Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities

Molecular Analysis for Screening Human Bacterial Pathogens in Municipal Wastewater Treatment and Reuse

(2014) Rajkumari Kumaraswamy et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Meta-analyses of studies of the human microbiota

(2013) C. A. Lozupone et al.   GENOME RESEARCH

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

The environment ontology: contextualising biological and biomedical entities

(2013) Pier Buttigieg et al.   Journal of Biomedical Semantics

Comparing clustering and pre-processing in taxonomy analysis

(2012) Marc J. Bonder et al.   BIOINFORMATICS

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples

(2012) Steven N. Evans et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

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

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

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

(2011) Lucie Zinger et al.   PLoS One

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

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

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CLEAN: CLustering Enrichment ANalysis

(2009) Johannes M Freudenberg et al.   BMC BIOINFORMATICS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Evaluating different approaches that test whether microbial communities have the same structure

(2008) Patrick D Schloss   ISME Journal