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IT at the Broad, iFRET, Core Labs, and How to Succeed in Systems Bio


On the cover of Genome Technology in November 2002 was Jill Mesirov, then the CIO of the Whitehead Institute Center for Genome Research. That story followed how Mesirov built up and kept the genome center on the forefront of life sciences computing. The center has since become the Broad Institute, where Mesirov remains chief informatics officer and directs the Computational Biology and Bioinformatics Organization. The goal of that group is to provide and coordinate computational support to the Broad, including bioinformatics, computational biology, and information technology.

A feature story in that same issue profiled Cari Soderlund, who wrote the Finger Printed Contigs program in the 1990s that assembles clones into contigs and has been used in a number of genome projects, such as rice, mice, and humans. More recently, the tool has been used in comparative genomic studies as well. Soderlund heads up the Arizona Genome Computational Laboratory, which was just being set up in 2002.

For another story, GT spoke with Mathias Howell, who combined FRET with SYBR Green to create iFRET, which has a signal strength twice as strong as SYBR Green and 40 times as strong as FRET. Howell formed a company called DynaMetrix with Anthony Brookes and Magnus Jobs, also at the Karolinska Institute, in 2002. Howell is now a postdoc at Uppsala University.

Last year’s November cover story was based on a reader survey about core labs — whether researchers used them, how they rated them, and what core lab employees say themselves. This survey found that, despite grumblings, researchers take advantage of their local core labs. In academia, 18.6 percent of the 438 academic respondents sent work their way all the time, 33.6 percent did so often, while 37.7 percent occasionally did, and 10.1 percent never did. From the core labs’ perspective, 72 percent reported an increase in workload between 2005 and 2006.

Also in the November 2006 issue was a roundtable discussion of how to succeed in systems biology. The panel featured Pfizer’s Christopher Bouton, the Broad’s Marcia Nizzari, Dana-Farber’s John Quackenbush, Isaac Kohane from Harvard, and David Sedlock from Millennium. In it, they dispensed such advice as Quackenbush’s take on systems biology: “It has to be more team-oriented and project-oriented than the way we think about traditional biology; you need to get people talking to each other.” Bouton noted, “I think it all comes back to people who are able to work in teams are going to be those people who succeed.”

In last year’s Under One Roof, GT examined the California Institute for Quantitative Biomedical Research, a collaboration of three of the Universities of California: Berkeley, San Francisco, and Santa Cruz. Since last year, QB3 hosted the Eleventh Annual International Conference on Research in Computational Molecular Biology, with speakers including Patrick Brown and Jay Keasling. In June, QB3 purchased a 900 MHz magnet for its NMR facility with funds from a $6 million NIH grant. Three QB3 synthetic biology engineers, J. Christopher Anderson, Kristala Jones, and Neil Renninger, were also chosen by Technology Review as top innovators under the age of 35.

The Scan

Should've Been Spotted Sooner

Scientists tell the Guardian that SARS-CoV-2 testing issues at a UK lab should have been noticed earlier.

For Martian Fuel

Researchers have outlined a plan to produce rocket fuel on Mars that uses a combination of sunlight, carbon dioxide, frozen water, cyanobacteria, and engineered E. coli, according to Gizmodo.

To Boost Rapid Testing

The Washington Post writes that new US programs aim to boost the availability of rapid at-home SARS-CoV-2 tests.

PNAS Papers on Strawberry Evolution, Cell Cycle Regulators, False-Positive Triplex Gene Editing

In PNAS this week: strawberry pan-genome, cell cycle-related roles for MDM2 and MDMX, and more.