Herbold Computational Biology Job Openings

We welcome both computational researchers who want to learn about biology, as well as biologists who want to learn computational methods. 

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2 Found open positions

Post-Doctoral Researcher

FH Public Health Sciences Division
Category: Biostatistics, Bioinformatics and Computational Biology
Seattle, WA, US
Job ID: 20593

Overview

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.

 

At Fred Hutch, we believe that the innovation, collaboration, and rigor that result from diversity and inclusion are critical to our mission of eliminating cancer and related diseases. We seek employees who bring different and innovative ways of seeing the world and solving problems. Fred Hutch is in pursuit of becoming an antiracist organization.  We are committed to ensuring that all candidates hired share our commitment to diversity, antiracism, and inclusion.   


 

Matsen Lab Environment
The environment in the Matsen group is lively yet casual, with a strong emphasis on collaborative work between postdocs, PhD students, interns, and programmers. 

 

The Center is housed in a lovely campus on Lake Union a short walk from downtown, and a slightly longer walk from the University of Washington. The Matsen group is in the newly-remodeled Steam Plant building overlooking the lake. We believe that science is for everyone. We have had researchers with a variety of backgrounds, including Latinx, Black, Asian, and Middle Eastern. We have had women, men, gay, and straight, and we welcome people of all sexual orientations and gender identities. We have had successful high schoolers, postdocs, people who were the first in their family to attend college, and one who had decided that college wasn’t for them. We have had researchers with backgrounds in biology, physics, statistics, math, and computer science.

 

We acknowledge the historical and present barriers for underrepresented groups, and work to increase diversity, equity and inclusion in computational biology. Members of underrepresented groups are especially encouraged to apply.

 

Please read our expectations of group members. By applying for this position, we expect that you will fulfill these expectations. We enthusiastically solicit feedback on these expectations or requests for clarification.

Responsibilities

During the next few years we expect SARS-CoV-2 to continue its transformation into an endemic virus, as vaccines mitigate but do not eliminate its circulation. In many ways we expect SARS-CoV-2 to become analogous to flu, where yearly vaccinations are designed to be as effective as possible against the most important circulating strains. However, because of the time required to manufacture and then administer the vaccine, we must decide months ahead of time what the most important strains are to include. 

 

The purpose of this position is to develop algorithms to forecast the dominant viral variants given a diverse collection of densely sampled data. In addition to epidemiological data, we will have experimentally-derived estimates of the phenotype of large pools of spike variants, both in terms of their function and their ability to escape antibody-mediated immune pressure. Using machine-learning techniques we will predict the fitness of additional combinations of mutations alongside experimentally inferred phenotypes, and use these predictions as part of our overall system to predict the long-term trajectory of viral variants. This will be a close collaboration with the Bedford and Bloom labs.

 

We are seeking a postdoc to develop predictive algorithms and help bring them into production on nextstrain.org. This includes:

  • Reading relevant literature to understand the current state of the art.
  • Develop new models integrating diverse data types.
  • Developing benchmarks and working together with staff to evaluate algorithms on those benchmarks.
  • Working with the Bedford lab to put a prediction system into production.
  • Collaborating with trainees and staff from three labs.
  • Contributing to writing papers and software testing.
     

This position will be housed in the Matsen lab; see our website for more information about what we do.

Qualifications

MINIMUM QUALIFICATIONS:

  • The successful applicant will have a PhD in statistics, mathematics, computer science, or another relevant discipline, and will have a successful track record of independent research.
  • Creative and thoughtful
  • Solid in their mathematics/statistics background
  • A capable computer programmer
  • Familiar with modern Python-based tooling in machine-learning
  • A careful writer and diligent editor
  • Excited to contribute to an important goal

APPLICATION INSTRUCTIONS:
If you are interested in this position, please submit the following materials:

  • A CV summarizing your education and work experience so far.
  • The names and email addresses of two references.
  • Two publications featuring your work.
  • A code sample representing code that you are proud of. This doesn’t have to be long or especially fancy, but should be clean and do something non-trivial. Ideally this would be present as a commit to a code repository such as GitHub, but emailed code is fine as well.

 

Fred Hutch has a mandatory COVID-19 vaccine requirement, with exceptions only for approved medical or religious accommodations.
As a condition of employment, newly hired employees must provide proof of vaccination or initiate the accommodations process before their first day of employment. 

 

A statement describing your commitment and contributions toward greater diversity, equity, inclusion, and antiracism in your career or that will be made through your work at Fred Hutch is requested of all finalists.

 

 

Project Manager II/III - Matsen Research Group

FH Public Health Sciences Division
Category: Biostatistics, Bioinformatics and Computational Biology
Seattle, WA, US
Job ID: 21044

Overview

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.

 

At Fred Hutch, we believe that the innovation, collaboration, and rigor that result from diversity and inclusion are critical to our mission of eliminating cancer and related diseases. We seek employees who bring different and innovative ways of seeing the world and solving problems. Fred Hutch is in pursuit of becoming an antiracist organization.  We are committed to ensuring that all candidates hired share our commitment to diversity, antiracism, and inclusion.   

 

The Matsen research group at the Fred Hutchinson Cancer Research Center in Seattle, WA develops and applies methods to learn about evolution and immunology from molecular sequence data. This position will involve work at the immune/pathogen interface, including studying pathways of antibody evolution via affinity maturation, and analyzing functional assays such as deep mutational scans. There will be substantial collaborative work understanding the evolution of and the immune response to SARS-CoV-2 in a large, funded collaboration including the Baker, Bedford, Bloom, Shendure, and Veesler labs. See our website for more information about what we do.

 

Responsibilities

We are seeking a Research Project Manager with a biological background at the immune/pathogen interface who is interested in moving into the computational sphere. The successful candidate will partner with us for the full life cycle of project development. This includes

  • brainstorming areas where new computational research would be useful

  • reading relevant literature to define our potential contribution

  • writing a project specification with benchmark targets

  • managing the project, including interfacing between computational staff and biologist collaborators

  • contributing to writing papers and software testing.

 

The Research Project Manager will also share some administrative tasks with the PI.

 

Environment

The environment is lively yet casual, with a strong emphasis on collaborative work between postdocs, PhD students, interns, and programmers.

The Center is housed in a lovely campus on Lake Union a short walk from downtown, and a slightly longer walk from the University of Washington. The Matsen group is in the newly remodeled Steam Plant building overlooking the lake. We believe that science is for everyone. We have had researchers with a variety of backgrounds and believe in the importance of diversity, equity, and inclusion.

 

Please read our expectations of group members. By applying for this position, we expect that you will fulfill these expectations. We enthusiastically solicit feedback on these expectations or requests for clarification.

Qualifications

Qualifications

  • Bachelor's or Master's degree required. The successful candidate will have extensive knowledge/experience (PhD preferred) in adaptive immunology, protein science, biochemistry, structural biology, or another related field, along with a successful track record of independent research.
  • Minimum of 5 years post-master's or five years post-bachelor's related project/study management experience. 

Essential Skills

In addition to the core qualifications, we are looking for someone who is:

  • creative and thoughtful

  • able to synthesize between fields

  • comfortable with project management

  • a careful writer and diligent editor

  • highly organized

  • able to write scripts in Python, R, or shell to perform basic data analysis

  • willing to handle some administrative tasks

  • interested in the group's research, passionate about science, and excited to contribute

Application Instructions

If you are interested in this position, please submit the following materials (preferably as one PDF):

  • A CV summarizing your education and work experience so far.

  • The names, phone numbers, and email addresses of at least two references.

  • Two publications featuring your work.

Physical Requirements

Remaining in a normal seated or standing position for extended periods of time; reaching and grasping by extending hand(s) or arm(s); dexterity to manipulate objects with fingers, for example using a keyboard; communication skills using the spoken word; ability to see and hear within normal parameters; ability to move about workspace. The position requires mobility, including the ability to move materials weighing up to several pounds (such as a laptop computer or tablet). Work may involve possible exposure to malodorous vapors, low dose radiation, contamination by toxic chemicals and acids and presence of carcinogenic substances.

 

Persons with disabilities may be able to perform the essential duties of this position with reasonable accommodation. Requests for reasonable accommodation will be evaluated on an individual basis.

 

Please Note:

This job description sets forth the job’s principal duties, responsibilities, and requirements; it should not be construed as an exhaustive statement, however.  Unless they begin with the word “may,” the Essential Duties and Responsibilities described above are “essential functions” of the job, as defined by the Americans with Disabilities Act.

 

Fred Hutch has a mandatory COVID-19 vaccine requirement, with exceptions only for approved medical or religious accommodations.
As a condition of employment, newly hired employees must provide proof of vaccination or initiate the accommodations process before their first day of employment. 

 

A statement describing your commitment and contributions toward greater diversity, equity, inclusion, and antiracism in your career or that will be made through your work at Fred Hutch is requested of all finalists.

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