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Several of the most celebrated milestones in medicine can be attributed to immunological research, stemming from Edward Jenner’s pioneering smallpox vaccinations and key contributions from Pasteur and Koch resolving the germ theory of infectious disease. Advances in the many years since have produced life-saving vaccines and anti-microbial therapeutics targeting a vast range of pathogens. Coupling these interventions with epidemiological insights into pathogen spread, evolution, and transmission has sharpened our ability to fight infection. Nevertheless, the modern era is still confronted with significant challenges. The emergence and re-emergence of viral pathogens such as Zika and Ebola, as well as an antimicrobial resistance crisis, pose serious global public-health threats and can lead to significant morbidity and mortality. In addition, key therapies such as successful human immunodeficiency virus (HIV)-1 or universal flu vaccines are still lacking, and a new focus on the microbiome has uncovered the consequential influence of broad-spectrum antibiotics, aimed at pathogenic microbes, on the commensal microbiome and human health [1]. These limitations call for refinement and innovation beyond current paradigms of understanding infection and immunity and developing effective therapies, via new methodologies, analytical vantage points, and collaborative research. This special issue of Genome Medicine highlights the ways in which state-of-the-art genomic-sequencing technologies, systems biology, and bioinformatics are advancing research into pathogens and the immune response, as well as applications in surveillance, detection, biomarker discovery, and therapeutic design to prevent and treat infection. New insights into the immune system gained from high-resolution genomics approaches are facilitating the

Infection and immunity: insights and therapeutic strategies through genomic analysis of the host, pathogen, and host–pathogen interaction