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Daniel McDonald
Daniel McDonald
American Gut, Knight Lab, Department of Pediatrics, UCSD
Verifisert e-postadresse på ucsd.edu - Startside
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QIIME allows analysis of high-throughput community sequencing data
JG Caporaso, J Kuczynski, J Stombaugh, K Bittinger, FD Bushman, ...
Nature methods 7 (5), 335-336, 2010
364362010
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, CC Abnet, GA Al-Ghalith, ...
Nature biotechnology 37 (8), 852-857, 2019
175602019
Structure, function and diversity of the healthy human microbiome
nature 486 (7402), 207-214, 2012
110072012
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
MGI Langille, J Zaneveld, JG Caporaso, D McDonald, D Knights, ...
Nature biotechnology 31 (9), 814-821, 2013
90252013
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
D McDonald, MN Price, J Goodrich, EP Nawrocki, TZ DeSantis, A Probst, ...
The ISME journal 6 (3), 610-618, 2012
54672012
The treatment-naive microbiome in new-onset Crohn’s disease
D Gevers, S Kugathasan, LA Denson, Y Vázquez-Baeza, W Van Treuren, ...
Cell host & microbe 15 (3), 382-392, 2014
35452014
A communal catalogue reveals Earth’s multiscale microbial diversity
LR Thompson, JG Sanders, D McDonald, A Amir, J Ladau, KJ Locey, ...
Nature 551 (7681), 457-463, 2017
25232017
A framework for human microbiome research
Nature 486 (7402), 215-221, 2012
17782012
Best practices for analysing microbiomes
R Knight, A Vrbanac, BC Taylor, A Aksenov, C Callewaert, J Debelius, ...
Nature Reviews Microbiology 16 (7), 410-422, 2018
16862018
Deblur rapidly resolves single-nucleotide community sequence patterns
A Amir, D McDonald, JA Navas-Molina, E Kopylova, JT Morton, Z Zech Xu, ...
MSystems 2 (2), 10.1128/msystems. 00191-16, 2017
15452017
Strains, functions and dynamics in the expanded Human Microbiome Project
J Lloyd-Price, A Mahurkar, G Rahnavard, J Crabtree, J Orvis, AB Hall, ...
Nature 550 (7674), 61-66, 2017
12782017
Dynamics of the human gut microbiome in inflammatory bowel disease
J Halfvarson, CJ Brislawn, R Lamendella, Y Vázquez-Baeza, WA Walters, ...
Nature microbiology 2 (5), 1-7, 2017
11972017
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, C Abnet, GA Al-Ghalith, ...
PeerJ Preprints, 2018
10372018
GABA-modulating bacteria of the human gut microbiota
P Strandwitz, KH Kim, D Terekhova, JK Liu, A Sharma, J Levering, ...
Nature microbiology 4 (3), 396-403, 2019
9652019
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
D McDonald, JC Clemente, J Kuczynski, JR Rideout, J Stombaugh, ...
Gigascience 1 (1), 2047-217X-1-7, 2012
8322012
Regional variation limits applications of healthy gut microbiome reference ranges and disease models
Y He, W Wu, HM Zheng, P Li, D McDonald, HF Sheng, MX Chen, ...
Nature medicine 24 (10), 1532-1535, 2018
8312018
Forensic identification using skin bacterial communities
N Fierer, CL Lauber, N Zhou, D McDonald, EK Costello, R Knight
Proceedings of the National Academy of Sciences 107 (14), 6477-6481, 2010
7992010
American gut: an open platform for citizen science microbiome research
D McDonald, E Hyde, JW Debelius, JT Morton, A Gonzalez, G Ackermann, ...
Msystems 3 (3), 10.1128/msystems. 00031-18, 2018
7722018
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
JR Rideout, Y He, JA Navas-Molina, WA Walters, LK Ursell, SM Gibbons, ...
PeerJ 2, e545, 2014
6452014
Qiita: rapid, web-enabled microbiome meta-analysis
A Gonzalez, JA Navas-Molina, T Kosciolek, D McDonald, ...
Nature methods 15 (10), 796-798, 2018
6112018
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Artikler 1–20