Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells

Mechanisms of Pediatric Inflammatory Bowel Disease

(2016) Joanna M. Peloquin et al.   Annual Review of Immunology

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity

(2016) Melanie Schirmer et al.   CELL

Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients

(2016) Jessica D. Forbes et al.   INFLAMMATORY BOWEL DISEASES

Helminth infection promotes colonization resistance via type 2 immunity

(2016) Deepshika Ramanan et al.   SCIENCE

An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses

(2015) Teruyuki Sano et al.   CELL

Isolation and cytokine analysis of lamina propria lymphocytes from mucosal biopsies of the human colon

(2015) Rowann Bowcutt et al.   JOURNAL OF IMMUNOLOGICAL METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Transcriptomic landscape of lncRNAs in inflammatory bowel disease

(2015) Aashiq H Mirza et al.   Genome Medicine

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease

(2015) Xochitl C Morgan et al.   GENOME BIOLOGY

Individuality and Variation of Personal Regulomes in Primary Human T Cells

(2015) Kun Qu et al.   Cell Systems

Variable selection for generalized canonical correlation analysis

(2014) A. Tenenhaus et al.   BIOSTATISTICS

Inflammatory Bowel Disease as a Model for Translating the Microbiome

(2014) Curtis Huttenhower et al.   IMMUNITY

Bacterial Sensor Nod2 Prevents Inflammation of the Small Intestine by Restricting the Expansion of the Commensal Bacteroides vulgatus

(2014) Deepshika Ramanan et al.   IMMUNITY

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

(2014) Yael Haberman et al.   JOURNAL OF CLINICAL INVESTIGATION

IL-22-producing CD4+ cells are depleted in actively inflamed colitis tissue

(2013) J M Leung et al.   Mucosal Immunology

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Colonic Crohn Disease

(2013) Charles Friel et al.   Clinics in Colon and Rectal Surgery

A novel approach for biomarker selection and the integration of repeated measures experiments from two assays

(2012) Benoit Liquet et al.   BMC BIOINFORMATICS

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

(2012) Erwin G Zoetendal et al.   ISME Journal

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

TH17, TH22 and TReg Cells Are Enriched in the Healthy Human Cecum

(2012) Martin J. Wolff et al.   PLoS One

Fecal Lipocalin 2, a Sensitive and Broadly Dynamic Non-Invasive Biomarker for Intestinal Inflammation

(2012) Benoit Chassaing et al.   PLoS One

Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems

(2011) Kim-Anh Lê Cao et al.   BMC BIOINFORMATICS

Commensal Bacteroides Species Induce Colitis in Host-Genotype-Specific Fashion in a Mouse Model of Inflammatory Bowel Disease

(2011) Seth M. Bloom et al.   Cell Host & Microbe

Early Mucosal Healing With Infliximab Is Associated With Improved Long-term Clinical Outcomes in Ulcerative Colitis

(2011) Jean Frédéric Colombel et al.   GASTROENTEROLOGY

Neutrophil gelatinase-associated lipocalin (NGAL) in inflammatory bowel disease: association with pathophysiology of inflammation, established markers, and disease activity

(2011) K. A. Oikonomou et al.   JOURNAL OF GASTROENTEROLOGY

High temporal and inter-individual variation detected in the human ileal microbiota

(2010) Carien C. G. M. Booijink et al.   ENVIRONMENTAL MICROBIOLOGY

IL-22+ CD4+ T Cells Are Associated with Therapeutic Trichuris trichiura Infection in an Ulcerative Colitis Patient

(2010) M. J. Broadhurst et al.   Science Translational Medicine

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Foxp3+ Regulatory T Cells, Th17 Effector Cells, and Cytokine Environment in Inflammatory Bowel Disease

(2009) Nicola Eastaff-Leung et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Human gut microbiome adopts an alternative state following small bowel transplantation

(2009) A. L. Hartman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA