| 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 | 15615 | 2019 |
| Metagenomic biomarker discovery and explanation N Segata, J Izard, L Waldron, D Gevers, L Miropolsky, WS Garrett, ... Genome biology 12, 1-18, 2011 | 12998 | 2011 |
| Structure, function and diversity of the healthy human microbiome nature 486 (7402), 207-214, 2012 | 10515 | 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), 814-821, 2013 | 8808 | 2013 |
| PICRUSt2 for prediction of metagenome functions GM Douglas, VJ Maffei, JR Zaneveld, SN Yurgel, JR Brown, CM Taylor, ... Nature biotechnology 38 (6), 685-688, 2020 | 3640 | 2020 |
| 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 | 3442 | 2014 |
| Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment XC Morgan, TL Tickle, H Sokol, D Gevers, KL Devaney, DV Ward, ... Genome biology 13, 1-18, 2012 | 2959 | 2012 |
| A framework for human microbiome research nature 486 (7402), 215-221, 2012 | 2616 | 2012 |
| Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases J Lloyd-Price, C Arze, AN Ananthakrishnan, M Schirmer, J Avila-Pacheco, ... Nature 569 (7758), 655-662, 2019 | 2193 | 2019 |
| Genomic analysis identifies association of Fusobacterium with colorectal carcinoma AD Kostic, D Gevers, CS Pedamallu, M Michaud, F Duke, AM Earl, ... Genome research 22 (2), 292-298, 2012 | 2117 | 2012 |
| MetaPhlAn2 for enhanced metagenomic taxonomic profiling DT Truong, EA Franzosa, TL Tickle, M Scholz, G Weingart, E Pasolli, ... Nature methods 12 (10), 902-903, 2015 | 2094 | 2015 |
| Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis JU Scher, A Sczesnak, RS Longman, N Segata, C Ubeda, C Bielski, ... elife 2, e01202, 2013 | 1996 | 2013 |
| The healthy human microbiome J Lloyd-Price, G Abu-Ali, C Huttenhower Genome medicine 8, 1-11, 2016 | 1983 | 2016 |
| Metagenomic microbial community profiling using unique clade-specific marker genes N Segata, L Waldron, A Ballarini, V Narasimhan, O Jousson, ... Nature methods 9 (8), 811-814, 2012 | 1933 | 2012 |
| Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity A Zhernakova, A Kurilshikov, MJ Bonder, EF Tigchelaar, M Schirmer, ... Science 352 (6285), 565-569, 2016 | 1834 | 2016 |
| Temporal development of the gut microbiome in early childhood from the TEDDY study CJ Stewart, NJ Ajami, JL O’Brien, DS Hutchinson, DP Smith, MC Wong, ... Nature 562 (7728), 583-588, 2018 | 1688 | 2018 |
| Microbial co-occurrence relationships in the human microbiome K Faust, JF Sathirapongsasuti, J Izard, N Segata, D Gevers, J Raes, ... PLoS computational biology 8 (7), e1002606, 2012 | 1561 | 2012 |
| Gut microbiome structure and metabolic activity in inflammatory bowel disease EA Franzosa, A Sirota-Madi, J Avila-Pacheco, N Fornelos, HJ Haiser, ... Nature microbiology 4 (2), 293-305, 2019 | 1452 | 2019 |
| Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine LT Geller, M Barzily-Rokni, T Danino, OH Jonas, N Shental, D Nejman, ... Science 357 (6356), 1156-1160, 2017 | 1426 | 2017 |
| Species-level functional profiling of metagenomes and metatranscriptomes EA Franzosa, LJ McIver, G Rahnavard, LR Thompson, M Schirmer, ... Nature methods 15 (11), 962-968, 2018 | 1384 | 2018 |
