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Jai Ram Rideout
Jai Ram Rideout
One Codex
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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
129652019
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
129622019
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
129622019
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
NA Bokulich, BD Kaehler, JR Rideout, M Dillon, E Bolyen, R Knight, ...
Microbiome 6, 1-17, 2018
35632018
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
9632018
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
7832012
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
6172014
Qiita: rapid, web-enabled microbiome meta-analysis
A Gonzalez, JA Navas-Molina, T Kosciolek, D McDonald, ...
Nature methods 15 (10), 796-798, 2018
5192018
Temporal variability is a personalized feature of the human microbiome
GE Flores, JG Caporaso, JB Henley, JR Rideout, D Domogala, J Chase, ...
Genome biology 15, 1-13, 2014
4312014
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites
LK Ursell, JC Clemente, JR Rideout, D Gevers, JG Caporaso, R Knight
Journal of Allergy and Clinical Immunology 129 (5), 1204-1208, 2012
3852012
q2-longitudinal: longitudinal and paired-sample analyses of microbiome data
NA Bokulich, MR Dillon, Y Zhang, JR Rideout, E Bolyen, H Li, PS Albert, ...
MSystems 3 (6), 10.1128/msystems. 00219-18, 2018
1872018
Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity
Y He, JG Caporaso, XT Jiang, HF Sheng, SM Huse, JR Rideout, ...
Microbiome 3, 1-10, 2015
1822015
QIIME 2: reproducible, interactive, scalable, and extensible microbiome data science. PeerJ
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, C Abnet, GA Al-Ghalith, ...
Inc 6, e27295v2, 2018
1692018
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience 1: 7
D McDonald, JC Clemente, J Kuczynski, JR Rideout, J Stombaugh, ...
1272012
mockrobiota: a public resource for microbiome bioinformatics benchmarking
NA Bokulich, JR Rideout, WG Mercurio, A Shiffer, B Wolfe, CF Maurice, ...
Msystems 1 (5), 10.1128/msystems. 00062-16, 2016
692016
Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone
DW Kang, JK DiBaise, ZE Ilhan, MD Crowell, JR Rideout, JG Caporaso, ...
Anaerobe 33, 33-41, 2015
612015
Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
J Fouquier, JR Rideout, E Bolyen, J Chase, A Shiffer, D McDonald, ...
Microbiome 4, 1-10, 2016
572016
Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets
JR Rideout, JH Chase, E Bolyen, G Ackermann, A González, R Knight, ...
Gigascience 5 (1), s13742-016-0133-6, 2016
442016
A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments
NA Bokulich, JR Rideout, E Kopylova, E Bolyen, J Patnode, Z Ellett, ...
PeerJ PrePrints 3, e934v2, 2015
342015
Optimizing taxonomic classification of marker gene amplicon sequences
NA Bokulich, BD Kaehler, JR Rideout, M Dillon, E Bolyen, R Knight, ...
PeerJ Preprints 6, e3208v2, 2018
322018
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