James Kent on Involvement in Genomics
  James Kent     Biography    
Recorded: 31 May 2003

We had been doing software and the software was just getting more and more complicated. And I guess that we had one thing for this new operating system for Microsoft where the developer’s kit for us programmers came on twelve CD-Rom’s. And I just could have exploded at that point because, you know, I was thinking that the human genome fits on one CD-Rom and it doesn’t change every three months. Now little did I realize then that now [that] I’m working with the human genome and effectively it does change every three months because we get an assembly. I think now that it’s finished actually that will settle down and we’ll be able to sort of, you know, look at it in detail.

I felt pretty strongly as I was coming in to it. I mean, you know, you had the human genome. And you can say that, you know, it fits on one CD-Rom. It’s pretty amazing considering, you know, these days, you know, just simple computer programs sometimes will take up that much. But still nobody understands it. I mean, in fact, we find out that you could probably fit on a tenth of a CD-Rom all that’s actually really needed to make a human. But figuring out what it is still too vast; its way too vast for anybody to sort of understand on their own so you need some sort of system to sort of index it. I mean I guess we’re in the age of hypertext and the web and stuff and basically, I guess, my view back in ’95 was that the human genome would probably need a really good on-line help system where people could sort of follow it and ask questions about it and lookup parts of it. I was thinking of that for quite some time, but then that was only part of my motivation. I mean, I like biology a lot for its own sake and I sort of got into the lab and I really like microscopes. I don’t actually like gels so much because they’re kind of boring to look at.

I was just working through the program and I think it was in ’99 the worm genome had just been finished and it was clear that at that point, you know, there was a lot of research that you just do with the computer. There was at that point in___when you were working on the worm a lot of the stuff you no longer needed to go do PCR experiments or go do wet lab experiments if you had just the right computer skills since there was so much data already there you could take it from that. And my advisor then knew I had done some stuff with the computers and so he had a little lab project for me that started with the computers. And it’s sort of one thing led to another from that and eventually, I guess, about three months later I met David Haussler and he was—when I went to Santa Cruz actually, I didn’t know him. And it was just lucky that I ended up in the place that had good computational biology. I had been there for the biology itself.

Jim Kent is a research scientist at the University of California, Santa Cruz's Center for Biomolecular Science and Engineering. After a stint working in the computer animation industry, he entered the Molecular, Cell, and Developmental Biology Ph.D. program at Santa Cruz. While completing his degree, he became increasingly interested in bioinformatics. Concurrently, the human genome was being sequenced, accumulating in the databases and was scheduled to be released in one month’s time—however, still no technology was in place to assemble its many sequences. In one month, Jim Kent created a computer program called the GigAssembler and computationally compiled for the first time, the entire human genome so that it could be released to the public at its intended deadline.

Jim Kent focuses on understanding the way in which genes are turned on and off to create varying outcomes.