Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

VAMPS: a website for visualization and analysis of microbial population structures

(2014) Susan M Huse et al.   BMC BIOINFORMATICS

Host-specificity among abundant and rare taxa in the sponge microbiome

(2014) Julie Reveillaud et al.   ISME Journal

Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals?

(2014) Amy Apprill et al.   PLoS One

PNAS Plus: From the Cover: Oligotyping analysis of the human oral microbiome

(2014) A. M. Eren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecological Succession and Stochastic Variation in the Assembly of Arabidopsis thaliana Phyllosphere Communities

(2014) L. Maignien et al.   mBio

HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences

(2013) João F. Matias Rodrigues et al.   BIOINFORMATICS

Sewage reflects the distribution of human faecalLachnospiraceae

(2013) Sandra L. McLellan et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

Distinct antimicrobial peptide expression determines host species-specific bacterial associations

(2013) S. Franzenburg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

DySC: software for greedy clustering of 16S rRNA reads

(2012) Zejun Zheng et al.   BIOINFORMATICS

Growing Unculturable Bacteria

(2012) E. J. Stewart   JOURNAL OF BACTERIOLOGY

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

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

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald 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

Exploring the Diversity of Gardnerella vaginalis in the Genitourinary Tract Microbiota of Monogamous Couples Through Subtle Nucleotide Variation

(2011) A. Murat Eren et al.   PLoS One

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

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

Species boundaries and phylogenetic relationships between Atlanto-Mediterranean shallow-water and deep-sea coral associated Hexadella species (Porifera, Ianthellidae)

(2010) Julie Reveillaud et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

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

On the origin of prokaryotic species

(2009) W. F. Doolittle et al.   GENOME RESEARCH

A single regulatory gene is sufficient to alter bacterial host range

(2009) Mark J. Mandel et al.   NATURE

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

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

(2009) Yijun Sun et al.   NUCLEIC ACIDS RESEARCH

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics