Genomic, transcriptomic, proteomic, and metabolomic projects exemplify the “omics” era, and have significantly expanded available data for biomedical research. Recently, next generation sequencing technologies have even more greatly expanded DNA and RNA information. The present challenge is mining this information to obtain meaningful data such as that identifying novel drug targets and vaccine candidates. Several bioinformatics tools and new technologies have been used to high-throughput identification of potential candidates. We illustrate the utilization of new strategies in the study of two major parasitic diseases: schistosomiasis and malaria.