Bilkent University
Department of Computer Engineering


Big mechanisms for big data


Prof. Dr. Emek Demir
Oregon Health & Science University, USA

Genomics and imaging data produced by large NIH projects now reaches to Exabyte scale. Current mechanisms of knowledge representation and scientific communication in biology cannot adequately deal with the complexity and volume of this informationa serious bottleneck for developing a causal, predictive understanding of the cell. This is the key observation that guides our teams research.

I will discuss multiple algorithms and tools we developed over the years that bridges causal mechanistic knowledge obtained through decades of low-throughput biology research with big data and share insights we gained during this process. I will also talk briefly about applications of these algorithms to modern molecular tumor boards and precision medicine.

Bio: I have unique expertise in integrating rich, detailed pathway information to build large scale cell maps and using them to answer cancer biology problems in conjunction with omic data. While at MSKCC, I led the development of BioPAX standard for pathway information and built an extensive software stack for aggregating and using pathway information from all major public data sources. Pathway Commons, our aggregation server, now has more than 3 million interactions and more than 400.000 highly detailed reactions of human pathways and it is the largest process-level pathway database. For the last five years, with the completion of key informatics components, I have shifted my focus to using this platform for answering cancer biology questions. I 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 exclusively altered pathway modules. I also worked on NLP, crowd sourcing and smart assistant solutions to accelerate pathway curation as a part of three DARPA projects.


DATE: 24 May 2019, Friday @ 13:30