Rachel is working with Brian King on a new method that can predict a contact map of a protein from its sequence, which is an important step toward predicting the fold of a protein. Rachel has presented her work at two conferences, will be presenting at an ACM international conference for bioinformatics in the fall. Her work will culminate in an honors thesis this coming year.

 Student Reflection

I have been doing research with Professor Brian King in the Computer Science Department since my sophomore year. Our research is to predict protein contact map (PCM) using machine learning algorithm. Protein's functionality and its 3-dimensional (3D) structure are intrinsically related. However, determination of a protein's 3D structure is hindered by the inefficiency of traditional experimental methods such as NMR spectroscopy or X-ray crystallography. Protein residue contact map is an intermediate to protein's tertiary structure and prior research has successfully predicted a protein's 3D structure from PCM. Our goal is to predict PCM from a protein's secondary structure using Quinlan's C4.5 decision tree algorithm. Our result is promising. We published and presented our work at the 5th Association for Computing Machinery (ACM) conference in Bioinformatics, Computational Biology and Health Informatics at Newport Beach, California.

My research experience with Professor King is one of the best parts in my life as an undergraduate student. It enables me to use the knowledge I learned in class, but it also requires me to explore new territories by myself. Before doing research with Professor King, I had limited background in both computer science and biology. I still remember spending a whole week reading articles and textbooks in machine learning, in order to learn about the PCM and the decision tree algorithm. Also, this experience motivates me to continue my education in graduate school. As the only undergraduate student in the ACM conference, I am very proud of our research. I really appreciate Professor King, along with the Computer Science Department at Bucknell, giving me this precious opportunity to delve into this emerging area.

Read about Rachel Ren's Paper being selected for the National Bioinformatics Conference