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CORNELL UNIVERSITY EXPLORES THE WORLD OF BIOINFORMATICS

The Cornell Theory Center (CTC) awarded three undergraduate summer internships in Computational Biology this year. Cornell computer science major Keith Jamison '04 and chemical engineer majors Sam Lai '03 and Keiichiro Kushiro '04 will spend the summer in Rhodes Hall working with scientists at CTC's Computational Biology Service Unit (CBSU). Internships carry an award of $3,500; Lai and Kushiro, who are working together on a project, are sharing the award.

Jamison will use high-performance computing applications to study the structures of proteins in an effort to understand more about proteins in our bodies and how they function. Understanding the three-dimensional shape, or structure, of proteins can lead to advances in the medical field. Proteins are responsible for all processes in the body, with the success of the process determined by the protein's structure.

"Proteins are behind every biological function," said Jamison, who hails from El Paso, Texas. "Ultimately, knowing the shape of proteins will allow you to determine how best to interact with the molecule. This research allows me to combine my interest in two fields: the medical field and computer science."

Advised by assistant professor of computer science Golan Yona, Jamison will use existing measures of similarity to induce a new measure of similarity for all protein pairs, by mapping each protein to a high dimensional proximity space.

"Although Keith is a computer science major, he has taken many courses in biology and biochemistry, and he is now taking my class, machine learning," said Yona, who indicated that the project will make extensive use of threading algorithms. "His background matches the project requirements perfectly. Knowledge in biology and machine learning are essential to the project, and he is excited about the prospects of integrating both."

Lai, of Hong Kong, and Kushiro, of Japan, are simulating a virtual Escherichia coli cell that accounts for cell geometry, cell-cycle times, ATP usage, genetic mechanisms, and concentrations of various components for each generation. The CBSU internship provides access to high-performance computing, enabling them to extract highly specific and accurate biological predictions pertinent to E. coli without the existing limitations of tedious measurements of kinetic rate constants.

"We needed intense computer power because we are simulating a vast number of parameter combinations," said Kushiro. "Parallel processing is so much more efficient than trying to analyze the data on a single processor."

Lai and Kushiro, working under the direction of Professor Michael Shuler, Cornell's director of the Bioengineering and Biomedical Engineering programs, and graduate student Mariajose Castellanos, are conducting this research in collaboration with Kevin Brown of the Sethna Group at the Physics department on the use of statistical mechanics techniques applied to parameter evaluation for complex biological system models. Based on the results of Lai's and Kushiro's efforts, they will find out if Brown's research can be applied to an entire cell system.

"Specifically, though, the goal of our internship is to enable further medical research as well as the creation of a minimal cell model," said Lai. "If E. coli can be simulated on a computer, researchers will have an additional resource to complement their work with the organism in a laboratory environment."

CTC's Undergraduate Summer Internships in Computational Biology are funded through an IBM University Partnership award. The program runs from June through mid-August. The call for proposals for 2004 will be available in February of next year.

"We were very impressed by the quality of proposals that we received for this program," says CTC executive director Linda Callahan. "And we were very pleased with the breadth of the fields from which we received applicants. This is a great opportunity for such exceptional students to immerse themselves in bioinformatics with the staff at CTC's CBSU."

The students will discuss results of their internship in a project report and a seminar this fall.

The Cornell Theory Center's Computational Biology Service Unit (CBSU) is a dynamic institute that conducts research and develops tools in conjunction with collaborative partners at Cornell University, Cornell's Weill Medical College, Rockefeller University and Memorial Sloan-Kettering Cancer Center. Professors and researchers from many different departments within Cornell University use CBSU and CTC's resources in their research projects. CBSU is also affiliated with the Cornell Genomics Initiative. Current activities at CBSU include collaborative research, Web computing, software development and the creation of Web resources for biological researchers.