Decoding cell division history and lineage-resolved phenotypic patterns from single-cell barcode and transcriptomic data.

FateScape accurately reconstructs lineage topology and reveals depth-resolved phenotypic patterns in single-cell data from C. elegans and mouse embryos.

• Why it matters: Understanding cell division history and phenotypic diversity is crucial for deciphering multicellular development, yet current methods lack integrated approaches to infer lineage and phenotype simultaneously.
• What they did: FateScape combines paired lineage barcodes and transcriptomic profiles using statistical methods, including overlapping state-lineage decomposition and barcode-guided subtree integration, validated through simulations and biological data.
• The result: FateScape reliably recovers lineage structures and quantifies phenotypic dispersion and concentration across lineage depths, enabling detailed insights into developmental cell state organization.