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

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

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

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

Diversity, compositional and functional differences between gut microbiota of children and adults

(2020) Djawad Radjabzadeh et al.   Scientific Reports

The Role of the Gut Microbiome in Cattle Production and Health: Driver or Passenger?

(2020) Eóin O'Hara et al.   Annual Review of Animal Biosciences

SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole genome sequencing of tank milk

(2020) Wouter Coppieters et al.   GENOME RESEARCH

An improved pig reference genome sequence to enable pig genetics and genomics research

(2020) Amanda Warr et al.   GigaScience

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

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

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals

(2019) FER Vuik et al.   United European Gastroenterology Journal

Gut Microbiota Plays a Central Role to Modulate the Plasma and Fecal Metabolomes in Response to Angiotensin II

(2019) Muhammad Umar Cheema et al.   HYPERTENSION

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

An enzymatic pathway in the human gut microbiome that converts A to universal O type blood

(2019) Peter Rahfeld et al.   Nature Microbiology

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Prospecting for microbial α-N-acetylgalactosaminidases yields a new class of GH31 O-glycanase

(2019) Peter Rahfeld et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals

(2018) Andrey Ziyatdinov et al.   BMC BIOINFORMATICS

Disease Heritability Inferred from Familial Relationships Reported in Medical Records

(2018) Fernanda C.G. Polubriaginof et al.   CELL

The Human Gut Microbiome: From Association to Modulation

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

Determination of complete sequence information of the human ABO blood group orthologous gene in pigs and breed difference in blood type frequencies

(2018) Min-Kyeung Choi et al.   GENE

IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes

(2018) Yukihide Momozawa et al.   Nature Communications

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

Harnessing genomic information for livestock improvement

(2018) Michel Georges et al.   NATURE REVIEWS GENETICS

Genomes of the Mouse Collaborative Cross

(2017) Anuj Srivastava et al.   GENETICS

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Fine-mapping inflammatory bowel disease loci to single-variant resolution

(2017) Hailiang Huang et al.   NATURE

Genomes of the Mouse Collaborative Cross

(2017) Anuj Srivastava et al.   GENETICS

Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning

(2017) Christopher Staley et al.   Microbiome

Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides

(2017) Dmitry A. Ravcheev et al.   Frontiers in Genetics

ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins

(2016) Emily R. Davenport et al.   BMC GENOMICS

Genetic Determinants of the Gut Microbiome in UK Twins

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

NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock

(2016) Carole Charlier et al.   GENOME RESEARCH

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

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

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice

(2016) Taichi A. Suzuki et al.   PLoS One

Blood Groups in Infection and Host Susceptibility

(2015) Laura Cooling   CLINICAL MICROBIOLOGY REVIEWS

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

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

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

(2015) Huashui Ai et al.   NATURE GENETICS

Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes

(2015) Laurent A F Frantz et al.   NATURE GENETICS

Meta-analysis of the heritability of human traits based on fifty years of twin studies

(2015) Tinca J C Polderman et al.   NATURE GENETICS

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Design of Glycosyltransferase Inhibitors: Serine Analogues as Pyrophosphate Surrogates?

(2015) Shuai Wang et al.   ChemPlusChem

Two novel regulators ofN-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections

(2015) Huimin Zhang et al.   MicrobiologyOpen

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

(2015) Christopher C Chang et al.   GigaScience

Mucin glycan foraging in the human gut microbiome

(2015) Louise E. Tailford et al.   Frontiers in Genetics

Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves

(2014) Nilusha Malmuthuge et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

A unique gene cluster for the utilization of the mucosal and human milk-associated glycans galacto-N-biose and lacto-N-biose inLactobacillus casei

(2014) Gonzalo N. Bidart et al.   MOLECULAR MICROBIOLOGY

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Genetic analysis of the roles of agaA, agaI, and agaS genes in the N-acetyl-D-galactosamine and D-galactosamine catabolic pathways in Escherichia coli strains O157:H7 and C

(2013) Zonglin Hu et al.   BMC MICROBIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Association between the ABO blood group and the human intestinal microbiota composition

(2012) Harri Mäkivuokko et al.   BMC MICROBIOLOGY

N-Acetylgalactosamine Utilization Pathway and Regulon in Proteobacteria

(2012) Semen A. Leyn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The ABO blood group is a trans-species polymorphism in primates

(2012) L. Segurel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

(2011) Mohammadreza Ghodsi et al.   BMC BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

GCTA: A Tool for Genome-wide Complex Trait Analysis

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

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

METAL: fast and efficient meta-analysis of genomewide association scans

(2010) C. J. Willer et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Genomic encyclopedia of sugar utilization pathways in the Shewanella genus

(2010) Dmitry A Rodionov et al.   BMC GENOMICS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors

(2010) A. K. Benson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Evolution of genome architecture

(2008) Eugene V. Koonin   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes

(2008) ARMANDO GERALDES et al.   MOLECULAR ECOLOGY