When Terry Furey enrolled in the Ph.D. program in Computer Science at the Baskin School of Engineering, he had no idea that he would soon become a part of one of the greatest scientific feats in modern history.
As a computer scientist with an interest in biology, Furey had originally been excited to work with David Haussler, then a professor of computer science at UC Santa Cruz, who was known for his work in what would today be considered computational biology. Furey began his studies working with support vector machines and microarrays in Haussler’s lab, but then, as he describes it, “David just kind of disappeared for six months.”
It turned out that Haussler was deeply involved in talks with the Human Genome Project consortium. When he resurfaced, he had a new project: to help the consortium complete their assembly of the first draft of the human genome.
As Haussler’s only graduate student at the time, Furey quickly went to work performing some of the initial analyses for the assembly project. His work helped to ensure the accuracy of the ordering sequence by comparing it to existing genome-wide marker maps while Jim Kent, a graduate student in UCSC’s biology department, was putting together the assembly.
“While David and Jim were off doing the whole assembly thing, I was working with some of the different sequencing centers in the consortium as they were starting to put together their sets of BAC clones in order to complete each of the chromosomes,” Furey explains. “This was before the wide adoption of shotgun sequencing, so we were putting together a tiling path, and a lot of what I was doing was ensuring that these clones actually did go together the way the sequencing centers thought they did and providing feedback on when I saw things that didn’t seem like they belonged.”
As the project evolved, Furey accompanied Kent and Haussler to many of the consortium meetings that were hosted by Cold Spring Harbor Laboratory. It was at the first of these meetings that the scale of what they were doing began to dawn on him. “I was interacting with these luminary scientists, and it really started to sink in what this project was,” Furey notes.
In July of 2000, UC Santa Cruz published the first draft of the assembled human genome on the internet, but there was still plenty left to be done. By this point, Haussler’s lab had expanded to include graduate students Chuck Sugnet and Sanja Rogic, and the three of them went to work on helping Jim Kent launch the UCSC Genome Browser, a new tool that would act essentially as a digital microscope for visualizing the genome online. The work Furey had done on mapping during the sequencing portion of the project ended up providing much of the foundation for the UCSC Genome Browser’s mapping tracks, and the software he had written to map chromosome bands became the ideogram that appears on the top of the Browser.
“It was humble beginnings,” Furey says of their small team, but as the UCSC Genome Browser proved to be a popular and widely used tool among researchers, Haussler’s lab and Kent’s Browser team exploded. “David had a knack for being able to get some smart and talented people there, and it was just a really exciting time. Thinking now of some of the people who were there and what they have gone on and done, I feel very fortunate to have been able to be a part of that.”
Before Furey began his program at the Baskin School of Engineering, his career ambitions had been directed mostly toward teaching, but the experience he gained during the Human Genome Project ignited his passion for research. After graduating with his Ph.D., he continued to engage in large consortium work through the ENCODE Project, for which he researched open chromatin and DNase-seq assays.
Today, Furey is combining his interests in teaching and research as a professor at the University of North Carolina at Chapel Hill, where he holds dual appointments in the genetics and biology departments. He is currently working on two different projects involving functional genomics assays. The first of these projects looks at the effects of environmental toxicants and variations in how bodies respond to those toxicants, while the other looks at inflammatory bowel diseases like Crohn's disease to better understand their molecular basis and heterogeneity.
On the latter project, Furey is collaborating with a physician-scientist, which he says has been both an interesting and challenging experience. “It took awhile for us to really be able to communicate well together because we come from such very different backgrounds,” he says. “I’ve learned a lot about intestinal biology and the disease, and I have tried to teach him what analyses are possible and what we just can’t do. I think it has been informative both ways.”
One of the most rewarding aspects of working with a physician, however, has been that it has helped direct research questions toward what will make the biggest practical difference for treatment. Furey is excited by the prospect that the work he is doing could be contributing to making patients' lives better, even if it might take time to see the full impact. “With research, nothing is ever immediate,” he explains. “You always have to imagine that in the long term the knowledge that you are gaining now might make a difference ten years down the line.”
Furey, of course, knows this from experience. Twenty years after the Human Genome Project was completed, he has been able to witness breakthroughs in disease research that would have never been possible before the genome was sequenced, and he is proud of the contribution he made.
When he is mentoring his students, Furey often uses his story as an example of how research and career trajectories can take unexpected turns. “I tell all my grad students now that there are some things that you just can’t plan for,” he says. “I really think that perseverance is one of the most important traits... Everyone is smart. A lot of times it is not the ‘smartest’ ones who end up being most successful, but the ones who don’t give up, who look for opportunities and make the most of those opportunities. ”