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
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."