The ultimate network
With NSF grant, Rice professor is building new tools to probe genomes

BY MIKE WILLIAMS
Rice News staff

A Rice University computer scientist has won a National Science Foundation grant worth $1.2 million to create tools that will simplify the task of understanding the evolution of whole-genome sequences.

	LUAY NAKHLEH

Luay Nakhleh, associate professor of computer science, is principal investigator for the project that includes researchers at the University of Michigan and the University of Texas at Austin.

Over the term of the three-year grant, the team will develop software tools to analyze gene genealogies — aka gene trees — through which researchers model how genes replicate and are transmitted during evolution.

Nakhleh’s project will produce algorithms to look for key similarities and differences among gene genealogies across species in the hope of refining information about where branching in the tree of life may have occurred.

“The way biologists traditionally build species trees, or evolutionary histories, is by sequencing a single gene,” Nakhleh said. “They say, for example, ‘Let’s get the human/chimp/mouse evolutionary history.’ So they will find a gene or genomic sequence from each and then build a tree from these sequences. There are tons for methods for things like that.

“But now that whole-genome sequences are available, biologists are saying, ‘OK, why are we doing just a single gene? Let’s try to build it on multiple genes.'”

Nakhleh said advances in genetic research have brought forth new questions, as gene trees built from corresponding sequences in, say, humans, chimps and gorillas now give confusing results. “Some gene trees will tell you that humans are closer to chimps than gorillas. Others will tell you humans are closer to gorillas than to chimps. And then you will see other genes telling you chimps and gorillas are closer to each other than to humans.

“So now the question is, which one is it? And why are these gene trees telling us different stories?”

Hybridization in plants and horizontal gene transfer among bacteria add more variables, as they allow genetic sequences to be shared in a nonvertical fashion. Nakhleh said geneticists are beginning to understand they’re looking at something more like a network than a tree.

“The question is, can we still construct something? Is there a network we can make sense of? This is what we are going after.”

Nakhleh said the project will conclude with a two-day national workshop to train students and postdoctoral fellows in use of the new tools.