Daniel McDonald
Daniel McDonald
American Gut, Knight Lab, Department of Pediatrics, UCSD
Verified email at ucsd.edu - Homepage
TitleCited byYear
QIIME allows analysis of high-throughput community sequencing data
JG Caporaso, J Kuczynski, J Stombaugh, K Bittinger, FD Bushman, ...
Nature methods 7 (5), 335, 2010
177122010
Structure, function and diversity of the healthy human microbiome
C Huttenhower, D Gevers, R Knight, S Abubucker, JH Badger, ...
nature 486 (7402), 207, 2012
48482012
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, 2013
32892013
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, 2012
27132012
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
14582014
A framework for human microbiome research
BA Methé, KE Nelson, M Pop, HH Creasy, MG Giglio, C Huttenhower, ...
nature 486 (7402), 215, 2012
12842012
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
4742010
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, 2017
4442017
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), 7, 2012
3742012
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
3502014
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, 2017
2842017
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), 17004, 2017
2412017
Rethinking “enterotypes”
D Knights, TL Ward, CE McKinlay, H Miller, A Gonzalez, D McDonald, ...
Cell host & microbe 16 (4), 433-437, 2014
2322014
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
J Kuczynski, Z Liu, C Lozupone, D McDonald, N Fierer, R Knight
Nature methods 7 (10), 813, 2010
2282010
PyCogent: a toolkit for making sense from sequence
R Knight, P Maxwell, A Birmingham, J Carnes, JG Caporaso, BC Easton, ...
Genome biology 8 (8), R171, 2007
1942007
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
1842018
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
1712018
Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins
EE Hansen, CA Lozupone, FE Rey, M Wu, JL Guruge, A Narra, ...
Proceedings of the National Academy of Sciences 108 (Supplement 1), 4599-4606, 2011
1692011
Deblur rapidly resolves single-nucleotide community sequence patterns
A Amir, D McDonald, JA Navas-Molina, E Kopylova, JT Morton, ZZ Xu, ...
MSystems 2 (2), e00191-16, 2017
1642017
A wellness study of 108 individuals using personal, dense, dynamic data clouds
ND Price, AT Magis, JC Earls, G Glusman, R Levy, C Lausted, ...
Nature biotechnology 35 (8), 747, 2017
1382017
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