Failure of cells to respond to DNA damage is a primary determinant of cancer progression and is a key mechanism of toxicity by pharmacologic agents. Modeling of the molecular interaction networks induced by DNA damaging agents is likely to reveal new insights into the mechanisms of the cellular DNA damage response. To further elucidate DNA alkylation damage response in eukaryotes, we have developed network models of regulatory pathways responding to the DNA damaging agent methyl methanesulfonate (MMS) in yeast. Models were constructed using data derived from classical genomic and microarray approaches, and were refined using computational systems biology approaches. A phenotypic screening was used to identify a set of transcription factors important for DNA damage response, and the implicated regulatory pathways were systematically interrogated using chromatin immunoprecipitation (chIP-chip) and DNA microarrays to monitor protein-DNA interactions and genome-wide expression patterns in single gene-knockout strains. These data were integrated and modeled using Bayesian statistics to identify expression-activated network regions, and visualized using software we have developed for operating on network models (www.cytoscape.org). Using this systems approach, we have generated new hypotheses revealing the complex web of interactions, cellular factors, and mechanisms involved in DNA damage response.