Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease

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

TRIM27 mediates STAT3 activation at retromer-positive structures to promote colitis and colitis-associated carcinogenesis

(2018) Hong-Xia Zhang et al.   Nature Communications

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

(2018) Yael Haberman et al.   Nature Communications

A microbial signature for Crohn's disease

(2017) Victoria Pascal et al.   GUT

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation

(2017) Koji Atarashi et al.   SCIENCE

CCDC88B is required for pathogenesis of inflammatory bowel disease

(2017) Nassima Fodil et al.   Nature Communications

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Genomic Alterations Observed in Colitis-Associated Cancers Are Distinct From Those Found in Sporadic Colorectal Cancers and Vary by Type of Inflammatory Bowel Disease

(2016) Rona Yaeger et al.   GASTROENTEROLOGY

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

Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis

(2016) Marlies Meisel et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Colonic Mucosal Epigenome and Microbiome Development in Children and Adolescents

(2016) R. Alan Harris et al.   Journal of Immunology Research

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

(2016) Shoko Iwai et al.   PLoS One

Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium

(2016) Qianpeng Zhang et al.   Scientific Reports

Mucosa-Associated Faecalibacterium prausnitzii Phylotype Richness Is Reduced in Patients with Inflammatory Bowel Disease

(2015) Mireia Lopez-Siles et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SPINGO: a rapid species-classifier for microbial amplicon sequences

(2015) Guy Allard et al.   BMC BIOINFORMATICS

Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci

(2015) Imge Hulur et al.   BMC GENOMICS

Identification of a common variant with potential pleiotropic effect on risk of inflammatory bowel disease and colorectal cancer

(2015) Hamed Khalili et al.   CARCINOGENESIS

Autophagy and inflammatory bowel disease: Association between variants of the autophagy-related IRGM gene and susceptibility to Crohn's disease

(2015) Sara Rufini et al.   DIGESTIVE AND LIVER DISEASE

The Crohn’s disease-associated polymorphism in ATG16L1 (rs2241880) reduces SHIP gene expression and activity in human subjects

(2015) E N Ngoh et al.   GENES AND IMMUNITY

Bacterial infection remodels the DNA methylation landscape of human dendritic cells

(2015) Alain Pacis et al.   GENOME RESEARCH

Deep resequencing of 131 Crohn's disease associated genes in pooled DNA confirmed three reported variants and identified eight novel variants

(2015) Sung Noh Hong et al.   GUT

Impact of Drug Therapy and Surgery on Quality of Life in Crohnʼs Disease

(2015) Emily K. Wright et al.   INFLAMMATORY BOWEL DISEASES

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Expression of CCL20 and Its Corresponding Receptor CCR6 Is Enhanced in Active Inflammatory Bowel Disease, and TLR3 Mediates CCL20 Expression in Colonic Epithelial Cells

(2015) Helene Kolstad Skovdahl et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease

(2014) Britt-Sabina Petersen et al.   BMC GENOMICS

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

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

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota

(2014) Lindsey Albenberg et al.   GASTROENTEROLOGY

Effects of bowel cleansing on the intestinal microbiota

(2014) Jonna Jalanka et al.   GUT

Bacteroides fragilis subverts mucosal biology: from symbiont to colon carcinogenesis

(2014) Cynthia L. Sears et al.   JOURNAL OF CLINICAL INVESTIGATION

Associations between STAT3 rs744166 Polymorphisms and Susceptibility to Ulcerative Colitis and Crohn's Disease: A Meta-Analysis

(2014) Jixiang Zhang et al.   PLoS One

Ulcerative colitis neoplasia is not associated with common inflammatory bowel disease single-nucleotide polymorphisms

(2014) Tara M. Connelly et al.   SURGERY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Possible role of Escherichia coli in propagation and perpetuation of chronic inflammation in ulcerative colitis

(2013) Magdalena Pilarczyk-Zurek et al.   BMC GASTROENTEROLOGY

Association of gut microbiota with post-operative clinical course in Crohn’s disease

(2013) Neelendu Dey et al.   BMC GASTROENTEROLOGY

Inflammatory Bowel Disease in Chinese Children

(2013) Xin-qiong Wang et al.   INFLAMMATORY BOWEL DISEASES

Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis

(2013) Lionel Rigottier-Gois   ISME Journal

Bacterial colonization factors control specificity and stability of the gut microbiota

(2013) S. Melanie Lee et al.   NATURE

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Molecular Reclassification of Crohn’s Disease: A Cautionary Note on Population Stratification

(2013) Bärbel Maus et al.   PLoS One

Identification of Novel Predictor Classifiers for Inflammatory Bowel Disease by Gene Expression Profiling

(2013) Trinidad Montero-Meléndez et al.   PLoS One

Anaerostipes hadrus comb. nov., a dominant species within the human colonic microbiota; reclassification of Eubacterium hadrum Moore et al. 1976

(2012) Emma Allen-Vercoe et al.   ANAEROBE

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

(2012) Andrew E. Teschendorff et al.   BIOINFORMATICS

Association Study of a Polymorphism in Clock GenePERIOD3and Risk of Inflammatory Bowel Disease

(2012) Gianluigi Mazzoccoli et al.   CHRONOBIOLOGY INTERNATIONAL

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

(2012) Núria Planell et al.   GUT

Gut microbiota composition correlates with diet and health in the elderly

(2012) Marcus J. Claesson et al.   NATURE

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

(2012) Luke Jostins et al.   NATURE

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Analysis of IL12B Gene Variants in Inflammatory Bowel Disease

(2012) Jürgen Glas et al.   PLoS One

TRIM27 Negatively Regulates NOD2 by Ubiquitination and Proteasomal Degradation

(2012) Birte Zurek et al.   PLoS One

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease

(2011) Alan W Walker et al.   BMC MICROBIOLOGY

Twin Study Indicates Loss of Interaction Between Microbiota and Mucosa of Patients With Ulcerative Colitis

(2011) Patricia Lepage et al.   GASTROENTEROLOGY

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota

(2011) Ian B Jeffery et al.   GUT

Sociodemographic, health and lifestyle predictors of poor diets

(2011) Janas Harrington et al.   PUBLIC HEALTH NUTRITION

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations

(2010) Erica D. Sonnenburg et al.   CELL

A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes

(2010) Ben P. Willing et al.   GASTROENTEROLOGY

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY