Cracking the Case

If USC life sciences forms a web of interdisciplinary research, computational biologist Simon Tavaré sits smack in the center.

A professor of mathematics, biological sciences and preventive medicine, Tavaré collaborates with paleontologists, pathologists, cancer epidemiologists, statistical geneticists, molecular biologists, population geneticists and, of course, his close colleagues at the College’s Center for Computational and Experimental Genomics.

The holder of the George and Louise Kawamoto Chair in Biological Sciences, Tavaré’s expertise lies in the application of statistics and probability theory to problems arising in molecular biology, human genetics, population genetics, molecular evolution and bioinformatics.

Tavaré is one of the pioneers in the field of computational biology and has made key contributions in statistical genetics. He is most famous for his work on how to use gene sequences to trace the lineage of a cell, an individual or a species back through time.

“What I do is to use statistics to infer the [genetic] history of organisms or tumors,” says Tavaré. “Biology motivates my mathematical work. But what most interests me is thinking up new methods in statistics.” Formally trained in probability and statistics, Tavaré began his informal education in biology in college, eventually working as a fellow with mathematician-biologist Sam Karlin of Stanford University, whose group was among the first to study the statistics of genetics.

In his current work, Tavaré continues to apply the power of math to help solve complex biological problems. “Efforts to map genes correlated with complex and common diseases rely heavily on sophisticated mathematical techniques,” he says.

At the Keck School of Medicine of USC, Tavaré works on two separate projects related to tumor progression in colon cancer, one with molecular pathologist Darryl Shibata and the other with cancer epidemiologist Duncan Thomas. Tavaré also studies evolution and genetic variation in collaboration with College molecular and marine biologists, and in another project with fossil expert Robert Martin of the Chicago Field Museum.

In the summer of 2002, the National Institutes of Health awarded Tavaré $1.65 million to tackle the computational problems presented by the powerful technology of DNA chips. DNA chips allow biologists to compare the activity of all genes in cells, shedding light on what genes make a liver cell distinct from a brain cell or a cancerous cell different from a normal cell. The problem has been that just one experiment can result in a million data points. Analyzing the data has presented a formidable challenge. Tavaré’s project focuses on developing new mathematical tools that will help scientists interpret the data.

The DNA-chip research represents exactly the kind of challenge that most intrigues Tavaré: to develop new mathematical theories, interesting in their own right, that will prove invaluable to core issues in biology. “Tavaré’s strength is that he has taught himself so much biology that he has truly become, not just an applied mathematician, but a computational biologist concerned with questions at the core of biology,” says Sarah Bottjer, professor and chair of the biological sciences department at the College.