ArticleScience (New York, N.Y.)2020
Massively multiplex chemical transcriptomics at single-cell resolution.
Article in Science (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 220 papers.
What it found
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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.
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Who cites it
220 citing papers in PubMed, 389 citations in OpenAlex.
- Latent causal diffusions for single-cell perturbation modeling.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- TechBio 3.0 closes the drug discovery loop with multimodal AI and generative chemistry.npj drug discovery · 2026Review
- Dynamic graph prior-guided latent adaptation for generalizable single-cell perturbation response prediction.Bioinformatics (Oxford, England) · 2026Article
- Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments.Genome research · 2026Article
- Review
- Single-cell mapping of homocysteine-induced perturbations in avian embryogenesis using LMO and BD rhapsody transcriptomics.iScience · 2026Article
- Learning chemical-induced gene expression perturbations with WAVE.Nature communications · 2026Article
- Single-cell RNA profiling suggests goflikicept-mediated immune modulation in idiopathic recurrent pericarditis.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Article
- GEM-GPT Enables Personalized Cell Type-Resolved Therapeutic Design for Systems Pharmacology.bioRxiv : the preprint server for biology · 2026Article
- A systematic comparison of single-cell perturbation response prediction models.Science advances · 2026Article
- PHAROS: turning single-cell perturbation models into target-directed drug-combination screens.bioRxiv : the preprint server for biology · 2026Article
- Multiplexed single cell transcriptomics optimizes mesodermal patterning and hemogenic endothelial output from murine embryonic stem cells.Research square · 2026Article
- Alpha protein kinase 3 gene therapy restores heart function in mouse and human models of cardiomyopathy.Nature cardiovascular research · 2026Article
- Virtual cells: progress and challenges from mechanistic modeling to data-driven integration.Briefings in bioinformatics · 2026Review
- CFM-GP: unified conditional flow matching to learn gene perturbation across cell types.NAR genomics and bioinformatics · 2026Article
- DECANT: decoupling mechanism from context in single-cell drug perturbation representation.Bioinformatics (Oxford, England) · 2026Article
- Data-centric feedback loops for next-generation immunotherapy development.Nature biomedical engineering · 2026Review
- Pre-Existing Heterogeneity Predicts Rare Proteostasis-Stress Programs Across Diverse Perturbations.Biology · 2026Article
- Article
- Synthesizing Mechanistic Hypotheses from Single-Cell Omics via Discretized Feature Attribution and Empirical Language Model Grounding.bioRxiv : the preprint server for biology · 2026Article
160 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
14 authors at 4 institutions in 1 country.
Funding
Abstract
High-throughput chemical screens typically use coarse assays such as cell survival, limiting what can be learned about mechanisms of action, off-target effects, and heterogeneous responses. Here, we introduce "sci-Plex," which uses "nuclear hashing" to quantify global transcriptional responses to thousands of independent perturbations at single-cell resolution. As a proof of concept, we applied sci-Plex to screen three cancer cell lines exposed to 188 compounds. In total, we profiled ~650,000 single-cell transcriptomes across ~5000 independent samples in one experiment. Our results reveal substantial intercellular heterogeneity in response to specific compounds, commonalities in response to families of compounds, and insight into differential properties within families. In particular, our results with histone deacetylase inhibitors support the view that chromatin acts as an important reservoir of acetate in cancer cells.
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Identifiers
What 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.