Stephen Nayfach

Bioinformaticist Research Scientist

DOE Joint Genome Institute

Science Programs

Secondary Affiliation: Environmental Genomics and Systems Biology

Biosystems Data Science

Building: 91, Room 0450J2
Mail Stop: 91R0183
Phone: (925) 296-5848
snayfach@lbl.gov
https://github.com/snayfach/

Research Interests

Stephen’s research is focusing on population genomics and on the development of computational methods for large scale reconstruction of genomes from metagenomes.

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JGI Adds Actinobacteria Chapter in the Genomic Encyclopedia of Bacteria and Archaea

November 11, 2022

In Cell Genomics, an international consortium led by researchers at the Joint Genome Institute team generated 824 new Actinobacteria genomes, which were were combined with nearly 5,000 publicly available ones and 1,100 metagenome-assembled genomes (MAGs) reconstructed from sequenced environmental samples in a previous study.

JGI’s CheckV Tool to Assess Virus Data Quality

December 22, 2020

Assembling viral genomes from metagenomes is challenging and often results in highly fragmented data, which limits the ability of researchers to accurately perform functional assessment, host prediction, and phylogenetic analysis. As reported in Nature Biotechnology, a team including JGI’s Stephen Nayfach, Frederik Schulz, Emiley Eloe-Fadrosh, Simon Roux and Nikos Kyrpides developed an automated tool called CheckV (pronounced “Check-Vee”) to help researchers assess and improve the quality of metagenome-assembled viral genomes. CheckV has already been applied to over 2.4 million viral genomes available in the latest release of IMG/VR, a database that is part of the Integrated Microbial Genomes & Microbiomes (IMG/M) suite. Learn more here on the JGI website.

JGI Leads Large-Scale Effort to Develop a Genomic Catalog of Earth’s Microbiomes

November 9, 2020

Microorganisms play key roles in regulating global nutrient cycles but only a small fraction has been identified and an even smaller number has been successfully cultured in a lab for study. In Nature Biotechnology, the known diversity of bacteria and archaea has now expanded by 44% through a publicly available collection of more than 52,000 microbial genomes from environmental samples. Of that number, 70% of the novel genome sequences were previously unknown, not yet cultured in the lab. The work results from a JGI-led collaboration involving more than 200 scientists around the world, KBase and NERSC. Read more about the genomic catalog of Earth’s microbiomes on the JGI website.

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