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Items: 1 to 20 of 206

1.

Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis.

Schloss PD, Westcott SL.

Appl Environ Microbiol. 2011 May;77(10):3219-26. doi: 10.1128/AEM.02810-10. Epub 2011 Mar 18.

2.

Distribution-based clustering: using ecology to refine the operational taxonomic unit.

Preheim SP, Perrotta AR, Martin-Platero AM, Gupta A, Alm EJ.

Appl Environ Microbiol. 2013 Nov;79(21):6593-603. doi: 10.1128/AEM.00342-13. Epub 2013 Aug 23.

3.

A comparison of methods for clustering 16S rRNA sequences into OTUs.

Chen W, Zhang CK, Cheng Y, Zhang S, Zhao H.

PLoS One. 2013 Aug 13;8(8):e70837. doi: 10.1371/journal.pone.0070837. eCollection 2013.

4.

Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units.

Glassman SI, Martiny JBH.

mSphere. 2018 Jul 18;3(4). pii: e00148-18. doi: 10.1128/mSphere.00148-18.

5.

DBH: A de Bruijn graph-based heuristic method for clustering large-scale 16S rRNA sequences into OTUs.

Wei ZG, Zhang SW.

J Theor Biol. 2017 Jul 21;425:80-87. doi: 10.1016/j.jtbi.2017.04.019. Epub 2017 Apr 26.

PMID:
28454900
6.

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes.

Kim M, Morrison M, Yu Z.

J Microbiol Methods. 2011 Jan;84(1):81-7. doi: 10.1016/j.mimet.2010.10.020. Epub 2010 Oct 31.

PMID:
21047533
7.

Ironing out the wrinkles in the rare biosphere through improved OTU clustering.

Huse SM, Welch DM, Morrison HG, Sogin ML.

Environ Microbiol. 2010 Jul;12(7):1889-98. doi: 10.1111/j.1462-2920.2010.02193.x. Epub 2010 Mar 11.

8.

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering.

Franzén O, Hu J, Bao X, Itzkowitz SH, Peter I, Bashir A.

Microbiome. 2015 Oct 5;3:43. doi: 10.1186/s40168-015-0105-6. Erratum in: Microbiome. 2015;3:57.

9.

Sources of clostridia in raw milk on farms.

Julien MC, Dion P, Lafrenière C, Antoun H, Drouin P.

Appl Environ Microbiol. 2008 Oct;74(20):6348-57. doi: 10.1128/AEM.00913-08. Epub 2008 Aug 29.

10.

MtHc: a motif-based hierarchical method for clustering massive 16S rRNA sequences into OTUs.

Wei ZG, Zhang SW.

Mol Biosyst. 2015 Jul;11(7):1907-13. doi: 10.1039/c5mb00089k.

PMID:
25912934
11.

Microbial diversity in ostrich ceca as revealed by 16S ribosomal RNA gene clone library and detection of novel Fibrobacter species.

Matsui H, Kato Y, Chikaraishi T, Moritani M, Ban-Tokuda T, Wakita M.

Anaerobe. 2010 Apr;16(2):83-93. doi: 10.1016/j.anaerobe.2009.07.005. Epub 2009 Jul 24.

PMID:
19632349
12.

Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data.

Koskinen K, Auvinen P, Björkroth KJ, Hultman J.

J Comput Biol. 2015 Aug;22(8):743-51. doi: 10.1089/cmb.2014.0268. Epub 2014 Dec 19.

PMID:
25525895
13.

hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Units Based on Homopolymer Compaction.

Park S, Choi HS, Lee B, Chun J, Won JH, Yoon S.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Mar-Apr;15(2):441-451. doi: 10.1109/TCBB.2016.2535326. Epub 2016 Feb 26.

PMID:
26930691
14.

DMclust, a Density-based Modularity Method for Accurate OTU Picking of 16S rRNA Sequences.

Wei ZG, Zhang SW, Zhang YZ.

Mol Inform. 2017 Dec;36(12). doi: 10.1002/minf.201600059. Epub 2017 Jun 6.

PMID:
28586119
15.

bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences.

Chen SY, Deng F, Huang Y, Jia X, Liu YP, Lai SJ.

J Comput Biol. 2016 Apr;23(4):229-38. doi: 10.1089/cmb.2015.0214. Epub 2016 Mar 7.

PMID:
26950196
16.

16S rRNA metagenome clustering and diversity estimation using locality sensitive hashing.

Rasheed Z, Rangwala H, Barbará D.

BMC Syst Biol. 2013;7 Suppl 4:S11. doi: 10.1186/1752-0509-7-S4-S11. Epub 2013 Oct 23.

17.

MSClust: A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence.

Chen W, Cheng Y, Zhang C, Zhang S, Zhao H.

J Microbiol Methods. 2013 Sep;94(3):347-55. doi: 10.1016/j.mimet.2013.07.004. Epub 2013 Jul 28.

18.

ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time.

Cai Y, Sun Y.

Nucleic Acids Res. 2011 Aug;39(14):e95. doi: 10.1093/nar/gkr349. Epub 2011 May 19.

19.
20.

OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units.

Westcott SL, Schloss PD.

mSphere. 2017 Mar 8;2(2). pii: e00073-17. doi: 10.1128/mSphereDirect.00073-17. eCollection 2017 Mar-Apr.

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