ArticleNature communications2018
Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 221 papers, 2 of them syntheses that pooled it.
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Who cites it
221 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- Medical Treatment of Lung Cancer: Can Immune Cells Predict the Response? A Systematic Review.Frontiers in immunology · 2020Pooled it
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- Spatially resolved chromatin architectures in mammalian brain tissues.Nature methods · 2026Article
- Three dimensional reconstruction of the human nucleus accumbens reveals topographic organization and molecular heterogeneity of D1-islands across the anterior posterior axis.bioRxiv : the preprint server for biology · 2026Article
- A comparative single-cell transcriptomic atlas for diverse populations of vertebrate hair cells.bioRxiv : the preprint server for biology · 2026Article
- Developing mouse inhibitory neuron single-cell transcriptomes reveal distinct modes of cell-type diversification.Nature neuroscience · 2026Article
- The cellular and molecular basis of gyrus-sulcus specialization in the primate brain.Nature communications · 2026Article
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- An Integrated Multi-omics Single Cell Atlas of the Human RPE and Choroid.bioRxiv : the preprint server for biology · 2026Article
- A consensus atlas of human brain development defines cell type-specific maturation trajectories across the lifespan.bioRxiv : the preprint server for biology · 2026Article
- Single-nucleus transcriptomic atlas of postnatal camel liver development identifies candidate adaptive features.BMC genomics · 2026Article
- A single-cell atlas of alternative wing development in two hemipteran species.Nature communications · 2026Article
- Generation of human appetite-regulating neurons and tanycytes from pluripotent stem cells.Cell stem cell · 2026Article
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- Genomic sequence evolution underlying human neocortical interareal diversification.Genome biology · 2026Article
- IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches.bioRxiv : the preprint server for biology · 2026Article
161 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Single-cell RNA-sequencing (scRNA-seq) technology provides a new avenue to discover and characterize cell types; however, the experiment-specific technical biases and analytic variability inherent to current pipelines may undermine its replicability. Meta-analysis is further hampered by the use of ad hoc naming conventions. Here we demonstrate our replication framework, MetaNeighbor, that quantifies the degree to which cell types replicate across datasets, and enables rapid identification of clusters with high similarity. We first measure the replicability of neuronal identity, comparing results across eight technically and biologically diverse datasets to define best practices for more complex assessments. We then apply this to novel interneuron subtypes, finding that 24/45 subtypes have evidence of replication, which enables the identification of robust candidate marker genes. Across tasks we find that large sets of variably expressed genes can identify replicable cell types with high accuracy, suggesting a general route forward for large-scale evaluation of scRNA-seq data.
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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.