19.

Kraken: ultrafast metagenomic sequence classification using exact alignments.

Wood DE, Salzberg SL.

Genome Biol. 2014 Mar 3;15(3):R46. doi: 10.1186/gb-2014-15-3-r46.

PMID:
24580807
[PubMed - in process]
Free PMC Article
20.

The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.

Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R.

Syst Appl Microbiol. 2008 Sep;31(4):241-50. doi: 10.1016/j.syapm.2008.07.001. Epub 2008 Aug 9.

PMID:
18692976
[PubMed - indexed for MEDLINE]

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