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Gene Myers, computer algorithm pioneer in human genome sequencing, to join UC Berkeley faculty
29 October 2002

By Sarah Yang, Media Relations

Berkeley - More than two years after the landmark sequencing of the human genome, the computer whiz behind the algorithms used to decipher millions of pieces of the genetic material is coming to the University of California, Berkeley, for his next big challenge.


Gene Myers
Gene Myers

Gene Myers, former vice president of Informatics Research at Celera Genomics in Rockville, Md., is joining UC Berkeley as a professor in the Department of Electrical Engineering & Computer Sciences, effective Jan. 1. As part of his work in computational biology, he will work closely with researchers at the campus's Department of Molecular & Cell Biology, Lawrence Berkeley National Laboratory and the Department of Energy's Joint Genome Institute.

"The addition of Myers to the faculty exemplifies the commitment of UC Berkeley and the College of Engineering to outstanding research in bioinformatics," said Jitendra Malik, professor and associate chair of computer sciences. "I believe the interplay of computation and biology will dominate science in the 21st century."

Myers' research is sure to contribute to the campus's Health Sciences Initiative, which unites hundreds of scientists from diverse research fields for the common goal of stimulating advances in health and medicine.

"He's exactly what the Health Sciences Initiative is all about," said Robert Tjian, professor of molecular and cell biology and chair of the initiative. "The UC Berkeley culture has long been characterized by interdisciplinary collaboration. Many of the innovations that have come out of this campus are a result of the fact that our researchers thrive in this cooperative atmosphere."

The move to UC Berkeley marks a return to academia for Myers, who taught at the University of Arizona in Tucson for 17 years before the race to sequence the human genome inspired him to pack up for Celera in 1998.

"The caliber of the researchers at UC Berkeley is excellent," said Myers. "It's also a very rich, collegial environment, which is part of why I'm coming here. Universities are places where lots of individually talented people are spinning and exchanging ideas and creating new concepts. New concepts are needed to understand life at the genomic level."

Myers will play an active role in UC Berkeley's Center for Integrative Genomics, which brings together researchers interested in molecular evolution, biodiversity and genomics, with a heavy emphasis on computation.

"Right now, seven different animal genomes have been sequenced and assembled, but that number is likely to shoot up to 50 to 100 in the next five years," said Michael Levine, professor of molecular and cell biology and director of the center. "Specifically, researchers at the center will look at the role of regulatory DNA in animal evolution. We'll be mining a treasure trove of data, and we need to have a way to compare these genomes in order to understand the mechanisms of evolutionary change and innovation, to essentially understand the diversity of life on earth."

Myers developed his background in traditional sciences as an undergraduate at the California Institute of Technology, where he received his bachelor's degree with honors in mathematics. At Caltech, Myers supplemented his math curriculum with courses in physics, chemistry and biology.

In 1981, after he received his PhD in computer science from the University of Colorado, Myers joined the faculty of the University of Arizona. There, Myers received a Faculty of Science Distinguished Teaching Award in 1989.

During Myers' tenure in Arizona, he worked with Jim Weber, a geneticist at the Marshfield Clinic in Wisconsin, on a radical concept: Sequence the human genome by mathematically chopping the entire genome into random bits, sequencing those pieces and then reassembling them in correct order.

The technique, called "whole genome shotgun sequencing," had been used successfully to sequence and assemble the genome of microbes, most notably the Haemophilus influenza bacteria in 1995. But skeptics rejected the idea that shotgun sequencing could be used for animal genomes, which have far more repeating structures than microbial genomes. With so many bits and pieces that look alike, conventional wisdom held that a computer couldn't possibly reassemble them in exactly the right order.

Scientists in the publicly funded Human Genome Project were instead using a divide-and-conquer approach by taking medium-sized chunks of the genome and sequencing those sections one at a time.

"It was a tedious method that involved many more steps and was much more expensive," said Richard Karp, University Professor at UC Berkeley and a leader in modern theoretical computer science. "Myers was clever and insightful enough to develop a computer algorithm that resolved the concerns people had about using shotgun sequencing for mammalian genomes. He was so confident this would work that he took the plunge and joined Celera. It was a gutsy move."

It was at Celera that Myers had free rein to test run his algorithms.

The first key, Myers explained, was to modify the traditional shotgun protocol to deliver the genome bits in pairs separated by known distances of 2,000, 10,000, and 50,000 letters. The second key was to design algorithms that identified the non-repeating parts of the genome that are easy to reconstruct and then link those parts to pairs that bookend a repeat sequence. This self-checking system was built into the algorithm so the probability of reassembling any piece incorrectly was virtually zero.

"They all said we were nuts, but nobody could give me a logical reason why it wouldn't work," said Myers. "That's when I knew we had a winner."

By 1999, one year after signing on with J. Craig Venter, former president of Celera, Myers and a team of 10 researchers - including Gerald Rubin, professor of molecular and cell biology at UC Berkeley - proved this refined version of shotgun sequencing worked. In 11 months, they wrote 500,000 lines of code to sequence the genome of the Drosophila fruit fly. The research was dubbed "Best Paper of the Year" in 2000 by Science magazine.

"It was a heady time, and great fun," said Myers. In June 2000, Venter and Dr. Francis Collins, who led the publicly funded Human Genome Project, stood by President Bill Clinton to announce the completion of a working draft of the 30,000 genes in the human genome.

Myers flourishes by thinking unconventionally. He developed an appreciation for different points of view through his extraordinary travels as a child. His father's position as a financial officer for Esso, part of the ExxonMobil Corp., required the family to relocate every few years. Myers was born in Boise, Idaho, but didn't stay there long.

"I spent my first birthday on a ship crossing the Pacific on our way to Karachi, Pakistan," he said. Myers called many areas of the world home - including India, Indonesia, Japan and Hong Kong - before returning to the United States to complete his last two years in high school. "That gave me an appreciation for the variety that exists in the world, and I think it helped me develop an open mind about different, non-traditional points of view," said Myers.

While his work at Celera propelled Myers onto the bioinformatics world stage, his contributions to computational biology predated human genome sequencing with his work on the Blast software program, created in 1990. Myers helped develop the algorithms that allow geneticists to compare new DNA sequences or new proteins against known sequences in the GenBank database. He pioneered a scoring method that allowed for approximate rather than exact string matching. That allowed biologists to find "close match" sequences that may play similar functional roles. Not surprisingly, Blast has become an essential search tool in biology labs worldwide.

Among the many honors Myers has earned are the Paris Kanellakis Theory and Practice Prize in 2002, awarded by the Association for Computing Machinery for work in applied algorithms, and the 3rd Millennium Achievement Award in 2000 by the Institute of Electrical and Electronics Engineers. In 2001, Myers was named "Most Influential in Bioinformatics" by Genome Technology Magazine.

With the sequencing of the human genome complete, Myers is now preparing himself for new frontiers in bioinformatics.

"We've decoded the human genome," said Myers. "Now, I want to decode the cell."