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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Posted ContentDOI
Reference data based insights expand understanding of human metabolomes
Julia M. Gauglitz,Julia M. Gauglitz,Wout Bittremieux,Wout Bittremieux,Wout Bittremieux,Candace L. Williams,Kelly C. Weldon,Kelly C. Weldon,Morgan Panitchpakdi,Morgan Panitchpakdi,Francesca Di Ottavio,Christine M. Aceves,Christine M. Aceves,Elizabeth Brown,Elizabeth Brown,Nicole Sikora,Nicole Sikora,Alan K. Jarmusch,Alan K. Jarmusch,Cameron Martino,Anupriya Tripathi,Anupriya Tripathi,Erfan Sayyari,Justin P. Shaffer,Roxana Coras,Fernando Vargas,Fernando Vargas,Lindsay DeRight Goldasich,Tara Schwartz,MacKenzie Bryant,Gregory Humphrey,Abigail J. Johnson,Katharina Spengler,Pedro Belda-Ferre,Edgar Diaz,Daniel McDonald,Qiyun Zhu,Dominic S. Nguyen,Emmanuel O. Elijah,Emmanuel O. Elijah,Mingxun Wang,Mingxun Wang,Clarisse Marotz,Kate E. Sprecher,Kate E. Sprecher,Daniela Vargas Robles,Dana Withrow,Gail Ackermann,Lourdes Herrera,Barry J. Bradford,Lucas Miranda Marques,Juliano Geraldo Amaral,Rodrigo Moreira da Silva,Flávio Protaso Veras,Thiago M. Cunha,Renê Donizeti Ribeiro de Oliveira,Paulo Louzada-Junior,Robert H. Mills,Douglas Galasko,Parambir S. Dulai,Curt Wittenberg,David Gonzalez,Robert Terkeltaub,Megan M. Doty,Megan M. Doty,Jae H. Kim,Kyung E. Rhee,Julia Beauchamp-Walters,Kenneth P. Wright,Maria Gloria Dominguez-Bello,Mark J. Manary,Michelli F. Oliveira,Brigid S. Boland,Norberto Peporine Lopes,Monica Guma,Austin D. Swafford,Rachel J. Dutton,Rob Knight,Pieter C. Dorrestein +78 more
TL;DR: It is discovered that food-based annotations increase the interpreted fraction of molecular features 7-fold, providing a general framework for expanding the interpretability of human metabolomic “dark matter.”
Posted ContentDOI
Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs
Jeremiah J. Minich,Farhana Ali,Clarisse Marotz,Pedro Belda-Ferre,Leslie Y. Chiang,Justin P. Shaffer,Carolina S. Carpenter,Daniel McDonald,Jack A. Gilbert,Sarah M. Allard,Eric E. Allen,Rob Knight,Daniel A. Sweeney,Austin D. Swafford +13 more
TL;DR: The feasibility of using alternative consumer-grade swabs stored in 95% ethanol rather than viral transport media to detect SARS-CoV-2 from ten hospitalized persons and hospital rooms is demonstrated.
Journal ArticleDOI
Reply to: Examining microbe-metabolite correlations by linear methods
James T. Morton,Daniel McDonald,Alexander A. Aksenov,Alexander A. Aksenov,Louis-Félix Nothias,Louis-Félix Nothias,James R. Foulds,Robert A. Quinn,Michelle H. Badri,Tami L. Swenson,Marc W. Van Goethem,Trent R. Northen,Trent R. Northen,Yoshiki Vázquez-Baeza,Mingxun Wang,Mingxun Wang,Nicholas A. Bokulich,Aaron Watters,Se Jin Song,Richard Bonneau,Pieter C. Dorrestein,Pieter C. Dorrestein,Rob Knight +22 more
TL;DR: Morton, James T; McDonald, Daniel; Aksenov, Alexander A; Nothias, Louis Felix; Foulds, James R; Quinn, Robert A; Badri, Michelle H; Swenson, Tami L; Van Goethem, Marc W; Northen, Trent R; Vazquez-Baeza, Yoshiki; Wang, Mingxun; Bokulich, Nicholas A; Watters, Aaron; Song, Se Jin; Bonneau, Richard; Dorrestein, Pieter C; Knight, Rob RE
Posted ContentDOI
Greengenes2 enables a shared data universe for microbiome studies
Daniel McDonald,Yueyu Jiang,M. Erdal Balaban,Kalen Cantrell,Qiyun Zhu,Antonio Gonzalez,James T. Morton,Giorgia Nicolaou,Donovan H. Parks,Søren Michael Karst,Mads Albertsen,Philip Hugenholtz,Todd Z. DeSantis,Se Jin Song,Andrew Bartko,Aki S. Havulinna,Pekka Jousilahti,Susan Cheng,Teemu J. Niiranen,Mohit P. Jain,Veikko Salomaa,Leo Lahti,Siavash Mirarab,Rob Knight +23 more
TL;DR: Greengenes2 as mentioned in this paper showed that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy, and in phenotype effect size when analyzed with the same tree.
Proceedings ArticleDOI
Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment
TL;DR: A new ensemble-based task dispatching system is designed and implemented that is deployed on a Blue Gene/L system in conjunction with the Blue Gene's High Throughput Computing (HTC) capability, able to efficiently process and dispatch large numbers of very short tasks to over a thousand cores.