Comparing clustering and pre-processing in taxonomy analysis

Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments

(2012) A. R. Özok et al.   INTERNATIONAL ENDODONTIC JOURNAL

TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage

(2012) B. W. Brandt et al.   NUCLEIC ACIDS RESEARCH

Two-Stage Clustering (TSC): A Pipeline for Selecting Operational Taxonomic Units for the High-Throughput Sequencing of PCR Amplicons

(2012) Xiao-Tao Jiang et al.   PLoS One

The Relation between Oral Candida Load and Bacterial Microbiome Profiles in Dutch Older Adults

(2012) Eefje A. Kraneveld et al.   PLoS One

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

(2011) Patrick D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

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

(2011) Y. Sun et al.   BRIEFINGS IN BIOINFORMATICS

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences

(2011) Xiaoyu Wang et al.   ISME Journal

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

(2011) Jeffrey J Werner et al.   ISME Journal

Saliva microbiomes distinguish caries-active from healthy human populations

(2011) Fang Yang et al.   ISME Journal

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

(2011) Yunpeng Cai et al.   NUCLEIC ACIDS RESEARCH

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

The Human Oral Microbiome

(2010) F. E. Dewhirst et al.   JOURNAL OF BACTERIOLOGY

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Pyrosequencing analysis of the Oral Microflora of healthy adults

(2009) B.J.F. Keijser et al.   JOURNAL OF DENTAL RESEARCH