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The Center for Applied Pathogen Epidemiology and Outbreak Control (CAPE) is dedicated to advancing the use of pathogen sequence data to inform public health response. This center operates as a public health-academic collaboration network, uniting Georgia Department of Public Health (GDPH) with researchers from the University of Georgia (UGA), Georgia Tech Research Institute (GTRI), Augusta University (AU), Georgia State University (GSU), Emory University, and The University of Texas School of Public Health (UTSPH). The collective goal is to operationalize innovative solutions and construct robust computational infrastructure, empowering public health partners to more effectively combat epidemic and pandemic diseases. This entails overcoming technical challenges, fostering innovative solutions, delivering educational materials for workforce development and providing a framework to support an applied infectious disease research program that can inform real-time public health responses.