ReviewNature methods2025
Considerations for building and using integrated single-cell atlases.
Review in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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The trial behind it
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
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Deep representation learning for temporal inference in cancer omics: a systematic literature review.Briefings in bioinformatics · 2026Pooled it
- Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments.Genome research · 2026Article
- Predictive control of human pancreatic cell fate using a digital model ofbioRxiv : the preprint server for biology · 2026Article
- Article
- Are different populations fairly represented in single-cell omic atlases?Cell genomics · 2026Review
- Unleashing innovative cross-organ fibrosis therapies by harnessing the omics revolution.JCI insight · 2026Review
- Are Different Populations Fairly Represented in Single-Cell Omic Atlases?bioRxiv : the preprint server for biology · 2026Article
- Epigenetic biomarkers in inflammatory bowel diseases-computational challenges and opportunities.Journal of Crohn's & colitis · 2026Review
- Review
- Defining the role of natural killer cells in acute myeloid leukemia through the lens of single-cell omics.Frontiers in immunology · 2026Review
- A comparative review of single-cell atlases: mapping cellular diversity across species and tissues.Cellular and molecular life sciences : CMLS · 2025Review
- Decoding cell fate: integrated experimental and computational analysis at the single-cell level.Bioinformatics (Oxford, England) · 2025Review
- Integrating single-cell RNA-seq datasets with substantial batch effects.BMC genomics · 2025Article
- Insights, opportunities, and challenges provided by large cell atlases.Genome biology · 2025Review
- Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments.bioRxiv : the preprint server for biology · 2025Article
- Galaxy single-cell & spatial omics community update: Navigating new frontiers in 2025.Cell genomics · 2025Review
- Biology-driven insights into the power of single-cell foundation models.Genome biology · 2025Article
- Integrated single-cell atlas of human atherosclerotic plaques.Nature communications · 2025Article
- Design specifications for biomedical virtual twins in engineered adoptive cellular immunotherapies.NPJ digital medicine · 2025Review
- Exploring the untapped potential of single-cell and spatial omics in plant biology.The New phytologist · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rapid adoption of single-cell technologies has created an opportunity to build single-cell 'atlases' integrating diverse datasets across many laboratories. Such atlases can serve as a reference for analyzing and interpreting current and future data. However, it has become apparent that atlasing approaches differ, and the impact of these differences are often unclear. Here we review the current atlasing literature and present considerations for building and using atlases. Importantly, we find that no one-size-fits-all protocol for atlas building exists, but rather we discuss context-specific considerations and workflows, including atlas conceptualization, data collection, curation and integration, atlas evaluation and atlas sharing. We further highlight the benefits of integrated atlases for analyses of new datasets and deriving biological insights beyond what is possible from individual datasets. Our overview of current practices and associated recommendations will improve the quality of atlases to come, facilitating the shift to a unified, reference-based understanding of single-cell biology.
Indexed as
Identifiers
39672979What OpenQuestion holds
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.