Doubling Down on Known Protein Families
Through a novel approach detailed in Nature, a massive computational analysis of microbiome datasets focuses on unveiling protein functional diversity. [Read More]
Content Tagged "Nikos Kyrpides"
From Life at the Extremes to Editing Genomes
Jennifer Doudna and Emmanuelle Charpentier were recognized for their work on CRISPR-Cas9, technology described by the Nobel Foundation as having “a revolutionary impact on the life sciences.” For the past few years, Doudna’s lab has partnered with JGI’s Microbiome Data Science group led by Nikos Kyrpides, mining the IMG/M system for novel Cas genes and CRISPR systems. [Read More]
Termite diets dictate microbes in their guts
Realtors and homeowners cringe at the thought of termites on their properties, but for bioenergy researchers, these insects are rich harbors of microbial communities that can break down woody lignocellulose. In 2007, the DOE Joint Genome Institute sequenced the microbes in the hindgut of termites from Costa Rica (from the Nasutitermesgenus) to identify the genes… [Read More]
DOE JGI’s IMG/M data system in Berkeley Lab’s release on the Human Microbiome Project
Berkeley Lab’s role in mapping the human microbiome revolves around big data, both analyzing it and making it available for scientists to use worldwide…. Berkeley Lab scientists developed and maintain a comparative analysis system called the Integrated Microbial Genomes and Metagenomes for the Human Microbiome Project (IMG/M HMP). It allows scientists to study the human microbiome… [Read More]
Analyzing enzymes for a PAH degradation pathway
Microbial activity is crucial for breaking down compounds, removing pollutants and chemically transforming organic compounds. Some of these pollutants are polycyclic aromatic hydrocarbons (PAHs) found in contaminated soils. The PAH phenanthrene, for example, can be broken down by the bacterium Arthobacterphenanthrenivorans, which was isolated from a creosote-polluted site in Greece, and used by the microbe… [Read More]
New tools for the IMG/M analysis system
Since the initial release of the Integrated Microbial Genomes with Microbiome samples (IMG/M) system in 2007 to support the comparative analysis of metagenomic data sets, DOE JGI researchers have made several updates in order to keep pace with the rapid increase in data set generation due to advances in sequencing technologies. As reported by researchers… [Read More]
Consortium Drives Genome Standards
As technology for sequencing genomes has become cheaper and more widely accessible, there is a greater urgency to institute a standardized, comprehensive language for researchers to share their findings. The Genomic Standards Consortium (GSC), an open-membership organization, is building a culture of collaboration to achieve greater efficiencies by spending less time combing through and interpreting inconsistent… [Read More]
How salt-loving archaea can assist with biofuel production
Halophilic bacteria thrive in environments with very high concentrations of salt such as the waters and sediments of salt lakes and saline soils. One of the reasons why the DOE JGI has been sequencing halophiles under the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project and the Community Sequencing Program is because they have salt-adapted… [Read More]
Rhizobial project on The West Australian
The Centre for Rhizobium Studies, the Australian side of the project led by Dr Wayne Reeve, has the task of sequencing the genomes of rhizobia selected from distinct geographic regions across the globe.The US side of the project will be run at the Joint Genome Institute, led by head of the microbial program Dr Nikos… [Read More]
Making Science’s Insights of the Decade list – twice
The December 17 issue of Science includes a special feature called “Insights of the Decade” and two of them feature work done by DOE JGI researchers. (Note: Free registration is required to read the articles online.) Genome research features prominently in Science’s Insights of the Decade list. (DNA helix image by DS from Flickr via… [Read More]