Bioinformatics Analyst I/II - Computational Cancer Genomics and Data Science

Fred Hutchinson Cancer Center is an independent, nonprofit organization providing adult cancer treatment and groundbreaking research focused on cancer and infectious diseases. Based in Seattle, Fred Hutch is the only National Cancer Institute-designated cancer center in Washington.

With a track record of global leadership in bone marrow transplantation, HIV/AIDS prevention, immunotherapy and COVID-19 vaccines, Fred Hutch has earned a reputation as one of the world’s leading cancer, infectious disease and biomedical research centers. 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 value collaboration, compassion, determination, excellence, innovation, integrity and respect. These values are grounded in and expressed through the principles of diversity, equity and inclusion. Our mission is directly tied to the humanity, dignity and inherent value of each employee, patient, community member and supporter. Our commitment to learning across our differences and similarities make us stronger. We seek employees who bring different and innovative ways of seeing the world and solving problems. Fred Hutch is in pursuit of becoming an anti-racist organization. We are committed to ensuring that all candidates hired share our commitment to diversity, anti-racism and inclusion.

The Ha Lab is a computational biology team working with interdisciplinary collaborators with expertise in experimental biology, cancer biology, and clinical cancer research. We are part of the Computational Biology Program and are housed in the newly remodeled Steam Plant building overlooking Lake Union near downtown Seattle and the University of Washington. We are seeking a highly motivated individual who is interested in applying computational and analytical approaches to study genetics and epigenetics of cancer from tumor and liquid biopsies. A Bioinformatics Analyst position in the laboratory of Dr. Gavin Ha (https://GavinHaLab.org/) and the Computational Biology Program is available immediately. Candidates who are excited about research in bioinformatics, data science, machine learning, and explainable AI approaches to large/complex ‘omics’ data in the field of cancer research are encouraged to apply. The position has a competitive salary with great benefits.

 

Dr. Ha is a recipient of an NIH Director’s New Innovator Award, an NCI Transition Career Development Award, a Prostate Cancer Foundation Young Investigator Award, and a V Foundation Scholar Grant. His laboratory develops computational approaches to study cancer genomes from tumors and liquid biopsies, such as circulating tumor DNA, and leverages these data for genome discovery and disease monitoring. Their goals are to uncover mechanisms of treatment resistance, to identify blood-based genetic biomarkers, and to translate these findings to help improve clinical applications. 

 

See the lab website and GitHub for more details on current projects and software:

https://gavinhalab.org/

https://github.com/GavinHaLab

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, explainable AI to study cancer and genetics
• Analysis of large, complex genome, epigenome or transcriptome data

This position requires onsite work at our South Lake Union campus in Seattle a minimum of 3 days per week.

The research interests/projects and responsibilities for this Analyst position in the Ha lab include:

 

Bioinformatics Analyst I

• Under the direction of senior personnel, run established bioinformatic tools and pipelines for analysis of normal and cancer “omics” datasets for various research projects
• Work with research team to document, process, manage and store large datasets
• Generate figures and tables summarizing data outputs
• Beta test new bioinformatic tools in development

Bioinformatics Analyst II

• Analyze cancer genomes to understand tumor progression/evolution/heterogeneity, metastatic disease, non-coding genome alterations, copy number alterations, genome rearrangements and 3D structure, mutational signatures.
• Partner with Fred Hutch scientists to refine computational research questions and design analytical processes that can be applied to these genomic datasets.
• Develop and/or apply machine learning techniques to analyze large cancer datasets.
• Identify and implement appropriate bioinformatic tools for analyzing sequence data from tumor genomes including long-range sequencing technologies (linked-reads, long-reads, optical mapping).
• Develop and implement computational approaches to analyze circulating tumor DNA from liquid biopsies.
• Prepare figures and written sections to document methods and results for manuscripts, presentations, and grant applications.
• Implement and maintain best practices in large-scale data management and database development.

Bioinformatics Analyst I

 

MINIMUM QUALIFICATIONS:

• Applicants must have at least a bachelor’s degree in one of these disciplines: Computational biology, bioinformatics, computer science, data science, statistics, biostatistics, biomedical engineering, computer/electrical engineering, physics, or other related fields, with some prior experience applying computation analysis of large sequence-based molecular data in an academic research lab or industry setting
• Minimum 1 year experience with analyzing genome sequencing data
• Strong programming skills in R and Python

PREFERRED QUALIFICATIONS:

• Previous experience working with cancer genomics datasets
• A background in cancer biology
• Experience working in and developing workflows for cloud computing environments
• Experience with high performance computing environments
• Strong skills in implementation of analytical tools at scale
• Experience with pipeline management tools (Snakemake, WDL, Nextflow)
• Works well in team environments; strong communication skills; detail-oriented

Bioinformatics Analyst II

 

MINIMUM QUALIFICATIONS:

• Applicants must have at least a bachelor’s degree in one of these disciplines: Computational biology, bioinformatics, computer science, data science, statistics, biostatistics, biomedical engineering, computer/electrical engineering, physics, or other related fields, with some prior experience applying computation analysis of large sequence-based molecular data in an academic research lab or industry setting
• 3+ years relevant experience, or a master’s degree with a minimum 1 full year of relevant experience outside the degree requirements
• Effective use of shell scripting and significant fluency in R and Python 3
• Familiarity with workflow and scheduling software (e.g. Slurm)

PREFERRED QUALIFICATIONS:

• Facility with commonly used Bioconductor packages, ggplot, tidyverse etc.
• Ability to generate and customize common data visualizations (PCA plots, volcano plots, Circos plots, etc)
• Excellent written and verbal communication skills

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:
  • An attachment or;
  • Link(s) to public repositories (e.g. GitHub)
• Names and email addresses of three professional references
• Statement on commitment to Diversity, Equity, and Inclusion

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.

Bioinformatics Analyst I: The annual base salary range for this position is from $68,162 to $102,211, and pay offered will be based on experience and qualifications.
Bioinformatics Analyst II: The annual base salary range for this position is from $78,894 to $118,310, and pay offered will be based on experience and qualifications. This position may be eligible for relocation assistance.

Fred Hutchinson Cancer Center offers employees a comprehensive benefits package designed to enhance health, well-being, and financial security. Benefits include medical/vision, dental, flexible spending accounts, life, disability, retirement, family life support, employee assistance program, onsite health clinic, tuition reimbursement, paid vacation (12-22 days per year), paid sick leave (12-25 days per year), paid holidays (13 days per year), paid parental leave (up to 4 weeks), and partially paid sabbatical leave (up to 6 months). 

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 Human Resources at hrops@fredhutch.org or by calling 206-667-4700.