| 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 | 454 | 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 | 444 | 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 | 376 | 2016 |
| A genomic catalog of Earths microbiomes S Nayfach, S Roux, R Seshadri, D Udwary, N Varghese, F Schulz, D Wu, ... Nature biotechnology 39 (4), 499-509, 2021 | 349 | 2021 |
| 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 | 348 | 2021 |
| Toward accurate and quantitative comparative metagenomics S Nayfach, KS Pollard Cell 166 (5), 1103-1116, 2016 | 241 | 2016 |
| 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), 1-18, 2015 | 205 | 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 | 195 | 2016 |
| 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 | 185 | 2017 |
| 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 | 166 | 2021 |
| Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earths biomes S Roux, M Krupovic, RA Daly, AL Borges, S Nayfach, F Schulz, A Sharrar, ... Nature microbiology 4 (11), 1895-1906, 2019 | 165 | 2019 |
| 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 | 128 | 2021 |
| 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), e00332-18, 2019 | 89 | 2019 |
| 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 | 68 | 2015 |
| 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 | 52 | 2020 |
| MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome S Nayfach, MA Fischbach, KS Pollard Bioinformatics 31 (20), 3368-3370, 2015 | 51 | 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 | 40 | 2019 |
| Phylogeny-corrected identification of microbial gene families relevant to human gut colonization PH Bradley, S Nayfach, KS Pollard PLoS computational biology 14 (8), e1006242, 2018 | 34 | 2018 |
| Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis JK Jarett, S Nayfach, M Podar, W Inskeep, NN Ivanova, J Munson-McGee, ... Microbiome 6, 1-14, 2018 | 32 | 2018 |
| Global ecotypes in the ubiquitous marine clade SAR86 A Hoarfrost, S Nayfach, J Ladau, S Yooseph, C Arnosti, CL Dupont, ... The ISME journal 14 (1), 178-188, 2020 | 30 | 2020 |
