| 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 | 5723 | 2019 |
| 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 | 1437 | 2017 |
| 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), e00191-16, 2017 | 832 | 2017 |
| 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 | 750 | 2018 |
| Advancing our understanding of the human microbiome using QIIME JA Navas-Molina, JM Peralta-Sánchez, A González, PJ McMurdie, ... Methods in enzymology 531, 371-444, 2013 | 536 | 2013 |
| 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 | 528 | 2014 |
| 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), e00031-18, 2018 | 416 | 2018 |
| Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity S Shalapour, XJ Lin, IN Bastian, J Brain, AD Burt, AA Aksenov, ... Nature 551 (7680), 340-345, 2017 | 320 | 2017 |
| Qiita: rapid, web-enabled microbiome meta-analysis A Gonzalez, JA Navas-Molina, T Kosciolek, D McDonald, ... Nature methods 15 (10), 796-798, 2018 | 298 | 2018 |
| Phylogenetic placement of exact amplicon sequences improves associations with clinical information S Janssen, D McDonald, A Gonzalez, JA Navas-Molina, L Jiang, ZZ Xu, ... Msystems 3 (3), e00021-18, 2018 | 220 | 2018 |
| Balance trees reveal microbial niche differentiation JT Morton, J Sanders, RA Quinn, D McDonald, A Gonzalez, ... MSystems 2 (1), e00162-16, 2017 | 193 | 2017 |
| Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2: e00191-16 A Amir, D McDonald, JA Navas-Molina, E Kopylova, JT Morton, Z Zech Xu, ... | 151 | 2017 |
| Open-source sequence clustering methods improve the state of the art E Kopylova, JA Navas-Molina, C Mercier, ZZ Xu, F Mahé, Y He, HW Zhou, ... MSystems 1 (1), e00003-15, 2016 | 125 | 2016 |
| Bringing the dynamic microbiome to life with animations Y Vázquez-Baeza, A Gonzalez, L Smarr, D McDonald, JT Morton, ... Cell host & microbe 21 (1), 7-10, 2017 | 69 | 2017 |
| American Gut: an open platform for citizen science microbiome research. mSystems 3: e00031-18 D McDonald, E Hyde, JW Debelius, JT Morton, A Gonzalez, G Ackermann, ... DOI 10, 00031-18, 2018 | 56 | 2018 |
| Correcting for microbial blooms in fecal samples during room-temperature shipping A Amir, D McDonald, JA Navas-Molina, J Debelius, JT Morton, E Hyde, ... Msystems 2 (2), e00199-16, 2017 | 54 | 2017 |
| From sample to multi-omics conclusions in under 48 hours RA Quinn, JA Navas-Molina, ER Hyde, SJ Song, Y Vázquez-Baeza, ... Msystems 1 (2), e00038-16, 2016 | 42 | 2016 |
| The oral and skin microbiomes of captive komodo dragons are significantly shared with their habitat ER Hyde, JA Navas-Molina, SJ Song, JG Kueneman, G Ackermann, ... Msystems 1 (4), e00046-16, 2016 | 41 | 2016 |
| Balance trees reveal microbial niche differentiation. mSystems 2: e00162-16 JT Morton, J Sanders, RA Quinn, D McDonald, A Gonzalez, ... | 29 | 2017 |
| Bacterial density rather than diversity correlates with hatching success across different avian species JM Peralta-Sanchez, AM Martín-Platero, L Wegener-Parfrey, ... FEMS microbiology ecology 94 (3), fiy022, 2018 | 21 | 2018 |
