ArticleNature genetics2025
Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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Who cites it
10 citing papers in PubMed.
- Systematic benchmarking and optimal strategy selection of cross-species integration methods.Briefings in bioinformatics · 2026Article
- Insights from integrative spatial transcriptomics in sepsis-associated acute kidney injury.Nature reviews. Nephrology · 2026Review
- ELF3 links kidney function GWAS loci to maladaptive epithelial inflammation.Science advances · 2026Article
- Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- Single-cell omics in tumor lymph node metastasis: mechanisms and therapeutic implications.Molecular cancer · 2026Review
- A Manifold-Based Measure of Transcriptional Entropy for Quantifying Aging in Single Cells.bioRxiv : the preprint server for biology · 2026Article
- An Ex Vivo Patient-Derived Tumor-Bearing Human Kidney Model Recapitulates Drug Toxicity and Metabolic Distribution.Research (Washington, D.C.) · 2026Article
- Design of precision therapeutics for a CKD risk allele by targeting Shroom3-Rock interaction.Nature communications · 2025Article
- Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas.Nature genetics · 2025Article
Corrections and comments
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Authors and funding
16 authors.
Funding
Abstract
The use of single-cell RNA sequencing in clinical and translational research is limited by the challenge of identifying cell-type-specific, targetable molecular changes in individual patients and cross-species differences. Here we created an integrated single-cell kidney atlas including over 1 million cells from 140 samples, defining more than 70 conserved cell states in human and rodent models. We developed CellSpectra, a computational tool that quantifies changes in gene expression coordination across cellular functions, which we applied to kidney and lung cancer data. This tool powers our patient-level single-cell functional profiling report, which highlights cell-type-specific changes in the coordination of pathway gene expression in individuals. Our cross-species atlas facilitates the selection of a rodent model that closely reflects the cellular and pathway-level signatures observed in patient samples, advancing the application of single-cell methodologies in clinical precision medicine. Finally, using experimental models, we demonstrate how our informatics approach can be applied for the potential selection of suitable therapeutics.
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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.