ArticleScience (New York, N.Y.)2018
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis.
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 467 papers.
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Who cites it
467 citing papers in PubMed.
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- Electrophysiological Profiling of Exocytosis during Early-Stage Development of the Zebrafish Lateral Line.eNeuro · 2026Article
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- A genetic model for development, physiology and behavior of catecholamine-deficient zebrafish larvae.Communications biology · 2026Article
- Lineage Tracing Reveals atoh7-Positive and Negative Retinal Ganglion Cell Populations in the Zebrafish Retina.Investigative ophthalmology & visual science · 2026Article
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- Distinct transcriptional programs define cranial motor neuron subtypes during vertebrate development.bioRxiv : the preprint server for biology · 2026Article
- Lineage-specific change in craniofacial gene regulatory networks of syngnathid fishes revealed by integrating multiomics across fishes.bioRxiv : the preprint server for biology · 2026Article
- PseudoVelo: Inferring Gene Expression Derivatives Along Pseudotime as Pseudo-Velocity.International journal of molecular sciences · 2026Article
- Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration.bioRxiv : the preprint server for biology · 2026Article
- SupeRJump: Determining normal and leukemic differentiation fate through semi-supervised jump diffusion modeling.bioRxiv : the preprint server for biology · 2026Article
- Conserved and lineage-specific mechanisms drive chromatophore differentiation in reptiles.Nature communications · 2026Article
- Extreme conservation of cnidarian stinging cell identity despite 600 million years of evolution.bioRxiv : the preprint server for biology · 2026Article
407 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. Analysis of Nodal signaling mutants revealed that their transcriptomes were canalized into a subset of wild-type transcriptional trajectories. Some wild-type developmental branch points contained cells that express genes characteristic of multiple fates. These cells appeared to trans-specify from one fate to another. These findings reconstruct the transcriptional trajectories of a vertebrate embryo, highlight the concurrent canalization and plasticity of embryonic specification, and provide a framework with which to reconstruct complex developmental trees from single-cell transcriptomes.
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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.