Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

Microbiome sequencing: challenges and opportunities for molecular medicine

(2016) Thomas Clavel et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability

(2016) Andreas Hiergeist et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Gut barrier impairment by high-fat diet in mice depends on housing conditions

(2016) Veronika Maria Müller et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Helicobacter pylori strains harboring babA2 from Indian sub population are associated with increased virulence in ex vivo study

(2016) Prachetash Ghosh et al.   Gut Pathogens

IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

(2016) Ilias Lagkouvardos et al.   Scientific Reports

Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence

(2015) Monika Schaubeck et al.   GUT

Physiological relevance of food grade microcapsules: Impact of milk protein based microcapsules on inflammation in mouse models for inflammatory bowel diseases

(2015) Rebecca Würth et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men

(2015) Ilias Lagkouvardos et al.   MOLECULAR NUTRITION & FOOD RESEARCH

De novo assembly of bacterial transcriptomes from RNA-seq data

(2015) Brian Tjaden   GENOME BIOLOGY

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking

(2014) P. J. McMurdie et al.   BIOINFORMATICS

Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?

(2014) Fionn Murtagh et al.   JOURNAL OF CLASSIFICATION

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

(2014) Brandon Brooks et al.   Microbiome

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Long-Term Temporal Analysis of the Human Fecal Microbiota Revealed a Stable Core of Dominant Bacterial Species

(2013) Inés Martínez et al.   PLoS One

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Independent filtering increases detection power for high-throughput experiments

(2010) R. Bourgon 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