I was a PhD student in Computer Science
at Duke University until 2015, working with Prof. Bruce R. Donald.
My research focused on protein design methods and applications.
Specifically, I developed protein design algorithms to accurately and realistically model how protein
structure and function changes when mutations occur in the protein's gene.
I applied these algorithms to several biomedically important problems, such as: (i) predict how pathogens, such as Methicillin-resistant
You can find my old CV at CV here and you can also visit our lab's webpage.
I've now moved to the Laboratory of Protein Design and Engineering at EPFL!
Ph.D. in Computer Science, Fall 2008-June 2015
University of Costa Rica
Masters in Computer Science, 2004-2007
Bachelor in Computer Science, 2000-2003
Pablo Gainza, Hunter Nisonoff, Bruce R. Donald. Algorithms for Protein Design. Curr Opin in Struct Biol, In Press 2016
Adegoke Ojewole, Anna Lowegard, Pablo Gainza, Stephanie Reeve, Ivelin S. Georgiev, Amy C. Anderson, Bruce R. Donald. OSPREY Predicts Resistance Mutations using Positive and Negative Computational Protein Design. Methods in Molecular Biology, In Press 2016Kyle E. Roberts*, Pablo Gainza*, Mark A. Hallen, Bruce R. Donald. Fast gap-free enumeration of conformations and sequences for protein design. Proteins doi=10.1002/prot.24870, 2015 (* equal contribution)
Mark A. Hallen, Pablo Gainza, Bruce R. Donald. A compact representation of continuous energy surfaces for more efficient protein design. J Chem Theory Comput, 11 (5), pp 2292–2306, 2015
Stephanie Reeve*, Pablo Gainza*, Kathleen M. Frey, Ivelin S. Georgiev, Bruce R. Donald, and Amy C. Anderson. Protein Design Algorithms Predict Viable Resistance to an Experimental Antifolate. Proc Nat Acad Sci USA 112 (3), 749-754, 2015 (* equal contribution)
Pablo Gainza*, 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. OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms. Methods in Enzymology, Vol. 523, Methods in Protein Design, pp87-107. , 2013. (* equal contribution)Design and implementation of a scalable constraint-based routing module for QoS path computation
Last modified: 2016/03/21