Computational Biologist

Department Overview

The OHSU Knight Cancer Institute is internationally recognized for pioneering advances in personalized cancer treatment and early detection. From transforming Chronic Myeloid Leukemia with Gleevec to driving precision oncology, the institute is dedicated to ending cancer as we know it. Our culture is guided by three principles: we are bold, we are supportive, and we work as a connected team. The Knight Diagnostic Laboratories (KDL) is a CLIA/CAP-accredited diagnostic laboratory with decades of expertise in molecular oncology, rare genetic disorders, and cytogenetics.

Our team of medical directors, scientists, and technical specialists provide cutting-edge diagnostic testing to enable personalized medicine. Additionally, through close partnerships with the Knight Bio Library and Histopathology Shared Resource Laboratories, our clients can also gain access to biospecimens, histology, and immunohistochemistry services.

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

We are seeking a Computational Biologist / Clinical Bioinformatician to join our multidisciplinary team. This role provides bioinformatics expertise in support of clinical test development and will work closely with medical directors, bioinformaticians, and wet-lab scientists to develop, validate, and maintain clinical workflows in accordance with CAP and regulatory standards. The successful candidate will bring strong experience in next-generation sequencing (NGS) data processing and analysis (tissue, blood, and cell-free specimens;

OR: DNA, RNA, epigenomics), and bioinformatics tool development and biostatistics, with a commitment to teamwork, reproducibility, and clinical best practices.

• Support clinical test development through computational analysis of data and development of computational tools.
• Develop, validate, and maintain bioinformatics pipelines aligned with CAP/CLIA requirements.
• Implement and benchmark tools, algorithms, and workflows for variant calling, expression analysis, and proteomic profiling.
• Collaborate with medical directors, clinical bioinformatics teams, and wet bench scientists in a cross-disciplinary environment.
• Contribute to SOP-driven analysis workflows, ensuring reproducibility and regulatory compliance.
• Manage and maintain code, data, and version control repositories (e.g., Git Hub).
• Provide bioinformatics support for clinical reporting and test development.
• Stay current with emerging literature, methods, and tools in computational biology and clinical bioinformatics.
• Participates in the supervision of trainees involved in computational projects

• 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
• 1 year of clinical experience in NGS data analysis including variant calling, copy number analysis and structural variant interpretation
• 1 year of clinical Bioinformatics Tools & Pipelines:
  Alignment (BWA, STAR, HISAT2);
  Variant callers (Mutect2, Var Scan, Strelka, Free Bayes);
  Annotation tools (ANNOVAR, VEP, Oncotator);
  Workflow management (Nextflow, Snakemake, WDL/Cromwell)
• Demonstrated ability to develop genomic analysis workflows.
• Demonstrated skills in a high-level programming language, preferably Python or R, Pearl, preferably in Linux or Unix, optionally with Java or C/C++
• Experience with artificial intelligence methods.
• Experience with SOP-driven workflows for reproducibility and accreditation compliance
• Experience with statistics and its applications to data analysis and interpretation
• 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…