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
2432016
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
1892019
Toward accurate and quantitative comparative metagenomics
S Nayfach, KS Pollard
Cell 166 (5), 1103-1116, 2016
1682016
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
1402015
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
1272017
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
1142016
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
79*2021
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
672019
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
542015
A genomic catalog of Earth’s microbiomes
S Nayfach, S Roux, R Seshadri, D Udwary, N Varghese, F Schulz, D Wu, ...
Nature biotechnology, 1-11, 2020
442020
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
412019
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
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, 1-8, 2020
302020
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
192020
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
182018
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
162018
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
152019
Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria
S Nayfach, KS Pollard
bioRxiv, 031757, 2015
132015
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
102021
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
92018
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Articles 1–20