Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses

Richness and ecosystem development across faecal snapshots of the gut microbiota

(2018) Gwen Falony et al.   Nature Microbiology

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD

(2016) João Sabino et al.   GUT

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Brief Report:Dialisteras a Microbial Marker of Disease Activity in Spondyloarthritis

(2016) Raul Y. Tito et al.   Arthritis & Rheumatology

ACG Clinical Guideline: Primary Sclerosing Cholangitis

(2015) Keith D Lindor et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

fitdistrplus: AnRPackage for Fitting Distributions

(2015) Marie Laure Delignette-Muller et al.   Journal of Statistical Software

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Immunomodulatory Properties of Streptococcus and Veillonella Isolates from the Human Small Intestine Microbiota

(2014) Bartholomeus van den Bogert et al.   PLoS One

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fusobacterium nucleatum Potentiates Intestinal Tumorigenesis and Modulates the Tumor-Immune Microenvironment

(2013) Aleksandar D. Kostic et al.   Cell Host & Microbe

Primary sclerosing cholangitis

(2013) Gideon M Hirschfield et al.   LANCET

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

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

Monitoring microbiological changes in drinking water systems using a fast and reproducible flow cytometric method

(2013) E.I. Prest et al.   WATER RESEARCH

Second European evidence-based consensus on the diagnosis and management of ulcerative colitis Part 1: Definitions and diagnosis

(2012) Axel Dignass et al.   Journal of Crohns & Colitis

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

SlyA Is a Transcriptional Regulator Involved in the Virulence of Enterococcus faecalis

(2011) Charlotte Michaux et al.   INFECTION AND IMMUNITY

The second European evidence-based Consensus on the diagnosis and management of Crohn's disease: Definitions and diagnosis

(2010) Gert Van Assche et al.   Journal of Crohns & Colitis

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH