ArticleCell reports. Medicine2024
scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network.
Article in Cell reports. Medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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
29 citing papers in PubMed.
- Integrative transcriptomic and experimental analysis identifies GREM1 as a pro-metastatic mediator in lung adenocarcinoma.Journal of translational medicine · 2026Article
- Myofibroblastic CAF and Malignant Ductal Cell Crosstalk Drives Epithelial-Mesenchymal Transition and Progression in Pancreatic Ductal Adenocarcinoma via THBS2-SDC/Integrin Axes.International journal of molecular sciences · 2026Article
- Integrating single-nucleus RNA sequencing and gene perturbation reveals regulatory networks of intramuscular fat deposition in bovine skeletal muscle.Animal bioscience · 2026Article
- scMagnifier: Resolving fine-grained cell subtypes via GRN-informed perturbations and consensus clustering.PLoS computational biology · 2026Article
- Cross-tissue atlas of mucosa-associated lymphoid tissue lymphomas reveals intratumoral heterogeneity and microenvironmental subtypes.Cell reports. Medicine · 2026Article
- Decoding drug-responsive cell subpopulations in triple-negative breast cancer using single-cell multiomics.iScience · 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
- Multi-lineage hepatic organoids reveal toxic exosome mediated indirect hepatotoxicity.Nature communications · 2026Article
- Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.Genome medicine · 2026Article
- SDMap: a comprehensive database of spatial drug perturbation maps.Nucleic acids research · 2026Article
- VASN Enhances IGF2BP3 Stability via USP10 Deubiquitination to Promote Triple-negative Breast Cancer Paclitaxel Resistance.International journal of biological sciences · 2026Article
- Personalized chronotherapy in glioblastoma: integrating circadian profiling and PK-PD modelling to optimize temozolomide timing.NPJ precision oncology · 2025Article
- Immunological dynamics in orthotopic compared with subcutaneous murine models of HPV-positive oropharyngeal cancer.Disease models & mechanisms · 2025Article
- Transfer Learning and Permutation-Invariance Improving Predicting Genome-Wide, Cell-Specific and Directional Interventions Effects of Complex Systems.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Identification of gene modules associated with B cell activation and tissue remodeling in primary Sjögren's syndrome.BMC immunology · 2025Article
- IgRENE: integrating gene regulatory networks and drug ontologies towards selected modification of target gene's expression.Briefings in bioinformatics · 2025Article
- Decoding meningioma prognosis with multi-omics: macrophage diversity, immune-CNV interplay, and novel SPP1-targeted strategies.Journal of neuro-oncology · 2025Article
- Mapping Macrophage Diversity in Coats' Disease: A Lipid-Associated Subset in the Pathogenesis of Exudative Retinopathy.Investigative ophthalmology & visual science · 2025Article
- Epigenetic synthetic lethality as a cancer therapeutic strategy: synergy of experimental and computational approaches.Epigenomics · 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
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cells respond divergently to drugs due to the heterogeneity among cell populations. Thus, it is crucial to identify drug-responsive cell populations in order to accurately elucidate the mechanism of drug action, which is still a great challenge. Here, we address this problem with scRank, which employs a target-perturbed gene regulatory network to rank drug-responsive cell populations via in silico drug perturbations using untreated single-cell transcriptomic data. We benchmark scRank on simulated and real datasets, which shows the superior performance of scRank over existing methods. When applied to medulloblastoma and major depressive disorder datasets, scRank identifies drug-responsive cell types that are consistent with the literature. Moreover, scRank accurately uncovers the macrophage subpopulation responsive to tanshinone IIA and its potential targets in myocardial infarction, with experimental validation. In conclusion, scRank enables the inference of drug-responsive cell types using untreated single-cell data, thus providing insights into the cellular-level impacts of therapeutic interventions.
Indexed as
Identifiers
What Socratic 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 Socratic graph.