ArticleNature biotechnology2021
Quantifying the effect of experimental perturbations at single-cell resolution.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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Who cites it
125 citing papers in PubMed.
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- A targeted vector for brain endothelial cell gene delivery and cerebrovascular malformation modelling.Nature biomedical engineering · 2026Article
- Gut microbiome modulation by Veillonella ratti induces resistance to EAE pathogenesis via microbe-derived metabolites.Experimental & molecular medicine · 2026Article
- A progeria syndrome links DNA hypermethylation to age-related pathology.Nature genetics · 2026Article
- Autoinhibitory feedback preserves intestinal stem cell maintenance and fate commitment.The EMBO journal · 2026Article
- Article
- APOE4 Drives Uniquely Dysfunctional Human Microglial States in Alzheimer's Disease.bioRxiv : the preprint server for biology · 2026Article
- SOFisher: reinforcement learning-guided experiment designs for spatial omics.Nature communications · 2026Article
- scArchon: a scalable benchmarking framework for assessing single-cell perturbation models.Genome biology · 2026Article
- Interpretation, extrapolation and perturbation of single cells.Nature reviews. Genetics · 2026Review
- In Silico Perturbation Identifies Transcription Factors as Protective Targets in HSPCs After Irradiation.International journal of molecular sciences · 2026Article
- Characterizing gene perturbations in single cells via network divergence analysis.Nature communications · 2026Article
- Single-cell analysis of the human immune system reveals sex-specific dynamics of immunosenescence.Nature aging · 2026Article
- Decoding myeloid heterogeneity in glioblastoma: spatial insights from transcriptomics.Journal of translational medicine · 2026Review
- Single-cell transcriptional changes of artemisinin-sensitive K13Frontiers in cellular and infection microbiology · 2026Article
- Skin-derived myeloid precursors and joint-resident fibroblasts spread psoriatic disease from skin to joints.Nature immunology · 2026Article
- Programmable pH-responsive DNA inter-strand matching (PRISM) for precision molecular band-pass actuation.Theranostics · 2026Article
- Interpretable Differential Abundance Signature (iDAS).Small methods · 2026Article
- VIP-OT: Dissecting Single-Cell Biochemical State Dynamics under Perturbation via Vibrational Painting and Optimal Transport.bioRxiv : the preprint server for biology · 2025Article
- Haruka Resolves Perturbation Response Heterogeneity in Spatial Cell Niches.bioRxiv : the preprint server for biology · 2025Article
65 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
10 authors.
Funding
Abstract
Current methods for comparing single-cell RNA sequencing datasets collected in multiple conditions focus on discrete regions of the transcriptional state space, such as clusters of cells. Here we quantify the effects of perturbations at the single-cell level using a continuous measure of the effect of a perturbation across the transcriptomic space. We describe this space as a manifold and develop a relative likelihood estimate of observing each cell in each of the experimental conditions using graph signal processing. This likelihood estimate can be used to identify cell populations specifically affected by a perturbation. We also develop vertex frequency clustering to extract populations of affected cells at the level of granularity that matches the perturbation response. The accuracy of our algorithm at identifying clusters of cells that are enriched or depleted in each condition is, on average, 57% higher than the next-best-performing algorithm tested. Gene signatures derived from these clusters are more accurate than those of six alternative algorithms in ground truth comparisons.
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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.