Understanding the gene regulatory circuits that control development is a central problem in biology. Over the past several years, I have worked with scientists with backgrounds in physics and mathematics to understand the general mechanisms in development, reprogramming, transdifferentiation as well as other cellular fate conversions. These projects worked toward a mathematical description of the famous embryologist Conrad Waddington’s “epigenetic landscape”. With the advent of single-cell RNA-seq, we may now be able to reconstruct the cellular trajectories across this landscape during differentiation. However, doing so will require sophisticated statistical models and powerful computational tools to interpret the enormous datasets generated by single-cell sequencing. In the Trapnell lab, I am working on such tools.