ArticleNature2025
The Human Cell Atlas from a cell census to a unified foundation model.
Article in Nature, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
87 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A multiscale growth atlas of Arabidopsis: linking cell dynamics to organ development.The New phytologist · 2026Pooled it
- Genetic and genomic insights into male reproductive tract development.Fertility and sterility · 2025Pooled it
- B-Cell Aware Analysis of Single-Cell Transcriptomics Data.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Reclaiming Anatomy as Method: From Morphological Reasoning to Clinical Relevance.Clinical anatomy (New York, N.Y.) · 2026Review
- Fast, flexible analysis of differences in cellular composition with crumblr.Nature communications · 2026Article
- A systematic comparison of single-cell perturbation response prediction models.Science advances · 2026Article
- scDiagnostics: systematic assessment of cell type annotation in single-cell transcriptomics data.Briefings in bioinformatics · 2026Article
- Donor-specific, but not sex-specific, signatures dominate cell-type classification in lung scRNA-seq data.Biochemistry and biophysics reports · 2026Article
- scProtoTransformer: Scalable reference mapping across molecules, cells, and donors.Science advances · 2026Article
- Increasing usable reads in RNA-seq protocols.iScience · 2026Article
- Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data.Nature biotechnology · 2026Article
- Are different populations fairly represented in single-cell omic atlases?Cell genomics · 2026Review
- Using Disease-Agnostic Genomic Liquid Biopsy in Complex Diagnoses: Real-Life Example of cfChIP-Seq in a Fever of Unknown Origin.JCO precision oncology · 2026Article
- Epigenetics in lung cancer precision medicine: from bench to bedside-a narrative review.Translational lung cancer research · 2026Review
- cellGeometry: ultra-fast single-cell deconvolution of bulk RNA-Seq using a geometric solution.Nature communications · 2026Article
- Human genetics across levels of biological organization.Nature reviews. Genetics · 2026Review
- Decoding neuronal gene expression: integrative insights from omics and AI.Brain informatics · 2026Review
- NERINE reveals rare variant associations in gene networks across phenotypes and implicates an SNCA-PRL-LRRK2 subnetwork in Parkinson's disease.Cell genomics · 2026Article
- Myocardial Immune Niches in Homeostasis and Inflammation.Immunological reviews · 2026Review
- Evaluating the learnability of single-cell large language models on multiple tasks.BMC genomics · 2026Article
27 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the convergence of notable advances in molecular and spatial profiling methods and new computational approaches taking advantage of artificial intelligence and machine learning, the construction of cell atlases is progressing from data collection to atlas integration and beyond. Here, we explore five ways in which cell atlases, including the Human Cell Atlas, are already revealing valuable biological insights, and how they are poised to provide even greater benefits in the coming years. In particular, we discuss cell atlases as censuses of cells; as 3D maps of cells in the body, across modalities and scales; as maps connecting genotype causes to phenotype effects; as 4D maps of development; and, ultimately, as foundation models of biology unifying all of these aspects and helping to transform medicine.
Indexed as
Identifiers
39566552What 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.