I am a fifth-year PhD student in Computer Science at Duke University, working with Bruce R. Donald. My research focuses on protein design methods and applications. Specifically, I develop protein design algorithms to accurately and realistically model how protein structure and function changes when mutations occur in the protein's gene. I apply these algorithms to predict how pathogens, such as Methicillin-resistant Staphylococcus aureus, can evolve resistance to new drugs.

You can find my CV here and you can also visit our lab's webpage.

Education Background

Duke University
Ph.D. candidate in Computer Science, Fall 2008-now

University of Costa Rica
Masters in Computer Science, 2004-2007
Bachelor in Computer Science, 2000-2003

Publications

OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms.
with Kyle E. Roberts, Ivelin Georgiev, Ryan Lilien, Daniel Keedy,Cheng-Yu Chen, Faisal Reza, Amy C. Anderson, David Richardson, Jane S. Richardson, and Bruce R. Donald
Methods in Enzymology, Vol. 523, Methods in Protein Design, pp87-107. , March 2013.

Protein Design using Continuous Rotamers
with Kyle E. Roberts and Bruce R. Donald
PLoS Computational Biology (2012) 8(1): e1002335., January 2012.

Graduate coursework

Spring 2012
CPS 296.2: Topics in Computational Structural Biology

Spring 2011
CPS 196.1: Algorithms in Drug Design

Spring 2010
CPS 250: Numerical Analysis
BCH 222: Structure of Biological Macromolecules

Fall 2009
CPS 230: Design and Analysis of Algorithms

Spring 2009
CPS 262: Computational Systems Biology
CPS 296.4: Topics in Computational Structural Biology

Fall 2008
STA 213: Advanced Statistical Methods
CPS 220: Advanced Computer Architecture I
CPS 270: Artificial Intelligence

Other stuff

I also worked on optimization problems in Computer Networks for a while; specifically, on optimizing packet delivery while maintaining Quality of Service guarantees (a known NP-Hard problem) in a practical scenario:
Design and implementation of a scalable constraint-based routing module for QoS path computation
P. Gainza, H. Cancela, E. Grampin, M.E. Urquhart.
Proceedings of the 4th international IFIP/ACM Latin American conference on Networking 2007 (LANC'07). (Chevron Award for top student paper).

I am on facebook and google+.

Last modified: 2013/3/23