Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling

Association between specific mucosa-associated microbiota in Crohn's disease at the time of resection and subsequent disease recurrence: A pilot study

(2015) Peter De Cruz et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

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

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

CGAT: computational genomics analysis toolkit

(2014) D. Sims et al.   BIOINFORMATICS

Epithelial IL-22RA1-Mediated Fucosylation Promotes Intestinal Colonization Resistance to an Opportunistic Pathogen

(2014) Tu Anh N. Pham et al.   Cell Host & Microbe

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

(2014) Aleksandar D. Kostic et al.   GASTROENTEROLOGY

The Diagnostic Approach to Monogenic Very Early Onset Inflammatory Bowel Disease

(2014) Holm H. Uhlig et al.   GASTROENTEROLOGY

Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery

(2014) Clarissa Schwab et al.   ISME Journal

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

(2014) Michelle G Rooks et al.   ISME Journal

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

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

The alarmin IL-33 promotes regulatory T-cell function in the intestine

(2014) Chris Schiering et al.   NATURE

Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness

(2014) Joseph M. Pickard et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The gut microbiota in mouse models of inflammatory bowel disease

(2014) Kalliopi K. Gkouskou et al.   Frontiers in Cellular and Infection Microbiology

Transition metal ions at the crossroads of mucosal immunity and microbial pathogenesis

(2014) Vladimir E. Diaz-Ochoa et al.   Frontiers in Cellular and Infection Microbiology

Genetic Susceptibility in IBD

(2013) James D. Doecke et al.   INFLAMMATORY BOWEL DISEASES

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer

(2013) Shun’ichi Ishii et al.   Nature Communications

CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data

(2012) Jason E Shoemaker et al.   BMC GENOMICS

Loss of Interleukin-10 Signaling and Infantile Inflammatory Bowel Disease: Implications for Diagnosis and Therapy

(2012) Daniel Kotlarz et al.   GASTROENTEROLOGY

Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis

(2012) David Berry et al.   ISME Journal

Dextran Sodium Sulphate Colitis Mouse Model: Traps and Tricks

(2012) Martina Perše et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

(2012) Alison R. Erickson et al.   PLoS One

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

(2011) N. P. McNulty et al.   Science Translational Medicine

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

(2010) Wendy S. Garrett et al.   Cell Host & Microbe

Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases

(2010) Daniel N. Frank et al.   INFLAMMATORY BOWEL DISEASES

ProteinS-Thiolation by Glutathionylspermidine (Gsp)

(2010) Bing-Yu Chiang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Use of superoxide dismutase and catalase producing lactic acid bacteria in TNBS induced Crohn's disease in mice

(2010) Jean Guy LeBlanc et al.   JOURNAL OF BIOTECHNOLOGY

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

(2010) Andre Franke et al.   NATURE GENETICS

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

(2010) P. J. Turnbaugh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Biosynthesis and Degradation of H2O2 by Vaginal Lactobacilli

(2009) R. Martin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases

(2009) Christopher D Packey et al.   CURRENT OPINION IN INFECTIOUS DISEASES

Inflammatory Bowel Disease and Mutations Affecting the Interleukin-10 Receptor

(2009) Erik-Oliver Glocker et al.   NEW ENGLAND JOURNAL OF MEDICINE

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

Interleukin-23 Restrains Regulatory T Cell Activity to Drive T Cell-Dependent Colitis

(2008) Ana Izcue et al.   IMMUNITY

Analysis of bacterial bowel communities of IBD patients: What has it revealed?

(2008) Harry Sokol et al.   INFLAMMATORY BOWEL DISEASES

The yejABEF operon of Salmonella confers resistance to antimicrobial peptides and contributes to its virulence

(2008) Sandeepa M. Eswarappa et al.   MICROBIOLOGY-SGM

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

New substrates for TonB-dependent transport: do we only see the ‘tip of the iceberg’?

(2008) Kristine Schauer et al.   TRENDS IN BIOCHEMICAL SCIENCES