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
168202010
Structure, function and diversity of the healthy human microbiome
C Huttenhower, D Gevers, R Knight, S Abubucker, JH Badger, ...
nature 486 (7402), 207, 2012
46392012
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
30712013
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
25992012
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
13892014
A framework for human microbiome research
BA Methé, KE Nelson, M Pop, HH Creasy, MG Giglio, C Huttenhower, ...
nature 486 (7402), 215, 2012
12412012
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
4622010
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
3862017
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
3552012
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
3332014
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
2462017
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
2222017
Rethinking “enterotypes”
D Knights, TL Ward, CE McKinlay, H Miller, A Gonzalez, D McDonald, ...
Cell host & microbe 16 (4), 433-437, 2014
2212014
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
2192010
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
1932007
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
1662011
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
1572017
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
1462018
Best practices for analysing microbiomes
R Knight, A Vrbanac, BC Taylor, A Aksenov, C Callewaert, J Debelius, ...
Nature Reviews Microbiology 16 (7), 410, 2018
1402018
Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat
JK Harris, JG Caporaso, JJ Walker, JR Spear, NJ Gold, CE Robertson, ...
The ISME journal 7 (1), 50, 2013
1312013
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Articles 1–20