Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Metatranscriptome of human faecal microbial communities in a cohort of adult men

(2018) Galeb S. Abu-Ali et al.   Nature Microbiology

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Maximal viral information recovery from sequence data using VirMAP

(2018) Nadim J Ajami et al.   Nature Communications

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

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

(2017) Subra Kugathasan et al.   LANCET

Fine-mapping inflammatory bowel disease loci to single-variant resolution

(2017) Hailiang Huang et al.   NATURE

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Human genetic variation and the gut microbiome in disease

(2017) Andrew Brantley Hall et al.   NATURE REVIEWS GENETICS

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Comparison of Collection Methods for Fecal Samples in Microbiome Studies

(2016) Emily Vogtmann et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies

(2016) E. Loftfield et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Complement in disease: a defence system turning offensive

(2016) Daniel Ricklin et al.   Nature Reviews Nephrology

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Aleksandar D. Kostic et al.   Cell Host & Microbe

Micronutrient deficiencies in inflammatory bowel disease

(2015) Roni Weisshof et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

Bile Acid Malabsorption in Inflammatory Bowel Disease

(2015) Libor Vítek   INFLAMMATORY BOWEL DISEASES

Carnitine in bacterial physiology and metabolism

(2015) Jamie A. Meadows et al.   MICROBIOLOGY-SGM

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

The global burden of IBD: from 2015 to 2025

(2015) Gilaad G. Kaplan   Nature Reviews Gastroenterology & Hepatology

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

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

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Temporal and technical variability of human gut metagenomes

(2015) Anita Y Voigt et al.   GENOME BIOLOGY

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

(2015) Xochitl C Morgan et al.   GENOME BIOLOGY

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

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

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

Environmental Risk Factors for Inflammatory Bowel Diseases: A Review

(2014) Ashwin N. Ananthakrishnan   DIGESTIVE DISEASES AND SCIENCES

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

(2014) Aleksandar D. Kostic et al.   GASTROENTEROLOGY

The Complement System in Inflammatory Bowel Disease

(2014) Umang Jain et al.   INFLAMMATORY BOWEL DISEASES

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

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

Intestinal transport and metabolism of bile acids

(2014) Paul A. Dawson et al.   JOURNAL OF LIPID RESEARCH

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

Complex host genetics influence the microbiome in inflammatory bowel disease

(2014) Dan Knights et al.   Genome Medicine

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

MetaRef: a pan-genomic database for comparative and community microbial genomics

(2013) Katherine Huang et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

(2013) Jose U Scher et al.   eLife

Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases

(2012) Henri Duboc et al.   GUT

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

(2012) J Gregory Caporaso et al.   ISME Journal

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

(2012) Luke Jostins et al.   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

Advances in Analysis of Longitudinal Data

(2010) Robert D. Gibbons et al.   Annual Review of Clinical Psychology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Intestinal Epithelial Serum Amyloid A Modulates Bacterial Growth In Vitro and Pro-Inflammatory Responses in Mouse Experimental Colitis

(2010) Erik RM Eckhardt et al.   BMC GASTROENTEROLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

An improved approximation to the precision of fixed effects from restricted maximum likelihood

(2009) Michael G. Kenward et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

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

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

Mucosal Lipocalin 2 Has Pro-Inflammatory and Iron-Sequestering Effects in Response to Bacterial Enterobactin

(2009) Michael A. Bachman et al.   PLoS Pathogens

The Human CXC Chemokine Granulocyte Chemotactic Protein 2 (GCP-2)/CXCL6 Possesses Membrane-Disrupting Properties and Is Antibacterial

(2008) H. M. Linge et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA