TECHNOLOGY CORE SUMMARY Systematic characterization of protein and genetic interaction networks of respiratory pathogens in disease- relevant cells and 3D culture is critical for the identification of functional host-pathogen complexes and targets for therapeutic development. Systems biology approaches that determine protein-protein interactions (PPIs), characterize protein and posttranslational modification (PTM) abundance changes during infection, and classify functional host factors that regulate infectious disease pathogenesis, can provide strategic insight and generate models of respiratory pathogen infection. Combined with visualization of key host-pathogen complexes at atomic level through structural biology, and integrating with clinical and patient data related to disease severity, our innovative “systems to mechanism, bedside to benchtop” approach can be incredibly powerful for the identification of new therapeutic targets and for predicting respiratory disease outcome. The Technology Core will provide the infrastructure and technological expertise essential to the completion of the overall Host Pathogen Map Initiative (HPMI) 2.0 objectives. With support of Core facilities, the Technology Core will provide a suite of state-of-the-art proteomic technologies (Thermo Fisher Scientific Proteomics Facility for Disease Target Discovery, UCSF, Quantitative Biosciences Institute (QBI), Gladstone Institute), genetic screens (Innovative Genomics Institute, UCBerkeley), and structural biology approaches (UCSF Advanced Microscopy Laboratory and Crystallography Facilities, UCSF) for the generation of high-quality data, which will be integrated in collaboration with the Data Management and Bioinformatics and Modeling Core with clinical and patient derived data. Our goal is to provide PPI and global proteomic analyses, genome-wide and targeted knockdown and knockout genetic screens, and structural characterization of host-pathogen interactions for Mycobacterium tuberculosis (Mtb) (Project 1), and respiratory viruses: SARS-CoV-2, IAV, IBV, RSV, and HPIV (Project 2). We will analyze selected variants and clinical isolates for each pathogen in disease-relevant cell lines, primary cells isolated from healthy donors or mice, 3D-culture models including human airway epithelial organoids, and infected patient samples. Finally, we will continue to develop, optimize, and innovate new technological advances as needed to support Project 1 and 2 and HPMI 2.0 overall goals.