Prof. Andrew Ferguson has an RA Opportunity in Computational Biomaterials Research

Prof. Andrew Ferguson is recruiting for an RA opportunity in his computational biomaterials group in the Department of Materials Science and Engineering. Prof. Ferguson's research interests lie in the application of molecular simulation, statistical mechanics, and machine learning / data mining tools to problems in biomaterials and the life sciences. The particular research opening available is in the computational inference of viral fitness landscapes for rational vaccine design.

In brief, we are developing a Bayesian inference algorithm to compute Ising/Potts model descriptions of viral "fitness landscapes" by data mining protein sequence databases. These landscapes quantify the capacity of a virus to replicate in a host as a function of its amino acid sequence, and permit the theoretical prediction of the fitness of mutant viral strains. We shall apply this approach to key proteins in the HIV virus, and will test our predictions against in vitro assays performed by collaborators in the HIV Pathogenesis Program at the University of KwaZulu-Natal. Further, we shall integrate these data-driven fitness landscapes with bioinformatic models of host-pathogen predator-prey dynamics to develop realistic statistical predictions of the infection course, and identify immune responses expected to be particularly efficacious in targeting vulnerable regions of the virus and controlling viral replication. This computational platform is expected to be of value in guiding the development of prophylactic and therapeutic strategies for HIV and other viral pathogens. We will work with experimental and clinical collaborators at the Ragon Institute of MGH, MIT and Harvard to test our designed vaccines in vitro and in small animal models.

We are seeking motivated students with a strong background in mathematics and physics. Although we work closely with experimental collaborators, this project is exclusively computational/theoretical in nature. Previous experience in computational work is desirable, but not necessary. No prior background in biology/immunology is required.

Please contact Prof. Ferguson (alf@illinois.edu) directly for more information, or visit his faculty page.