Slingshot is a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. It addresses the challenge of accurately characterizing multiple branching lineages in noisy single-cell data. The method consists of two main stages: identifying the global lineage structure and inferring pseudotimes for cells along each lineage. Slingshot uses a cluster-based minimum spanning tree (MST) to identify the number and shape of lineages, and then employs simultaneous principal curves to fit smooth branching curves to these lineages. This approach allows Slingshot to capture complex lineage structures while maintaining stability in noisy data. The method is evaluated on real datasets and simulated datasets, demonstrating its robustness to noise and its ability to correctly identify multiple lineages. Compared to other methods, Slingshot shows higher accuracy in inferring pseudotimes, especially in the presence of multiple branching lineages. The flexibility and modularity of Slingshot make it suitable for integration into existing analysis pipelines, making it a valuable tool for single-cell transcriptomics research.Slingshot is a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. It addresses the challenge of accurately characterizing multiple branching lineages in noisy single-cell data. The method consists of two main stages: identifying the global lineage structure and inferring pseudotimes for cells along each lineage. Slingshot uses a cluster-based minimum spanning tree (MST) to identify the number and shape of lineages, and then employs simultaneous principal curves to fit smooth branching curves to these lineages. This approach allows Slingshot to capture complex lineage structures while maintaining stability in noisy data. The method is evaluated on real datasets and simulated datasets, demonstrating its robustness to noise and its ability to correctly identify multiple lineages. Compared to other methods, Slingshot shows higher accuracy in inferring pseudotimes, especially in the presence of multiple branching lineages. The flexibility and modularity of Slingshot make it suitable for integration into existing analysis pipelines, making it a valuable tool for single-cell transcriptomics research.