Description:
The past decade has seen an explosion in “genome‐era” technologies which profile genes, proteins, metabolites and the intricate web of interconnections among them. Much of bioinformatics and functional genomics is now focused on methods to assemble these diverse measurements into models of functional networks and pathways within the cell.Mapping the genetic network underlying the response to DNA damage. We will describe our ongoing efforts to apply ChIP‐sequencing and synthetic‐lethal screens to map how the cellˈs transcriptional network is remodeled by DNA‐damaging conditions.Network‐based biomarkers for disease diagnosis and personalized medicine. Recently, we have shown that networks can also serve as powerful biomarkers and in many cases are more predictive than any individual gene. Our approach is to project gene and/or protein expression profiles of each patient onto the known human genetic network map to identify pathways that are predictive of disease.Protein network comparative genomics. We are developing a library of standard approaches for comparing protein interaction networks across species, conditions, and network types.We are developers of the Cytoscape platform, an Open‐Source software environment for visualization and analysis of biological networks and models (http://www.cytoscape.org/).