Molecular and genetic network analysis in yeast

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Experimental determination of interactions between cellular components, such as biochemical reactions, protein-protein and genetic interactions, charts a map of the cell. The interaction network map defines gene function and forms the basis for our models of biological processes. This knowledge will eventually enable us to predict phenotype from genotype, understand the genetic basis of disease and engineer new biological systems for industrial applications.Recent biotechnology advances and the availability of completely sequenced genomes for hundreds of organisms has led to genome-scale mapping of networks of interacting proteins, genes and molecules. For instance, over 80,000 protein-protein, protein-DNA and genetic interactions for the yeast Saccharomyces cerevisiae have been mapped using techniques such as yeast two-hybrid, chromatin immunoprecipitation on microarrays and immunoprecipitation coupled to mass spectrometry, with a significant contribution by Canadian research groups. Further, molecular profiling methods, such as RNA level measurement by microarray or protein quantitation by mass spectrometry, provide insight into the dynamic levels of cellular pathway components.This extensive information about the cellular network demands the development of powerful computational tools to facilitate interpretation outside of the direct capacity of the human brain. I aim to address this by developing novel biological network analysis methods to discover new protein complexes, summarize dependency or buffering relationships between biological processes and find pathways that are active at specific life cycle states of the cell. Network analysis methods will help us, as biologists, effectively navigate the cell map at multiple levels of detail and use it to make new discoveries.