Pablo Gainza-Cirauqui
Pablo Gainza-Cirauqui

Department of Computer Science
Duke University
Phone: (919) 660-6512
Office: D206 LSRC
balls

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 Staphylococcus aureus, can evolve resistance to new drugs, (ii) nanobody deimmunization and (iii) antibody design.
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!

Education Background

Duke University
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

Publications

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 2016

Kyle 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)

Pablo Gainza*, Kyle E. Roberts* and Bruce R. Donald. Protein Design using Continuous Rotamers PLoS Computational Biology (2012) 8(1): e1002335., 2012. (* equal contribution)

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).

Last modified: 2016/03/21