A method for automated pathogenic content estimation with application to rheumatoid arthritis

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

(2015) Simone Rampelli et al.   CURRENT BIOLOGY

Prevalence of and Outcomes Associated with Corticosteroid Prescription in Inflammatory Bowel Disease

(2014) Laura E. Targownik et al.   INFLAMMATORY BOWEL DISEASES

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

The dynamics of gut-associated microbial communities during inflammation

(2013) Sebastian E Winter et al.   EMBO REPORTS

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

(2013) Jose U Scher et al.   eLife

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli et al.   NATURE

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

(2011) Jeffrey J Werner et al.   ISME Journal

GeneDB--an annotation database for pathogens

(2011) F. J. Logan-Klumpler et al.   NUCLEIC ACIDS RESEARCH

Gut microbiome-host interactions in health and disease

(2011) James M Kinross et al.   Genome Medicine

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Metagenomic Analyses: Past and Future Trends

(2010) Carola Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effect ofPorphyromonas gingivalis-induced inflammation on the development of rheumatoid arthritis

(2010) P. Mark Bartold et al.   JOURNAL OF CLINICAL PERIODONTOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

Methotrexate-induced nitrosative stress may play a critical role in small intestinal damage in the rat

(2008) Viswa Kalyan Kolli et al.   ARCHIVES OF TOXICOLOGY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH