Stephen Nayfach
Stephen Nayfach
DOE Joint Genome Institute
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Cited by
Cited by
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
Toward accurate and quantitative comparative metagenomics
S Nayfach, KS Pollard
Cell 166 (5), 1103-1116, 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), 51, 2015
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
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
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
Automated and accurate estimation of gene family abundance from shotgun metagenomes
S Nayfach, PH Bradley, SK Wyman, TJ Laurent, A Williams, JA Eisen, ...
PLoS Comput Biol 11 (11), e1004573, 2015
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
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
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, 1-10, 2020
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), 2019
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), 1-14, 2018
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
Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria
S Nayfach, KS Pollard
bioRxiv, 031757, 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
CheckV: assessing the quality of metagenome-assembled viral genomes
S Nayfach, AP Camargo, E Eloe-Fadrosh, S Roux, N Kyrpides
BioRxiv, 2020
A most wanted list of conserved microbial protein families with no known domains
SK Wyman, A Avila-Herrera, S Nayfach, KS Pollard
PloS one 13 (10), e0205749, 2018
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), 157, 2019
Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community
P Panwar, MA Allen, TJ Williams, AM Hancock, S Brazendale, ...
Microbiome 8 (1), 1-24, 2020
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
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