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Post-Doctoral Research Fellow Computational Biology

Company name
Fred Hutchinson Cancer Research Center

Location
Seattle, WA

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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. The Center's five scientific divisions collaborate to form a unique environment for conducting basic and applied science. Vaccine and Infectious Diseases Division (VIDD), works to eliminate or minimize the impact of globally significant infectious diseases. Within VIDD is the Statistical Center for HIV/AIDS Research & Prevention (SCHARP) which provides statistical support and data management to researchers worldwide in the fight against HIV/AIDS with active studies in the U.S., Africa, Latin America, Asia and Europe. Join us and make a difference!

Careers Start Here.

We have an open postdoc position in the lab of Dr. Frederick (Erick) A. Matsen of at least two years duration with solid pay and great benefits

The project is to learn about anti-HIV antibody development and coevolution using data coming from a unique HIV superinfection cohort for which the viral history has been carefully characterized

There will be many opportunities to develop and deploy new methods in a team pushing the boundaries of Bayesian phylogenetic analysis

We will work with collaborators to validate inferences using lab techniques

The larger research group is highly collaborative, with deep expertise in virology, protein evolution, and structural/functional analysis

We're a Python shop looking for someone who isn't afraid of large-scale data analysis and has high standards for organization and code clarity

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

Julie Overbaugh's lab

brings decades of experience analyzing HIV infection and the corresponding immune response.

Jesse Bloom's lab does groundbreaking work understanding protein evolution at the pathogen-immune interface; they recently did deep mutational scanning on

HIV env , influenza

in the presence of antibody selection

and are gearing up to do more in HIV, including DMS on anti-HIV antibodies.

Kelly Lee's lab

brings a full stack of cutting-edge technology to study virus/immune reactions from a structural perspective.

My group

works to develop advanced Bayesian phylogenetic techniques and tools to understand antibody sequences.

(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:

from evolutionary biology who are interested in a field awash with data with real biomedical consequences (and job opportunities!)

from immunology who want to be immersed in a group with tons of computational evolutionary biology experience and ambition to advance Bayesian methods

from other fields who are just really good at getting computers to process a lot of data with complex models.

The formal requirements are:

an open and curious mind, ready to learn what's needed

desire to advance understanding of a biological problem

serious Python programming chops

expertise in large-scale computing pipelines with a passion for reproducibility (this certainly includes Git and Linux-fu)

a team spirit, ready to work with diverse group

Ideally we'd recruit someone with:

understanding of evolutionary biology, including coevolution

knowledge of adaptive immunology

expertise in Bayesian statistics

C experience

To apply,

please submit your application with the following. Code samples may be emailed directly to Dr. Matsen:

a substantial code sample

two representative publications or preprints

a several paragraph statement of research interests

names and email addresses of three references

CV

We are committed to cultivating a workplace in which diverse perspectives and experiences are welcomed and respected. We are proud to be an Equal Opportunity and VEVRAA Employer. We do not discriminate on the basis of race, color, religion, creed, ancestry, national origin, sex, age, disability, marital or veteran status, sexual orientation, gender identity, political ideology, or membership in any other legally protected class. We are an Affirmative Action employer. We encourage individuals with diverse backgrounds to apply and desire priority referrals of protected veterans. If due to a disability you need assistance/and or a reasonable accommodation during the application or recruiting process, please send a request to our Employee Services Center at (see application details) or by calling (see application details).

Company info

Fred Hutchinson Cancer Research Center
Website : https://www.fredhutch.org/en.html

Company Profile
About Fred Hutchinson Cancer Research Center Arnold Building and Vessel sculpture on the Hutchinson Center campus The Arnold Building and Vessel sculpture sit at the heart of the Hutchinson Center campus. At Fred Hutch, our interdisciplinary teams of world-renowned scientists and humanitarians work together to prevent, diagnose and treat cancer, HIV/AIDS and other diseases. Our researchers, including three Nobel laureates, bring a relentless pursuit of, and passion for, health knowledge and hope to their work and the world. Together, our researchers are discovering new ways to detect cancers earlier, when cure rates are highest; developing effective treatments with fewer side effects; and learning how to prevent cancers from growing in the first place. Our groundbreaking discoveries began in the 1970s with Dr. E. Donnall Thomas’s pioneering work in bone marrow transplantation, which led to him receiving the 1990 Nobel Prize in physiology or medicine. Since then, Hutch researchers have made a number of breakthroughs, including developing immunotherapies that use the immune system to defeat cancer and advancing the understanding of human biology. Admittedly, the eradication of cancer and other life-threatening diseases is an ambitious goal, one that demands tenacity, scientific excellence, collaboration and breakthrough creativity. To accomplish this, Fred Hutch attracts some of the world's greatest minds. Nobel laureate medal Dr. E. Donnall Thomas won the 1990 Nobel Prize for physiology or medicine for pioneering bone marrow transplantation. Our roster of internationally acclaimed scientists includes a MacArthur fellow, seven members of the National Academy of Sciences, five members of the Institute of Medicine, six members of the American Academy of Arts and Sciences, nine members of the American Association for the Advancement of Science and eight current and former Howard Hughes Medical Institute investigators. Fred Hutch understands that disease research means more than searching for new treatments. We are home to the country's largest and oldest cancer prevention program, which has made key contributions to understanding how diet, exercise and other factors reduce the risk of acquiring the disease. To accelerate our progress, we are part of the Fred Hutch / University of Washington Cancer Consortium. This research and clinical collaboration between the Hutch, the University of Washington, Seattle Children’s and Seattle Cancer Care Alliance enables our researchers to leverage each institution’s strengths and develop premier research programs across many types of disease. The Consortium is among 45 National Cancer Institute-designated comprehensive cancer centers nationwide.

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