Nayfach, Stephen

A unified catalog of 204,938 reference genomes from the human gut microbiome

Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 1,367

New insights from uncultivated genomes of the global human gut microbiome

Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature

Gut microbiota and healthGenomics and Phylogenetic Studies

Cited by 737

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Nayfach, S., Páez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., Proal, A. D., Fischbach, M. A., Bhatt, A. S., Hugenholtz, P., et al. (2021) · Nature Microbiology

Bacteriophages and microbial interactionsGenomics and Phylogenetic Studies

Cited by 580

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

Nayfach, S., Rodriguez-Mueller, B., Garud, N., & Pollard, K. S. (2016) · Genome Research

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 470

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

Camargo, A. P., Nayfach, S., Chen, I.-M. A., Palaniappan, K., Ratner, A., Chu, K., Ritter, S. J., Reddy, T. B. K., Mukherjee, S., Schulz, F., et al. (2023) · Nucleic Acids Research

Bacteriophages and microbial interactionsGenomics and Phylogenetic Studies

Cited by 446

Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences

Ruffolo, J. A., Nayfach, S., Gallagher, J., Bhatnagar, A., Beazer, J., Hussain, R., Russ, J., Yip, J., Hill, E., Pacesa, M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

CRISPR and Genetic EngineeringRNA regulation and disease

Cited by 90

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Camargo, A. P., Call, L., Roux, S., Nayfach, S., Huntemann, M., Palaniappan, K., Ratner, A., Chu, K., Mukherjeep, S., Reddy, T. B. K., et al. (2024) · Nucleic Acids Research

Genomics and Phylogenetic StudiesBacterial Genetics and Biotechnology

Cited by 87

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro

Shi, Z. J., Dimitrov, B., Zhao, C., Nayfach, S., & Pollard, K. S. (2022) · Nature Biotechnology

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 42