Computational approaches for multimodal lineage tracing

Understanding how cells commit to distinct fates over time is fundamental to elucidating the principles and mechanisms that govern organismal development, tissue regeneration and disease progression. Multimodal lineage tracing, which couples heritable lineage information with single-cell multi-omics, has revolutionized our ability to chart cellular dynamics and fate decisions at unprecedented resolution. However, the resulting datasets are inherently complex and heterogeneous, calling for sophisticated computational frameworks capable of transforming raw measurements into coherent biological insights. Here we comprehensively survey recent methodological advances that substantially expand the computational toolkit for analysing lineage-resolved, single-cell multi-omic data, enabling more accurate lineage reconstruction, trajectory inference, ancestral state estimation and identification of molecular programmes driving cell-state transitions. Emerging high-resolution lineage-tracing technologies and deep learning-based analytical models promise to further unlock the full potential of multimodal lineage tracing, offering an increasingly complete and quantitative view of cellular evolution in both health and disease.