Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Increased Effectiveness of Early Therapy With Anti-Tumor Necrosis Factor-α vs an Immunomodulator in Children With Crohn's Disease

(2013) Thomas D. Walters et al.   GASTROENTEROLOGY

Specific Gut Commensal Flora Locally Alters T Cell Tuning to Endogenous Ligands

(2013) Pascal Chappert et al.   IMMUNITY

Proteomic patterns of colonic mucosal tissues delineate Crohn's colitis and ulcerative colitis

(2013) Erin H. Seeley et al.   Proteomics Clinical Applications

Host-Derived Nitrate Boosts Growth of E. coli in the Inflamed Gut

(2013) S. E. Winter et al.   SCIENCE

Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity

(2013) J. G. M. Markle et al.   SCIENCE

Functional profiling of the gut microbiome in disease-associated inflammation

(2013) Daniela Börnigen et al.   Genome Medicine

Bioinformatics analysis reveals transcriptome and microRNA signatures and drug repositioning targets for IBD and other autoimmune diseases

(2012) Peter M. Clark et al.   INFLAMMATORY BOWEL DISEASES

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

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

(2012) Luke Jostins et al.   NATURE

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

Ustekinumab Induction and Maintenance Therapy in Refractory Crohn's Disease

(2012) William J. Sandborn et al.   NEW ENGLAND JOURNAL OF MEDICINE

Preoperative Diagnosis of Benign Thyroid Nodules with Indeterminate Cytology

(2012) Erik K. Alexander et al.   NEW ENGLAND JOURNAL OF MEDICINE

Patients with Inflammatory Bowel Disease Exhibit Dysregulated Responses to Microbial DNA

(2012) Naomi S. C. Hotte et al.   PLoS One

Host Genes Related to Paneth Cells and Xenobiotic Metabolism Are Associated with Shifts in Human Ileum-Associated Microbial Composition

(2012) Tianyi Zhang et al.   PLoS One

An Ileal Crohn's Disease Gene Signature Based on Whole Human Genome Expression Profiles of Disease Unaffected Ileal Mucosal Biopsies

(2012) Tianyi Zhang et al.   PLoS One

Analysis of Candidate Colitis Genes in the Gdac1 Locus of Mice Deficient in Glutathione Peroxidase-1 and -2

(2012) R. Steven Esworthy et al.   PLoS One

A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response

(2012) Scott Schwartz et al.   GENOME BIOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Increasing Incidence and Prevalence of the Inflammatory Bowel Diseases With Time, Based on Systematic Review

(2011) Natalie A. Molodecky et al.   GASTROENTEROLOGY

Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88

(2011) Erik Larsson et al.   GUT

Vedolizumab for the Treatment of Active Ulcerative Colitis: A Randomized Controlled Phase 2 Dose-ranging Study

(2011) Asit Parikh et al.   INFLAMMATORY BOWEL DISEASES

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Characterization of intestinal gene expression profiles in Crohnʼs disease by genome-wide microarray analysis

(2010) Colin L. Noble et al.   INFLAMMATORY BOWEL DISEASES

Predictive value of epithelial gene expression profiles for response to infliximab in Crohnʼs disease‡

(2010) Ingrid Arijs et al.   INFLAMMATORY BOWEL DISEASES

Supervised classification of microbiota mitigates mislabeling errors

(2010) Dan Knights et al.   ISME Journal

Diet, gut microbiota and immune responses

(2010) Kendle M Maslowski et al.   NATURE IMMUNOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Infliximab, Azathioprine, or Combination Therapy for Crohn's Disease

(2010) Jean Frédéric Colombel et al.   NEW ENGLAND JOURNAL OF MEDICINE

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

(2010) V. Kaimal et al.   NUCLEIC ACIDS RESEARCH

Mucosal healing predicts long-term outcome of maintenance therapy with infliximab in Crohnʼs disease

(2009) Fabian Schnitzler et al.   INFLAMMATORY BOWEL DISEASES

DUOX2-derived reactive oxygen species are effectors of NOD2-mediated antibacterial responses

(2009) S. Lipinski et al.   JOURNAL OF CELL SCIENCE

How to map billions of short reads onto genomes

(2009) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Loss of Hepatocyte-Nuclear-Factor-4α Affects Colonic Ion Transport and Causes Chronic Inflammation Resembling Inflammatory Bowel Disease in Mice

(2009) Mathieu Darsigny et al.   PLoS One

Activation of an IL-6:STAT3-dependent transcriptome in pediatric-onset inflammatory bowel disease

(2007) Rebecca Carey et al.   INFLAMMATORY BOWEL DISEASES