Cures Start Here. At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the development of immunotherapy, which harnesses the power of the immune system to treat cancer. An independent, nonprofit research institute based in Seattle, Fred Hutch houses the nation’s first cancer prevention research program, as well as the clinical coordinating center of the Women’s Health Initiative and the international headquarters of the HIV Vaccine Trials Network. Careers Start Here
This is a unique time, full of opportunity, to be working on B cell receptor (antibody) sequences. The field is awash with data, and methods haven’t really caught up: there is still lots to do to develop methods that fully make use of the data but also scale to large data sets.
The Fred Hutch is also a unique place to be doing this work, with a convergence of many very strong research programs. This project is a collaborative endeavor between
(In passing, I also note that the HIV Vaccine Trials Network has its primary leadership here, and they are very interested in using B cell sequencing to understand vaccine response.)
This project is to analyze the antibody immune response in Dr. Overbaugh’s priceless samples from a cohort of Kenyan sex workers in the era before widely-available antiretrovirals. The general goal is to understand the broad and potent antibody responses raised by these women. Our part of that goal will be to perform sequence analysis to understand the events leading to, selective pressures on, and co-evolution of HIV-responsive lineages. This will include close inspection of individual data sets as well as methods development to characterize the antibody response in more detail.
This project will entail be a convergence of the two primary themes in my group: Bayesian phylogenetics and B cell receptor sequence analysis. Our recent work has convinced us that Bayesian methods are needed for antibody ancestral sequence reconstruction, and we’re going all-in. There special challenges, such as context sensitive mutation and strong natural selection, and also special opportunities.
One of the special opportunities that this work provides is that these inferences can be validated by lab work.
The Overbaugh lab is expert at expressing antibodies and testing their properties, in particular against viruses isolated from these same individuals. This will create a beautiful dynamic feedback loop that we can use to learn about coevolution.
In case you aren’t already stoked, here’s an image from Liao et al 2013 showing the epic evolutionary battle between HIV (top) and antibodies (bottom):
This is a great opportunity for people with a few different backgrounds, so drop us a line even if you don’t already know how to approach all aspects of this work. In particular, this would be a good fit for folks:
The formal requirements are:
Ideally we’d recruit someone with: