Whole exome sequencing analyses reveal gene–microbiota interactions in the context of IBD

Genetic effects on the commensal microbiota in inflammatory bowel disease patients

(2019) Hugues Aschard et al.   PLoS Genetics

Genetic Factors and the Intestinal Microbiome Guide Development of Microbe-based Therapies for Inflammatory Bowel Diseases

(2019) Louis J. Cohen et al.   GASTROENTEROLOGY

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

(2019) Jason Lloyd-Price et al.   NATURE

Microbial genes and pathways in inflammatory bowel disease

(2019) Melanie Schirmer et al.   NATURE REVIEWS MICROBIOLOGY

Genome-wide analysis identifies rare copy number variations associated with inflammatory bowel disease

(2019) Svetlana Frenkel et al.   PLoS One

Determinants of IBD Heritability: Genes, Bugs, and More

(2018) Williams Turpin et al.   INFLAMMATORY BOWEL DISEASES

Analysis of predicted loss-of-function variants in UK Biobank identifies variants protective for disease

(2018) Connor A. Emdin et al.   Nature Communications

Host genetic variation and its microbiome interactions within the Human Microbiome Project

(2018) Raivo Kolde et al.   Genome Medicine

Abstract 2287: Precise common and rare germline CNV calling with GATK

(2018) Mehrtash Babadi et al.   CANCER RESEARCH

Age-dependent changes in GI physiology and microbiota: time to reconsider?

(2018) Ran An et al.   GUT

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells

(2018) A. Butera et al.   Scientific Reports

Species-level functional profiling of metagenomes and metatranscriptomes

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

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome

(2018) Arnau Vich Vila et al.   Science Translational Medicine

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies

(2017) Siew C Ng et al.   LANCET

A functional genomics predictive network model identifies regulators of inflammatory bowel disease

(2017) Lauren A Peters et al.   NATURE GENETICS

Human genetic variation and the gut microbiome in disease

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

Host Genetics and Gut Microbiome: Challenges and Perspectives

(2017) Alexander Kurilshikov et al.   TRENDS IN IMMUNOLOGY

Functional mapping and annotation of genetic associations with FUMA

(2017) Kyoko Watanabe et al.   Nature Communications

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity

(2016) Melanie Schirmer et al.   CELL

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Genetic Determinants of the Gut Microbiome in UK Twins

(2016) Julia K. Goodrich et al.   Cell Host & Microbe

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease

(2016) Floris Imhann et al.   GUT

Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota

(2016) Jun Wang et al.   NATURE GENETICS

The effect of host genetics on the gut microbiome

(2016) Marc Jan Bonder et al.   NATURE GENETICS

Association of host genome with intestinal microbial composition in a large healthy cohort

(2016) Williams Turpin et al.   NATURE GENETICS

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease

(2016) James E. Peters et al.   PLoS Genetics

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

(2016) David Ríos-Covián et al.   Frontiers in Microbiology

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis et al.   Cell Host & Microbe

Exome Sequencing Analysis Reveals Variants in Primary Immunodeficiency Genes in Patients With Very Early Onset Inflammatory Bowel Disease

(2015) Judith R. Kelsen et al.   GASTROENTEROLOGY

Genetics and Genetic Biomarkers in Sporadic Colorectal Cancer

(2015) John M. Carethers et al.   GASTROENTEROLOGY

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

Effect of predicted protein-truncating genetic variants on the human transcriptome

(2015) M. A. Rivas et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Pooled Sequencing of 531 Genes in Inflammatory Bowel Disease Identifies an Associated Rare Variant in BTNL2 and Implicates Other Immune Related Genes

(2015) Natalie J. Prescott et al.   PLoS Genetics

Interactions Between the Dietary Polyunsaturated Fatty Acid Ratio and Genetic Factors Determine Susceptibility to Pediatric Crohn's Disease

(2014) Irina Costea et al.   GASTROENTEROLOGY

TheATG16L1–T300Aallele impairs clearance of pathosymbionts in the inflamed ileal mucosa of Crohn's disease patients

(2014) Mehdi Sadaghian Sadabad et al.   GUT

A polygenic burden of rare disruptive mutations in schizophrenia

(2014) Shaun M. Purcell et al.   NATURE

Complex host genetics influence the microbiome in inflammatory bowel disease

(2014) Dan Knights et al.   Genome Medicine

General Framework for Meta-analysis of Rare Variants in Sequencing Association Studies

(2013) Seunggeun Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome

(2013) Dan Knights et al.   GUT

Polyunsaturated Fatty Acids in Inflammatory Bowel Diseases

(2013) Rachel Marion-Letellier et al.   INFLAMMATORY BOWEL DISEASES

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

HVEM signalling at mucosal barriers provides host defence against pathogenic bacteria

(2012) Jr-Wen Shui et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Nod2 is essential for temporal development of intestinal microbial communities

(2011) A. Rehman et al.   GUT

Altered gut microbiota composition in immune-impairedNod2−/−mice

(2011) Stanislas Mondot et al.   GUT

Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers

(2011) Tingting Wang et al.   ISME Journal

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL)

(2010) Andre Franke et al.   NATURE GENETICS

Data quality control in genetic case-control association studies

(2010) Carl A Anderson et al.   Nature Protocols

A genome-wide perspective of genetic variation in human metabolism

(2009) Thomas Illig et al.   NATURE GENETICS

Genetic Analysis of Innate Immunity in Crohn's Disease and Ulcerative Colitis Identifies Two Susceptibility Loci Harboring CARD9 and IL18RAP

(2008) Alexandra Zhernakova et al.   AMERICAN JOURNAL OF HUMAN GENETICS

CD160 inhibits activation of human CD4+ T cells through interaction with herpesvirus entry mediator

(2008) Guifang Cai et al.   NATURE IMMUNOLOGY