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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

Bioinformatics Analyst I/II

FH Public Health Sciences Division
Category: Biostatistics, Bioinformatics and Computational Biology
Seattle, WA, US
Job ID: 23207

Overview

Fred Hutchinson Cancer Center is an independent, nonprofit, unified adult cancer care and research center that is clinically integrated with UW Medicine, a world leader in clinical care, research and learning. The first National Cancer Institute-designated cancer center in the Pacific Northwest, Fred Hutch’s global leadership in bone marrow transplantation, HIV/AIDS prevention, immunotherapy, and COVID-19 vaccines has confirmed our reputation as one of the world’s leading cancer, infectious disease and biomedical research centers. Based in Seattle, Fred Hutch operates eight clinical care sites that provide medical oncology, infusion, radiation, proton therapy, and related services, and network affiliations with hospitals in five states. Together, our fully integrated research and clinical care teams seek to discover new cures to the world’s deadliest diseases and make life beyond cancer a reality.

 

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.

 

A Bioinformatics Analyst I/II position in the laboratory of Dr. Gavin Ha (https://GavinHaLab.org/) and the Computational Biology Program is available immediately. We are seeking a highly motivated individual who is interested in studying the genetics and epigenetics of cancer using computational approaches. Candidates who are excited about large/complex ‘omics’ data analysis and cancer research are encouraged to apply. The position has a competitive salary with great benefits.

Responsibilities

The Ha lab is establishing a research program that uses new DNA sequencing technologies to study cancer genomes. The lab is also focused on research involving liquid biopsies, such as cell-free DNA, and developing new computational approaches to leverage these data for genome discovery and disease monitoring. The research interests/projects and responsibilities in the Ha lab include:

  • Analysis of cancer genomes to understand tumor progression/evolution/heterogeneity, metastatic disease, non-coding genome alterations, copy number alterations, genome rearrangements and 3D structure, mutational signatures.
  • Partnering with Hutch scientists to refine computational research questions and design analytical processes that can be applied to these genomic datasets.
    Identifying and implementing appropriate bioinformatic tools for analyzing sequence data from tumor genomes including long-range sequencing technologies (linked-reads, long-reads, optical mapping)
  • Development and use of computational approaches to analyze circulating tumor DNA from liquid biopsies.
  • Preparing figures and written sections to document methods and results for manuscripts, presentations, and grant applications. Contribute to manuscript preparation by
  • Interfacing with Ha lab and collaborators to validate results using functional experiments.
  • For examples of recent studies, see PMID:29909985, PMID:29109393, PMID:25060187, doi:10.1101/2022.06.21.496879, doi:10.1101/2021.08.31.21262867, doi:10.1101/2022.01.09.475586
  • See the lab website for more details: https://GavinHaLab.org/  

Candidates with strong interest and/or expertise in any of these research areas are highly encouraged to apply:

  • Cancer genomics, liquid biopsies, tumor evolution/heterogeneity, epigenetics, single-cell omics.
  • Application of statistical modeling, algorithm design, artificial intelligence and machine learning to study cancer and genetics.
  • Analysis of large, complex genome, epigenome or transcriptome data.

Qualifications

Bioinformatics Analyst I Minimum Qualifications:

  • Bachelor’s degree in Computational Biology, Bioinformatics, Computer Science, Data Science, Statistics, Biostatistics, Biomedical Engineering, Computer/Electrical Engineering, Physics, or other related fields.
  • 1 year of cumulative experience in computation analysis of large sequence-based molecular data.
  • Ability to work well in team environments; strong communication skills; detail-oriented.
  • Strong programming experience (R, Python, Matlab, Java, C/C++, Perl or other languages for research)
  • Experience with analyzing genome sequencing data.

Bioinformatics Analyst II Minimum Qualifications:

  • Master’s degree in bioinformatics, computational biology, genetics, or related field with at least three years’ direct experience in computational analysis of large sequence-based molecular data sets.
  • Ability to work well in team environments; strong communication skills; detail-oriented.
  • Strong programming experience (R, Python, Matlab, Java, C/C++, Perl or other languages for research)
  • Experience with analyzing genome sequencing data.

PREFERRED:

  • Previous experience working with cancer datasets is considered a strong asset.
  • A background in cancer biology is considered a strong asset.
  • Experience with high performance computing environments or cloud computing environments is considered a strong asset.
  • Candidates who are skilled at implementation of analytical tools at scale and who enjoy driving projects are preferred.

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.


To apply, please submit your application with the following:

  • Cover letter describing your experience and/or research interests is required.
  • Curriculum vitae
  • Example of your code either as (1) an attachment or (2) link(s) to public repositories (e.g. GitHub)
  • Names and email addresses of three professional references

Post-Doctoral Researcher

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

Overview

Fred Hutchinson Cancer Center is an independent, nonprofit, unified adult cancer care and research center that is clinically integrated with UW Medicine, a world leader in clinical care, research and learning. The first National Cancer Institute-designated cancer center in the Pacific Northwest, Fred Hutch’s global leadership in bone marrow transplantation, HIV/AIDS prevention, immunotherapy, and COVID-19 vaccines has confirmed our reputation as one of the world’s leading cancer, infectious disease and biomedical research centers. Based in Seattle, Fred Hutch operates eight clinical care sites that provide medical oncology, infusion, radiation, proton therapy, and related services, and network affiliations with hospitals in five states. Together, our fully integrated research and clinical care teams seek to discover new cures to the world’s deadliest diseases and make life beyond cancer a reality.

 

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.

 

 

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