Emek is an associate professor in OHSU’s Department of Molecular and Medical Genetics and the program director of OHSU’s Brenden-Colson Center for Pancreatic Care Computational Biology. He received his Ph.D. in computer engineering from Bilkent University in Turkey in 2005 under the direction of Ugur Dogrusoz, Ph.D., and completed his postdoctoral training with Chris Sander at the Computational Biology Center at the Memorial Sloan Kettering Cancer Center (MSKCC) in New York. Before coming to OHSU, he was a manager at Pathway Informatics at MSKCC.
Emek focuses on integrating rich, detailed pathway information and using the resulting "cell maps" to answer cancer biology problems in conjunction with omic data. His work runs the gamut on Pathway Informatics, from pathway curation, visualization, NLP, data standardization and integration to machine learning, mechanistic assembly and simulation. He led the development of the BioPAX standard for pathway information and built an extensive software stack for aggregating and using pathway information from all major public data sources. These efforts resulted in Pathway Commons, a resource with more than 2 million interactions and more than 400,000 highly-detailed reactions of human pathways. Pathway Commons is the largest process-level pathway database.
Emek also led the development of several pathway analysis algorithms for detecting highly-altered sub-networks in a cancer context, finding modulators of transcription factors, inferring differentially active networks from proteomic measurements and finding mutually exclusive altered pathway modules.Read more