A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

Associations between usual diet and gut microbiota composition: results from the Milieu Intérieur cross-sectional study

(2019) Valentin Partula et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

The Human Gut Microbiome: From Association to Modulation

(2018) Thomas S.B. Schmidt et al.   CELL

Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

(2018) Etienne Patin et al.   NATURE IMMUNOLOGY

The gut–liver axis and the intersection with the microbiome

(2018) Anupriya Tripathi et al.   Nature Reviews Gastroenterology & Hepatology

Gut microbiota associations with common diseases and prescription medications in a population-based cohort

(2018) Matthew A. Jackson et al.   Nature Communications

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

(2018) Raivo Kolde et al.   Genome Medicine

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

(2018) Jun Wang et al.   Microbiome

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines

(2018) Petar Scepanovic et al.   Genome Medicine

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life

(2018) Tommi Vatanen et al.   Nature Microbiology

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

(2017) Ilias Lagkouvardos et al.   PeerJ

An insider's perspective: Bacteroides as a window into the microbiome

(2017) Aaron G. Wexler et al.   Nature Microbiology

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

(2016) Toshitaka Odamaki et al.   BMC MICROBIOLOGY

Genetic Determinants of the Gut Microbiome in UK Twins

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

Reference-based phasing using the Haplotype Reference Consortium panel

(2016) Po-Ru Loh et al.   NATURE GENETICS

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

A reference panel of 64,976 haplotypes for genotype imputation

(2016)   NATURE GENETICS

Signals from the gut microbiota to distant organs in physiology and disease

(2016) Bjoern O Schroeder et al.   NATURE MEDICINE

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

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Imputation of KIR Types from SNP Variation Data

(2015) Damjan Vukcevic et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

The Milieu Intérieur study — An integrative approach for study of human immunological variance

(2015) Stéphanie Thomas et al.   CLINICAL IMMUNOLOGY

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

TheVGAMPackage for Categorical Data Analysis

(2015) Thomas W. Yee   Journal of Statistical Software

mice: Multivariate Imputation by Chained Equations inR

(2015) Stef van Buuren et al.   Journal of Statistical Software

Genome-Wide Association Studies of the Human Gut Microbiota

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

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter

(2014) Mariel M. Finucane et al.   PLoS One

A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

(2014) Jared O'Connell et al.   PLoS Genetics

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens

(2013) Xiaoming Jia et al.   PLoS One

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

The Microbiome in Infectious Disease and Inflammation

(2012) Kenya Honda et al.   Annual Review of Immunology

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

The Effects from DNA Extraction Methods on the Evaluation of Microbial Diversity Associated with Human Colonic Tissue

(2010) Páraic Ó Cuív et al.   MICROBIAL ECOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Gut Microbiota in Health and Disease

(2010) Inna Sekirov et al.   PHYSIOLOGICAL REVIEWS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Predominant Role of Host Genetics in Controlling the Composition of Gut Microbiota

(2008) Zaruhi A. Khachatryan et al.   PLoS One