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Author Details

Justin P Shaffer
University of California San Diego
2017
26
12
PMIDPaper TitleJournal TitlePublished Year
36814836Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies.Cell Rep Methods2023
37853256Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation.Nat Biotechnol2023
35293790Transcriptional Profiles of a Foliar Fungal Endophyte (<i>Pestalotiopsis</i>, Ascomycota) and Its Bacterial Symbiont (<i>Luteibacter</i>, <i>Gammaproteobacteria</i>) Reveal Sulfur Exchange and Growth Regulation during Early Phases of Symbiotic Interaction.mSystems2022
35477286Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype.mSystems2022
35798960Enhancing untargeted metabolomics using metadata-based source annotation.Nat Biotechnol2022
35369727Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy.mSystems2022
35713407A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities.Biotechniques2022
36179670Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions.Cell2022
35968805Postnatal exposure to ambient air pollutants is associated with the composition of the infant gut microbiota at 6-months of age.Gut Microbes2022
35293792Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases.mSystems2022
33947809Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".mSystems2021
33622857Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.mSystems2021
33512248A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.Biotechniques2021
33482920Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment.Microbiome2021
34424832Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California.Gut Microbes2021
33941606Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information.Genome Res2021
34103074SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment.Microbiome2021
32540955Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information.Genome Res2020
33200135A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.bioRxiv2020
33236030Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment.medRxiv2020
32839765Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment.Res Sq2020
32184365Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome.mSystems2020
31671129Soil-borne fungi influence seed germination and mortality, with implications for coexistence of desert winter annual plants.PLoS One2019
31672155Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity.Genome Biol2019
28936944Bacterial Endosymbionts: Master Modulators of Fungal Phenotypes.Microbiol Spectr2017
28382021An Endohyphal Bacterium (<i>Chitinophaga</i>, Bacteroidetes) Alters Carbon Source Use by <i>Fusarium keratoplasticum</i> (<i>F. solani</i> Species Complex, Nectriaceae).Front Microbiol2017
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Collaborators

University of California San Diego
Co-authored papers 12
University of California San Diego
Co-authored papers 11
Center for Microbiome Innovation, University of California San Diego
Co-authored papers 11
Center for Microbiome Innovation, University of California San Diego
Co-authored papers 10
University of California
Co-authored papers 9
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Co-authored papers 8
University of California
Co-authored papers 8
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Co-authored papers 6
Center for Microbiome Innovation, University of California San Diego
Co-authored papers 6
Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University
Co-authored papers 5
Center for Microbiome Innovation, University of California San Diego
Co-authored papers 4
Co-authored papers 3
Cumming School of Medicine, University of Calgary
Co-authored papers 3
University of Maryland School of Medicine, Institute for Genome Sciences
Co-authored papers 2
Co-authored papers 2
University of Minnesota
Co-authored papers 2
San Diego State University
Co-authored papers 2
University of California San Diego
Co-authored papers 2
The University of Arizona
Co-authored papers 2
University of California
Co-authored papers 2
Pacific Northwest National Laboratory
Co-authored papers 2
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 2
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 2
University of Minnesota
Co-authored papers 2
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 2
Oak Ridge National Laboratory
Co-authored papers 2
Co-authored papers 2
Lawrence Berkeley National Laboratory
Co-authored papers 2
The Scripps Research Institute
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