Our lab combines stem cell engineering with systems biology and tissue engineering to model and control blood stem cells and their immune, vascular, and bone niches. We study stem cells differentiated as three-dimensional aggregates, or spheroids, which exhibit fascinating levels of organization and patterning. By collecting high throughput data, such as RNA-seq, we quantify the expression of genes, networks, and signaling pathways across different cell types. We use these approaches to ask how cells communicate and work together to make decisions about cell fate and respond to changes in their local environment. A more comprehensive understanding of these complex systems is needed to empower stem cell engineering and to realize translational applications ranging from drug screening to transplantation and regeneration.