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Stephen Nayfach
Stephen Nayfach
Profluent Bio
Verified email at profluent.bio
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Cited by
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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
7182021
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
6362021
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
5392019
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
5262021
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
4192016
Toward accurate and quantitative comparative metagenomics
S Nayfach, KS Pollard
Cell 166 (5), 1103-1116, 2016
2722016
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
S Nayfach, D Pez-Espino, L Call, SJ Low, H Sberro, NN Ivanova, ...
Nature microbiology 6 (7), 960-970, 2021
2492021
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses
S Roux, D Pez-Espino, IMA Chen, K Palaniappan, A Ratner, K Chu, ...
Nucleic acids research 49 (D1), D764-D775, 2021
2492021
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
2432015
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
2422016
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
2202019
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
2072017
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
1022019
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
782023
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
712015
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
682020
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
572019
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
532015
You can move, but you can't hide: identification of mobile genetic elements with geNomad
AP Camargo, S Roux, F Schulz, M Babinski, Y Xu, B Hu, PSG Chain, ...
bioRxiv, 2023.03. 05.531206, 2023
492023
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
452023
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