A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases

Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases

(2020) Kazuyoshi Ishigaki et al.   NATURE GENETICS

The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases

(2020) Fengzhe Xu et al.   Microbiome

The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches

(2019) D B Dhakan et al.   GigaScience

Genetic analyses of diverse populations improves discovery for complex traits

(2019) Genevieve L. Wojcik et al.   NATURE

Potential roles of gut microbiome and metabolites in modulating ALS in mice

(2019) Eran Blacher et al.   NATURE

Large Covariance Estimation for Compositional Data via Composition-Adjusted Thresholding

(2018) Yuanpei Cao et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses

(2018) Mo Han et al.   Microbiome

A One-Penny Imputed Genome from Next-Generation Reference Panels

(2018) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

US Immigration Westernizes the Human Gut Microbiome

(2018) Pajau Vangay et al.   CELL

The role of sex in the genomics of human complex traits

(2018) Ekaterina A. Khramtsova et al.   NATURE REVIEWS GENETICS

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention

(2017) Ruixin Liu et al.   NATURE MEDICINE

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

(2017) Zefang Tang et al.   NUCLEIC ACIDS RESEARCH

Nucleoredoxin guards against oxidative stress by protecting antioxidant enzymes

(2017) Sophie Kneeshaw et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) Koji Atarashi et al.   SCIENCE

Functional mapping and annotation of genetic associations with FUMA

(2017) Kyoko Watanabe et al.   Nature Communications

The gut microbiome in atherosclerotic cardiovascular disease

(2017) Zhuye Jie et al.   Nature Communications

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing

(2017) Chao Fang et al.   GigaScience

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

Genetic Determinants of the Gut Microbiome in UK Twins

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

The Human Microbiome during Bacterial Vaginosis

(2016) Andrew B. Onderdonk et al.   CLINICAL MICROBIOLOGY REVIEWS

The effect of heritability and host genetics on the gut microbiota and metabolic syndrome

(2016) Mi Young Lim 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

Integrative approaches for large-scale transcriptome-wide association studies

(2016) Alexander Gusev et al.   NATURE GENETICS

Metagenome-wide association studies: fine-mining the microbiome

(2016) Jun Wang et al.   NATURE REVIEWS MICROBIOLOGY

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome

(2016) Hailiang Xie et al.   Cell Systems

Species–function relationships shape ecological properties of the human gut microbiome

(2016) Sara Vieira-Silva et al.   Nature Microbiology

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

Focal Adhesion Proteins α- and β-Parvin are Overexpressed in Human Colorectal Cancer and Correlate with Tumor Progression

(2015) Vasiliki Bravou et al.   CANCER INVESTIGATION

Genetic and environmental control of host-gut microbiota interactions

(2015) Elin Org et al.   GENOME RESEARCH

A catalog of the mouse gut metagenome

(2015) Liang Xiao et al.   NATURE BIOTECHNOLOGY

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment

(2015) Xuan Zhang et al.   NATURE MEDICINE

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database

(2014) R. Leslie et al.   BIOINFORMATICS

Rethinking “Enterotypes”

(2014) Dan Knights et al.   Cell Host & Microbe

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

The Database of Genomic Variants: a curated collection of structural variation in the human genome

(2013) Jeffrey R. MacDonald et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Categorization of the gut microbiota: enterotypes or gradients?

(2012) Ian B. Jeffery et al.   NATURE REVIEWS MICROBIOLOGY

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

Novel Genetic Loci Identified for the Pathophysiology of Childhood Obesity in the Hispanic Population

(2012) Anthony G. Comuzzie et al.   PLoS One

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test

(2011) Michael C. Wu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Oxr1 Is Essential for Protection against Oxidative Stress-Induced Neurodegeneration

(2011) Peter L. Oliver et al.   PLoS Genetics

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

(2010) A. McKenna et al.   GENOME RESEARCH

Sex differences in the activity of signalling pathways and expression of G-protein-coupled receptor kinases in the neonatal ventral hippocampal lesion model of schizophrenia

(2010) Evgeny Bychkov et al.   INTERNATIONAL JOURNAL OF NEUROPSYCHOPHARMACOLOGY

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS