Chuqiao Ren, ’15

Project: A novel ensemble classifier for protein contact map prediction
Duration: Summer 2013 – Spring 2015
Funding: Bucknell University Program for Undergraduate Research, BRK Startup Fund, Geisinger BGRI Grant, CS Dept. Fund


One of the greatest challenges in bioinformatics is how to predict the 3-D structure of a protein by understanding the relationship between a sequence and its amino acid structure.  A protein contact map is a useful way of representing protein 3-D conformations. It is based on a distance matrix, which is a symmetric matrix that contains the Euclidean distance between each pair of C-alpha atoms in each residue in the folded protein.  

Our goal is to improve existing machine learning algorithms for predicting a protein contact map from protein sequence, and develop a novel algorithm that improves the performance of existing contact map predictors.


  • Honors Thesis – Successfully defended, April 2015
  • Short paper and poster – ACB BCB ’14 – ACM International Conference on Bioinformatics, Computational Biology and Biomedicine, Sept 20-23, Newport Beach, CA [link]
  • Poster Presentation – Fourth Annual Susquehanna Valley Undergraduate Research Symposium, SVURS 2014, August 5, Geisinger Research, Danville, PA
  • Poster – Kalman Research Symposium 2014, March 29, Bucknell University, Lewisburg, PA.


Chuqiao successfully defended her honors thesis in April, 2015. She is staying for a bit longer this summer to help finish a journal publication and submit before she departs us. She is currently planning on pursuing her graduate degree in computer science at Columbia University, starting Fall 2015. Congratulations, Chuqiao!

Spring 2015

Rachel Ren successfully defended her honors thesis, titled, “Predicting Protein Contact Maps by Bagging Decision Trees”. Congratulations, Rachel! Additionally, Rachel will be attending graduate school starting in the fall at Columbia University, where she will pursue a Masters in Computer Science. Rachel intends to focus on research in machine learning.

Congratulations, Rachel! Bucknell is proud of you! We wish you the very best as you pursue your graduate work.