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Results: 1 to 20 of 116

1.

Comparing clustering and pre-processing in taxonomy analysis.

Bonder MJ, Abeln S, Zaura E, Brandt BW.

Bioinformatics. 2012 Nov 15;28(22):2891-7. doi: 10.1093/bioinformatics/bts552. Epub 2012 Sep 8.

PMID:
22962346
[PubMed - indexed for MEDLINE]
Free Article
2.

CLUSTOM: a novel method for clustering 16S rRNA next generation sequences by overlap minimization.

Hwang K, Oh J, Kim TK, Kim BK, Yu DS, Hou BK, Caetano-Anollés G, Hong SG, Kim KM.

PLoS One. 2013 May 1;8(5):e62623. doi: 10.1371/journal.pone.0062623. Print 2013. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/bb3baaad-6b58-41a0-96cc-7bdc819de411.

PMID:
23650520
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
23899776
[PubMed - indexed for MEDLINE]
4.

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers.

Liu Z, DeSantis TZ, Andersen GL, Knight R.

Nucleic Acids Res. 2008 Oct;36(18):e120. doi: 10.1093/nar/gkn491. Epub 2008 Aug 22.

PMID:
18723574
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
21716311
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.

Schloss PD, Gevers D, Westcott SL.

PLoS One. 2011;6(12):e27310. doi: 10.1371/journal.pone.0027310. Epub 2011 Dec 14.

PMID:
22194782
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.

Sun Y, Cai Y, Huse SM, Knight R, Farmerie WG, Wang X, Mai V.

Brief Bioinform. 2012 Jan;13(1):107-21. doi: 10.1093/bib/bbr009. Epub 2011 Apr 27.

PMID:
21525143
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering.

Sul WJ, Cole JR, Jesus Eda C, Wang Q, Farris RJ, Fish JA, Tiedje JM.

Proc Natl Acad Sci U S A. 2011 Aug 30;108(35):14637-42. doi: 10.1073/pnas.1111435108. Epub 2011 Aug 22.

PMID:
21873204
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
23974136
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities.

Stoeck T, Behnke A, Christen R, Amaral-Zettler L, Rodriguez-Mora MJ, Chistoserdov A, Orsi W, Edgcomb VP.

BMC Biol. 2009 Nov 3;7:72. doi: 10.1186/1741-7007-7-72.

PMID:
19886985
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A novel method for determining microflora composition using dynamic phylogenetic analysis of 16S ribosomal RNA deep sequencing data.

Chan ER, Hester J, Kalady M, Xiao H, Li X, Serre D.

Genomics. 2011 Oct;98(4):253-9. doi: 10.1016/j.ygeno.2011.04.002. Epub 2011 Apr 15.

PMID:
21515358
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Rethinking microbial diversity analysis in the high throughput sequencing era.

Lemos LN, Fulthorpe RR, Triplett EW, Roesch LF.

J Microbiol Methods. 2011 Jul;86(1):42-51. doi: 10.1016/j.mimet.2011.03.014. Epub 2011 Mar 30.

PMID:
21457733
[PubMed - indexed for MEDLINE]
Free Article
13.

Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing.

Zakrzewski M, Goesmann A, Jaenicke S, Jünemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sørensen S, Pühler A, Schlüter A.

J Biotechnol. 2012 Apr 30;158(4):248-58. doi: 10.1016/j.jbiotec.2012.01.020. Epub 2012 Feb 8.

PMID:
22342600
[PubMed - indexed for MEDLINE]
14.

Low sequencing efforts bias analyses of shared taxa in microbial communities.

Lemos LN, Fulthorpe RR, Roesch LF.

Folia Microbiol (Praha). 2012 Sep;57(5):409-13. doi: 10.1007/s12223-012-0155-0. Epub 2012 May 5.

PMID:
22562492
[PubMed - indexed for MEDLINE]
15.

Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.

Jiang XT, Zhang H, Sheng HF, Wang Y, He Y, Zou F, Zhou HW.

PLoS One. 2012;7(1):e30230. doi: 10.1371/journal.pone.0030230. Epub 2012 Jan 11.

PMID:
22253923
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Experimental factors affecting PCR-based estimates of microbial species richness and evenness.

Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, Hugenholtz P.

ISME J. 2010 May;4(5):642-7. doi: 10.1038/ismej.2009.153. Epub 2010 Jan 21.

PMID:
20090784
[PubMed - indexed for MEDLINE]
17.

Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data.

Helal M, Kong F, Chen SC, Bain M, Christen R, Sintchenko V.

PLoS One. 2011;6(6):e19517. doi: 10.1371/journal.pone.0019517. Epub 2011 Jun 8.

PMID:
21687706
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.

Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, Sogin ML.

PLoS Genet. 2008 Nov;4(11):e1000255. doi: 10.1371/journal.pgen.1000255. Epub 2008 Nov 21. Erratum in: PLoS Genet. 2008 Dec;4(12). doi: 10.1371/annotation/3d8a6578-ce56-45aa-bc71-05078355b851. Welch, David Mark [corrected to Mark Welch, David].

PMID:
19023400
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Quantitatively evaluating mistaken clone assignments by RFLP analysis of 16S rRNA genes: a case study.

Zhang HB, Xu CW, Wang MM, Li T, Zhao ZW.

Can J Microbiol. 2008 Jun;54(6):479-82. doi: 10.1139/w08-031.

PMID:
18535634
[PubMed - indexed for MEDLINE]
20.

TBC: a clustering algorithm based on prokaryotic taxonomy.

Lee JH, Yi H, Jeon YS, Won S, Chun J.

J Microbiol. 2012 Apr;50(2):181-5. doi: 10.1007/s12275-012-1214-6. Epub 2012 Apr 27.

PMID:
22538644
[PubMed - indexed for MEDLINE]

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