Gene regulation and metabolism lie at the heart of most biological processes. Both are accomplished by complex networks harboring hundreds of nodes and thousands of edges. We study these networks and the interactions between them mainly in the nematode C. elegans, because it is amenable to high-throughput, large-scale genetics and genomics. In addition, we study interspecies network interactions between C. elegans and bacteria, that may help illuminate connections between mammalian intestinal cells and the gut microbiota.