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Author Details

Yoshiki V??zquez-Baeza
Center for Microbiome Innovation, University of California San Diego
2013
70
36
PMIDPaper TitleJournal TitlePublished Year
36587850The gut microbiome is a significant risk factor for future chronic lung disease.J Allergy Clin Immunol2023
37372419Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases.Genes (Basel)2023
36814836Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies.Cell Rep Methods2023
35115689Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.Nat Genet2022
35477286Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype.mSystems2022
35369727Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy.mSystems2022
35354069Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting.Cell Metab2022
33914902Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data.Biometrics2022
35042975Correction to: Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers.ISME J2022
35087228Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity.Nat Microbiol2022
32868914Context-aware dimensionality reduction deconvolutes gut microbial community dynamics.Nat Biotechnol2021
33651661Links between gut microbiome composition and fatty liver disease in a large population sample.Gut Microbes2021
33709132Dietary factors, gut microbiota, and serum trimethylamine-N-oxide associated with cardiovascular disease in the Hispanic Community Health Study/Study of Latinos.Am J Clin Nutr2021
33727399EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets.mSystems2021
34893089Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity.Genome Biol2021
34609167Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data.mSystems2021
34479875Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes.Genome Res2021
34079079Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers.ISME J2021
34103074SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment.Microbiome2021
33986544Challenges in benchmarking metagenomic profilers.Nat Methods2021
34193290Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome.Microbiome2021
34166363Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.PLoS Comput Biol2021
33199911Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.Nat Chem Biol2021
33026068Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity.Inflamm Bowel Dis2021
33398188Reply to: Examining microbe-metabolite correlations by linear methods.Nat Methods2021
33098964Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk.Brain Behav Immun2021
32343490QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.Curr Protoc Bioinformatics2020
31930986Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations.Gastroenterology2020
32047061Human Skin, Oral, and Gut Microbiomes Predict Chronological Age.mSystems2020
33236030Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment.medRxiv2020
32576651High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy.mSystems2020
32839779Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity.bioRxiv2020
30801026Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease.mSystems2019
31672155Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity.Genome Biol2019
31686038Learning representations of microbe-metabolite interactions.Nat Methods2019
30240894Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.Clin Gastroenterol Hepatol2019
31551401Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.mSystems2019
31399723Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.Nat Biotechnol2019
31341288Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.Nat Biotechnol2019
30714619Suppression of the gut microbiome ameliorates age-related arterial dysfunction and oxidative stress in mice.J Physiol2019
29055911Guiding longitudinal sampling in IBD cohorts.Gut2018
30059804Are microbiome studies ready for hypothesis-driven research?Curr Opin Microbiol2018
30377368Striped UniFrac: enabling microbiome analysis at unprecedented scale.Nat Methods2018
30275573Qiita: rapid, web-enabled microbiome meta-analysis.Nat Methods2018
29438507Bacterial density rather than diversity correlates with hatching success across different avian species.FEMS Microbiol Ecol2018
29487294Creating a 3D microbial and chemical snapshot of a human habitat.Sci Rep2018
29795809American Gut: an Open Platform for Citizen Science Microbiome Research.mSystems2018
28968189Impacts of the Human Gut Microbiome on Therapeutics.Annu Rev Pharmacol Toxicol2018
28506317Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease.Microbiome2017
28253908Normalization and microbial differential abundance strategies depend upon data characteristics.Microbiome2017
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University of California San Diego School of Medicine
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Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University
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Cumming School of Medicine, University of Calgary
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Co-authored papers 6
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Co-authored papers 6
University of Minnesota
Co-authored papers 5
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Scripps Institution of Oceanography, University of California San Diego
Co-authored papers 4
Institute for Minority Health Research, University of Illinois at Chicago
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