Our research will provide insight into how plants sense and respond to nitrogen (N) at the molecular level, a largely unanswered question in plants. Identifying factors involved in the regulation of gene networks in response to N could be used to optimize N-assimilation and use in vivo. Improving N-use efficiency is economically beneficial, and would also serve to reduce ground water contamination by nitrite, a health and environmental concern. Understanding this process could also be used to devise strategies to improve the amino acid content of seeds, and important issue for agriculture and human nutrition. Our work iteratively combines experimental (molecular genetics, genomics) and informatics approaches (data integration, mining and network analysis) to generate and test hypotheses for how nitrogen regulates metabolic and other cellular processes at the gene network level. Research in our laboratory includes integration of publicly available genomic data, literature mining and the use of this data to make predictions about the regulation of molecular networks. Our approach will help to identify the pathways for intervention and to enable the results of such interventions (e.g. genetic modifications) to be evaluated experimentally. We hope our functional studies will contribute to the efforts of the plant community to understand the function of every Arabidopsis gene by the end of the year 2010. Although our main interest is in plants and using Arabidopsis thaliana as a model system, the methods and tools we develop will be generic and applicable to any organism whose genome is sequenced. Our research will deliver a list of target genes to modify plant traits of interest, such as enhanced growth in N-limiting conditions. Orthologs of such genes in species with agronomic importance could be targeted for genetic engineering programs.