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Puzzling Protein Structures, Collaborations and Participants' Proximity, Advances in Synthetic Genomics, More


Ten years ago, Genome Technology spoke with the University of Washington's David Baker, who was making strides in protein structure predictions using his Rosetta algorithm. Irwin Kuntz told GT that Baker's "Rosetta program ... and his ability to do ab initio structure objectivity is perhaps the best thing going in the field." Last year, Baker and his collaborators described in Nature their interactive online game Foldit, which invites players to "interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology." This September, Baker and his colleagues reported in Nature Structural & Molecular Biology that Foldit players had solved the crystal structure of the M-PMV retroviral protease, which had puzzled researchers for more than a decade.

For its November 2006 issue, GT spoke with systems biology experts about how to succeed in the field. At the time, Children's Hospital Boston's Isaac Kohane said researchers with both biological and computational expertise were being stretched thin. "Leaders in this area — people who are able to do this integrative, quantitative, and biological thinking — are being asked to do a whole range of efforts," he said, notably through collaborations. In a December 2010 PLoS One paper, Kohane and his colleagues showed that participants' physical closeness correlates with the impact of a collaboration, such that proximity is predictive of a group's success.

Last year, researchers at the J. Craig Venter Institute reported in Nature Methods their use of isothermal DNA assembly to create a synthetic mouse mitochondrial genome, the first synthetic organellar genome reported. In GT's November 2010 issue, JCVI's Daniel Gibson said that because his team's method "is so simple and robust, and only requires a few steps, it can be automated." Writing in Nature this September, a team led by investigators at the Johns Hopkins University School of Medicine described its synthetic yeast genome project, Sc2.0, as well as "the first partially synthetic eukaryotic chromosomes, Saccharomyces cerevisiae chromosome synIXR, and semi-synVIL." The team also reported on an approach it created to generate complex genotypes. "When complete, the fully synthetic genome will allow massive restructuring of the yeast genome, and may open the door to a new type of combinatorial genetics based entirely on variations in gene content and copy number," the Hopkins-led team wrote.

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