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| 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 | 2041 | 2015 |
| A proteome-scale map of the human interactome network T Rolland, M Taşan, B Charloteaux, SJ Pevzner, Q Zhong, N Sahni, S Yi, ... Cell 159 (5), 1212-1226, 2014 | 1463 | 2014 |
| 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 | 1353 | 2019 |
| 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 | 1316 | 2018 |
| Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans T Vatanen, AD Kostic, E d’Hennezel, H Siljander, EA Franzosa, ... Cell 165 (4), 842-853, 2016 | 1305 | 2016 |
| The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes AD Kostic, D Gevers, H Siljander, T Vatanen, T Hyötyläinen, ... Cell host & microbe 17 (2), 260-273, 2015 | 1203 | 2015 |
| 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), 61-66, 2017 | 1167 | 2017 |
| Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 F Beghini, LJ McIver, A Blanco-Míguez, L Dubois, F Asnicar, S Maharjan, ... elife 10, e65088, 2021 | 1114 | 2021 |
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| Multivariable association discovery in population-scale meta-omics studies H Mallick, A Rahnavard, LJ McIver, S Ma, Y Zhang, LH Nguyen, TL Tickle, ... PLoS computational biology 17 (11), e1009442, 2021 | 1055 | 2021 |
| Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability M Yassour, T Vatanen, H Siljander, AM Hämäläinen, T Härkönen, ... Science translational medicine 8 (343), 343ra81-343ra81, 2016 | 945 | 2016 |
| The human gut microbiome in early-onset type 1 diabetes from the TEDDY study T Vatanen, EA Franzosa, R Schwager, S Tripathi, TD Arthur, K Vehik, ... Nature 562 (7728), 589-594, 2018 | 743 | 2018 |
| Sequencing and beyond: integrating molecular 'omics' for microbial community profiling EA Franzosa, T Hsu, A Sirota-Madi, A Shafquat, G Abu-Ali, XC Morgan, ... Nature Reviews Microbiology, 2015 | 718 | 2015 |
| Relating the metatranscriptome and metagenome of the human gut EA Franzosa, XC Morgan, N Segata, L Waldron, J Reyes, AM Earl, ... Proceedings of the National Academy of Sciences 111 (22), E2329-E2338, 2014 | 668 | 2014 |
| Indoleacrylic acid produced by commensal peptostreptococcus species suppresses inflammation M Wlodarska, C Luo, R Kolde, E d’Hennezel, JW Annand, CE Heim, ... Cell host & microbe 22 (1), 25-37. e6, 2017 | 664 | 2017 |
| Identifying personal microbiomes using metagenomic codes EA Franzosa, K Huang, JF Meadow, D Gevers, KP Lemon, ... Proceedings of the National Academy of Sciences 112 (22), E2930-E2938, 2015 | 538 | 2015 |
| Dynamics of metatranscription in the inflammatory bowel disease gut microbiome M Schirmer, EA Franzosa, J Lloyd-Price, LJ McIver, R Schwager, ... Nature microbiology 3 (3), 337-346, 2018 | 479 | 2018 |
| Global chemical effects of the microbiome include new bile-acid conjugations RA Quinn, AV Melnik, A Vrbanac, T Fu, KA Patras, MP Christy, Z Bodai, ... Nature 579 (7797), 123-129, 2020 | 405 | 2020 |
| Obese individuals with and without type 2 diabetes show different gut microbial functional capacity and composition LB Thingholm, MC Rühlemann, M Koch, B Fuqua, G Laucke, R Boehm, ... Cell host & microbe 26 (2), 252-264. e10, 2019 | 362 | 2019 |
