Human gut bacteria produce ΤΗ17-modulating bile acid metabolites

Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease

(2021) Jonathan Wei Jie Lee et al.   Cell Host & Microbe

Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians

(2021) Yuko Sato et al.   NATURE

Multivariable association discovery in population-scale meta-omics studies

(2021) Himel Mallick et al.   PLoS Computational Biology

A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria

(2020) Jordan E. Bisanz et al.   Cell Host & Microbe

Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells

(2020) Clarissa Campbell et al.   NATURE

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Streamlined Genetic Manipulation of Diverse Bacteroides and Parabacteroides Isolates from the Human Gut Microbiota

(2019) Leonor García-Bayona et al.   mBio

Bile acid metabolites control TH17 and Treg cell differentiation

(2019) Saiyu Hang et al.   NATURE

Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis

(2019) Xinyang Song et al.   NATURE

Gut microbiome–mediated bile acid metabolism regulates liver cancer via NKT cells

(2018) Chi Ma et al.   SCIENCE

IL-23 and IL-1β Drive Human Th17 Cell Differentiation and Metabolic Reprogramming in Absence of CD28 Costimulation

(2018) Shankar Revu et al.   Cell Reports

A selective gut bacterial bile salt hydrolase alters host metabolism

(2018) Lina Yao et al.   eLife

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

(2018) Guangchuang Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Genomes OnLine database (GOLD) v.7: updates and new features

(2018) Supratim Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

The Xenobiotic Transporter Mdr1 Enforces T Cell Homeostasis in the Presence of Intestinal Bile Acids

(2017) Wei Cao et al.   IMMUNITY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Bile Acids Control Inflammation and Metabolic Disorder through Inhibition of NLRP3 Inflammasome

(2016) Chuansheng Guo et al.   IMMUNITY

Development of a real-time PCR assay for quantification of Citrobacter rodentium

(2016) Sofia Sagaidak et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

A biosynthetic pathway for a prominent class of microbiota-derived bile acids

(2015) A Sloan Devlin et al.   Nature Chemical Biology

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

Bile Acid-Activated Receptors, Intestinal Microbiota, and the Treatment of Metabolic Disorders

(2015) Stefano Fiorucci et al.   TRENDS IN MOLECULAR MEDICINE

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Gut Microbiota Regulates Bile Acid Metabolism by Reducing the Levels of Tauro-beta-muricholic Acid, a Naturally Occurring FXR Antagonist

(2013) Sama I. Sayin et al.   Cell Metabolism

Bile acid receptors as targets for drug development

(2013) Frank G. Schaap et al.   Nature Reviews Gastroenterology & Hepatology

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Small molecule inhibitors of RORγt: Targeting Th17 cells and other applications

(2012) Jun R. Huh et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Control of TH17 cells occurs in the small intestine

(2011) Enric Esplugues et al.   NATURE

Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci

(2010) Eli A Stahl et al.   NATURE GENETICS

Systemic gut microbial modulation of bile acid metabolism in host tissue compartments

(2010) J. R. Swann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Genome-wide scan reveals association of psoriasis with IL-23 and NF-κB pathways

(2009) Rajan P Nair et al.   NATURE GENETICS

Relative Abundance of Bacteroides spp. in Stools and Wastewaters as Determined by Hierarchical Oligonucleotide Primer Extension

(2008) P.-Y. Hong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

T Helper 17 Lineage Differentiation Is Programmed by Orphan Nuclear Receptors RORα and RORγ

(2008) Xuexian O. Yang et al.   IMMUNITY

Regulatory T Cells: Mechanisms of Differentiation and Function

(2007) Steven Z. Josefowicz et al.   Annual Review of Immunology