The Infectious Disease Epidemiology (IDE) Laboratory offers an excellent interdisciplinary environment where experimentalists work closely with computational experts utilizing state-of-the-art genomic technologies. We ask fundamental questions on how bacterial phenotypes are determined by their genotypes in natural settings. We therefore utilize a broad range of high-throughput genomic and phenomic technologies to obtain whole genome sequencing of clinical and environmental bacterial strains and their key clinical phenotypes under various conditions. We then employ computational methods, in particular machine learning methods, to integrate the phenome and genome data with the goal of reconstructing the genotype-phenotype map and identifying robust causative and informative genomic biomarkers.