Bioinformatics Analyst I-II, Computational Analyses of Microbial Genomic/Metagenomic/Epigenomic Data

Job ID
Regular Full-Time
Fred Hutchinson Cancer Research Center
Biostatistics, Bioinformatics and Computational Biology


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 Johnston Laboratory in the Vaccine and Infectious Disease Division at the Fred Hutchinson Cancer Research Center is recruiting a highly motivated and creative Bioinformatics Analyst to analyze multiple unique data sets primarily associated with long-read sequencing technologies (PacBio) including large scale computational genomics of microbial genomes, patient tumor and tissue metagenomics, and microbial/eukaryote epigenetics.


The Johnston Laboratory is an interdisciplinary and highly collaborative team of classically trained microbiologists, synthetic microbiologists, bioinformaticians and engineers. Using cutting edge technologies and methodologies, we seek to gain a deeper functional understanding of what bacteria are doing and how they are doing it. We then use that information to create novel therapeutics and engineer the next generation of microbe-based technologies for application in human medicine, synthetic microbiology and bioengineering.


The Bioinformatics Analyst will be responsible for working with our team to provide data analyses and visualizations of primarily microbial datasets (Genomic/Metagenomic/Epigenomic data). A successful candidate will have experience in data analysis, generating visualizations, writing analyses summaries and abstracts, and managing time across various projects with different collaborators. Responsibilities and essential job functions include but are not limited to the following:

  • Supports the maintenance of computational infrastructure and the flow of samples and information for large-scale studies.
  • Contributes to web-based bioinformatics and public and proprietary relational databases. Assists in the development and application of computational tools.
  • Interpret complex biological information, conduct statistical and genomic analysis.
  • Write custom scripts to access databases, perform and evaluate quality control and analyze Next Generation Sequencing (NGS) data.
  • Assist in the development and refinement of data analysis and integration methodology and pipelines.
  • Develop modular and reusable software for use in basic science research and genomic analysis in a cost-effective and efficient manner with limited instruction or guidance.
  • Engage in bioinformatics literature to ensure the availability of robust methods, resources, and data sources. Work with research collaborators to gather requirements and create processes and pipelines to meet their research goals
  • Candidate must demonstrate outstanding personal initiative and creativity in problem solving
  • Excellent written and oral communication skills are required for manuscripts/grants preparation, public presentation, and collaboration with other researchers


The successful candidate will be involved in multiple funded projects and work closely with bench scientists during project design, method development, and data acquisition; executing, improving, and developing informatics pipelines based on evaluation of computational tools and reference databases; and conducting and reporting data analysis using principles of good statistical scientific practice and reproducible research.


We are accepting applications for either a Bioinformatics Analyst Level I (min 0-2 years) or Level II (min 3-6 years).


Minimum Qualifications:

  • Bioinformatics Analyst I Education: BS degree in Biology, Statistics, Computer Science or equivalent education with 0-2 years of work experience with bioinformatics in relevant scientific domain
  • Bioinformatics Analyst II Education: BS degree in Biology, Statistics, Computer Science or equivalent education with 3-6 years of work experience with bioinformatics in relevant scientific domain
  • 2+ years of experience in software development, data engineering, data science, or related field with a track record of manipulating, processing, and extracting value from large datasets
  • Extensive experience working with at least one of the following datasets, e.g. whole genome analyses (assembly and annotation tools, Pangenomics), Metagenome analyses (community compositional assessment and comparisons), epigenome analysis (SMRTseq, ChipSeq, ATACseq - data pipelines)
  • Proficiency in, at least, one modern scripting or programming language (Python, R, Node, or C++)
  • Ability to learn new tools and content quickly and independently
  • Strong oral and communication skills

Desired Qualifications:

  • MS degree with 2+ years of work experience with bioinformatics in relevant scientific domain
  • Beneficial experience relative to this role:
  • Experience with workflow solutions (e.g. NextFlow, Airflow, Luigi, Cromwell)
  • Experience using source code management and CI/CD solutions (e.g., Git, GitHub, Jenkins, GitLabCI)
  • Experience with AWS services (e.g. EC2, S3, Batch, Lambda)
  • Experience with application container solutions (e.g. Docker, Singularity)


Application Instructions:

Applications will be considered commensurate with experience and track record of achievement. Please include a cover letter with your application, detailing your interest and suitability for this position.


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

Our Commitment to Diversity

We are proud to be an Equal Employment Opportunity (EEO) and Vietnam Era Veterans Readjustment Assistance Act (VEVRAA) Employer. We are committed to cultivating a workplace in which diverse perspectives and experiences are welcomed and respected. We do not discriminate on the basis of race, color, religion, creed, ancestry, national origin, sex, age, disability (physical or mental), marital or veteran status, genetic information, 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 or by calling 206-667-4700.


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