Computational Biology

Informatics, systems analysis, and modeling

There is a wide range of computational biology research in the Biomedical Engineering Department and at OHSU generally, ranging from genomics to molecular simulation to organ-scale modeling, and beyond. Faculty bring to bear expertise in machine learning, statistics, computer science, and physical sciences. BME faculty participate in the National Cancer Institute's Genomic Data Analysis Network, consisting of the nation's top cancer research institutes that provide the first line analysis on some of the largest cohorts of cancer data on the planet. OHSU also collaborates with industry partners, such as Intel, to improve methods in cutting edge big data analysis for biological problems. Other work pursues machine-learning-based image analysis of cutting edge microscopy data generated at OHSU, physiological modeling of diabetes and blood-flow pathologies, and molecular-dynamics-based drug design.

Associated faculty

Ozgun Babur, Ph.D.

Ozgun Babur

Modeling and analyzing human cellular and molecular pathways, and learning from omic data using pathway knowledge.

Young Hwan Chang, Ph.D.

Young Hwan Chang
Multi-scale image analysis based on machine learning.

Emek Demir, Ph.D.

Emek Demir
Integrating pathway information and "cell maps" to answer cancer biology problems in conjunction with omic data.

Kyle Ellrott, Ph.D.

Kyle Ellrott
Large-scale integrative computing and analysis.

Jeremy Goecks, Ph.D.

Jeremy Goecks
Computational tools and platforms for precision medicine.

Laura Heiser, Ph.D.

Laura Heiser
Integrative systems biology modeling of cancer processes.

Yali Jia, Ph.D.

Yali Jia
Deep learning for classification and segmentation, optical imaging, ocular diseases.

Peter G. Jacobs, Ph.D.

Peter G. Jacobs
Mathematical modeling of the glucoregulatory system, drug delivery, and diagnostics.
Jacobs Lab

Abhinav Nellore, Ph.D.

Abhi Nellore
Large-scale analysis of publicly available genomics data.

Sandra Rugonyi, Ph.D.

Sandra Rugonyi
Blood flow simulations of subject-specific cardiovascular pathologies.

Reid Thompson, M.D., Ph.D.

Reid Thompson
Computational immunogenomics and early cancer detection.

Zheng Xia, Ph.D.

Zheng Xia
Machine Learning algorithms for large-scale omics data mining.

Daniel M. Zuckerman, Ph.D.

Daniel Zuckerman
Molecular through cell-scale simulations using physics-based algorithms.

OHSU is also home to significant computational research outside of the BME Department. See the Computational Biology Group, the Department of Medical Informatics and Clinical Epidemiology, the Department of Computer Science and Electrical Engineering, as well as other departments which are home to computational faculty: Molecular and Medical GeneticsRadiation Medicine, and Molecular Microbiology and Immunology.