Oregon Health & Science University

Computational Biologist 1

Job Locations US-OR-Portland
Requisition ID
2022-18503
Position Category
Research
Position Type
Regular Full-Time
Job Type
Research
Department
Knight Cancer Institute, Knight Diagnostic Laboratories
Salary Range
$57,969 - $79,600, commensurate with experience, education, and equity. (Starting pay $57,969 - $72,400)
FTE
1.00
Schedule
Monday - Friday, occasional nights and weekends
Hours
8:30 am - 5 pm

Department Overview

The OHSU Knight Cancer Institute is a pioneer in personalized cancer treatment and research, led by Dr. Brian Druker, whose development of Gleevec transformed Chronic Myeloid Leukemia from a fatal disease to a manageable one and proved that targeted therapies can work. The institute focuses on precision oncology, the early detection, prevention, and treatment of cancer, and creating a welcoming and supportive environment for its caregivers, researchers, and support personnel. Knight affiliates subscribe to three guiding principles: we are bold, we are supportive, and we work as a connected team in our fight to end cancer as we know it.  We’d love for you to join us! 

With decades of academic laboratory experience in pathology and genetics, the Knight Diagnostic Laboratories deliver advanced diagnostic testing to make personalized medicine a reality. Specializing in oncology, rare genetic disorders, and infectious disease, the laboratories are CLIA certified and CAP accredited.  Our Medical Directors and seasoned technical staff have many years of experience in clinical testing and test development and are dedicated to providing the best quality service for physicians and their patients.

Through our close partnership with the Knight BioLibrary and Histopathology Shared Resource Laboratories, research investigators can gain access to human biological specimens, histology, and immunohistochemistry services.

This position provides clinical bioinformatics expertise to the Knight Diagnostic Labs at OHSU.  Computational biologists support investigators in the development of clinical analysis methods that contribute to OHSU’s mission to improve human health, building and leveraging platform-based tools and biological understanding while working in a team-oriented data processing, data analysis, and software development environment, working with next-generation sequencing data, following best practices such as literature currency, tool benchmarking and code sharing through GitHub. Duties include teamwork, client interaction, cross-core collaboration, code and data management, maintenance and development of tools and pipelines, and support of investigators’ discoveries and scholarly work.

Function/Duties of Position

1. 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

2. Collaboration: Work with team members to build and maintain common code repository, bioinformatic best practices and team engagement.  Work with investigators to understand and clarify requests, document requirements, communicate ongoing work, assist with interpretation of results and build community.  Work with other cores to collaborate on support of investigator projects and to build and maintain shared workflows and seamless services. 

3. Data Management: Wrangle, clean, structure and store investigator data.  Assist in building, populating and/or maintaining a searchable, browsable system storing raw omics and imaging data, sample metadata, data generation and data processing provenance, and custom analysis results. 

4. Pipelines: Assist platform development teams implementing scalable high-performance workflows to support the research community with analytical advances and to disseminate best practices to the computational community.  Assist with documentation and user support that enable computational researchers across campus to access and re-use analysis pipelines.

5. Tools: Assist with software development, using structured software engineering best practices.  Collaborate with team members in building, publishing and re-using high-performance open-source code

6. Custom Analysis: Employ best practices for omics, imaging and integrative data representation and analysis.  Provide processed data and technical support to biostatisticians and computational scientists, helping to identify technical factors in data generation and processing and supporting development of biological conclusions that drive the next generation of research and advance human health. 

7. Career Development:  Participate in appropriate activities that enhance general knowledge of or ability to do assigned work. This includes, but is not limited to, the following:  attend classes, seminars, and other training forums; stay current in relevant literature; participate in preparation of scholarly work; participate in staff meetings and other informational sessions; read vendor documentation as appropriate to position; interact with peers and other employees to receive and disseminate information.

Required Qualifications

  • 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
  • Demonstrated ability in research related to genomic analysis, machine learning, or image analysis, which may include experience with next-gen sequencing or medical imaging
  • Demonstrated skills in a high-level programming language, preferably Python or R, preferably in Linux or Unix, optionally with Java or C/C++
  • Understanding of basic statistics and some of its applications to biomedical science
  • Experience with structured data storage and with multi-component data processing systems
  • Experience with architecture or tools for managing “omics” or imaging data
  • Ability to prioritize multiple tasks at one time
  • Excellent communication, analytical and organizational skills, both written and verbal
  • Ability to work independently and as part of a team while being collaborative in resolving problems
  • A desire to change the world and contribute to the elimination of human disease

Preferred Qualifications

  • 3 years of relevant experience, including one year of hands-on experience with generation or analysis of omics or imaging data
  • Experience as a data analyst, software developer or biological researcher, including at least 6 months in a collaborative team work environment.
  • At least 6 months of work experience in a professional, team-oriented computational biology environment
  • High performance computing experience
  • A passion for open-access innovation

Additional Details

Please submit a resume and cover letter for your application to be considered. 

Please note: As of Oct. 18, 2021, all OHSU employees are required to be fully vaccinated against COVID-19. Fully vaccinated means you have received both doses of a two-dose, or one dose of a single-dose, FDA- or WHO-authorized COVID-19 vaccine and at least 14 days have passed since your final dose of COVID-19 vaccine. If you apply for and are offered a position, you must be fully vaccinated prior to starting work. 

If the position you are offered does not require direct, in-person patient care contact, you may request an exception to the vaccine policy for medical or religious reasons. OHSU uses very narrow criteria under the law to allow an exception and very few requests are being approved.

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