ArticleNature methods2026
Inferring cell differentiation maps from lineage tracing data.
Article in Nature methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- The tree labeling polytope: A unified approach to ancestral reconstruction problems.Cell systems · 2026Article
- Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data.Cell genomics · 2026Article
- Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings.PLoS computational biology · 2026Article
- SCOPE: Localizing fate-decision states and their regulatory drivers in single-cell differentiation.bioRxiv : the preprint server for biology · 2026Article
- Spatial transcriptomics and artificial intelligence: a scoping review of emerging applications in head and neck pathology.Head and neck pathology · 2026Article
- Inferring Cell Differentiation Dynamics with Unobserved Progenitors.bioRxiv : the preprint server for biology · 2025Article
- Riemannian Metric Learning for Alignment of Spatial Multiomics.bioRxiv : the preprint server for biology · 2025Article
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Abstract
During development, cells differentiate through a hierarchy of increasingly restricted cell types, a process that is summarized by a cell differentiation map. Recent technologies profile lineages and cell types at scale, but existing methods to infer cell differentiation maps from these data rely on heuristic models with restrictive assumptions about the developmental process. Here we introduce a quantitative framework to evaluate cell differentiation maps and develop an algorithm, called Carta, that infers an optimal differentiation map from single-cell lineage tracing data. The key insight in Carta is to balance the tradeoff between the complexity of the map and the number of unobserved cell type transitions on the lineage tree. We show that, in models of mammalian trunk development and mouse hematopoiesis, Carta identifies important features of development that are not revealed by other methods, including convergent differentiation of cell types, progenitor differentiation dynamics and new intermediate progenitors.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.