ArticleNature cell biology2025
Decoding heterogeneous single-cell perturbation responses.
Article in Nature cell biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- Buffering of gene dosage response curves for human complex traits.Cell genomics · 2026Article
- Causal effect estimation from trans-regulatory single-cell CRISPR screens.Cell genomics · 2026Review
- Brieflow: an integrated computational pipeline for high-throughput analysis of optical pooled screening data.Nature communications · 2026Article
- CAPTAIN: a multimodal foundation model pretrained on co-assayed single-cell RNA and protein.Nature communications · 2026Article
- Interpretation, extrapolation and perturbation of single cells.Nature reviews. Genetics · 2026Review
- pertTF: context-aware AI modeling for genome-scale and cross-system perturbation prediction.bioRxiv : the preprint server for biology · 2026Article
- Strategies to control cellular spatial organization in microphysiological systems.Microsystems & nanoengineering · 2026Review
- MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation prediction.PLoS computational biology · 2026Article
- Therapeutic target database 2026: facilitating targeted therapies and precision medicine.Nucleic acids research · 2026Article
- A stem cell knockout village reveals lineage rewiring and a non-canonical islet cell fate in monogenic diabetes.bioRxiv : the preprint server for biology · 2025Article
- Decoding cell fate: integrated experimental and computational analysis at the single-cell level.Bioinformatics (Oxford, England) · 2025Review
- Fluctuation structure predicts genome-wide perturbation outcomes.Research square · 2025Article
- Fluctuation structure predicts genome-wide perturbation outcomes.bioRxiv : the preprint server for biology · 2025Article
- Integrated machine learning and single-cell RNA sequencing reveal COL4A2 and CXCL6 as oxidative stress-associated biomarkers in periodontitis.Frontiers in immunology · 2025Article
- Unraveling the future of genomics: CRISPR, single-cell omics, and the applications in cancer and immunology.Frontiers in genome editing · 2025Review
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24 authors.
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Abstract
Understanding how cells respond differently to perturbation is crucial in cell biology, but existing methods often fail to accurately quantify and interpret heterogeneous single-cell responses. Here we introduce the perturbation-response score (PS), a method to quantify diverse perturbation responses at a single-cell level. Applied to single-cell perturbation datasets such as Perturb-seq, PS outperforms existing methods in quantifying partial gene perturbations. PS further enables single-cell dosage analysis without needing to titrate perturbations, and identifies 'buffered' and 'sensitive' response patterns of essential genes, depending on whether their moderate perturbations lead to strong downstream effects. PS reveals differential cellular responses on perturbing key genes in contexts such as T cell stimulation, latent HIV-1 expression and pancreatic differentiation. Notably, we identified a previously unknown role for the coiled-coil domain containing 6 (CCDC6) in regulating liver and pancreatic cell fate decisions. PS provides a powerful method for dose-to-function analysis, offering deeper insights from single-cell perturbation 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.