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Updating Genomics and Bioinformatics Courses for Undergraduates

Responding to the National Research Council of the National Academies’ call to “involve students in working with real data and tolls that reflect the nature of life sciences research in the 21st century,” the DOE JGI’s Education Program, headed by Cheryl Kerfeld, collaborated with faculty members from several universities around the country to develop bioinformatics… [Read More]

Characterizes/Publishes Anti-Reservoir-Souring Microbe

Reservoir souring, the production of hydrogen sulfide in oil wells as a result of downhole activity by a specialized group of microorganisms called sulfate-reducing bacteria (SRB), is a detrimental process of great concern to the oil industry. As petroleum reserves age and water injection is implemented for pressure maintenance, there is an inherent risk of… [Read More]

GEBA Project: “Beyond Darwin’s Wildest Dreams”

Recently, Eisen and his colleagues unveiled a pilot project that they hope will help the community make the most of existing microbial genome data with a phylogeny-driven resource called the Genomic Encyclopedia of Bacteria and Archaea at the Joint Genome Institute. Currently available genomic resources for microbes are from a very narrow phylogenetic distribution of… [Read More]

GEBA project on Microbe World

The Joint Genome Institute at the Energy Department has started what it calls a “genomic encyclopedia,” a collection of genomes from diverse microbes. Using an evolutionary approach that differs in strategy from how scientists originally chose organisms for sequencing, researchers hope to discover many new kinds of genes. According the New York Times, “the genomic… [Read More]

GEBA project on OpenHelix

Just caught the announcement via GenomeWeb that the GEBA project paper has been published with 53 bacterial genomes (see Nature for a summary article that is available, and the paper itself is here).  They deliver 53 bacteria and 3 archaea. GEBA is the Genomic Encyclopedia of Bacteria and Archaea.  They developed a strategy to select… [Read More]

GEBA project on Green Car Congress

Genome researchers from the US and Germany have published the initial “volume” of the Genomic Encyclopedia of Bacteria and Archaea (GEBA)—an analysis of the first 56 genomes sequenced from the two domains. The paper appeared in the 24 December edition of the journal Nature. Read more on Green Car Congress. [Read More]

GEBA project on Scientific Blogging

In hopes of exploring that realm and expanding our understanding of microbes, a team from the the Department of Energy’s Joint Genome Institute (DOE JGI) have released the first volume of the Genomic Encyclopedia of Bacteria and Archaea (GEBA), an analysis of the first 56 genomes representing two of the three domains of the tree… [Read More]

GEBA project on 7th Space Interactive

The Earth is estimated to have about a nonillion (1,000,000,000,000,000,000,000,000,000,000) microbes in, on, around, and under it, comprised of an unknown but very large number of distinct species. Despite the widespread availability of microbial genome data—close to 2,000 microbes have been and are being decoded to date—a vast unknown realm awaits scientists intent on exploring… [Read More]

GEBA project in DOE Office of Science’s National Impact series

Think of phylogenetic diversity as all of the separate branches growing from the main “trunk” of the Tree of Life.  “Most of these separate branches within the bacteria and archaea have not yet been sampled in regard to genome sequencing” said Eisen. To expand the genomic sampling of bacterial and microbial diversity, Eisen and others… [Read More]

GEBA project on UC Newsroom

Genome scientists from the U.S. and Germany have assembled the first pages of a comprehensive encyclopedia of genomes of all the microbes on Earth. The results, published Dec. 24 in the journal Nature, will help biologists find new genes and fill out the branches of the “Tree of Life.”…. The project was funded primarily by… [Read More]