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.
Papers
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Proceedings ArticleDOI
Galileo: Citizen-led Experimentation Using a Social Computing System
Vineet Pandey,Tushar Koul,Chen Yang,Daniel McDonald,Mad Price Ball,Bastian Greshake Tzovaras,Rob Knight,Scott R. Klemmer +7 more
TL;DR: The Galileo system as discussed by the authors provides procedural support using three techniques: 1) experimental design workflow that provides just-in-time training; 2) review workflow with scaffolded questions; and 3) automated routines for data collection.
Journal ArticleDOI
Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases
George Armstrong,Cameron Martino,Justin Morris,Behnam Khaleghi,Jaeyoung Kang,Jeff DeReus,Qiyun Zhu,Daniel Roush,Daniel McDonald,Antonio Gonazlez,Justin P. Shaffer,Carolina S. Carpenter,Mehrbod Estaki,Stephen Wandro,Sean Eilert,Ameen Akel,Justin Eno,Kenneth E Curewitz,Austin D. Swafford,Niema Moshiri,Tajana Rosing,Rob Knight +21 more
TL;DR: Fastp and Minimap2 as discussed by the authors can reduce the computational complexity of preprocessing tasks such as adaptor and primer trimming and host removal by 5-fold or more on the same hardware while maintaining a high degree of correctness, greatly reducing the time to interpret results.
Posted ContentDOI
Rapid, large-scale wastewater surveillance and automated reporting system enabled early detection of nearly 85% of COVID-19 cases on a University campus
Smruthi Karthikeyan,Andrew Nguyen,Daniel McDonald,Yijian Zong,Nancy Ronquillo,Junting Ren,Jingjing Zou,Sawyer Farmer,Greg Humphrey,D. M. Henderson,Tara Javidi,Karen Messer,Cheryl L. Anderson,Robert T. Schooley,Natasha K Martin,Rob Knight +15 more
TL;DR: In this paper, a large-scale GIS enabled building-level wastewater monitoring system associated with the on-campus residences of 7614 individuals was employed to detect COVID-19 infection dynamics.
Journal ArticleDOI
Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References
Daniel Hakim,Stephen Wandro,Karsten Zengler,Livia S. Zaramela,Brent Nowinski,Austin D. Swafford,Qiyun Zhu,Se Jin Song,Antonio Gonzalez,Daniel McDonald,Rob Knight +10 more
TL;DR: Zebra, a method to compute and threshold the genome cover metric across like samples, a recurrence to estimate genome cover and confirm saturation, and guidance for choosing cover thresholds in real world scenarios are presented.
Journal ArticleDOI
Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles
James T. Morton,Dongxue Jin,Robert H. Mills,Yan Shao,Gibraan Rahman,Daniel McDonald,Qiyun Zhu,M. Erdal Balaban,Yueyu Jiang,Kalen Cantrell,Antonio Gonzalez,Linoy Mia Frankiensztajn,Sandra Martin-Brevet,Kirsten Berding,Brittany D. Needham,María Fernanda Zurita,Maude M. David,Olga V. Averina,Alexey S. Kovtun,Antonio Noto,Michele Mussap,Mingbang Wang,Daniel N. Frank,Ellen Li,Wenhao Zhou,Vassilios Fanos,Valery N. Danilenko,Dennis P. Wall,Paul Cardenas,Manuel E. Baldeón,Sébastien Jacquemont,Omry Koren,Evan Elliott,Ramnik J. Xavier,Sarkis K. Mazmanian,Rob Knight,Jack A. Gilbert,Sharon M. Donovan,Trevor D. Lawley,Bob Carpenter,Richard Bonneau,Gaspar Taroncher-Oldenburg +41 more
TL;DR: In this paper , a Bayesian differential ranking algorithm was used to identify ASD-associated molecular and taxa profiles across 10 cross-sectional microbiome datasets and 15 other datasets, including dietary patterns, metabolomics, cytokine profiles and human brain gene expression profiles.