Genome-wide associations of human gut microbiome variation and implications for causal inference analyses

GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals

(2019) Valentina Iotchkova et al.   NATURE GENETICS

PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations

(2019) Mihir A Kamat et al.   BIOINFORMATICS

pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)

(2019) Stefan Graw et al.   BMC BIOINFORMATICS

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative

(2018) Jun Wang et al.   Microbiome

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

Population-level analysis ofBlastocystissubtype prevalence and variation in the human gut microbiota

(2018) Raul Y Tito et al.   GUT

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Robust inference in summary data Mendelian randomization via the zero modal pleiotropy assumption

(2017) Fernando Pires Hartwig et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Commensal bacteria make GPCR ligands that mimic human signalling molecules

(2017) Louis J. Cohen et al.   NATURE

Functional mapping and annotation of genetic associations with FUMA

(2017) Kyoko Watanabe et al.   Nature Communications

Genetic Determinants of the Gut Microbiome in UK Twins

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

Consistent Estimation in Mendelian Randomization with Some Invalid Instruments Using a Weighted Median Estimator

(2016) Jack Bowden et al.   GENETIC EPIDEMIOLOGY

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

Haplotype estimation for biobank-scale data sets

(2016) Jared O'Connell 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

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic 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

LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants: Fig. 1.

(2015) Mitchell J. Machiela et al.   BIOINFORMATICS

Mendelian randomization with invalid instruments: effect estimation and bias detection through Egger regression

(2015) J. Bowden et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

New genetic loci link adipose and insulin biology to body fat distribution

(2015) Dmitry Shungin et al.   NATURE

Genetic studies of body mass index yield new insights for obesity biology

(2015) Adam E. Locke 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

Genome-Wide Association Study with Targeted and Non-targeted NMR Metabolomics Identifies 15 Novel Loci of Urinary Human Metabolic Individuality

(2015) Johannes Raffler et al.   PLoS Genetics

Genome-Wide Association Studies of the Human Gut Microbiota

(2015) Emily R. Davenport et al.   PLoS One

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands’

(2014) Patrick Deelen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Mendelian randomization: genetic anchors for causal inference in epidemiological studies

(2014) G. Davey Smith et al.   HUMAN MOLECULAR GENETICS

Correction: LotuS: an efficient and user-friendly OTU processing pipeline

(2014) Falk Hildebrand et al.   Microbiome

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

A mega-analysis of genome-wide association studies for major depressive disorder

(2012)   MOLECULAR PSYCHIATRY

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

(2012)   NATURE GENETICS

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

Murine Gut Microbiota Is Defined by Host Genetics and Modulates Variation of Metabolic Traits

(2012) Autumn M. McKnite et al.   PLoS One

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Meta-analysis and imputation refines the association of 15q25 with smoking quantity

(2010) Jason Z Liu et al.   NATURE GENETICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Butyrate Improves Insulin Sensitivity and Increases Energy Expenditure in Mice

(2009) Z. Gao et al.   DIABETES

Genome-wide association study reveals genetic risk underlying Parkinson's disease

(2009) Javier Simón-Sánchez et al.   NATURE GENETICS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics