A powerful combination: computer science, biology- Emerging Field is Subject of Stanford Conference

It was a case of learning from their child’s homework.

Peter and Vicky Markstein had long careers in computer science with no interest in biology. But the two researchers helped their daughter Michele with her biology doctorate research in 1999 and so stumbled onto the emerging field of bioinformatics.

By Dean Takahashi
Mercury News

Now the study of bioinformatics — the use of computing in biological research — is the subject of a second annual conference at Stanford University starting Monday, organized in part by the Marksteins. Topics at the conference vary widely from decoding proteins to a panel on bioethics.

Bioinformatics is luring hundreds of researchers from computing and biology because it takes heavy-duty computing methods to search for patterns in human and animal genetic codes.

“It’s an interdisciplinary approach to biology that brings mathematicians and computer scientists together to look at the vast amount of data that biologists can now generate,” Peter Markstein said.

Vicky Markstein added: “It’s a new kind of microscope for biologists.”

Interest in computing and biology spiked with the Human Genome Project, the 13-year federal research project that identified all 30,000 genes in human DNA and stored a mountain of data for analysis. Now that the genome has been decoded, the Marksteins and other researchers see an enormous task in analyzing and making sense of the data.

“It’s like a full alphabet available now,” Peter Markstein said. “The question is, what does it mean?”

RISC project

Both Marksteins worked many years at IBM and were part of the pioneering 1980s project dubbed “Reduced Instruction Set Computing,” which became the chip architecture behind computers at Sun Microsystem, IBM, Apple Computer and Hewlett-Packard. Peter Markstein joined HP in 1989, where he worked on technologies for the Itanium chip.

The Marksteins came upon their new field of study by accident. Michele Markstein, then a graduate student at the University of Chicago, was studying the genes of the fruit fly, or Drosophila melanogaster, and needed a way to quickly look for patterns in the DNA, particularly the parts of the DNA that turn functions on and off. She asked her parents and they created a computer program that could search for patterns in the DNA and quickly spit back results. Then Michele would verify the results in lab tests where she would mutate genes in order to discover their true functions.

The trio and another researcher, Michael Levine, published a paper on their results in 2000. With the paper authored by “`Markstein, Markstein, Markstein and Levine,” one researcher joked that it sounded like a Jewish deli, Peter Markstein said.

The elder Marksteins became addicted to the subject. They took classes at night at the University of California-Santa Cruz. Peter Markstein got permission from his boss at HP’s research lab in Palo Alto to study the field full time, while Vicky Markstein organized the first Stanford conference. Michele Markstein and researcher Ka-Ping Yee made their fruit-fly search tool available on the Web.

“This kind of tool allows us to ask basic questions about biology,” said Michele Markstein, 32, who is finishing up her doctorate and is a visiting scholar at the University of California-Berkeley.

It isn’t clear how much commercial opportunity will come from bioinformatics. Dave Berman, spokesman for HP Labs, said HP is sponsoring the Stanford conference and investing in the technology because it helps it understand customers in the life sciences.

Dick Lampman, director of HP Labs, said, “It’s an important field of research for the benefit of society.”

Some companies have already come and gone, though. One start-up, Double Twist in Oakland, hoped to commercialize bioinformatics, but it went out of business last year. Entigen of Sunnyvale also shut down in 2001. The companies that are left are generally larger diversified biotech companies that are using bioinformatics tools to arm their researchers in drug discovery.

Interest growing

Steve Madden, an organizer of the conference and a tech-support engineer for life sciences at Agilent Technologies, once worked at Double Twist. He said that most of the pure-play bioinformatics companies that got funding during the height of the human genome project found no market for their tools.

Nonetheless, academic interest is growing and the federal government is funding research through the Department of Energy’s Genomes to Life program. Some universities also are offering courses in bioinformatics. Madden said that at this year’s conference, there are 108 “posters,” or researchers who have proposed to present ideas for papers, compared with 39 last year.

Peter Markstein quipped, “Now I put on my tax return that I was a bioinformatician.”

Contact Dean Takahashi at [email protected] or (408) 920-5739.

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