| 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 | 16820 | 2010 |
| Structure, function and diversity of the healthy human microbiome C Huttenhower, D Gevers, R Knight, S Abubucker, JH Badger, ... nature 486 (7402), 207, 2012 | 4639 | 2012 |
| 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 | 3071 | 2013 |
| 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 | 2599 | 2012 |
| 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 | 1389 | 2014 |
| A framework for human microbiome research BA Methé, KE Nelson, M Pop, HH Creasy, MG Giglio, C Huttenhower, ... nature 486 (7402), 215, 2012 | 1241 | 2012 |
| 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 | 462 | 2010 |
| 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 | 386 | 2017 |
| 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 | 355 | 2012 |
| 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 | 333 | 2014 |
| 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 | 246 | 2017 |
| 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 | 222 | 2017 |
| Rethinking “enterotypes” D Knights, TL Ward, CE McKinlay, H Miller, A Gonzalez, D McDonald, ... Cell host & microbe 16 (4), 433-437, 2014 | 221 | 2014 |
| 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 | 219 | 2010 |
| 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 | 193 | 2007 |
| 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 | 166 | 2011 |
| 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 | 157 | 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 | 146 | 2018 |
| Best practices for analysing microbiomes R Knight, A Vrbanac, BC Taylor, A Aksenov, C Callewaert, J Debelius, ... Nature Reviews Microbiology 16 (7), 410, 2018 | 140 | 2018 |
| 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 | 131 | 2013 |
Rob KnightDirector, Center for Microbiome Innovation; Professor, Pediatrics, Bioengineering and CSE, UCSDVerified email at ucsd.edu