Bioinformatics Analyst I/II - Cancer Functional Genomics

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. 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.

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The laboratory of Dr. Xueqiu Lin in the Computational Biology Program of the Public Health Sciences and Human Biology Divisions has an open position for a Bioinformatics Analyst I/II. We are seeking a highly motivated individual who will bring their knowledge and computational skills to the study of cancer functional genomics. Candidates who are excited to be part of a team working on computational/statistical model development and large/complex ‘omics’ data analysis of cancer genomes to study cancer are encouraged to apply. Please visit the lab website for more information: https://research.fredhutch.org/lin/en.html. The position has a competitive salary with great benefits.

 

The Lin Laboratory uses CRISPR screen technologies, computational genomics, and interpretable deep learning models to study cancer risk and to advance precision medicine. We are building on this strong computational program by implementing wet-lab operations in a fully renovated laboratory space in the Lake Union Steam Plant Building, the newest Fred Hutch facility. The Steam Plant building is home to 23 laboratories consisting of 275 experts in computational biology, data science, and immunotherapy who use cutting-edge technologies and tools to revolutionize cancer treatment.

 

We work in an interdisciplinary team environment with many local and external experts. All our projects involve partnering with investigators and laboratories who have diverse expertise in computational, genomic, molecular, experimental, and cancer biology, and in clinical research. The study areas for this position center on genomic regulation, single cell sequencing, chromatin and epigenetic profiling, cancer GWAS studies, high-throughput CRISPR screening and translation of cancer biomarkers to improve treatment strategies and develop CRISPR targeted therapy.

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The Bioinformatics Analyst I/II will work under the direction of the senior computational scientist to develop deep learning models and algorithm for deciphering the logic of regulatory code, work on a variety of bioinformatics analysis projects including bioinformatics method and software development; executing, improving, and developing bioinformatics pipelines based on evaluation of computational tools and reference databases; and working with experimental researchers to conduct and report data analysis using principles of good statistical scientific practice and reproducible research.

 

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

• Application of statistical modeling, algorithm design, deep learning, machine learning and explainable artificial intelligence to study cancer and genetics.
• Gene regulation, gene regulatory elements, cancer genomics, epigenetics, CRISPR high-content screen, genotype-environment interaction.
• Analysis of large, complex CRISPR screen, genome, epigenome or transcriptome data

 

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)

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

 

Bioinformatics Analyst I

• Support and assist the senior computational scientist to develop deep learning models and implement algorithms.
• Assist in the development and refinement of data analysis and integration methodologies and pipelines.
• Generate figures and tables summarizing data outputs.
• Work with research team to document, process, manage and store large datasets.
• Developing and testing bioinformatics software.

Bioinformatics Analyst II:

• Interpret complex biological information, conduct statistical and genomic analysis.
• Implement and maintain best practices in large-scale data management and database development.
• Write custom scripts to access databases, perform and evaluate quality control and analyze Next Generation Sequencing (NGS) data.
• Analyze FFPE-CUTAC to identify non-coding genomic mutations and interpret their function in oncogenic regulatory networks for novel biomarker identification and risk model development.
• Develop and implement computational approaches to assist the design and development of high-throughput CRISPR screening.
• Integrate the high-throughput CRISPR screening data with multi-omics data.
• Prepare figures and written sections to document methods and results for manuscripts, presentations, and grant applications.
• Engage in bioinformatics literature to ensure the availability of robust methods, resources, and data sources.
• Present work at group meetings as well as occasional larger scientific meetings and contribute to scientific publications.

MINIMUM QUALIFICATIONS:

 

Bioinformatics Analyst I:

• Bachelor’s degree in one of these disciplines: Computer science, mathematics, statistics, physics, biostatistics, data science, bioinformatics, computational biology, computer/electrical engineering, or other related fields with at some prior experience applying computation analysis of large sequence-based molecular data in an academic research lab or industry setting.
• Up to 2 years of experience with analyzing genome sequencing data.
• Strong programming skills in R and Python.

Bioinformatics Analyst II:

All minimum qualifications from Level I, plus:

• 3 years relevant experience, or a master’s degree with at least 1 year of relevant experience outside of the degree requirements

 

PREFERRED QUALIFICATIONS:

• Previous experience working with deep learning or statistical modeling
• A background in cancer genomics
• 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
• Works well in team environments; strong communication skills; detail-oriented
• Experience with pipeline management tools (Snakemake, WDL, Nextflow)

 

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Bioinformatics Analyst I: The annual base salary range for this position is from $77,976 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 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 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.