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Items: 1 to 20 of 107

1.

BOTUX: bayesian-like operational taxonomic unit examiner.

Koparde VN, Adkins RS, Fettweis JM, Serrano MG, Buck GA, Reimers MA, Sheth NU.

Int J Comput Biol Drug Des. 2014;7(2-3):130-45. doi: 10.1504/IJCBDD.2014.061652. Epub 2014 May 28.

2.

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering.

Hao X, Jiang R, Chen T.

Bioinformatics. 2011 Mar 1;27(5):611-8. doi: 10.1093/bioinformatics/btq725. Epub 2011 Jan 13.

3.

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.

4.

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.

5.

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units.

Westcott SL, Schloss PD.

PeerJ. 2015 Dec 8;3:e1487. doi: 10.7717/peerj.1487. eCollection 2015.

6.

M-pick, a modularity-based method for OTU picking of 16S rRNA sequences.

Wang X, Yao J, Sun Y, Mai V.

BMC Bioinformatics. 2013 Feb 7;14:43. doi: 10.1186/1471-2105-14-43.

7.

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
8.

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
9.

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.

10.

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.

11.

TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences.

Tuzhikov A, Panchin A, Shestopalov VI.

Biotechniques. 2014 Feb 1;56(2):78-84. doi: 10.2144/000114135. eCollection 2014.

12.

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.

Wang Q, Garrity GM, Tiedje JM, Cole JR.

Appl Environ Microbiol. 2007 Aug;73(16):5261-7. Epub 2007 Jun 22.

13.

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.

14.

OTU analysis using metagenomic shotgun sequencing data.

Hao X, Chen T.

PLoS One. 2012;7(11):e49785. doi: 10.1371/journal.pone.0049785. Epub 2012 Nov 26.

15.

Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting.

Nguyen TD, Schmidt B, Zheng Z, Kwoh CK.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct;12(5):1060-73. doi: 10.1109/TCBB.2015.2407574.

PMID:
26451819
16.

Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs.

Mizrahi-Man O, Davenport ER, Gilad Y.

PLoS One. 2013;8(1):e53608. doi: 10.1371/journal.pone.0053608. Epub 2013 Jan 7.

17.

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.

18.

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.

Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE.

ISME J. 2012 Jan;6(1):94-103. doi: 10.1038/ismej.2011.82. Epub 2011 Jun 30.

19.

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW.

Microbiome. 2015 May 20;3:20. doi: 10.1186/s40168-015-0081-x. eCollection 2015. Erratum in: Microbiome. 2015;3:34.

20.

Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR.

Lazarevic V, Gaïa N, Girard M, Schrenzel J.

BMC Microbiol. 2016 Apr 23;16:73. doi: 10.1186/s12866-016-0689-4.

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