Functional & Integrative Genomics is devoted to large-scale studies of genomes and their functions, including systems analyses of biological processes. The journal will provide the research community an integrated platform where researchers can share, review and discuss their findings on important biological questions that will ultimately enable us to answer the fundamental question: How do genomes work?  Topics covered include but are not limited to:  Whole genome analyses of model and complex organisms  Genomics (Structural, comparative, integrative) and bioinformatics tools  Proteomics and Metabolomics (integrated with function)  Metagenomics  Ionomics  Large-scale/high-throughput analysis of biological systems Emphasis will be placed on manuscripts addressing important biological problems using large-scale systems and approaches. Studies on bacterial, fungal, protista, plant and animal genomes are welcome. Papers describing new genomics tools and databases will also be considered for publication.