D
Daniel McDonald
Researcher at University of California, San Diego
Publications - 157
Citations - 84726
Daniel McDonald is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Microbiome & Biology. The author has an hindex of 46, co-authored 128 publications receiving 64433 citations. Previous affiliations of Daniel McDonald include University of Colorado Boulder & University of California, Berkeley.
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Journal ArticleDOI
Comparison of methods for estimating the nucleotide substitution matrix
TL;DR: The availability of methods that are both fast and accurate will allow us to gain a global picture of change in the nucleotide substitution rate matrix on a genomewide scale across the tree of life.
Posted ContentDOI
Multi-omics profiling of Earth’s biomes reveals that microbial and metabolite composition are shaped by the environment
Justin P. Shaffer,Louis-Félix Nothias,Louis-Félix Nothias,Luke R. Thompson,Luke R. Thompson,Jon G. Sanders,Rodolfo A. Salido,Sneha P. Couvillion,Asker Daniel Brejnrod,Serina Huang,Franck Lejzerowicz,Holly L. Lutz,Qiyun Zhu,Cameron Martino,James T. Morton,Smruthi Karthikeyan,Mélissa Nothias-Esposito,Mélissa Nothias-Esposito,Kai Dührkop,Sebastian Böcker,Hyun-Woo Kim,Alexander A. Aksenov,Alexander A. Aksenov,Wout Bittremieux,Wout Bittremieux,Wout Bittremieux,Jeremiah J. Minich,Clarisse Marotz,Bryant Mm,Karenina Sanders,Tara Schwartz,Greg Humphrey,Vásquez-Baeza Y,Anupriya Tripathi,Anupriya Tripathi,Laxmi Parida,Anna Paola Carrieri,Niina Haiminen,Kristen L. Beck,Promi Das,A. Gonzalez,Daniel McDonald,Søren Michael Karst,Mads Albertsen,Gail Ackermann,Jeff DeReus,Torsten Thomas,Daniel Petras,Daniel Petras,Ashley Shade,James C. Stegen,Se Jin Song,Thomas O. Metz,Austin D. Swafford,Pieter C. Dorrestein,Pieter C. Dorrestein,Janet K. Jansson,Jack A. Gilbert,Rob Knight +58 more
TL;DR: In this paper, an integrated omics approach is used to describe the Earth's metabolome, which is a direct survey of metabolites associated with microbial communities spanning diverse environments using untargeted metabolomics coupled with metagenome analysis.
Posted ContentDOI
EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets
Kalen Cantrell,Marcus W. Fedarko,Gibraan Rahman,Daniel McDonald,Yimeng Yang,Thant Zaw,Antonio Gonzalez,Stefan Janssen,Mehrbod Estaki,Niina Haiminen,Kristen L. Beck,Qiyun Zhu,Qiyun Zhu,Erfan Sayyari,Jamie Morton,Anupriya Tripathi,Julia M. Gauglitz,Clarisse Marotz,Clarisse Marotz,Nathaniel L. Matteson,Cameron Martino,Jon G. Sanders,Anna Paola Carrieri,Se Jin Song,Austin D. Swafford,Pieter C. Dorrestein,Pieter C. Dorrestein,Kristian G. Andersen,Laxmi Parida,Ho-Cheol Kim,Yoshiki Vázquez-Baeza,Rob Knight +31 more
TL;DR: EMPress provides novel functionality—including ordination integration and animations—alongside many standard tree visualization features, and thus simplifies exploratory analyses of many forms of ‘omic data.
Journal ArticleDOI
Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species
Jeremiah J. Minich,Andreas Härer,Joseph Vechinski,Benjamin W. Frable,Zachary Skelton,Emily Kunselman,Michael A. Shane,Daniela S. Perry,Antonio Gonzalez,Daniel McDonald,Rob Knight,Todd P. Michael,Eric E. Allen +12 more
TL;DR: In this paper , the authors compared alpha, beta and gamma diversity while establishing a method to estimate microbial biomass associated with these host surfaces, showing that body site is the strongest driver of microbial diversity while microbial biomass and diversity is lowest in the gill of larger, pelagic fishes.