ArticleNature methods2021
Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ development.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- The development of single-cell lineage tracing technology and its application in immunotherapy.Molecular therapy. Advances · 2026Review
- Article
- BASELINE: a CRISPR base editing platform for mammalian-scale single-cell lineage tracing.Nucleic acids research · 2026Article
- Clonal drift in the aging gut: Mapping the fate of stem cells over time.PLoS biology · 2026Article
- Lineage tracing from cellular heritage to disease destiny.Nature genetics · 2026Review
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- Longitudinal lineage tracing reveals early clonal attrition during Drosophila midgut aging.PLoS biology · 2026Article
- Lighting the cell's path.Nature plants · 2026Article
- Mapping the zygote-to-adult developmental cell phylogeny in Arabidopsis thaliana reveals a three-cell rule of branching.Nature plants · 2026Article
- Single-cell mitochondrial lineage tracing: Opportunities and challenges.Quantitative biology (Beijing, China) · 2026Review
- Regenerative base editing enables deep lineage recording.bioRxiv : the preprint server for biology · 2026Article
- Cell lineage tracing: Methods, applications, and challenges.Quantitative biology (Beijing, China) · 2025Review
- Cell Fate Determination and Lineage Tracing: Technological Evolution and Multidimensional Applications.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity.Nature protocols · 2025Review
- ScGOclust: leveraging gene ontology to find functionally analogous cell types between distant species.Bioinformatics (Oxford, England) · 2025Article
- Advances in CRISPR-Cas9 in lineage tracing of model animals.Animal models and experimental medicine · 2025Review
- Detecting branching rate heterogeneity with tree balance statistics in lineage tracing trees.bioRxiv : the preprint server for biology · 2025Article
- Clonal expansion dictates the efficacy of mitochondrial lineage tracing in single cells.Genome biology · 2025Article
- Single-cell lineage tracing techniques in hematology: unraveling the cellular narrative.Journal of translational medicine · 2025Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mapping the cell phylogeny of a complex multicellular organism relies on somatic mutations accumulated from zygote to adult. Available cell barcoding methods can record about three mutations per barcode, enabling only low-resolution mapping of the cell phylogeny of complex organisms. Here we developed SMALT, a substitution mutation-aided lineage-tracing system that outperforms the available cell barcoding methods in mapping cell phylogeny. We applied SMALT to Drosophila melanogaster and obtained on average more than 20 mutations on a three-kilobase-pair barcoding sequence in early-adult cells. Using the barcoding mutations, we obtained high-quality cell phylogenetic trees, each comprising several thousand internal nodes with 84-93% median bootstrap support. The obtained cell phylogenies enabled a population genetic analysis that estimates the longitudinal dynamics of the number of actively dividing parental cells (Np) in each organ through development. The Np dynamics revealed the trajectory of cell births and provided insight into the balance of symmetric and asymmetric cell division.
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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 OpenQuestion graph.