Computational Biologist 1

Oregon Health & Science University•Portland, OR

11h•Onsite

About The Position

The OHSU Knight Cancer Institute is a pioneer in personalized cancer treatment and research. 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. We are seeking a highly motivated candidate with a strong mathematical background to fill a part-time, hourly position for a Computational Biologist 1 on the Reactome Project Team with Dr. Guanming Wu. This interdisciplinary role offers an exciting opportunity to work at the intersection of computational biology, bioinformatics, and applied mathematics (including statistical modeling and machine learning), in close collaboration with a leading wet-lab research team, Dr. Ted Braun’s group at the Knight Cancer Institute. The project focuses on developing multimodal AI/LLM-based models to predict the progression of aggressive myeloproliferative neoplasms (aMPN) to acute myeloid leukemia (AML). The successful candidate will be assisting with single-cell data analysis, developing machine learning (ML) and deep learning (DL) approaches for integrative pathway and network modeling with clinical variables, and applying AI technologies to build domain-specific knowledge graphs using Reactome’s pathway knowledgebase. The position requires a strong foundation in mathematics (e.g., linear algebra, probability, and optimization) and the ability to apply these concepts to complex biological data. Reactome is a leading open-source knowledgebase of human biological pathways. It provides tools for pathway curation, visualization, and enrichment analysis, serving the global research community. The Reactome project team is dedicated to integrating cutting-edge computational methods, including AI and ML, to continuously improve its offerings for large-scale data analysis and pathway-based research. The new team member will be working with Dr. Guanming Wu’s team, one of four organizations of the Reactome international consortium.

Requirements

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
AI/DL, mathematical or statistical modeling
Hands-on experience with the implementation of DL models
Graph-related research experience
AI/LLM program experience
Strong Python programming experience
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
Must possess energy and drive to coordinate multiple projects simultaneously
Ability to use tact and diplomacy to maintain effective working relationships

Nice To Haves

Single-cell omics data analysis
knowledge graph and graph neural network
Application of Reactome to data analysis and visualization
Experience with Pytorch or other DL packages
Experience with AI programming (e.g. GitHub Copilot, Claude Code)
Pathway and network analysis
Biology background

Responsibilities

Apply mathematical modeling, deep learning, and machine learning techniques to build a multimodal prediction model for aMPN progression.
Apply AI/LLM/NLP to build domain-specific knowledge graphs using Reactome, leveraging a strong background in graph theory.

Benefits

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