Tumors consist of cancer clones that are genetically and transcriptionally different from one another. This heterogeneity has shown to play a crucial role in tumor development and its response to treatment. We work on developing computational methods for inferring both the genetic alterations and the transcriptional cellular state in both bulk and single-cell RNA-seq data. This information is then used for linking the cell’s genotype to its phenotype, and for addressing questions related to cancer development and resistance to treatment.