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Content Tagged "bioinformatics"

Student tools for hands-on genomics and bioinformatics lessons

Driven in part by the increased emphasis to give life sciences students hands-on experience in “real research,” the DOE Joint Genome Institute’s Genomics and Bioinformatics Education Program developed a series of educational modules for undergraduate programs to explore and annotate publicly available microbial genome datasets. Known collectively as the Integrated Microbial Genomes Annotation Collaboration Toolkit… [Read More]

Cheryl Kerfeld on IMG-ACT in The Scientist

  “Bioinformatics has become such an integral part of research. And being able to do this, to use these tools in an informed way and in a way that’s somewhat discerning . . . is really important,” explains Cheryl Kerfeld, director of the Genomics and Bioinformatics Education Program at the Department of Energy’s Joint Genome… [Read More]

Fungal genomics and coal formation in BioBased Digest

In Massachusetts, a group of 70 researchers led by David S. Hibbett of Clark University, in Worcester, Mass. and Igor V. Grigoriev of the Department of Energy’s Joint Genome Institute comparing the genomes of 31 fungi to determine how white rot fungi breaks down lignin and could be a major breakthrough in cellulosic ethanol technology. Read… [Read More]

Linking white rot fungi and the Carboniferous period in Scientific American

Now a new genomic analysis suggests why Earth significantly slowed its coal-making processes roughly 300 million years ago—mushrooms evolved the ability to break down lignin. “These white rot fungi are major decomposers of wood and the only organism that achieves substantial degradation of lignin,” explains mycologist David Hibbett of Clark University in Massachusetts, who led the research… [Read More]

Kbase and DOE’s Susan Gregurick in GenomeWeb’s BioInform

Kbase is currently in alpha release and is targeted for full production release in early 2013.The community-driven and scalable open-source system is intended to provide a framework for evidence-based functional annotation of genome sequences. It will also enable the creation of metabolic and regulatory models that may be used to generate scientific hypotheses; as well… [Read More]

Bioinformatics challenges for metagenomic analyses

There are more microbes in, on and around the planet than there are stars in the sky. However, the vast majority of these microorganisms have not yet been studied, in part because many of them do not thrive when moved out of their natural environment. A spoonful of soil contains a complex and diverse microbial… [Read More]

DOE JGI’s role in managing Human Microbiome Project data

At JGI, Kyrpides oversees projects such as GenePRIMP, a highly rated quality control program for genome sequencing, and GOLD, the Genomes On-Line Database. GenePRIMP stands for “Gene PRediction IMprovement Pipeline, and it consists of a series of computational units that can be used to significantly improve the overall quality of the predicted genes in any… [Read More]

Peach genome project on WSU Today Online

The International Peach Genome Initiative’s decision to release the genetic makeup of the peach ahead of publication in a scientific journal could have far-reaching implications for the future of peaches and related Rosaceae plants like almonds, blackberries, apples, cherries, plums, raspberries, roses, strawberries and trees such as poplar, citrus and chestnut. “Having access to even… [Read More]

JGI’s new head of informatics

Svilen Tzonev has been named head of informatics at Department of Energy’s Joint Genome Institute in Walnut Creek, Calif. He was formerly at Illumina, where he was the senior director of software, bioinformatics and IT and helped to develop and commercialize the Genome Analyzer system. Prior to that post, he was director of software and… [Read More]