Computational Biology Turns 30 at USC Dornsife

This year marks three decades of research in computational biology at USC Dornsife. The year 1982 is also when Michael Waterman arrived at USC.

The USC Associates Chair in Natural Sciences and University Professor of Biological Sciences, Computer Science and Mathematics is widely considered the father of computational biology. Seven years later, Simon Tavaré, George and Louise Kawamoto Chair in Biological Sciences and professor of biological sciences, arrived and became a pioneer in the field.

From March 30 to April 1, USC Dornsife and the USC Office of the Provost sponsored a symposium celebrating 30 years of computational biology at USC Dornsife, Waterman’s 70th birthday and Tavaré’s 60th birthday.

The symposium included panel discussions, workshops, speakers from throughout the world, poster sessions, and a banquet.

“Being a computational physicist myself, I deeply admire what Mike and Simon have created here at USC,” Stephan Haas, professor of physics and astronomy, and vice dean of research in USC Dornsife, told the packed audience during opening remarks at Davidson Conference Center. “It’s not only their exemplary scientific achievement we are celebrating, but also their ability to build a dynamic and cohesive group of researchers of all ages who love working together.”

USC Dornsife’s computational biology breakthroughs have been a driving force behind USC’s continued investment into supercomputing infrastructures, making the campus a superb working environment for computational scientists, neurobiologists and researchers at the Southern California Earthquake Center (SCEC) housed in USC Dornsife, Haas said.

Michael Waterman, University Professor of Biological Sciences, Computer Science and Mathematics in USC Dornsife (left) is considered the father of computational biology, standing with Simon Tavaré, George and Louise Kawamoto Chair in Biological Sciences and professor of biological sciences, also credited with launching computational biology and bioinformatics in USC Dornsife. Photo by Pamela J. Johnson.

“Globally speaking, Mike and Simon have been among the very early leaders in making biology a fully quantitative science,” Haas said. “And they continue their visionary leadership by including other important areas — such as structural biology — into the portfolio of their group. In my view, probably their greatest achievement has been the successful nurturing of a new generation of quantitative biologists, many of whom are here today.”

Executive Vice Provost Michael Quick, professor of biological sciences, said Waterman and Tavaré are great scientists because their first thoughts — and second, and third — are about science.

“I’m lucky  to get to have a cup of coffee with both Simon and Mike several times a year — it is not enough — but while we often talk about a lot of different subjects, it always comes back to the science,” Quick said during opening remarks.  “And because they put science first — and the science of their colleagues — and because of the science that many of you in this room do, there is now a vibrant and growing field of study called computational biology, a field poised to take on some of the major questions in science in the coming decades.”

When addressing Waterman and Tavaré’s birthdays, Quick noted in his signature wit that he’s never been a fan of birthdays.

“It always seems that we did very little on our birthdays to warrant celebration,” Quick said. “So perhaps we should honor both Mike’s and Simon’s mothers for their hard work. I prefer to celebrate the science.”

Waterman could not have agreed more. He said the symposium coincidentally fell on his and Tavaré’s birthdays.

“The real theme of the conference was to celebrate the former and current students and postdocs from the program, Waterman later said. “Some of them are current leaders of the field and head their own programs at places like the National Institute for Research in Computer Science and Control (known as INRIA) and the Max Planck Institute.”

Many former students and postdoctoral researchers presented their work at the symposium.

“The impact of 30 years of generating a novel research area at USC came into sharp focus at the conference,” Waterman said.

Waterman recalled arriving at USC in 1982 eager to solve problems relating to biological sequences, in particular deoxyribonucleic acid (DNA), ribonucleic acid (RNA) and protein sequences.

“After a while I looked for a person we could bring to USC who had mathematical and statistical strengths, but also had an appreciation for the new data,” Waterman said. “The possibilities were not numerous at that time — in great contrast to today — but I found Simon Tavaré by spring 1983. He had done pioneering work on the coalescent, but was not yet famous for it.”

USC Dornsife organizers of the symposium from left: Ting Chen, professor of biology, computer science and mathematics; Xianghong Zhou, associate professor of biological sciences and computer science; Waterman; Tavaré; and Fengzhu Sun, professor of molecular and computational biology, who was lead organizer. Photo By Pamela J. Johnson.

Tavaré often spent time in Los Angeles beginning the summer of 1983 until 1987, when he worked as a visiting professor for a year before joining the faculty fulltime.

“For many years Simon and I shared grants, and postdoc and student researchers freely,” Waterman said, “and we together built what we now call the computational biology program.”

Waterman’s contributions include the dynamic programming algorithm for finding sequence homology and the algorithmic approach to RNA structure prediction. Tavaré has made significant contributions to methodology for the analysis and interpretation of DNA sequence and related genomic data, and to bioinformatics.

The computational biology and bioinformatics group Waterman and Tavaré have created has grown to a dozen faculty members as well as a large cohort of graduate students and postdoctoral fellows. Faculty members include National Science Foundation CAREER awardees as well as Pew and Sloan fellows.

Waterman was named a Guggenheim Fellow and elected to the American Academy of Arts and Sciences in 1995, and elected to the National Academy of Sciences in 2001.

Tavaré is an elected fellow of the Royal Society, the American Association for the Advancement of Science, the Institute of Mathematics and its Applications, the Society of Biology, the Institute of Mathematical Statistics and the American Statistical Association.

The symposium organizing committee included USC Dornsife’s Ting Chen, professor of biology, computer science and mathematics; Fengzhu Sun, professor of biological sciences; Xianghong Zhou, associate professor of biological sciences and computer science; and Paul Marjoram, assistant professor at USC’s Programs in Biomedical and Biological Sciences.

Keynote speakers included David Haussler, professor of biomolecular engineering at the University of California, Santa Cruz, who was the first to apply the latter methods to the genome-wide search for gene expression biomarkers in cancer; Barry Honig, professor of biochemistry and molecular biophysics at Columbia University, well known for his innovative methods to compute and display the electrostatic potentials of macromolecules based on their 3D structures; and Ron Shamir, Sackler Professor of Bioinformatics at Tel Aviv University, whose research interests include gene expression analysis, modeling and dissection of molecular networks, gene regulation and cancer genomics.

Also, Terry Speed, professor and head of bioinformatics at the Walter and Eliza Hall Institute in Australia, known for his analyses of variance and bioinformatics, particularly in microarrays data; and Wing H. Wong, professor of statistics and health research and policy at Stanford University, whose team developed the software dChip for the analysis microarray data and the programs CisGenome, SeqMap and SpliceMap for the study of next generation sequencing data.