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Author Details

Daniel McDonald
University of California San Diego
2007
119
49
PMIDPaper TitleJournal TitlePublished Year
37500913Greengenes2 unifies microbial data in a single reference tree.Nat Biotechnol2024
37853258Author Correction: Greengenes2 unifies microbial data in a single reference tree.Nat Biotechnol2024
37853257Author Correction: Generation of accurate, expandable phylogenomic trees with uDance.Nat Biotechnol2024
37500914Generation of accurate, expandable phylogenomic trees with uDance.Nat Biotechnol2024
36828255Diet Quality and the Fecal Microbiota in Adults in the American Gut Project.J Nutr2023
37853256Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation.Nat Biotechnol2023
37577622A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data.Res Sq2023
37350611Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution.mSystems2023
37339957Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors.Nat Commun2023
37372419Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases.Genes (Basel)2023
37365313Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles.Nat Neurosci2023
37231087You are what you excrete.Nat Microbiol2023
36814836Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies.Cell Rep Methods2023
36475896Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses.mSystems2023
33978602Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection.Female Pelvic Med Reconstr Surg2022
35477286Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype.mSystems2022
35411350Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.medRxiv2022
35798960Enhancing untargeted metabolomics using metadata-based source annotation.Nat Biotechnol2022
35798029Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.Nature2022
35369727Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy.mSystems2022
35638356Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase.mSystems2022
36396943Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species.Nat Commun2022
36073806Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References.mSystems2022
36245486The gastrointestinal and microbiome impact of a resistant starch blend from potato, banana, and apple fibers: A randomized clinical trial using smart caps.Front Nutr2022
36304280Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data.Front Bioinform2022
35293792Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases.mSystems2022
34617562A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project.Am J Clin Nutr2022
33011173Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry.Gastroenterology2021
35590169Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding.Med2021
33853672Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection.Microbiome2021
33906915Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition.mSystems2021
33482920Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment.Microbiome2021
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
34374562Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus.mSystems2021
34846164The Fecal Microbiome and Metabolome of Pitt Hopkins Syndrome, a Severe Autism Spectrum Disorder.mSystems2021
34479875Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes.Genome Res2021
34103074SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment.Microbiome2021
34283919Nutritional Interventions and the Gut Microbiome in Children.Annu Rev Nutr2021
33199911Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.Nat Chem Biol2021
33432244High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing.Nat Methods2021
33398188Reply to: Examining microbe-metabolite correlations by linear methods.Nat Methods2021
32868914Context-aware dimensionality reduction deconvolutes gut microbial community dynamics.Nat Biotechnol2021
32343490QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.Curr Protoc Bioinformatics2020
31857734The emergence of microbiome centres.Nat Microbiol2020
33051377Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV.mSystems2020
33236030Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment.medRxiv2020
32994287Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome.mSystems2020
32839779Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity.bioRxiv2020
32839765Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment.Res Sq2020
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Collaborators

University of California
Co-authored papers 95
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Co-authored papers 38
Center for Microbiome Innovation, University of California San Diego
Co-authored papers 30
Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University
Co-authored papers 24
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Co-authored papers 19
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Co-authored papers 14
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University of California San Diego
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University of California San Diego
Co-authored papers 12
University of Minnesota
Co-authored papers 9
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Broad Institute of MIT and Harvard
Co-authored papers 8
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Co-authored papers 7
Scripps Institution of Oceanography, University of California San Diego
Co-authored papers 6
Cumming School of Medicine, University of Calgary
Co-authored papers 6
Karolinska Institutet
Co-authored papers 6
Northern Gulf Institute, Mississippi State University
Co-authored papers 6
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Center for Computational Biology & Bioinformatics , University of California
Co-authored papers 5
University of California San Diego
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California Institute of Technology
Co-authored papers 4
Institute for Systems Biology
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