The Knight Cancer Institute (KCI) Center for Biomedical Data Science (CBDS) at Oregon Health & Science University seeks an experienced Computational Biologist Level 2-3 to support our Collaborative Nursery

Projects. The Collaborative Nursery is a new program designed to foster collaboration between CBDS faculty and other KCI investigators. The successful candidate must be prepared to work independently at all levels of data evaluation, curation, harmonization and analysis. The analyst will work closely and in person with both the computational and biology teams, and is expected to develop a strong working understanding of the biologic questions driving the research. The ability to be flexible and adapt to changing circumstances is essential for success in this role. This position will enjoy unique exposure and access to data relevant to cancer biology, detection, interception, and therapy. Data types may include multi-omic, genomic, transcriptomic, proteomic, imaging, and/or clinical

data. Duties will include requirements gathering, data management, pipeline building and execution, shared tool development, custom analysis with data modeling, machine learning, and contributions to manuscripts and grant applications.

 

Overview: The Knight Cancer Institute, known as one of the pioneers in personalized cancer medicine, is an international leader in research and cancer treatment. The Center for Biomedical Data Science (CBDS) has been created jointly with the University of Oregon to leverage the massive amounts of biomedical data that is being generated by advanced technologies. At CBDS, our mission is to harness large-scale, high dimensional data and develop informatics tools and computational approaches to enable the discovery of next-generation treatments and therapies and the advancement of cancer detection, interception and population science. This is an ambitious goal, one that requires novelty, creativity, and innovation. CBDS tackles this goal by working across a

variety of departments and units in basic, translational and clinical research at OHSU. Faculty and staff at CBDS have advanced training in machine learning and quantitative analysis of biomedical data, extensive platform development experience, and a track record of innovation in biomedical applications.

 

Our Commitment to Diversity: OHSU is committed to increasing the diversity of the campus community. We are dedicated to promoting inclusion and multiculturalism by having outstanding researchers of diverse backgrounds work together. We encourage extensive collaboration among researchers with diverse viewpoints and expertise because defeating cancer requires out-of-the-box thinking and new perspectives.

 

Every Knight Cancer employee is expected to embody our guiding principles:

• We act BOLDLY—Breakthroughs require pushing the boundaries of science, exploring new frontiers, and thinking differently
• We SUPPORT each other—Respect leads to trust, which leads to excellence
• We work as a CONNECTED team—We must leverage our collective brain power to conquer cancer because no one individual can do it alone

Data Organization and Management

• Clean and manage metadata
• Access, store, and document raw data
• Coordinate with project team members
• Meet publication requirements, including data and code repositing 

3 Data Analysis

• Sample/data quality control assessment
• Implement existing analytic packages and workflows
• Adapt existing resources and tools, as needed, to meet project needs
• Develop novel analyses and visualizations 

4 Technical Writing/Communication

• Present at regular team meetings
• Clear code documentation
• Support manuscript preparation
• Support grant writing efforts 

5 Computation Infrastructure Support

• Develop novel software tools or analytical pipelines
• Create or adapt data models/schemas for data management
• Provide technical support to other team members and participate in code reviews
• Assist in cross -platform and -tool integration

Education:

• PhD in Computational Biology or related field OR
• Master's Degree in Computational Biology, Bioinformatics, or related field AND 6 years relevant experience OR
• Equivalent combination of Bachelor’s in a relevant field in conjunction with training and experience may be considered.
• Candidates with fewer years’ experience than listed above per academic degree may be considered for a Computational Biologist Level 2 position

Experience:

• Significant experience with analysis of ‘omic or imaging data (genomic, transcriptomic, proteomic, medical imaging etc.)
• Experience in implementing statistical methods as appropriate for dataset treatment (e.g. quality inspection, normalization, differential feature detection, etc.)

Job Related Knowledge, Skills and Abilities (Competencies):

• High-level competency in an appropriate programming language (R or Python), preferably in Unix/Linux
• An understanding of statistical methods for data treatment
• Usage of structured engineering methods for specifying, designing, and implementing systems and pipelines in high performance computing environments
• Ability to effectively manage multiple projects
• Excellent written and verbal communication, analytical and organizational skills

Compliance:

• Code of conduct
• Respect in the workplace
• Applicable policies, procedures and agreements related to position, department or OHSU as a whole

Experience:

• Experience with machine learning
• Experience with high performance computing environments
• Experience developing pipelines to support analytics as described, to facilitate improved data management, and to generate complete workflows that are reproducible and scalable

Job Related Knowledge, Skills and Abilities (Competencies):

• Experience with version control in coding
• Experience using containers or package/environment management tools, such as Conda or Docker
• Experience with systems or tools for managing ‘omics or imaging data
• Experience with scientific and computation mentorship

We offer a variety of benefits on top of joining a thriving organization:

• Medical, dental and vision coverage at no or low cost to employees
  • Covered 100% for full-time employees and 88% for dependents
• Several retirement plans to choose from with contributions from OHSU
• 25 days a year of paid time off
• 8 days of sick time off
• Commuter subsidies
• Tuition reimbursement
• Access to group life insurance, disability insurance and other supplemental benefits
• Annual Merit Increase
• Growth/Development Opportunities
• Employee discounts to local and major businesses

 

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Oregon Health & Science University values a diverse and culturally competent workforce. We are proud of our commitment to being an equal opportunity, affirmative action organization that does not discriminate against applicants on the basis of any protected class status, including disability status and protected veteran status. Individuals with diverse backgrounds and those who promote diversity and a culture of inclusion are encouraged to apply. To request reasonable accommodation contact the Affirmative Action and Equal Opportunity Department at 503-494-5148 or aaeo@ohsu.edu.