Yichen Gu

CytoSignal detects and quantifies ligand-receptor signaling interactions at cellular resolution from spatial transcriptomic data, enabling spatial gradient analysis and temporal dynamics prediction.

This paper introduces TopoVelo, a method to infer spatial and temporal dynamics of cell fate transitions from spatial transcriptomic data, improving spatial coherence and accuracy in cell differentiation and migration analysis.

CytoSimplex visualizes cell differentiation trajectories using simplex geometry to represent cell fate commitment and potential in 2D and 3D plots.

This paper introduces VeloVAE, a Bayesian model for RNA velocity inference that improves accuracy and captures complex dynamics in multi-lineage single-cell data.