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
2602016
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
2422019
Toward accurate and quantitative comparative metagenomics
S Nayfach, KS Pollard
Cell 166 (5), 1103-1116, 2016
1842016
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
1552015
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
1352021
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
1342017
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
1322016
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
1022021
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
852019
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
612021
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
552015
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
442019
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
412015
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
352021
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
292020
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
212018
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), 1-14, 2019
202019
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
182018
Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria
S Nayfach, KS Pollard
bioRxiv, 031757, 2015
132015
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
122018
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Articles 1–20