ArticleCell systems2022
Morphology and gene expression profiling provide complementary information for mapping cell state.
Article in Cell systems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
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Who cites it
95 citing papers in PubMed.
- High-content morphological profiling by Cell Painting in 3D spheroids.Nature communications · 2026Article
- Multimodal Artificial Intelligence in Lung Cancer: From Data Integration to Precision Oncology.Cancers · 2026Review
- Scalable, generalizable and uncertainty-aware integration of spatial multiomics across diverse modalities and platforms with SCIGMA.Nature genetics · 2026Article
- Cell Painting in activated cells illuminates phenotypic dark space and drug mechanisms of action.Nature communications · 2026Article
- Sphingolipid Metabolism Links Morphological Signatures to Immunomodulatory Potency in Human Mesenchymal Stromal Cells.Cellular and molecular bioengineering · 2026Article
- A generative framework for predicting cellular morphological and transcriptomic perturbation responses.Cell reports methods · 2026Article
- Integrating chemical structures as treatments improves representations of microscopy images for morphological profiling.PLoS computational biology · 2026Article
- Retrieval-Based Evaluation of Cell Painting Feature Spaces Reveals Differences in the Preservation of Biologically Meaningful Phenotypic Similarity.International journal of molecular sciences · 2026Article
- Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.Cell · 2026Article
- Advances in high-throughput drug screening based on pharmacotranscriptomics.Journal of advanced research · 2026Review
- Identifying and targeting abnormal mitochondrial localization associated with psychosis.bioRxiv : the preprint server for biology · 2026Article
- Scalable data harmonization for single-cell image-based profiling with CytoTable.Patterns (New York, N.Y.) · 2026Article
- AI and network biology for rational polypharmacology in signaling drug design: a review.NPJ precision oncology · 2026Review
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- Predicting DNA damage response using synthetic cell painting profiles and experimental analysis.iScience · 2026Article
- Article
- Harnessing AI to fuse phenotypic signatures for drug target identification: progress in computational modeling.Briefings in bioinformatics · 2026Review
- Integrating artificial intelligence across the cancer drug discovery pipeline using a design-test-refine workflow.Frontiers in oncology · 2026Review
- Multi-view deep learning of highly multiplexed imaging data improves association of cell states with clinical outcomes.Bioinformatics advances · 2026Article
- Toward trustworthy virtual cells: a roadmap for perturbation-resolved, context-aware, and experimentally validated cell models.Frontiers in cell and developmental biology · 2026Review
35 more citing papers are in PubMed but not listed here.
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20 authors.
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Abstract
Morphological and gene expression profiling can cost-effectively capture thousands of features in thousands of samples across perturbations by disease, mutation, or drug treatments, but it is unclear to what extent the two modalities capture overlapping versus complementary information. Here, using both the L1000 and Cell Painting assays to profile gene expression and cell morphology, respectively, we perturb human A549 lung cancer cells with 1,327 small molecules from the Drug Repurposing Hub across six doses, providing a data resource including dose-response data from both assays. The two assays capture both shared and complementary information for mapping cell state. Cell Painting profiles from compound perturbations are more reproducible and show more diversity but measure fewer distinct groups of features. Applying unsupervised and supervised methods to predict compound mechanisms of action (MOAs) and gene targets, we find that the two assays not only provide a partially shared but also a complementary view of drug mechanisms. Given the numerous applications of profiling in biology, our analyses provide guidance for planning experiments that profile cells for detecting distinct cell types, disease phenotypes, and response to chemical or genetic perturbations.
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