Computational Biologist 1 or 2 - Oregon Health & Science University

Department Overview:

The Cancer Early Detection Advanced Research (CEDAR) center is a collaborative institution within the OHSU Knight Cancer Institute. The Knight Cancer Institute, known as one of the pioneers in personalized cancer medicine, is an international leader in research and cancer treatment. At CEDAR our mission is to detect and stop lethal cancers at the earliest stage because early detection saves lives. This is an ambitious goal, one that requires novelty, creativity, and innovation. We are comprised of biologists, chemists, biomedical engineers, computational biologists, and clinicians conducting groundbreaking translational cancer research to help people maintain a high quality of life and reduce cancer mortality, to create a global early detection community, and to have a positive impact on the Oregon economy.

 

Our Commitment to Diversity: CEDAR 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 on multiple projects. We encourage high-risk, high-reward research projects because defeating cancer requires out-of-the-box thinking and new perspectives. Our research is milestone driven to ensure that each project is fulfilling its stated goals.

 

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

Function/Duties of Position:

The Knight Cancer Institute Cancer Early Detection Advanced Research Center (CEDAR) at Oregon Health & Science University seeks an experienced Computational Biologist Level 1 or 2 who will develop custom computational methods, including construction of analytic pipelines and implementation of sophisticated statistical techniques to analyze spatial imaging data relevant to cancer biology and early detection. The position will enjoy unique exposure and access to single cell multiplex imaging data sets and single-cell transcriptomic data as a member of CEDAR¿s collaborative spatial imaging team, but no prior experience in image analysis specifically is required for this position.

 

The ideal candidate will have experience with analysis of `omic data (genomic, transcriptomic, proteomic etc.), particularly for target or biomarker discovery, experience in implementing statistical methods as appropriate for dataset treatment (e.g. quality inspection, normalization, differential feature detection, etc.), and experience in developing pipelines to support analytics as described to additionally facilitate improved data management, and to generate complete workflows that are reproducible and scalable. Experience with or knowledge regarding single-cell data and/or machine learning would be a bonus but is NOT required and should not be a deterrence from applying.

 

You will be part of multidisciplinary project-based teams developing novel approaches for the early detection of cancer. Duties include requirements gathering, data management, pipeline building, shared tool development, custom analysis with data modeling and machine learning, and contributions to manuscripts and grant applications, all under the supervision of senior level computational biologists. 

 

Duties Include:

Data Organization & Management 

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

Data Analysis 

• Sample quality control assessment
• Implement existing analytic packages and workflows
• Adapt existing resources as needed to meet project needs
• Develop novel analysis and visualization tools for spatial multi-omics data sets
• Support other team members in implementing analysis tools
• Additional duties as assigned by project leader

Technical Writing/Communication 

• Present at regular team meetings
• Clear code documentation
• Build, maintain, augment shared workflows
• Support manuscript preparation
• Support grant writing efforts

Career Development 

• Participate in activities that enhance general knowledge or ability to do assigned work

Protected Work Tme

• Protected time for non-research related CEDAR work, including time for CEDAR Council, Infrastructure, DEI, Engagement, Professional Development, etc.

Required Qualifications:

• CB1:
  • Master's Degree in Computational Biology or related field OR Bachelor's Degree in Computational Biology or related field AND 3 years of relevant experience
• CB2:
  • Master's Degree in Computational Biology or related field AND 3 years of relevant experience OR Bachelor's Degree in Computational Biology or related field AND 6 years of relevant experience

• Significant experience with analysis of ‘omic data (genomic, transcriptomic, proteomic etc.), particularly for target or biomarker discovery

• Experience in implementing statistical methods as appropriate for dataset treatment (e.g. quality inspection, normalization, differential feature detection, etc..

• Experience in developing pipelines to support analytics as described to additionally facilitate improved data management, and to generate complete workflows that are reproducible and scalable

• High-level competency in an appropriate programming language (R or Python)

• An understanding of a variety of sophisticated 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 prioritize multiple tasks at one time

• Good communication, analytical and organizational skills, both written and verbal

Preferred Qualifications:

• Experience with or knowledge regarding single-cell data (e.g. from single cell RNA sequencing) would be a bonus but is NOT required and should not be a deterrence from applying

• Experience with machine learning a bonus but not required

• A passion for open-access innovation

Additional Details:

Apply online. Please be sure to upload a Cover Letter and Resume/CV.

 

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
• Up to 208 hours (equal to 25 full days) a year of paid time off
• Commuter subsidies
• Tuition reimbursement
• Access to group life insurance, disability insurance and other supplemental benefits
• Annual Raises
• Growth/Development Opportunities
• Employee discounts to local and major businesses

 

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All are welcome: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.