ArticleNature methods2025
A comprehensive human embryo reference tool using single-cell RNA-sequencing data.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 64 papers.
What it found
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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.
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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
64 citing papers in PubMed.
- Endogenous retrovirus control of calbindin is essential for human early embryogenesis.Science advances · 2026Article
- The Building and Application of a Machine Learning Model on Predicting Euploid Blastocysts in IVF Treatments Without PGT-A.Reproductive sciences (Thousand Oaks, Calif.) · 2026Article
- Engineering the human endometrium at the intersection of development and reproduction.Nature biomedical engineering · 2026Review
- TGFβ-dependent upregulation of OCIAD2 is essential for epithelial-to-mesenchymal transition during mesendoderm differentiation.Stem cell reports · 2026Article
- Putting mammalian early embryonic cells into dormancy.Nature protocols · 2026Review
- A single small molecule-based human embryo model reveals V-ATPase requirement in mammalian blastocyst cavitation.Cell research · 2026Article
- Human stem cell-based embryo models: innovation, ethics, and policy.Human reproduction (Oxford, England) · 2026Article
- Direct Mapping of CDK2 Substrates in Embryonic Stem Cells Uncovers an AP-Site Repair Mechanism via HMCES Phosphorylation.bioRxiv : the preprint server for biology · 2026Article
- Sperm tRNA-derived fragments: molecular mechanisms and clinical implications for paternal epigenetic inheritance.Clinical epigenetics · 2026Review
- A transgene-free, human peri-gastrulation embryo model presents trilaminar embryonic disc-, amnion- and yolk sac-like structures.Nature cell biology · 2026Article
- Artificial Intelligence Virtual Organoids (AIVOs).Bioactive materials · 2026Review
- Beyond integration: towards benchmarks for developmental potential in human stem cell-derived embryo models.Human reproduction update · 2026Review
- Single-Cell Transcriptomic Analysis Reveals Multicellular Coordination and Signaling Rewiring During Fetal Goat Skeletal Muscle Development.Animals : an open access journal from MDPI · 2026Article
- The vertebrate yolk sac: evolutionary origins and current advances in in vitro models.Development (Cambridge, England) · 2026Review
- Stem cell-based embryo models as a tool for reproductive biology.Molecular human reproduction · 2026Review
- Cell type-agnostic transcriptomic signatures enable uniform comparisons of neural maturation.PLoS biology · 2026Article
- A guide to using embedded ethics in human stem-cell-based embryo model research.Nature cell biology · 2026Review
- Serum coating enables feeder-free culture of naive human pluripotent stem cells preserving developmental potential.The EMBO journal · 2026Article
- Decoding the modulatory role of long non-coding RNAs in embryogenesis: a comprehensive review.Molecular biology reports · 2026Review
- Progress in stem cell-based embryo models and their applications in developmental biology and biomedicine.Nature reviews. Molecular cell biology · 2026Review
4 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
15 authors.
Funding
Abstract
Stem cell-based embryo models offer unprecedented experimental tools for studying early human development. The usefulness of embryo models hinges on their molecular, cellular and structural fidelities to their in vivo counterparts. To authenticate human embryo models, single-cell RNA sequencing has been utilized for unbiased transcriptional profiling. However, an organized and integrated human single-cell RNA-sequencing dataset, serving as a universal reference for benchmarking human embryo models, remains unavailable. Here we developed such a reference through the integration of six published human datasets covering development from the zygote to the gastrula. Lineage annotations are contrasted and validated with available human and nonhuman primate datasets. Using stabilized Uniform Manifold Approximation and Projection, we constructed an early embryogenesis prediction tool, where query datasets can be projected on the reference and annotated with predicted cell identities. Using this reference tool, we examined published human embryo models, highlighting the risk of misannotation when relevant references are not utilized for benchmarking and authentication.
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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.