Rubin's highest public profile emerged from his partnership with the maverick scientist-entrepreneur J. Craig Venter to sequence the Drosophila genome as a warm-up to the contentious race to sequence the human genome. While the National Institutes of Health (NIH)-funded effort took a more cautious path to the enormous task, Venter and his company, Celera Genomics, gambled on a faster and less expensive—but potentially riskier—“whole-genome shotgun” method.

In 1998, when Venter approached Rubin, then head of the Berkeley Drosophila Genome Project, and proposed that they collaborate to perform the fruit fly genome sequencing at no cost to the public, many saw the deal as akin to selling one's soul to the devil. “That took a great deal of courage on Gerry's part, because Craig was being reviled by the [publicly funded genome sequencing] community,” says Michael Ashburner of the University of Cambridge, a biologist specializing in Drosophila genetics who recently published an account of the fruit fly genome effort.

The idea that the two might work together came up at a meeting at Cold Spring Harbor, just after Venter had been quoted in The New York Times as claiming that Celera would beat the NIH-funded effort to sequence the human genome—and do it cheaper. “It was a very tense atmosphere,” agrees Rubin. “But when Craig took me out in the corridor and asked me to collaborate on the Drosophila genome, I was instantly delighted. Celera wanted to prove that its shotgun sequencing method would work, and I wanted to get the genome done. It seemed like a no-brainer.”

Ultimately, Rubin's instincts and pragmatism, together with his insistence that the sequence immediately go into a public database, proved unerring and gained him wide respect. And, as it turns out, the collaboration worked brilliantly. In March of 2000, Venter and Rubin announced the nearly complete sequence of the 120 million units of DNA contained in the fruit fly's five chromosome arms. For this achievement, he and Venter, with their colleagues Mark D. Adams and Susan E. Celniker, shared the American Association for the Advancement of Science's Newcomb Cleveland Prize. “Gerry is a great scientific leader,” says Venter. “He proved it by going against the grain and following his own path, and as a result he really helped science move forward.”

With the raw sequence in hand, Rubin and about 60 Drosophila researchers, computer scientists, and staff gathered at Celera headquarters for a frenzied, 2-week-long “annotation jamboree.” Using algorithms being refined in all-night sessions, the scientists analyzed the sequence and discovered a total of 13,600 genes on the chromosomes. Rubin calls it “the most intellectually stimulating time of his career.” But he had another reason to be exhilarated: Confidentially, he had just accepted the position of vice president for biomedical research at HHMI, a job that would bring him back to the East Coast and, 2 years later, make him director of planning for Janelia.

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