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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A Tool to Find Nomadic Genes that Help Microbes Adapt

September 21, 2023

Mobile genetic elements (MGEs) are genetic entities that seek to replicate themselves and spread from cell to cell. Two of the most common forms of MGEs are viruses and plasmids. They can be found in virtually all of Earth’s ecosystems. A software tool recently described in Nature Biotechnology called geNomad identifies and classifies MGEs based upon their gene content and their genetic sequences. The software was created by researchers under the direction of JGI Microbiome Data Science Group Lead Nikos Kyrpides.

JGI Creates a New Matchmaker for Phages and their Hosts

June 7, 2023

To do anything, viruses must find a host, and not just any host will do. It must be a specific host the virus has adapted to commandeer. For bacteriophage viruses, these hosts are microbes like bacteria, not humans. With metagenomic sequencing, researchers have found more of these viruses than ever before, in all kinds of ecosystems. However, matching these viral genetic sequences to their hosts is crucial to understanding what these viruses can do. Building on existing virus-host prediction approaches, researchers have created a new program called iPHoP (pronounced “eye-pop”, freely available online).

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.

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