isCORAL: PKU team does in silico lineage tracing from transcriptome snapshots alone
arjunrajlab · x · 2026-10-22
A Peking University preprint (Yongjie Lin, Yihan Lin) introduces isCORAL, an in silico lineage-tracing framework that reconstructs clonal relationships from single-cell or spatial transcriptome snapshots alone.
- Approach: identifies memory genes with heritable expression differences, infers probabilistic clonal relationships, and builds clone-oriented embeddings plus dynamic cell-fate maps.
- Results: markedly outperforms tested alternatives on memory-gene identification and lineage reconstruction across diverse datasets.
- Applications: resolves early fate biases among transcriptionally similar hematopoietic stem cells, validates against an experimentally recorded lineage tree in mouse tumors, and infers early epiblast/amnion dynamics in a human embryo.
The authors suggest lineage tracing experiments could be virtualized at specific timescales, cutting cost while improving cell-fate inference.
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