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

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria

(2021) Koji Yahara et al.   Nature Communications

Genetic determinants of risk in autoimmune pulmonary alveolar proteinosis

(2021) Saori Sakaue et al.   Nature Communications

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

Responsible use of polygenic risk scores in the clinic: potential benefits, risks and gaps

(2021) et al.   NATURE MEDICINE

Whole genome sequences from non-invasively collected caribou faecal samples

(2021) Rebecca S. Taylor et al.   Conservation Genetics Resources

Genetic Ancestry Testing

(2020) Lynn B. Jorde et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment

(2020) Puzi Jiang et al.   BMC GENOMICS

Identification of type 2 diabetes loci in 433,540 East Asian individuals

(2020) Cassandra N. Spracklen et al.   NATURE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Insights into human genetic variation and population history from 929 diverse genomes

(2020) Anders Bergström et al.   SCIENCE

Metagenome-wide association of gut microbiome features for schizophrenia

(2020) Feng Zhu et al.   Nature Communications

Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species

(2020) Andie Ang et al.   Scientific Reports

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

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

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

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

(2019) Jason Lloyd-Price et al.   NATURE

CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies

(2019) Hrant Hovhannisyan et al.   BIOINFORMATICS

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

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

Accurate, scalable and integrative haplotype estimation

(2019) Olivier Delaneau et al.   Nature Communications

Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores

(2019) Julian R. Homburger et al.   Genome Medicine

The GenomeAsia 100K Project enables genetic discoveries across Asia

(2019)   NATURE

Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi

(2019) Siddhika Pareek et al.   npj Biofilms and Microbiomes

OUP accepted manuscript

(2018)   BIOINFORMATICS

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

(2018) Pamela Ferretti et al.   Cell Host & Microbe

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

(2018) Yukinori Okada et al.   Nature Communications

Improving saliva shotgun metagenomics by chemical host DNA depletion

(2018) Clarisse A. Marotz et al.   Microbiome

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

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

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study

(2018) Tommi Vatanen et al.   NATURE

A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixtures

(2017) Samuel H. Vohr et al.   Forensic Science International-Genetics

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research

(2017) Daria Shamarina et al.   Microbiome

Genotype Imputation with Millions of Reference Samples

(2016) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations

(2016) Aaron Y. Lee et al.   BMC BIOINFORMATICS

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

(2016) Suguru Nishijima et al.   DNA RESEARCH

Metagenome-wide association studies: fine-mining the microbiome

(2016) Jun Wang et al.   NATURE REVIEWS MICROBIOLOGY

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

(2016) Yuichi Maeda et al.   Arthritis & Rheumatology

Using populations of human and microbial genomes for organism detection in metagenomes

(2015) Sasha K. Ames et al.   GENOME RESEARCH

A global reference for human genetic variation

(2015) Richard A. Gibbs 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

Identifying personal microbiomes using metagenomic codes

(2015) Eric A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

minimac2: faster genotype imputation

(2014) Christian Fuchsberger et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Enabling the genomic revolution in Africa

(2014) et al.   SCIENCE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

A framework for human microbiome research

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Molecular pathogenesis of a novel mutation, G108D, in short-chain acyl-CoA dehydrogenase identified in subjects with short-chain acyl-CoA dehydrogenase deficiency

(2010) Kenichiro Shirao et al.   HUMAN GENETICS

Ancestry and Disease in the Age of Genomic Medicine

(2010) Charles N. Rotimi et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

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