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Abstract Cells with the same genome can exist in different phenotypes and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming for induced pluripotent stem cells and transdifferentiation, cancer metastasis and fibrosis progression. The regulation and dynamics of cell phenotypic conversion is a fundamental problem in biology, and has a long history of being studied within the formalism of dynamical systems. A main challenge for mechanism-driven modeling studies is acquiring sufficient amount of quantitative information for constraining model parameters. Advances in quantitative experimental approaches, especially high throughput single-cell techniques, have accelerated the emergence of a new direction for reconstructing the governing dynamical equations of a cellular system from quantitative single-cell data, beyond the dominant statistical approaches. Here I review a selected number of recent studies using live- and fixed-cell data and provide my perspective on future development. 

Summary Reversible transitions between epithelial and mesenchymal cell states are a crucial form of epithelial plasticity for development and disease progression. Recent experimental data and mechanistic models showed multiple intermediate epithelial–mesenchymal transition (EMT) states as well as trajectories of EMT underpinned by complex gene regulatory networks. In this review, we summarize recent progress in quantifying EMT and characterizing EMT paths with computational methods and quantitative experiments including omics‐level measurements. We provide perspectives on how these studies can help relating fundamental cell biology to physiological and pathological outcomes of EMT.