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

[1]  A. Bron,et al.  Age-Related Changes in the Gut Microbiota Modify Brain Lipid Composition , 2020, Frontiers in Cellular and Infection Microbiology.

[2]  D. Figeys,et al.  Advancing functional and translational microbiome research using meta-omics approaches , 2019, Microbiome.

[3]  B. Salehi,et al.  Gut Microbiota and Obesity: A Role for Probiotics , 2019, Nutrients.

[4]  Jack A Gilbert,et al.  Community ecology as a framework for human microbiome research , 2019, Nature Medicine.

[5]  Suzanne M. Paley,et al.  The MetaCyc database of metabolic pathways and enzymes , 2017, Nucleic Acids Res..

[6]  Arthur Brady,et al.  Strains, functions and dynamics in the expanded Human Microbiome Project , 2017, Nature.

[7]  A. Paterson,et al.  Association of host genome with intestinal microbial composition in a large healthy cohort , 2016, Nature Genetics.

[8]  T. Vatanen,et al.  The effect of host genetics on the gut microbiome , 2016, Nature Genetics.

[9]  A. K. Singh,et al.  Mobile genes in the human microbiome are structured from global to individual scales , 2016, Nature.

[10]  Emily R. Davenport,et al.  Genetic Determinants of the Gut Microbiome in UK Twins. , 2016, Cell host & microbe.

[11]  Allyson L. Byrd,et al.  Temporal Stability of the Human Skin Microbiome , 2016, Cell.

[12]  J. Raes,et al.  Population-level analysis of gut microbiome variation , 2016, Science.

[13]  Morris A. Swertz,et al.  Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity , 2016, Science.

[14]  Tony J. Kenna,et al.  Intestinal Dysbiosis in Ankylosing Spondylitis , 2016 .

[15]  Emily R. Davenport,et al.  Genome-Wide Association Studies of the Human Gut Microbiota , 2015, PloS one.

[16]  Duy Tin Truong,et al.  MetaPhlAn2 for enhanced metagenomic taxonomic profiling , 2015, Nature Methods.

[17]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[18]  Katherine H. Huang,et al.  Host genetic variation impacts microbiome composition across human body sites , 2015, Genome Biology.

[19]  Constantin Polychronakos,et al.  Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases , 2016 .

[20]  Eleazar Eskin,et al.  Genetic and environmental control of host-gut microbiota interactions , 2015, Genome research.

[21]  Qiang Feng,et al.  The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment , 2015, Nature Medicine.

[22]  S. T. de Farias,et al.  Qualitative analysis of the vaginal microbiota of healthy cattle and cattle with genital-tract disease. , 2015, Genetics and molecular research : GMR.

[23]  Jun S. Liu,et al.  The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.

[24]  A. Paterson,et al.  Determinants of Intestinal Permeability in Healthy First-Degree Relatives of Individuals with Crohn's Disease , 2015, Inflammatory bowel diseases.

[25]  Wei Chen,et al.  In vitro fermentation of fructooligosaccharides with human gut bacteria. , 2015, Food & function.

[26]  Mhairi Marshall,et al.  Brief Report: Intestinal Dysbiosis in Ankylosing Spondylitis , 2014, Arthritis & rheumatology.

[27]  Peter B. McGarvey,et al.  UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches , 2014, Bioinform..

[28]  Carson C Chow,et al.  Second-generation PLINK: rising to the challenge of larger and richer datasets , 2014, GigaScience.

[29]  Rohita Sinha,et al.  Host genetics and diet, but not immunoglobulin A expression, converge to shape compositional features of the gut microbiome in an advanced intercross population of mice , 2014, Genome Biology.

[30]  Dan Knights,et al.  Complex host genetics influence the microbiome in inflammatory bowel disease , 2014, Genome Medicine.

[31]  Angela C. Poole,et al.  Human Genetics Shape the Gut Microbiome , 2014, Cell.

[32]  Andrew H. Van Benschoten,et al.  Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. , 2014, Cell host & microbe.

[33]  Jacqueline A. Keane,et al.  Epithelial IL-22RA1-Mediated Fucosylation Promotes Intestinal Colonization Resistance to an Opportunistic Pathogen , 2014, Cell host & microbe.

[34]  F. Aujoulat,et al.  Veillonella seminalis sp. nov., a novel anaerobic Gram-stain-negative coccus from human clinical samples, and emended description of the genus Veillonella. , 2014, International journal of systematic and evolutionary microbiology.

[35]  Allyson L. Byrd,et al.  Biogeography and individuality shape function in the human skin metagenome , 2014, Nature.

[36]  Pieter B. T. Neerincx,et al.  Supplementary Information Whole-genome sequence variation , population structure and demographic history of the Dutch population , 2022 .

[37]  P. Schloss,et al.  Dynamics and associations of microbial community types across the human body , 2014, Nature.

[38]  Heng Li,et al.  Toward better understanding of artifacts in variant calling from high-coverage samples , 2014, Bioinform..

[39]  Se Jin Song,et al.  The treatment-naive microbiome in new-onset Crohn's disease. , 2014, Cell host & microbe.

[40]  Jesper V Olsen,et al.  Pathogens and host immunity in the ancient human oral cavity , 2014, Nature Genetics.

[41]  Peggy Hall,et al.  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..

[42]  Arthur Brady,et al.  MetaRef: a pan-genomic database for comparative and community microbial genomics , 2013, Nucleic Acids Res..

[43]  Eric J Alm,et al.  Host lifestyle affects human microbiota on daily timescales , 2014, Genome Biology.

[44]  A. Milosavljevic,et al.  mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities , 2014, BMC Genomics.

[45]  Peer Bork,et al.  Country-specific antibiotic use practices impact the human gut resistome , 2013, Genome research.

[46]  Akira Meguro,et al.  Genome-wide association analysis identifies new susceptibility loci for Behçet's disease and epistasis between HLA-B*51 and ERAP1 , 2013, Nature Genetics.

[47]  Mihai Pop,et al.  Bioinformatics for the Human Microbiome Project , 2012, PLoS Comput. Biol..

[48]  David C. Wilson,et al.  Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease , 2012, Nature.

[49]  K. Yanagihara,et al.  Multiple Lung Abscesses Caused by Actinomyces graevenitzii Mimicking Acute Pulmonary Coccidioidomycosis , 2012, Journal of Clinical Microbiology.

[50]  Bernard Henrissat,et al.  Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome , 2012, PLoS Comput. Biol..

[51]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.

[52]  Sven Laur,et al.  Robust rank aggregation for gene list integration and meta-analysis , 2012, Bioinform..

[53]  Andrey A. Shabalin,et al.  Matrix eQTL: ultra fast eQTL analysis via large matrix operations , 2011, Bioinform..

[54]  Paul Weston,et al.  Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility , 2011, Nature Genetics.

[55]  J. Nikkilä,et al.  Secretor Genotype (FUT2 gene) Is Strongly Associated with the Composition of Bifidobacteria in the Human Intestine , 2011, PloS one.

[56]  Jesse R. Zaneveld,et al.  Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins , 2011, Proceedings of the National Academy of Sciences.

[57]  Josyf Mychaleckyj,et al.  Robust relationship inference in genome-wide association studies , 2010, Bioinform..

[58]  Matti Pirinen,et al.  A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1 , 2010, Nature Genetics.

[59]  Min Zhang,et al.  Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors , 2010, Proceedings of the National Academy of Sciences.

[60]  Daniel Rios,et al.  Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor , 2022 .

[61]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[62]  Leena Peltonen,et al.  Identification of a variant associated with adult-type hypolactasia , 2002, Nature Genetics.

[63]  E. Baulieu,et al.  Dehydroepiandrosterone (DHEA), DHEA sulfate, and aging: contribution of the DHEAge Study to a sociobiomedical issue. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[64]  G. Lennon,et al.  Sequence and expression of a candidate for the human Secretor blood group alpha(1,2)fucosyltransferase gene (FUT2). Homozygosity for an enzyme-inactivating nonsense mutation commonly correlates with the non-secretor phenotype. , 1995, The Journal of biological chemistry.