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

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The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

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

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Downregulation of Expression of Xenobiotic Efflux Genes is Associated with Pelvic Pouch Inflammation in Ulcerative Colitis

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Memory Efficient Principal Component Analysis for the Dimensionality Reduction of Large Mass Spectrometry Imaging Data Sets

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High abundance and diversity of antimicrobial resistance determinants among early vancomycin-resistant Enterococcus faecium in Poland

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Recent Recombination Events in the Core Genome Are Associated with Adaptive Evolution in Enterococcus faecium

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Quantification and Characterization of Mucosa-Associated and Intracellular Escherichia coli in Inflammatory Bowel Disease

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Gene Expression Profiles of Ileal Inflammatory Bowel Disease Correlate with Disease Phenotype and Advance Understanding of Its Immunopathogenesis

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Diet rapidly and reproducibly alters the human gut microbiome

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Commensal Akkermansia muciniphila Exacerbates Gut Inflammation in Salmonella Typhimurium-Infected Gnotobiotic Mice

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Characterization of the Gut-Associated Microbiome in Inflammatory Pouch Complications Following Ileal Pouch-Anal Anastomosis

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Mother-to-Infant Transmission of Intestinal Bifidobacterial Strains Has an Impact on the Early Development of Vaginally Delivered Infant's Microbiota

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Extracellular Vesicles Derived from Gut Microbiota, Especially Akkermansia muciniphila, Protect the Progression of Dextran Sulfate Sodium-Induced Colitis

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Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity

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

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Increased abundance of Sutterella spp. and Ruminococcus torques in feces of children with autism spectrum disorder

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Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis

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Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

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TheNOD2insC polymorphism is associated with worse outcome following ileal pouch-anal anastomosis for ulcerative colitis

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

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Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

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Antibiotic Therapy in Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis

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Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives

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Etiology of pouchitis*

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

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Metagenomic biomarker discovery and explanation

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The Bacteriology of Pouchitis

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Metronidazole Is Still the Drug of Choice for Treatment of Anaerobic Infections

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Distinct microbiome in pouchitis compared to healthy pouches in ulcerative colitis and familial adenomatous polyposis

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Supervised classification of microbiota mitigates mislabeling errors

(2010) Dan Knights et al.   ISME Journal

Independent component analysis: Mining microarray data for fundamental human gene expression modules

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A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Succession of microbial consortia in the developing infant gut microbiome

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GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

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Pouchitis: lessons for inflammatory bowel disease

(2009) Hao Wu et al.   CURRENT OPINION IN GASTROENTEROLOGY

Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis

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What is principal component analysis?

(2008) Markus Ringnér   NATURE BIOTECHNOLOGY