ArticleNature genetics2022
Systematic reconstruction of cellular trajectories across mouse embryogenesis.
Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers.
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Who cites it
119 citing papers in PubMed, 201 citations in OpenAlex.
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- Systematic benchmarking and optimal strategy selection of cross-species integration methods.Briefings in bioinformatics · 2026Article
- Towards predictive virtual embryos with genomics and AI.Nature methods · 2026Article
- Regulation of mRNA poly(A) tail length governs mammalian body plan formation in gastruloids.Nature communications · 2026Article
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- Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis.bioRxiv : the preprint server for biology · 2026Article
- Developmental chronology of mouse embryo from 2-cell stage through birth.Nature cell biology · 2026Article
- Robust semi-supervised scRNA-seq integration from virtual adversarial learning.bioRxiv : the preprint server for biology · 2026Article
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- Maternal obesity remodels nutrient transport transcriptional programs in early mouse embryonic and extraembryonic cell lineages.Molecular metabolism · 2026Article
- Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes.bioRxiv : the preprint server for biology · 2026Article
- R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation.Genome research · 2026Article
- From chemically defined hiPSCs to self-organizing cardiac organoids: current strategies guided by developmental signaling.Stem cell research & therapy · 2026Review
- Quantifying stability via count splitting to guide model selection in RNA velocity analyses.bioRxiv : the preprint server for biology · 2026Article
- A cellular basis for the hourglass pattern in vertebrate embryogenesis.Nature communications · 2026Review
- stSCI: A multi-task learning framework for integrative analysis of single-cell and spatial transcriptomics data.Innovation (Cambridge (Mass.)) · 2026Article
- A benchmark of semi-supervised scRNA-seq integration methods in real-world scenarios.PLoS computational biology · 2026Article
59 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors at 6 institutions in 2 countries.
Funding
Abstract
Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single-cell zygote gives rise to millions of cells expressing a panoply of molecular programs. Although intensively studied, a comprehensive delineation of the major cellular trajectories that comprise mammalian development in vivo remains elusive. Here, we set out to integrate several single-cell RNA-sequencing (scRNA-seq) datasets that collectively span mouse gastrulation and organogenesis, supplemented with new profiling of ~150,000 nuclei from approximately embryonic day 8.5 (E8.5) embryos staged in one-somite increments. Overall, we define cell states at each of 19 successive stages spanning E3.5 to E13.5 and heuristically connect them to their pseudoancestors and pseudodescendants. Although constructed through automated procedures, the resulting directed acyclic graph (TOME (trajectories of mammalian embryogenesis)) is largely consistent with our contemporary understanding of mammalian development. We leverage TOME to systematically nominate transcription factors (TFs) as candidate regulators of each cell type's specification, as well as 'cell-type homologs' across vertebrate evolution.
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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.