| CheckV assesses the quality and completeness of metagenome-assembled viral genomes S Nayfach, AP Camargo, F Schulz, E Eloe-Fadrosh, S Roux, NC Kyrpides Nature biotechnology 39 (5), 578-585, 2021 | 929 | 2021 |
| A unified catalog of 204,938 reference genomes from the human gut microbiome A Almeida, S Nayfach, M Boland, F Strozzi, M Beracochea, ZJ Shi, ... Nature biotechnology 39 (1), 105-114, 2021 | 896 | 2021 |
| A genomic catalog of Earth’s microbiomes S Nayfach, S Roux, R Seshadri, D Udwary, N Varghese, F Schulz, D Wu, ... Nature biotechnology 39 (4), 499-509, 2021 | 635 | 2021 |
| New insights from uncultivated genomes of the global human gut microbiome S Nayfach, ZJ Shi, R Seshadri, KS Pollard, NC Kyrpides Nature 568 (7753), 505-510, 2019 | 622 | 2019 |
| An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography S Nayfach, B Rodriguez-Mueller, N Garud, KS Pollard Genome research 26 (11), 1612-1625, 2016 | 439 | 2016 |
| Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome S Nayfach, D Páez-Espino, L Call, SJ Low, H Sberro, NN Ivanova, ... Nature microbiology 6 (7), 960-970, 2021 | 339 | 2021 |
| Toward accurate and quantitative comparative metagenomics S Nayfach, KS Pollard Cell 166 (5), 1103-1116, 2016 | 294 | 2016 |
| IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses S Roux, D Páez-Espino, IMA Chen, K Palaniappan, A Ratner, K Chu, ... Nucleic acids research 49 (D1), D764-D775, 2021 | 292 | 2021 |
| Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome S Nayfach, KS Pollard Genome biology 16, 1-18, 2015 | 284 | 2015 |
| Modulation of a circulating uremic solute via rational genetic manipulation of the gut microbiota AS Devlin, A Marcobal, D Dodd, S Nayfach, N Plummer, T Meyer, ... Cell host & microbe 20 (6), 709-715, 2016 | 268 | 2016 |
| Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes S Roux, M Krupovic, RA Daly, AL Borges, S Nayfach, F Schulz, A Sharrar, ... Nature microbiology 4 (11), 1895-1906, 2019 | 251 | 2019 |
| Discovery of reactive microbiota-derived metabolites that inhibit host proteases CJ Guo, FY Chang, TP Wyche, KM Backus, TM Acker, M Funabashi, ... Cell 168 (3), 517-526. e18, 2017 | 227 | 2017 |
| Identification of mobile genetic elements with geNomad AP Camargo, S Roux, F Schulz, M Babinski, Y Xu, B Hu, PSG Chain, ... Nature Biotechnology, 1-10, 2023 | 193 | 2023 |
| IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata AP Camargo, S Nayfach, IMA Chen, K Palaniappan, A Ratner, K Chu, ... Nucleic acids research 51 (D1), D733-D743, 2023 | 162 | 2023 |
| iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria S Roux, AP Camargo, FH Coutinho, SM Dabdoub, BE Dutilh, S Nayfach, ... PLoS biology 21 (4), e3002083, 2023 | 120 | 2023 |
| A metagenomic meta-analysis reveals functional signatures of health and disease in the human gut microbiome CR Armour, S Nayfach, KS Pollard, TJ Sharpton MSystems 4 (4), 10.1128/msystems. 00332-18, 2019 | 108 | 2019 |
| Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria EN Bess, JE Bisanz, F Yarza, A Bustion, BE Rich, X Li, S Kitamura, ... Nature microbiology 5 (1), 56-66, 2020 | 87 | 2020 |
| Automated and accurate estimation of gene family abundance from shotgun metagenomes S Nayfach, PH Bradley, SK Wyman, TJ Laurent, A Williams, JA Eisen, ... PLoS computational biology 11 (11), e1004573, 2015 | 74 | 2015 |
| Diversity, evolution, and classification of virophages uncovered through global metagenomics D Paez-Espino, J Zhou, S Roux, S Nayfach, GA Pavlopoulos, F Schulz, ... Microbiome 7, 1-14, 2019 | 67 | 2019 |
| Unraveling the functional dark matter through global metagenomics GA Pavlopoulos, FA Baltoumas, S Liu, O Selvitopi, AP Camargo, ... Nature 622 (7983), 594-602, 2023 | 55 | 2023 |
