ArticleScience (New York, N.Y.)2018
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo.
Article in Science (New York, N.Y.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 448 papers.
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Who cites it
448 citing papers in PubMed, 899 citations in OpenAlex.
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- A 3D amphioxus brain atlas illuminates the blueprint of the ancestral chordate brain and highlights unique vertebrate innovations.Science advances · 2026Article
- Lineage tracing from cellular heritage to disease destiny.Nature genetics · 2026Review
- Transcriptional divergence of the zebrafishbioRxiv : the preprint server for biology · 2026Article
- ProtoCloud: A prototypical self-explaining model for single-cell analysis.Cell genomics · 2026Article
- barbieQ: an R software package for analysing barcode count data from clonal tracking experiments.Bioinformatics (Oxford, England) · 2026Article
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- Angptl5 restricts primitive hematopoiesis by promoting retinoic acid signaling in zebrafish.PLoS biology · 2026Article
- Intracellular pH dynamics promotes zebrafish larval tail regeneration.bioRxiv : the preprint server for biology · 2026Article
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- Met regulates endoderm migration in zebrafish.bioRxiv : the preprint server for biology · 2026Article
- Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data.bioRxiv : the preprint server for biology · 2026Article
- A fast-to-faithful transition shapes the DNA repair landscape during embryogenesis.bioRxiv : the preprint server for biology · 2026Article
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- Loss of MITF activity leads to emergent cell states from the melanocyte stem cell lineage.bioRxiv : the preprint server for biology · 2026Article
- Tree shrew immune cell atlas identifies NR1H3⁺ tissue macrophages with conserved anti-inflammatory function.Nature communications · 2026Article
388 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
High-throughput mapping of cellular differentiation hierarchies from single-cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single-cell RNA sequencing to >92,000 cells from zebrafish embryos during the first day of development. Using a graph-based approach, we mapped a cell-state landscape that describes axis patterning, germ layer formation, and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon-based barcoding approach (TracerSeq) for reconstructing single-cell lineage histories. Clonally related cells were often restricted by the state landscape, including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in embryos lacking the
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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.