A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases

[1]  Jian Yang,et al.  The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases , 2020, Microbiome.

[2]  Shiraz A. Shah,et al.  Genetics of human gut microbiome composition , 2020, bioRxiv.

[3]  M. Kanai,et al.  Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases , 2020, Nature Genetics.

[4]  Huijue Jia,et al.  Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omes , 2019, bioRxiv.

[5]  E. Segal,et al.  Potential roles of gut microbiome and metabolites in modulating ALS in mice , 2019, Nature.

[6]  Stephanie A. Bien,et al.  Genetic analyses of diverse populations improves discovery for complex traits , 2019, Nature.

[7]  Suisha Liang,et al.  A multi-omic cohort as a reference point for promoting a healthy human gut microbiome , 2019 .

[8]  J. Scaria,et al.  The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches , 2019, GigaScience.

[9]  Huanming Yang,et al.  Calorie restriction intervention induces enterotype-associated BMI loss in nonobese individuals , 2019, bioRxiv.

[10]  B. Stranger,et al.  The role of sex in the genomics of human complex traits , 2018, Nature Reviews Genetics.

[11]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[12]  Benjamin M Hillmann,et al.  US Immigration Westernizes the Human Gut Microbiome , 2018, Cell.

[13]  Brian L Browning,et al.  A One-Penny Imputed Genome from Next-Generation Reference Panels. , 2018, American journal of human genetics.

[14]  A. Yashin,et al.  Sex Differences in Genetic Associations With Longevity , 2018, JAMA network open.

[15]  Brian L. Browning,et al.  A one penny imputed genome from next generation reference panels , 2018, bioRxiv.

[16]  A. Kurilshikov,et al.  Environment dominates over host genetics in shaping human gut microbiota , 2018, Nature.

[17]  Jian Wang,et al.  A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses , 2018, Microbiome.

[18]  D. Posthuma,et al.  Functional mapping and annotation of genetic associations with FUMA , 2017, Nature Communications.

[19]  Jun Wang,et al.  Quantitative microbiome profiling links gut community variation to microbial load , 2017, Nature.

[20]  J. Segre,et al.  Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation , 2017, Science.

[21]  Xun Xu,et al.  The gut microbiome in atherosclerotic cardiovascular disease , 2017, Nature Communications.

[22]  T. Le Bihan,et al.  Nucleoredoxin guards against oxidative stress by protecting antioxidant enzymes , 2017, Proceedings of the National Academy of Sciences.

[23]  Huijue Jia,et al.  Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention , 2017, Nature Medicine.

[24]  Cheng Li,et al.  GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses , 2017, Nucleic Acids Res..

[25]  Y. Altuntas,et al.  [Microbiota and metabolic syndrome]. , 2017, Turk Kardiyoloji Dernegi arsivi : Turk Kardiyoloji Derneginin yayin organidir.

[26]  T. Spector,et al.  Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome. , 2016, Cell systems.

[27]  Helen E. Parkinson,et al.  The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) , 2016, Nucleic Acids Res..

[28]  U. Nöthlings,et al.  Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota , 2016, Nature Genetics.

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

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

[31]  Xun Xu,et al.  A reference gene catalogue of the pig gut microbiome , 2016, Nature Microbiology.

[32]  Jun Wang,et al.  Metagenome-wide association studies: fine-mining the microbiome , 2016, Nature Reviews Microbiology.

[33]  F. Hildebrand,et al.  Species–function relationships shape ecological properties of the human gut microbiome , 2016, Nature Microbiology.

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

[35]  Yun-Mi Song,et al.  The effect of heritability and host genetics on the gut microbiota and metabolic syndrome , 2016, Gut.

[36]  R. Fichorova,et al.  The Human Microbiome during Bacterial Vaginosis , 2016, Clinical Microbiology Reviews.

[37]  Wei Lin,et al.  Large Covariance Estimation for Compositional Data Via Composition-Adjusted Thresholding , 2016, Journal of the American Statistical Association.

[38]  E. Vogtmann,et al.  MicrobiomeGWAS: A Tool for Identifying Host Genetic Variants Associated with Microbiome Composition , 2015, bioRxiv.

[39]  T. R. Licht,et al.  A catalog of the mouse gut metagenome , 2015, Nature Biotechnology.

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

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

[42]  T. Lehtimäki,et al.  Integrative approaches for large-scale transcriptome-wide association studies , 2015, Nature Genetics.

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

[44]  A. Antonacopoulou,et al.  Focal Adhesion Proteins α- and β-Parvin are Overexpressed in Human Colorectal Cancer and Correlate with Tumor Progression , 2015, Cancer investigation.

[45]  Ryan M. Layer,et al.  SpeedSeq: Ultra-fast personal genome analysis and interpretation , 2014, Nature Methods.

[46]  Jens Roat Kultima,et al.  An integrated catalog of reference genes in the human gut microbiome , 2014, Nature Biotechnology.

[47]  Richard Leslie,et al.  GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database , 2014, Bioinform..

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

[49]  Susumu Goto,et al.  Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..

[50]  Lars Feuk,et al.  The Database of Genomic Variants: a curated collection of structural variation in the human genome , 2013, Nucleic Acids Res..

[51]  Richard A. Gibbs,et al.  Novel Genetic Loci Identified for the Pathophysiology of Childhood Obesity in the Hispanic Population , 2012, PloS one.

[52]  Qiang Feng,et al.  A metagenome-wide association study of gut microbiota in type 2 diabetes , 2012, Nature.

[53]  Timothy L. Tickle,et al.  Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment , 2012, Genome Biology.

[54]  F. Shanahan,et al.  Categorization of the gut microbiota: enterotypes or gradients? , 2012, Nature Reviews Microbiology.

[55]  C. Quince,et al.  Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics , 2012, PloS one.

[56]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy , 2011, Nucleic Acids Res..

[57]  P. Karp,et al.  The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases , 2011, Nucleic Acids Res..

[58]  K. Davies,et al.  Oxr1 Is Essential for Protection against Oxidative Stress-Induced Neurodegeneration , 2011, PLoS genetics.

[59]  Xihong Lin,et al.  Rare-variant association testing for sequencing data with the sequence kernel association test. , 2011, American journal of human genetics.

[60]  E. Gurevich,et al.  Sex differences in the activity of signalling pathways and expression of G-protein-coupled receptor kinases in the neonatal ventral hippocampal lesion model of schizophrenia. , 2011, The international journal of neuropsychopharmacology.

[61]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[62]  Suzanne M. Paley,et al.  The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases , 2009, Nucleic Acids Res..

[63]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[64]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[65]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[66]  G. Brand,et al.  Sex Differences in Human Olfaction: Between Evidence and Enigma , 2001, The Quarterly journal of experimental psychology. B, Comparative and physiological psychology.

[67]  Falk Hildebrand,et al.  Enterotypes in the landscape of gut microbial community composition , 2017, Nature Microbiology.

[68]  Jacob M. Luber,et al.  Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing , 2017 .

[69]  Christopher E. McKinlay,et al.  Rethinking "enterotypes". , 2014, Cell host & microbe.

[70]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..