Emek Demir got his Master of Science in Molecular Biology and Genetics at Bilkent University, Ankara, Turkey, in 2001. In 2005, he got his Ph.D. on Computer Science at the same University. Since then, he is working at the Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, USA, as Research Fellow and, since 2008, as Manager of the Pathway Information Resource.

Advances in molecular technologies have led to rapid generation of data and information about cellular processes at an increasing rate. Current means of knowledge representation and scientific communication in biology cannot adequately deal with the complexity and volume of this information – a serious bottleneck for developing a causal, predictive understanding of the cell.

Pathway Commons project aims to create a common language and platform for building cell maps – system level, integrated models of cellular processes. This talk will be about four applications of cell maps developed to (i) find causal explanations to correlations in large scale high throughput tumor profiles, (ii) improve network inference algorithms, (iii) find metabolic tumor vulnerabilities, (iv) finding mutually altered pathway fragments.
Emek Demir will then focus on the challenges one needs to consider when using qualitative large scale models to inform executable models or statistical inferences. He will discuss possible approaches and available tools.