| 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 | 13319 | 2019 |
| 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 | 3627 | 2018 |
| 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 | 970 | 2018 |
| Qiita: rapid, web-enabled microbiome meta-analysis A Gonzalez, JA Navas-Molina, T Kosciolek, D McDonald, ... Nature methods 15 (10), 796-798, 2018 | 525 | 2018 |
| QIIME 2 enables comprehensive end‐to‐end analysis of diverse microbiome data and comparative studies with publicly available data M Estaki, L Jiang, NA Bokulich, D McDonald, A González, T Kosciolek, ... Current protocols in bioinformatics 70 (1), e100, 2020 | 264 | 2020 |
| 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 | 189 | 2018 |
| 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 | 170 | 2018 |
| q2-sample-classifier: machine-learning tools for microbiome classification and regression NA Bokulich, MR Dillon, E Bolyen, BD Kaehler, GA Huttley, JG Caporaso Journal of open research software 3 (30), 2018 | 151 | 2018 |
| 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 | 57 | 2016 |
| 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 | 46 | 2016 |
| 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 | 34 | 2015 |
| 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 | 33 | 2018 |
| An early pandemic analysis of SARS-CoV-2 population structure and dynamics in Arizona JT Ladner, BB Larsen, JR Bowers, CM Hepp, E Bolyen, M Folkerts, ... MBio 11 (5), 10.1128/mbio. 02107-20, 2020 | 26 | 2020 |
| QIIME 2: reproducible, interactive, scalable, and extensible microbiome data science. PeerJ Preprints 6: e27295v2 E Bolyen, JR Rideout, MR Dillon, NA Bokulich, C Abnet, GA Al-Ghalith, ... | 26 | 2018 |
| Domestic canines do not display evidence of gut microbial dysbiosis in the presence of Clostridioides (Clostridium) difficile, despite cellular susceptibility to its toxins NE Stone, AE Nunnally, V Jimenez Jr, EK Cope, JW Sahl, K Sheridan, ... Anaerobe 58, 53-72, 2019 | 23 | 2019 |
| Predicting neurodegenerative disease using Prepathology gut microbiota composition: A longitudinal study in mice modeling Alzheimer’s disease pathologies EM Borsom, K Conn, CR Keefe, C Herman, GM Orsini, AH Hirsch, ... Microbiology Spectrum 11 (2), e03458-22, 2023 | 20 | 2023 |
| An Introduction to Applied Bioinformatics: a free, open, and interactive text. E Bolyen, JR Rideout, J Chase, TA Pitman, A Shiffer, W Mercurio, ... The Journal of open source education 1 (5), 2018 | 20 | 2018 |
| Optimizing taxonomic classification of marker gene sequences NA Bokulich, BD Kaehler, JR Rideout, M Dillon, E Bolyen, R Knight, ... PeerJ Preprints, 2017 | 18 | 2017 |
| Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity E Bolyen, MR Dillon, NA Bokulich, JT Ladner, BB Larsen, CM Hepp, ... F1000Research 9, 2020 | 17 | 2020 |
| q2-longitudinal: a QIIME 2 plugin for longitudinal and paired-sample analyses of microbiome data NA Bokulich, Y Zhang, M Dillon, JR Rideout, E Bolyen, H Li, PS Albert, ... BioRxiv, 223974, 2017 | 17 | 2017 |
