Analysis of gut microbiome, host genetics, and plasma metabolites reveals gut microbiome-host interactions in the Japanese population

Reconstruction of the personal information from human genome reads in gut metagenome sequencing data

(2023) Yoshihiko Tomofuji et al.   Nature Microbiology

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

(2022) Youwen Qin et al.   NATURE GENETICS

Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

(2022) Xiaomin Liu et al.   NATURE GENETICS

Challenges and future directions for studying effects of host genetics on the gut microbiome

(2022) Serena Sanna et al.   NATURE GENETICS

Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project

(2022) Esteban A. Lopera-Maya et al.   NATURE GENETICS

Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis

(2022) Jie Cai et al.   Cell Host & Microbe

ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs

(2022) Hui Yang et al.   NATURE

Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals

(2022) Aysu Okbay et al.   NATURE GENETICS

An online atlas of human plasma metabolite signatures of gut microbiome composition

(2022) Koen F. Dekkers et al.   Nature Communications

Genetic diversity fuels gene discovery for tobacco and alcohol use

(2022) Gretchen R. B. Saunders et al.   NATURE

Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome

(2021) Malte Christoph Rühlemann et al.   NATURE GENETICS

Large-scale association analyses identify host factors influencing human gut microbiome composition

(2021) Alexander Kurilshikov et al.   NATURE GENETICS

Human ABO Blood Groups and Their Associations with Different Diseases

(2021) Silamlak Birhanu Abegaz   Biomed Research International

Genetic determinants of risk in autoimmune pulmonary alveolar proteinosis

(2021) Saori Sakaue et al.   Nature Communications

Large-scale plasma-metabolome analysis identifies potential biomarkers of psoriasis and its clinical subtypes

(2021) Toshihiro Kishikawa et al.   JOURNAL OF DERMATOLOGICAL SCIENCE

Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese

(2021) Yoshihiko Tomofuji et al.   ANNALS OF THE RHEUMATIC DISEASES

Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease

(2021) Yoshihiko Tomofuji et al.   ANNALS OF THE RHEUMATIC DISEASES

Genetic architecture of microRNA expression and its link to complex diseases in the Japanese population

(2021) Kyuto Sonehara et al.   HUMAN MOLECULAR GENETICS

A cross-population atlas of genetic associations for 220 human phenotypes

(2021) Saori Sakaue et al.   NATURE GENETICS

Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation

(2020) Sidhartha R. Sinha et al.   Cell Host & Microbe

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

(2020) David A. Hughes et al.   Nature Microbiology

A Metagenome-Wide Association Study of Gut Microbiome in Patients With Multiple Sclerosis Revealed Novel Disease Pathology

(2020) Toshihiro Kishikawa et al.   Frontiers in Cellular and Infection Microbiology

Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota

(2020) Sachiko Ishida et al.   Communications Biology

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

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

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

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

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

(2019) Jason Lloyd-Price et al.   NATURE

Blood metabolome predicts gut microbiome α-diversity in humans

(2019) Tomasz Wilmanski et al.   NATURE BIOTECHNOLOGY

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

(2019) Petar Scepanovic et al.   Microbiome

Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population

(2019) Toshihiro Kishikawa et al.   ANNALS OF THE RHEUMATIC DISEASES

Characterizing rare and low-frequency height-associated variants in the Japanese population

(2019) Masato Akiyama et al.   Nature Communications

Interplay between the human gut microbiome and host metabolism

(2019) Alessia Visconti et al.   Nature Communications

Accurate, scalable and integrative haplotype estimation

(2019) Olivier Delaneau et al.   Nature Communications

Relationship between gut microbiota and circulating metabolites in population-based cohorts

(2019) Dina Vojinovic et al.   Nature Communications

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

(2018) Yukinori Okada et al.   Nature Communications

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

Leveraging Polygenic Functional Enrichment to Improve GWAS Power

(2018) Gleb Kichaev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Gut microbiome structure and metabolic activity in inflammatory bowel disease

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

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

The gut microbiome in atherosclerotic cardiovascular disease

(2017) Zhuye Jie et al.   Nature Communications

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

The gut microbiome of healthy Japanese and its microbial and functional uniqueness

(2016) Suguru Nishijima et al.   DNA RESEARCH

The effect of host genetics on the gut microbiome

(2016) Marc Jan Bonder et al.   NATURE GENETICS

Dysbiosis Contributes to Arthritis Development via Activation of Autoreactive T Cells in the Intestine

(2016) Yuichi Maeda et al.   Arthritis & Rheumatology

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

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

(2015) Xuan Zhang et al.   NATURE MEDICINE

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

(2015) Christopher C Chang et al.   GigaScience

minimac2: faster genotype imputation

(2014) Christian Fuchsberger et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Gut Microbiota Composition and Activity in Relation to Host Metabolic Phenotype and Disease Risk

(2012) Elaine Holmes et al.   Cell Metabolism

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

(2012) Junjie Qin et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Symptomatic atherosclerosis is associated with an altered gut metagenome

(2012) Fredrik H. Karlsson et al.   Nature Communications

Random-Effects Model Aimed at Discovering Associations in Meta-Analysis of Genome-wide Association Studies

(2011) Buhm Han et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

ABO blood group alleles and the risk of pancreatic cancer in a Japanese population

(2011) Makoto Nakao et al.   CANCER SCIENCE

LocusZoom: regional visualization of genome-wide association scan results

(2010) R. J. Pruim et al.   BIOINFORMATICS

Inhibiting the Initiation of Clostridium difficile Spore Germination using Analogs of Chenodeoxycholic Acid, a Bile Acid

(2010) J. A. Sorg et al.   JOURNAL OF BACTERIOLOGY

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles

(2009) Masahiro Sugimoto et al.   Metabolomics

Phosphodiesterase 1C is dispensable for rapid response termination of olfactory sensory neurons

(2009) Katherine D Cygnar et al.   NATURE NEUROSCIENCE

Bile Salts and Glycine as Cogerminants for Clostridium difficile Spores

(2008) J. A. Sorg et al.   JOURNAL OF BACTERIOLOGY