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A Tool to Find Nomadic Genes that Help Microbes Adapt

September 21, 2023

An illustration of a magnifying glass scoping out viruses from a larger field of microbes.

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

Schematic of the tool workflow. (Simon Roux)

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

Open book with circular representations of microbial genomes above, all against a green background

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 Helps Develop Computational Pipeline for RNA Virus Sequences

October 3, 2022

close up of a needle in a haystack. (judyanded via Flickr CC BY NC 2.0)

In the journal Cell, scientists from a team led by researchers at Tel Aviv University in Israel, the National Center for Biotechnology Information, and the DOE Joint Genome Institute (JGI) describe a computational pipeline that can specifically scan for RNA virus sequences.

Congratulations to Biosciences Area Director’s Award Recipients

September 22, 2021

Numerous Biosciences Area personnel are among the 2021 Berkeley Lab Director’s Awards honorees. This annual program recognizes outstanding contributions by employees to all facets of Lab activities. A complete list of winners can be found here. The 10th annual Director’s Awards ceremony will take place on November 18 at noon.

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