Using Computers to Study Disease: Speaks With a Siemens Prize Winner

Jan 27, 2011

Andrew Liu, a senior at Gunn High School in Palo Alto, was a regional finalist and national semifinalist in the 2010 Siemens Competition in Math, Science and Technology. Liu received these awards for his work in bioinformatics, using computer programming to better understand complications that arise after organ transplants.

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By Megan Driscoll

andrew liu You were a regional winner and national semifinalist in the 2010 Siemens Competition in Math, Science and Technology. Please describe for our readers the project that nabbed you this honor, and tell us how it can be used in modern medicine.

Andrew Liu: I studied transplant rejection using a computational approach called pathway analysis and discovered a novel explanation for transplant rejection, identifying molecular targets for potential patient drug treatment. To identify these targets, I developed an improved algorithm that analyzes genomics data to identify the genes and bodily pathways causing a given disease. Can you describe what pathway analysis is and how it applies principles of computer science to biology?

AL: Pathway analysis tries to identify the biological pathways causing a given disease based on gene expression data. Right now, there's plenty of data showing that certain genes are different (active at different levels) between diseased and non-diseased patients, and pathway analysis uses this data to identify the pathways that are different between the two conditions, thus responsible for the disease. The computer science challenge is to develop an algorithm to take gene expression data as input and output the correct pathways. I used my algorithm specifically to study transplant rejection, but the algorithm can also be used to study any disease with available data. What was the research process like? How did you plan and execute the project, and what was it like working with your Stanford mentor?

AL: I loved what I was doing, so I spent a lot of time (40-50 hours a week over the summer, and I'm still researching now). Once I had a picture of my project's direction in my head, it was just a matter of finishing each step - acquiring the gene expression data, storing pathway information in a database, etc. My mentor, Dr. Purvesh Khatri (a post-doctoral fellow in Stanford's Butte and Sarwal labs), was absolutely invaluable and has made my research experience more rewarding than I ever could have asked for. Especially when the results weren't what we were hoping for, Purvesh really helped me persist and motivated me with his passion. After winning the regional competition, you were still testing your explanation to see if it was the correct model. How did those tests come out?

AL: Unfortunately those tests were delayed, but the results should come out this month.

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  • Computer and Information Support Services, Other
  • Information Science and Studies General
  • Information Technology
  • Robotics and Artificial Intelligence How did you become interested in bioinformatics? Is this a field in which you envision yourself pursuing further research?

AL: I've been interested in math and computer science since middle school, so I applied to the Stanford Institutes of Medical Research when I heard about the opportunity in the Butte lab (which studies bioinformatics) to apply computer science to study disease. I was lucky to find a great mentor and lab as well as a cutting-edge field. I do envision myself pursuing further research in bioinformatics - I already am! You're also a two-time winner of the Intel Excellence in Computer Science award and a two-time qualifier for the USA Math Olympiad. What led you to computer science, and how did you develop such remarkable abilities?

AL: I started computer science out of my interest in math. In 7th grade, I designed a computer game called GeoQuest to teach my classmates about U.S. geography, and seeing my finished project made me really excited about programming. Eventually I got into research and programming contests like the USA Computing Olympiad, all of which developed my skills and showed me how widely applicable computer science is. What sort of plans have you considered for after high school? Have you had much time to think about college or career, and if so, what's your dream school? Dream career?

AL: I want to earn an undergraduate degree in computer science and a graduate degree in business or law. I don't have a definite choice for a career, but right now I think I'd like to start up a tech company or become an executive at an existing one. Finally, I'd like to give you the opportunity to share anything you'd like about your research, interests and prize-winning project.

AL: I'd again like to thank my mentor, Purvesh, and I'd like to thank for this opportunity to share.

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