Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome

(2018) Kate Joanne Howell et al.   GASTROENTEROLOGY

Cell-centred meta-analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of patients with IBD

(2018) Renaud Gaujoux et al.   GUT

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course

(2018) Melanie Schirmer et al.   Cell Host & Microbe

Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches

(2017) R. Balfour Sartor et al.   GASTROENTEROLOGY

Lessons Learned From Trials Targeting Cytokine Pathways in Patients With Inflammatory Bowel Diseases

(2017) Clara Abraham et al.   GASTROENTEROLOGY

Understanding and Preventing the Global Increase of Inflammatory Bowel Disease

(2017) Gilaad G. Kaplan et al.   GASTROENTEROLOGY

Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study

(2017) Subra Kugathasan et al.   LANCET

Clonal evolution of colorectal cancer in IBD

(2017) Chang-Ho R. Choi et al.   Nature Reviews Gastroenterology & Hepatology

Anti-inflammatory effect of IL-10 mediated by metabolic reprogramming of macrophages

(2017) W. K. Eddie Ip et al.   SCIENCE

Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates

(2017) Andreas Tuerk et al.   PLoS Computational Biology

Effect of vedolizumab (anti-α4β7-integrin) therapy on histological healing and mucosal gene expression in patients with UC

(2016) Ingrid Arijs et al.   GUT

Peroxisome Proliferator-activated Receptor-γ Coactivator 1-α (PGC1α) Protects against Experimental Murine Colitis

(2016) Kellie E. Cunningham et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic flexibility of mitochondrial respiratory chain disorders predicted by computer modelling

(2016) Łukasz P Zieliński et al.   MITOCHONDRION

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease

(2016) Walid Mottawea et al.   Nature Communications

Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function

(2015) Caleb J. Kelly et al.   Cell Host & Microbe

Pyruvate Kinase M2 Regulates Hif-1α Activity and IL-1β Induction and Is a Critical Determinant of the Warburg Effect in LPS-Activated Macrophages

(2015) Eva M. Palsson-McDermott et al.   Cell Metabolism

Strong Upregulation of AIM2 and IFI16 Inflammasomes in the Mucosa of Patients with Active Inflammatory Bowel Disease

(2015) Wiebe Vanhove et al.   INFLAMMATORY BOWEL DISEASES

A role for 12/15-lipoxygenase-derived proresolving mediators in postoperative ileus: protectin DX-regulated neutrophil extravasation

(2015) Kathy Stein et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

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

Transcriptome Profiling of Human Ulcerative Colitis Mucosa Reveals Altered Expression of Pathways Enriched in Genetic Susceptibility Loci

(2014) Christopher J. Cardinale et al.   PLoS One

Mitochondria and Tumor Progression in Ulcerative Colitis

(2013) Cigdem Himmetoglu Ussakli et al.   JNCI-Journal of the National Cancer Institute

Functional Comparison between Genes Dysregulated in Ulcerative Colitis and Colorectal Carcinoma

(2013) Wenyuan Zhao et al.   PLoS One

Burden of Gastrointestinal Disease in the United States: 2012 Update

(2012) Anne F. Peery et al.   GASTROENTEROLOGY

Transcriptional analysis of the intestinal mucosa of patients with ulcerative colitis in remission reveals lasting epithelial cell alterations

(2012) Núria Planell et al.   GUT

Mitochondrial electron transport chain complex dysfunction in the colonic mucosa in ulcerative colitis

(2012) Srikanth Santhanam et al.   INFLAMMATORY BOWEL DISEASES

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

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

(2011) Daniel McDonald et al.   ISME Journal

The expression of REG 1A and REG 1B is increased during acute amebic colitis

(2011) Kristine M. Peterson et al.   PARASITOLOGY INTERNATIONAL

Eosinophils promote resolution of acute peritonitis by producing proresolving mediators in mice

(2010) Tomohiro Yamada et al.   FASEB JOURNAL

Severe Pediatric Ulcerative Colitis: A Prospective Multicenter Study of Outcomes and Predictors of Response

(2010) Dan Turner et al.   GASTROENTEROLOGY

Clinical variables as prognostic tools in pediatric-onset ulcerative colitis: A retrospective cohort study

(2010) Jill C. Moore et al.   INFLAMMATORY BOWEL DISEASES

Resolution of Inflammation in Murine Autoimmune Arthritis Is Disrupted by Cyclooxygenase-2 Inhibition and Restored by Prostaglandin E2-Mediated Lipoxin A4 Production

(2010) M. M. Y. Chan et al.   JOURNAL OF IMMUNOLOGY

Mitochondrial respiratory chain in the colonic mucosal of patients with ulcerative colitis

(2010) Karla G. Sifroni et al.   MOLECULAR AND CELLULAR BIOCHEMISTRY

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

Influence of Phenotype at Diagnosis and of Other Potential Prognostic Factors on the Course of Inflammatory Bowel Disease

(2009) M J L Romberg-Camps et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

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

Mucosal Gene Expression of Antimicrobial Peptides in Inflammatory Bowel Disease Before and After First Infliximab Treatment

(2009) Ingrid Arijs et al.   PLoS One

Clonality, Founder Mutations, and Field Cancerization in Human Ulcerative Colitis–Associated Neoplasia

(2008) Simon J. Leedham et al.   GASTROENTEROLOGY

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

(2007) Rebecca Carey et al.   INFLAMMATORY BOWEL DISEASES