ArticleScience (New York, N.Y.)2018
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.
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 303 papers.
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Who cites it
303 citing papers in PubMed.
- Learning stochastic dynamics and cell-fate landscapes from single-cell snapshots via optimal transport.Science advances · 2026Article
- Conserved and lineage-specific mechanisms drive chromatophore differentiation in reptiles.Nature communications · 2026Article
- Sidekick2 facilitates multiciliated cell penetration through multicellular adherens junctions.bioRxiv : the preprint server for biology · 2026Article
- Epigenome regulators imbue a single eukaryotic promoter with diverse gene expression dynamics.iScience · 2026Article
- A method for CRISPR/Cas9-induced genetic barcoding and lineage tracing in sheep.Scientific reports · 2026Article
- A cellular basis for the hourglass pattern in vertebrate embryogenesis.Nature communications · 2026Review
- stVCR: spatiotemporal dynamics of single cells.Nature methods · 2026Article
- Kernel-DMD for multiome data integration and control.PLoS computational biology · 2026Article
- Parameter-free representations outperform single-cell foundation models on downstream benchmarks.ArXiv · 2026Article
- Parameter-free representations outperform single-cell foundation models on downstream benchmarks.bioRxiv : the preprint server for biology · 2026Article
- Cell atlases and the developmental foundations of the phenotype.PLoS computational biology · 2026Article
- NR6A1 is essential for neural crest cell specification, formation and survival.Nature communications · 2026Article
- Integrative Learning of Disentangled Representations from Single-Cell RNA-Sequencing Datasets.Computational and structural biotechnology journal · 2026Article
- Spatially varying gene regulation network inference from spatial transcriptomics.Bioinformatics advances · 2026Article
- Sex-specific functional evolution of Dmrt1 in African clawed frogs (Xenopus), and the importance of genetic tipping points in developmental biology.PLoS genetics · 2026Article
- Ric-8A controls Cited2 subcellular localization and transcriptional programs during neural crest development.Frontiers in cell and developmental biology · 2026Article
- Foxi1 regulates multipotent mucociliary progenitors and ionocyte specification through transcriptional and epigenetic mechanisms.PLoS biology · 2026Article
- TheBiomolecules · 2025Review
- A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells.BMC genomics · 2025Article
- Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors.The EMBO journal · 2025Article
243 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
Time series of single-cell transcriptome measurements can reveal dynamic features of cell differentiation pathways. From measurements of whole frog embryos spanning zygotic genome activation through early organogenesis, we derived a detailed catalog of cell states in vertebrate development and a map of differentiation across all lineages over time. The inferred map recapitulates most if not all developmental relationships and associates new regulators and marker genes with each cell state. We find that many embryonic cell states appear earlier than previously appreciated. We also assess conflicting models of neural crest development. Incorporating a matched time series of zebrafish development from a companion paper, we reveal conserved and divergent features of vertebrate early developmental gene expression programs.
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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.