ArticleeLife2021
Mapping single-cell atlases throughout Metazoa unravels cell type evolution.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 192 papers.
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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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Who cites it
192 citing papers in PubMed, 290 citations in OpenAlex.
- Ancient vocabulary for evolving cells.Nature ecology & evolution · 2026Article
- Flexible use of conserved motifs constrains genome access in cell type evolution.Nature ecology & evolution · 2026Article
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- Alignment-free integration of single-nucleus ATAC-seq across species with sPYce.Nature ecology & evolution · 2026Article
- Systematic benchmarking and optimal strategy selection of cross-species integration methods.Briefings in bioinformatics · 2026Article
- Pesci: fast and user-friendly software to compare single-cell gene expression across species.Bioinformatics (Oxford, England) · 2026Article
- Asymmetric Evolution of Antennal Cell Types Underlies a Derived Ammonia-Sensing Logic for Ecological Adaptation in Bactrocera dorsalis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The extreme diversity of retinal amacrine cells has deep evolutionary roots.Science advances · 2026Article
- Single-cell profiling decodes patagium development in gliding mammal.Nature communications · 2026Article
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- Unify learns cellular evolution with universal multimodal embeddings.Nature communications · 2026Article
- Single-cell foundation modeling with species-native protein tokens links regenerative competence across frog and mouse.bioRxiv : the preprint server for biology · 2026Article
- Evolution of compound eye cell types shapes visual behaviors acrossbioRxiv : the preprint server for biology · 2026Article
- Cross-species integration of single-cell data reveals conserved pathology-associated cell populations across animal models and human samples.Cell reports methods · 2026Article
- Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration.bioRxiv : the preprint server for biology · 2026Article
- Extreme conservation of cnidarian stinging cell identity despite 600 million years of evolution.bioRxiv : the preprint server for biology · 2026Article
- A 3D amphioxus brain atlas illuminates the blueprint of the ancestral chordate brain and highlights unique vertebrate innovations.Science advances · 2026Article
132 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison between distant relatives is hindered by complex gene histories and diversifications in expression programs. Previously, we introduced the self-assembling manifold (SAM) algorithm to robustly reconstruct manifolds from single-cell data (Tarashansky et al., 2019). Here, we build on SAM to map cell atlas manifolds across species. This new method, SAMap, identifies homologous cell types with shared expression programs across distant species within phyla, even in complex examples where homologous tissues emerge from distinct germ layers. SAMap also finds many genes with more similar expression to their paralogs than their orthologs, suggesting paralog substitution may be more common in evolution than previously appreciated. Lastly, comparing species across animal phyla, spanning sponge to mouse, reveals ancient contractile and stem cell families, which may have arisen early in animal 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.