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US-Russian collaboration develops new method for sequencing dark matter of life from a single cell
Date:8/10/2012

San Diego, Calif., and Saint Petersburg, Russia An international team of researchers led by computer scientist Pavel Pevzner, from the University of California, San Diego, have developed a new algorithm to sequence organisms' genomes from a single cell faster and more accurately. The new algorithm, called SPAdes, can be used to sequence bacteria that can't be submitted to standard cloning techniqueswhat researchers refer to as the dark matter of life, from pathogens found in hospitals, to bacteria living deep in ocean or in the human gut.

Ultimately, the researchers hope to apply this algorithm to cancer cells to monitor early stages of the disease when normal cells first turn into malignant ones. Pevzner and colleagues published their findings in the May issue of the Journal of Computational Biology. They released SPAdes Aug. 8.

Last fall, Pevzner's group, in collaboration with single-cell sequencing pioneer Roger Lasken at the J. Craig Venter Institute and researchers at Illumina Inc., developed the first software capable of handling single-cell sequencing. Researchers published those findings in Nature Biotechnology in September 2011. The fact that a new sequencing algorithm was developed in just months reflects the frenetic pace of progress in single-cell sequencing, one of the fastest-growing, and most important, areas in modern genomics.

Pevzner's group, which includes scientists from the Jacobs School of Engineering at UC San Diego and the Russian Academy of Sciences, along with Lasken's team, are now using SPAdes to sequence the bacterial dark matter of life and human pathogens.

The international collaboration is part of an ambitious "megagrant" initiative launched by then Russian President Dmitry Medvedev, including an invitation to 40 world-class scientists to help jumpstart Russian science, which has been faltering since the fall of the Soviet Union. Megagrants brought to Russia experts in various fields, including some
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Contact: Ioana Patringenaru
ipatrin@ucsd.edu
858-822-0899
University of California - San Diego
Source:Eurekalert

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