RESEARCH SUMMARY Embryonic development involves the formation of functional organs comprised of many different cell types, which often originate from different locations. Thus cell migration and differentiation must be tightly coordinated, but are typically studied as independent processes. Here we use a combination of gene expression profiling in single cells, zebrafish genetics and computational models to test the hypothesis that migration and differentiation are coordinated. This coordination requires specific regulators of cell adhesion dynamics and cell-cell signaling. We focus on neural crest cells, a transient embryonic population that migrates throughout the body to give rise to a huge range of different fates. One barrier to studying this problem has been the limited number of tools available to detect transitional states in individual cells as they differentiate and tie this to their migratory behaviors in a precise and quantitative manner. Here we develop new approaches for profiling gene expression in single cells from known locations and tracking their movements in vivo. We will analyze how genes required for cell adhesion and cell-cell signaling influence these processes, and use computational models to predict key features of neural crest cell responses. We expect that such a multidisciplinary approach will reveal insights into the mechanisms that integrate cell migration and fate.