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Grant Funding, Populus, and Defense

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One year ago, Genome Technology examined the state of US government grant funding for projects under the systems biology umbrella. We sifted and sorted through individual grants awarded by the NIH, NSF, USDA, and DOD to generate estimates of funding falling into broad discipline and technology categories. Our hard-won results indicated that a majority of NIH and USDA dollars flocked to research in genomics and gene expression, while NSF was a decent supporter of proteomics and bioinformatics projects. The DOD, meanwhile, had a hand in many pharmacogenomics studies, especially those concerning breast and prostate cancers.

The cover story in November 2005 also featured results from a survey of reader perspectives on public funding trends. At the time, 76 percent of you felt that the funding climate was cooler than it was 10 years ago, and many had reported that shifting funding priorities had urged them to take up research in greener fields. Since public coffers are promising to be emptier in coming years, and we are loath to see our readers search between couch cushions for pipette money, GT stepped in this year with another data crunching tour de force — our first-ever listing of private foundation grants. Check out the July/August issue for details, deadlines, and contact info for grant-giving NGOs with an interest in basic and biomedical research.

Last year’s issue also featured a news item on Stephen DiFazio, the West Virginia University researcher who was busy writing up the final draft of a paper reporting the poplar genome sequence. The poplar, also called the black cottonwood or Populus trichocarpa, is the first woody perennial plant to have its genome sequenced. This September, the paper was published in Science, which celebrated the event with a cover image of poplars against the night sky. DiFazio was second author on the paper, which featured more than 100 co-authors from institutions across the world.

It was only one year ago that GT reported on the rise of dual-core processors in bioinformatics applications. Before dual-core became ubiquitous in the personal computing world, researchers were already test driving the systems on Blast and HMMer. Fast forward 12 months, and the community is already looking down the barrel of multi-core and multi-thread-based systems. For starters, check out GT’s coverage of the Cell microprocessor and its potential for scientific computing on p. 18.

Five years ago, the magazine explored genomics research in biodefense. In the public sector, TIGR and the New Jersey School for Emerging and Reemerging Pathogens had just won a contract to develop array-based diagnostics for three classes of biological warfare agents. Industry contracts with the DOD abounded, especially with its Defense Advanced Research Projects Agency arm, with Bruker, Cepheid, Nanogen, and Transgenomic all working on defense-related tools. Since then, DARPA’s budget has continued to rise. Alnylam received funding for its pandemic flu program from the agency, while CombiMatrix signed a subcontract this year with Northrop Grumman to develop components for DARPA’s program to develop a handheld sensor capable of identifying biological weapons.    

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.