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

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile

(2015) Alyxandria M. Schubert et al.   mBio

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

(2015) Yan He et al.   Microbiome

Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis

(2015) Joseph P. Zackular et al.   mSphere

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations

(2014) Ali May et al.   BIOINFORMATICS

Limits to robustness and reproducibility in the demarcation of operational taxonomic units

(2014) Thomas S. B. Schmidt et al.   ENVIRONMENTAL MICROBIOLOGY

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

(2014) Thomas S. B. Schmidt et al.   PLoS Computational Biology

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

(2014) Jai Ram Rideout et al.   PeerJ

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit

(2013) Sarah P. Preheim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Streptomycin Application Has No Detectable Effect on Bacterial Community Structure in Apple Orchard Soil

(2013) Ashley Shade et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units

(2013) Alexander F. Koeppel et al.   NUCLEIC ACIDS RESEARCH

A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs

(2013) Wei Chen et al.   PLoS One

Comparing clustering and pre-processing in taxonomy analysis

(2012) Marc J. Bonder et al.   BIOINFORMATICS

Secondary structure improves OTU assignments of 16S rRNA gene sequences

(2012) Patrick D Schloss   ISME Journal

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

(2011) Jorge Barriuso 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

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert 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

Alignment and clustering of phylogenetic markers - implications for microbial diversity studies

(2010) James R White et al.   BMC BIOINFORMATICS

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

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

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

(2010) Minseok Kim et al.   JOURNAL OF MICROBIOLOGICAL METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies

(2010) Patrick D. Schloss   PLoS Computational Biology

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

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

(2009) Yijun Sun et al.   NUCLEIC ACIDS RESEARCH