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Need for standard definitions covered by PhysOrg

As the proverbial “fire hose of data” becomes a Niagara torrent, with conservative estimates of 12,000 draft genomes hitting the public databases by 2012, researchers may be surprised to find that these datasets describe genomes that are not complete. Recognizing the problem, a group of researchers from several sequencing centers, including the DOE Joint Genome… [Read More]

“Geneticists call for better draft sequences”

Researchers who have mapped a species’ genome need to be more explicit about the quality of their sequence, says an international team of genome researchers. “People generating these sequences should discriminate a bit more between the products that they provide to the rest of the scientific community,” says Patrick Chain of the Joint Genome Institute… [Read More]

Standard definitions for genome sequences on EurekAlert!

In 1996, researchers from major genome sequencing centers around the world convened on the island of Bermuda and defined a finished genome as a gapless sequence with a nucleotide error rate of one or less in 10,000 bases. This effectively set the quality target for the human genome effort and was quickly applied to other… [Read More]

For more data analysis at DOE JGI

The US Department of Energy Joint Genome Institute is in the process of hiring about 20 new staffers who will help analyze the growing amount of data it is generating through its sequencing activities. JGI, which is headquartered in Walnut Creek, Calif., says some of the new staffers will hold positions within its separate plant,… [Read More]

Shewanella research on ScienceDaily

Researchers have completed the first thorough, system-level assessment of the diversity of an environmentally important genus of microbes known as Shewanella. Microbes belonging to that genus frequently participate in bioremediation by confining and cleaning up contaminated areas in the environment. The team of researchers from the Georgia Institute of Technology, Michigan State University and the… [Read More]

T. reesei research a DOE National Impact story

In 2008, scientists funded in part by the U.S. Department of Energy (DOE) Office of Science at the DOE Joint Genome Institute (JGI) mapped the genome of this important organism using the Army reference strain. According to Eddy Rubin, DOE JGI Director in 2008 interview, “the genome of T. reesei provides us with a roadmap… [Read More]

Cheryl Kerfeld at iPlant Genomics Education Conference

We learned about many kinds of annotation projects. Charles Hardnet from Spelman College showed electron micrographs of the phage that his students isolated and annotated through their school’s partnership with HHMI. For the bacterial projects, Derek Wood, Brad Goodner, Daniel Rhoades, and Steve Slater from colleges across the US described a joint endeavor where students… [Read More]

“Bioprospecting Termites” at Spectre Footnotes

In 2005, the microbial ecologist Falk Warnecke, of the Department of Energy’s Joint Genome Institute, traveled with researchers from Caltech and the San Diego biotech company Diversa to Costa Rica, where they opened up a termite nest in a tree. The group dissected 165 worker termites, freezing the contents of their third guts in liquid… [Read More]

Nikos Kyrpides and the GSC on GenomeWeb

Genomics “is now mature enough to go ahead and develop all the standards that would facilitate the comparisons across different groups more efficiently, such as standards in gene calling and annotation,” Kyrpides said. Standards development in the area of metadata “is one of the most intensely developing area under the auspices of GSC,” and he… [Read More]

T. reesei research on ISA’s InTech

During World War II, Trichoderma reesei frustrated American Army quartermasters in the South Pacific by speeding up the rate at which canvas supplies wore out. Now the same fungus is a key producer of industrial enzymes that break down biomass for biofuel production. In 50 short years, the fungus has gone from being the bane… [Read More]