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

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

(2013) Xiaoyu Wang et al.   BMC BIOINFORMATICS

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Assessing the Consequences of Denoising Marker-Based Metagenomic Data

(2013) John M. Gaspar et al.   PLoS One

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

(2013) Sandra Kittelmann et al.   PLoS One

CLUSTOM: A Novel Method for Clustering 16S rRNA Next Generation Sequences by Overlap Minimization

(2013) Kyuin Hwang et al.   PLoS One

Comparing clustering and pre-processing in taxonomy analysis

(2012) Marc J. Bonder et al.   BIOINFORMATICS

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

(2012) Martin Hartmann et al.   ISME Journal

TBC: A clustering algorithm based on prokaryotic taxonomy

(2012) Jae-Hak Lee et al.   JOURNAL OF MICROBIOLOGY

Grinder: a versatile amplicon and shotgun sequence simulator

(2012) Florent E. Angly et al.   NUCLEIC ACIDS RESEARCH

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

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

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

High-Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of Extraction Procedure, Primer Length and Annealing Temperature

(2012) Martin J. Sergeant et al.   PLoS One

Implications of Pyrosequencing Error Correction for Biological Data Interpretation

(2012) Matthew G. Bakker 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

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Pyrosequencing as a tool for better understanding of human microbiomes

(2012) José F. Siqueira et al.   Journal of Oral Microbiology

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

(2011) Xiaolin Hao et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

(2011) Mohammadreza Ghodsi et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

(2011) André Gilles et al.   BMC GENOMICS

Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health

(2011) Wim Crielaard et al.   BMC Medical Genomics

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

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

(2011) Yunpeng Cai et al.   NUCLEIC ACIDS RESEARCH

CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome

(2011) Ann L. Griffen et al.   PLoS One

Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform

(2011) Hideyuki Tamaki et al.   PLoS One

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

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

Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim

(2010) S. Balzer et al.   BIOINFORMATICS

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

The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes

(2010) David L. Kirchman et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences

(2010) Martin Hartmann et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

(2008) P.C.Y. Woo et al.   CLINICAL MICROBIOLOGY AND INFECTION

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One