Genome sequencing technologies have enabled a rapid expansion into understanding cancer biology, drug development, and treatment resistance. A powerful application of these technologies is the ability to quantitatively interrogate the coding and non-coding components of entire transcriptomes. Work in our laboratory has focused on the application of transcriptome sequencing (RNA-seq) coupled with network and pathway analysis for translational research into breast cancers and rare tumors. This presentation will detail how we have harnessed RNA-seq on tumor tissues to reveal efficacious drug targets and implement rational drug combinations in triple-negative breast cancer. Further, ongoing work on how RNA-seq is being used for biomarker discovery in retrospective cancer clinical trials will also be presented.