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Chemical genomics, Beowulf clusters, and a genomics generation


In Genome Technology a year ago, we traced the backstory of NIH’s Molecular Libraries Initiative, which was formed to identify new small molecules that can be used as research tools. At the time, the project’s leaders were busy evaluating the 38 applications that came in from academic and private-sector groups interested in joining the initiative’s network of screening centers. The network came together this past June when NIH announced the names of nine winning groups. These joined NIH’s first screening center, the Chemical Genomics Center, headed by Chris Austin.

Last year’s issue also featured a news bulletin from the American Society of Human Genetics meeting where we talked with Francis Collins about the progress of the HapMap project. In February 2005, the International HapMap Consortium received a funding boost of $3.3 million for creating an improved map nearly five times denser than originally envisioned when the project was launched in 2002. The first draft of the HapMap was published last October; check out the story in this issue (p. 15) for more details.

Back in January 2001, our cover story looked at how Beowulf compute clusters were bringing supercomputing power to the genomics crowd. Named for the Old English hero “with the strength of 1,000 men,” Beowulf clusters are highly scalable systems based on a private network outfitted with commodity software and open source infrastructure. Five years ago, the Fox Chase Cancer Center had just received its own Beowulf cluster care of Paralogic, which specializes in building clusters for scientific applications. Doug Eadline, then president of Paralogic, has since become editor-in-chief of ClusterWorld magazine.

In the February 2001 issue, we profiled members of “Generation G,” our designation for 16 of the most promising young professionals of the new biology. Our instincts five years ago were right on the money, as yesterday’s rising stars have gone on to become fixed luminaries in their fields. Consider:

Ewan Birney received The Royal Society’s Francis Crick Award in 2003, and was recently selected to lead the EU’s five-year plan to establish ENFIN, a new network of excellence for computational biology. Although Birney resigned from his post as president of the Open Bioinformatics Foundation earlier last year, he remains on OBF’s board of directors along with Steve Brenner, another Generation G alumnus.

Speaking of Steve Brenner, the UC-Berkeley professor recently received an NIH grant to continue development of the ASTRAL collection of software and databases for the study of protein structure and evolution.

Christian Marcazzo hasn’t slowed down since his days as director of product marketing at Lion Biosciences. In November 2005, he was appointed senior director of life sciences marketing at Spotfire, after having served as vice president of business development at InforSense. Marcazzo now works with another rising star from 2001, Spotfire CEO Christopher Ahlberg.                                      

— Jen Crebs

Coming up
Next Month in GT

Don’t miss these features in the March issue:

Cancer special issue
In its second cancer-themed issue, Genome Technology looks at the most significant and innovative advances in cancer research from the last 12 months. We’ll profile researchers who are making strides against cancer from all the systems biology fronts, from proteomics to bioinformatics to RNAi and more.

Bioinformatics and microarrays

As chip density grows higher and higher, the amount of data being generated from microarrays has never been greater. How to handle it all? We’ll talk to informatics gurus about the best ways to deal with data, from software options to establishing parameters to make your algorithms as efficient and effective as possible.


The Scan

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.

US Survey Data Suggests Ancestry Testing Leads Way in Awareness, Use of Genetic Testing Awareness

Although roughly three-quarters of surveyed individuals in a Genetics in Medicine study reported awareness of genetic testing, use of such tests was lower and varied with income, ancestry, and disease history.

Coral Genome Leads to Alternative Amino Acid Pathway Found in Other Non-Model Animals

An alternative cysteine biosynthesis pathway unearthed in the Acropora loripes genome subsequently turned up in sequences from non-mammalian, -nematode, or -arthropod animals, researchers report in Science Advances.

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.