Despite the devastating global human toll of infectious diseases, we lack fundamental knowledge about the viruses, bacteria, fungi, parasites and insect vectors that cause and spread disease. This ignorance leaves us with very few opportunities to intervene in the cycle of infection and transmission, especially in the face of the emergence of new infectious diseases and the rapid rise in drug resistance. Our Genomic Center for Infectious Disease (GCID) develops and applies cutting-edge genomic technologies to address fundamental gaps in our knowledge of the basic biology that underlies the interactions between hosts, pathogens, and vectors. Our GCID is comprised of highly experienced managers with a history of working together effectively to develop and apply innovative genomic approaches. Our GCID employs industrial practices and management systems in directing the world-leading facilities of our Technology, Data and Administrative Cores. Outstanding scientists lead our four Research Projects, devoted to viral, bacterial, fungal, and parasitic diseases and vectors that transmit them. Our collective work will target high priority pathogens and pathogen-host-vector systems that have a major impact on the global burden of disease. Each Research Project leverages our expertise in genomics, technology development, bioinformatics and computational biology, and with collaborating researchers and clinicians applies them to thoughtfully acquired samples and proven model systems. Moreover, the laboratory and analytical methods we develop will have broad applicability to other pathogen-host systems. Our Research Projects benefit from synergies arising from their shared space, approaches and tools, and together they will pursue three long-range, cross-cutting objectives: 1) Explore the genomic epidemiology of pathogens and vectors at individual and population scales; 2) Understand interactions among vertebrate hosts, pathogens, and arthropod vectors using genomic and transcriptomic approaches; and, 3) Define the functional basis of virulence, immunity, and the functional consequences of metagenomic diversity. By applying powerful new genomic technologies to probe host and pathogen contributions to infection processes we will obtain crucial knowledge, and open new avenues for tracking, preventing and managing infectious diseases. We will produce and disseminate data, methodologies, and expertise, broaden participation in genomic research into infectious disease, and generate data and knowledge that will enable a wide community to benefit from our expertise, and, ultimately improve global public health.