Title: "Integrative -omics for the Systems Biology of Complex Phenotypes"
Speaker: Mehmet Koyutürk; Department of Electrical Engineering and Computer Science; Center for Proteomics and Bioinformatics, Case Western Reserve University
Place: HORT 117; April 12, 2011, Tuesday, 4:30pm


In the study of biological systems, many phenotypes, i.e., observed differences between the behavior of different organisms, are complex - that is, they are based on a set of complex interactions between multiple genetic and environmental factors. Genomic association studies provide significant information on the genetic bases of complex phenotypes, however so far have defined a limited set of phenotypes. Large scale monitoring of gene expression reveals underlying cellular mechanisms, however, it is limited in capturing the abundance and activity of functional proteins. Protein expression data provides more reliable information on function, but with limited coverage. Protein-protein interactions (PPI) highlight functional relationships between proteins, but PPI data is highly noisy, incomplete, and static. In this talk, we investigate how these useful, yet limited sources of biological data can be integrated through innovative use of computational approaches to gain insights on the molecular mechanisms of complex phenotypes. We introduce several algorithmic problems that stem from these applications, including (i) network-based prioritization of candidate disease genes, (ii) integration of protein and gene expression data to identify dysregulated subnetworks in cancer, and (iii) use of subnetwork markers in prediction of metastasis. Experimental results on various public and dedicated datasets show that such integrative approaches can provide significant insights into the systems biology of complex phenotypes.

Associated Reading:
Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, and Mehmet Koyuturk. 2010. Subnetwork State Functions Define Dysregulated Subnetworks in Cancer. B. Berger (Ed.): RECOMB 2010, LNBI 6044, pp. 80-95. Springer-Verlag Berlin Heidelberg.

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