Computational Biologist 1 at Oregon Health & Science University

Portland, Oregon, United States -

Full Time

Start Date

Immediate

Expiry Date

11 Sep, 26

Salary

69.32

Posted On

13 Jun, 26

Experience

2 year(s) or above

Remote Job

Yes

Telecommute

Yes

Sponsor Visa

Skills

Deep Learning, Machine Learning, Python, Mathematical Modeling, Statistical Modeling, Graph Theory, Natural Language Processing, Single-cell Data Analysis, Knowledge Graphs, Pytorch, Bioinformatics, Computational Biology, Linear Algebra, Probability, Optimization, Network Analysis

Industry

Higher Education

Description

Department Overview The OHSU Knight Cancer Institute is a pioneer in personalized cancer treatment and research, where the 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! 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 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. Duties include: 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. 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 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 Preferred Qualifications 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 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 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 #linkedin #indeed #knightcancerjobs #knightresearchandlabjobs #knightcompbiojobs #knightinternal Why apply to OHSU? We are Oregon's only public academic health center. In addition to caring for patients, we lead groundbreaking research. We also train the next generation of health care professionals. As Portland's largest employer, we give you opportunities to learn and advance in a system of hospitals and clinics across Oregon and Southwest Washington. All are welcome. OHSU welcomes people of all ages, ethnicities, genders, national origins, religions and sexual orientations. We are striving to build an anti-racist, multicultural institution and encourage people with diverse backgrounds to apply. To request reasonable accommodation, contact askhr@ohsu.edu

Responsibilities

Develop multimodal AI and LLM-based models to predict the progression of aggressive myeloproliferative neoplasms to acute myeloid leukemia. Build domain-specific knowledge graphs using the Reactome pathway knowledgebase and implement integrative network modeling with clinical variables.