Relationships between systems biology and genomics. Functional genomics assays like gene expression profiling, metabolomics and proteomics are used as input data by different systems-level analysis approaches such as Gene Regulatory Network (GRN) inference, Pathway Analysis (PA) and Flux Balance Analysis (FBA). Functional annotation, a core activity of genomics, is a prerequisite in PA and FBA, and helps in the interpretation of GRNs. GRN and FBA generate models of the biological system based on genomics data and can also use pathway databases as a priori information to help building models of the system. Alternatively, PA can be directly employed as an interpretative tool of the system. Systems Medicine relies on GRNs and pathways to develop personalized genomic diagnosis tools. Metagenomics expands the system under study to a supraorganismal level, whereas novel systems-level annotation paradigms such as transcript annotation expand the scope of functional annotations.