Cells make fate decisions in response to dynamic environmental and pathological stimuli as well as cell-to-cell communications. Recent technological breakthroughs have enabled to gather data in previously unthinkable quantities at single cell level, starting to suggest that cell fate decision is much more complex, dynamic, and stochastic than previously recognized. Multiscale interactions, sometimes through cell-cell communications, play a critical role in cell decision making. Dissecting cellular dynamics emerging from molecular and genomic scale in single-cell demands novel computational tools and multiscale models. In this talk, I will present our recent works on analyzing single cell molecular data, and their connections with cellular and spatial tissue dynamics. Our mathematical approaches bring together optimization, statistical physics, ODEs/PDEs, and stochastic simulations along with machine learning techniques. By utilizing our newly developed computational tools along with their close integrations with new datasets collected from our experimental collaborators, we are able to investigate several complex systems during development and regeneration to uncover new mechanisms in cell fate determination.