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Computational Genomics Whiz Came a Long Way

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With one keystroke, Jun Liu puts his computer to the task of identifying switches that turn on and off related genes among numerous DNA sequences of E. coli. Running on a program he created, the computer locates the switches in less than a second. The demonstration is remarkable not only because the technique is fast and accurate — 80 percent of the predictions have been right — but also because of Liu’s background in rural China during the Cultural Revolution. He never had a computer or calculator and rarely saw a math book.

Things have changed for Liu, 36, who’s now a tenured statistics professor at Harvard University. He came to the United States in 1986 for graduate school on a mathematics scholarship and joined Harvard’s faculty five years later, seeking a discipline that was “more connected to real life” than pure math. In 1992, he read a paper about using computer algorithms to find control switches for gene regulation. Realizing that an algorithm he developed might do even better, Liu began a collaboration with the author, New York Department of Health researcher Chip Lawrence.

Liu and Lawrence’s algorithms look for repetitive patterns in the promoter regions of DNA segments found upstream of genes. The search improves with multiple iterations, as the program converges on a common string of base pairs — sites where proteins are likely to bind to activate genes associated with a particular function. Although the technique works well with simple organisms like bacteria, yeast, and C. elegans, the team is now scaling up to handle the human genome.

Meanwhile, Liu is embarking on other ventures, such as finding novel approaches to identifying genetic disease markers. “I’m always looking for new problems to work on,” says Liu, who’s struck by the role that chance has played in sending him down the biology path. Observers might also be struck by how far he’s come from his modest origins. A couple of decades ago, he didn’t have a math text to call his own. Now he has shelves filled with math books, including one that he wrote.

— Steve Nadis

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