ArticleNature2019
Molecular recording of mammalian embryogenesis.
Article in Nature, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 225 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
225 citing papers in PubMed.
- Article
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis.Nature genetics · 2026Article
- Multichannel genomic recording of biological information with ENGRAM.Nature protocols · 2026Review
- Genomic repeats for single-cell molecular recording.bioRxiv : the preprint server for biology · 2026Article
- SPACE-seq integrates spatial transcriptomics and lineage tracing in native tissues.Cell stem cell · 2026Article
- Lineage tracing in gastruloids to understand determinants of early fate decisions.Current opinion in genetics & development · 2026Review
- SenFlag gene signature identifies senescent cells in mouse and human tissues through a conserved core transcriptional program.The EMBO journal · 2026Article
- BASELINE: a CRISPR base editing platform for mammalian-scale single-cell lineage tracing.Nucleic acids research · 2026Article
- The tree labeling polytope: A unified approach to ancestral reconstruction problems.Cell systems · 2026Article
- Lineage-aware stochastic modeling reveals gene-expression dynamics in development and disease.bioRxiv : the preprint server for biology · 2026Article
- Can you trust your reconstructed lineage tree? A homoplasy-based approach for irreversible evolution.bioRxiv : the preprint server for biology · 2026Article
- Lineage tracing from cellular heritage to disease destiny.Nature genetics · 2026Review
- LAML-Pro: joint maximum likelihood inference of cell genotypes and cell lineage trees.Bioinformatics (Oxford, England) · 2026Article
- Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data.Cell genomics · 2026Article
- SciPhy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.Nature communications · 2026Article
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- barbieQ: an R software package for analysing barcode count data from clonal tracking experiments.Bioinformatics (Oxford, England) · 2026Article
- Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining.Genome research · 2026Article
- Using CRISPR barcoding as a molecular clock to capture dynamic processes at single-cell resolution.Genome research · 2026Article
165 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
Funding
Abstract
Ontogeny describes the emergence of complex multicellular organisms from single totipotent cells. This field is particularly challenging in mammals, owing to the indeterminate relationship between self-renewal and differentiation, variation in progenitor field sizes, and internal gestation in these animals. Here we present a flexible, high-information, multi-channel molecular recorder with a single-cell readout and apply it as an evolving lineage tracer to assemble mouse cell-fate maps from fertilization through gastrulation. By combining lineage information with single-cell RNA sequencing profiles, we recapitulate canonical developmental relationships between different tissue types and reveal the nearly complete transcriptional convergence of endodermal cells of extra-embryonic and embryonic origins. Finally, we apply our cell-fate maps to estimate the number of embryonic progenitor cells and their degree of asymmetric partitioning during specification. Our approach enables massively parallel, high-resolution recording of lineage and other information in mammalian systems, which will facilitate the construction of a quantitative framework for understanding developmental processes.
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Registered trials
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.