Emek Demir

Emek Demir serves as an Associate Professor in the Department of Molecular and Medical Genetics at Oregon Health & Science University's School of Medicine, where he directs the Computational Biology program at the Brenden-Colson Center for Pancreatic Care. His academic journey includes a Ph.D. in Computer Engineering from Bilkent University (2005) under Ugur Dogrusoz and postdoctoral training with Chris Sander at Memorial Sloan Kettering Cancer Center's Computational Biology Center.

Dr. Demir's research centers on Pathway Informatics, integrating detailed biological pathway information with omic data to solve cancer biology problems. His work spans pathway curation, visualization, NLP, data standardization, machine learning, and mechanistic simulation. He pioneered the BioPAX pathway data standard and developed Pathway Commons—the largest process-level pathway database with over 2 million interactions and 400,000 detailed human reactions.

His publication record demonstrates consistent innovation in computational oncology, with recent work focusing on transcription factor activity prediction, spatial tumor mapping, and causal network analysis. Key contributions include algorithms for detecting altered cancer sub-networks, identifying transcription factor modulators, and inferring active networks from proteomic data. His research bridges computational methods with clinical applications in leukemia, prostate cancer, and glioblastoma.

• Recipient of leadership roles in major NIH-funded initiatives
• Principal developer of Pathway Commons and BioPAX standards
• Extensive collaborations with Memorial Sloan Kettering and OHSU clinical departments

Dr. Demir directs a computational biology program focused on translating pathway knowledge into clinical insights for pancreatic cancer, with ongoing projects in spatial omics, multi-dimensional tumor atlases, and antiviral nanomaterial applications.