More broadly, we develop computational methods for finding patterns in sequences and structures that allow us to make inferences about the relationships between sequence, structure, function, and evolution. These methods include elements of datamining, machine learning, modeling, and simulation in the context of biological data. One of our central emphases is using information from homologous molecules in different species to find the conserved structural elements that are associated with biological function. More recently we have extended these approaches to the analysis of biological networks using genome wide expression, protein interaction, genetic interaction and metabolite data.