Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

Host genetic and environmental effects on mouse intestinal microbiota

(2012) James H Campbell et al.   ISME Journal

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

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

Bambus 2: scaffolding metagenomes

(2011) Sergey Koren et al.   BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

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

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

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

(2011) Thomas M. Gihring et al.   ENVIRONMENTAL MICROBIOLOGY

Marine sponges and their microbial symbionts: love and other relationships

(2011) Nicole S. Webster et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Archaea in Yellowstone Lake

(2011) Jinjun Kan et al.   ISME Journal

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing

(2011) Ann L Griffen 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

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

(2011) Miguel Pignatelli 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

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

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

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

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

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

(2010) Anna Engelbrektson et al.   ISME Journal

Examining the global distribution of dominant archaeal populations in soil

(2010) Scott T Bates et al.   ISME Journal

Characterization of Archaeal Community in Contaminated and Uncontaminated Surface Stream Sediments

(2010) Iris Porat et al.   MICROBIAL ECOLOGY

Multiple displacement amplification compromises quantitative analysis of metagenomes

(2010) Suzan Yilmaz et al.   NATURE 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

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

(2010) Jenna L. Morgan et al.   PLoS One

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

(2010) J. McCarren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Empirical Testing of 16S rRNA Gene PCR Primer Pairs Reveals Variance in Target Specificity and Efficacy Not Suggested by In Silico Analysis

(2009) S. E. Morales et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Polymerase chain reaction primers miss half of rRNA microbial diversity

(2009) SunHee Hong et al.   ISME Journal

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

Mapping the Tree of Life: Progress and Prospects

(2009) N. R. Pace   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes

(2008) J. A. Frank et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A renaissance for the pioneering 16S rRNA gene

(2008) Susannah G Tringe et al.   CURRENT OPINION IN MICROBIOLOGY

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE