Stephen Nayfach
Stephen Nayfach
DOE Joint Genome Institute
Verified email at lbl.gov
Title
Cited by
Cited by
Year
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
1902016
Toward accurate and quantitative comparative metagenomics
S Nayfach, KS Pollard
Cell 166 (5), 1103-1116, 2016
1312016
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
1262015
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
1132017
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
1112019
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
922016
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
492015
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
422019
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
372015
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
19*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
182019
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
142018
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
142018
Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria
S Nayfach, KS Pollard
bioRxiv, 031757, 2015
112015
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
102020
CheckV: assessing the quality of metagenome-assembled viral genomes
S Nayfach, AP Camargo, E Eloe-Fadrosh, S Roux, N Kyrpides
BioRxiv, 2020
62020
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
52018
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
42019
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
22020
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
12020
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Articles 1–20