ArticleNucleic acids research2018
Systematic exploration of cell morphological phenotypes associated with a transcriptomic query.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
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Who cites it
44 citing papers in PubMed, 1 synthesis or guideline pooled it, 70 citations in OpenAlex.
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- Maximum Matching Accuracy: An Instance Segmentation Evaluation Metric Utilizing Globally Optimal Matching.ArXiv · 2026Article
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- Deep-DPC: Deep learning-assisted label-free temporal imaging discovery of anti-fibrotic compounds by controlling cell morphology.Journal of advanced research · 2025Article
- Joint profiling of cell morphology and gene expression during in vitro neurodevelopment.eLife · 2025Article
- Smaller scale, same impact: replicating high-throughput phenotypic profiling in a medium-throughput lab for use in chemical risk assessment.Archives of toxicology · 2025Article
- Prediction of cellular morphology changes under perturbations with a transcriptome-guided diffusion model.Nature communications · 2025Article
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- Cell Painting: a decade of discovery and innovation in cellular imaging.Nature methods · 2025Review
- Systematic data analysis pipeline for quantitative morphological cell phenotyping.Computational and structural biotechnology journal · 2024Review
- High-Throughput Transcriptomics Screen of ToxCast Chemicals in U-2 OS Cells.Toxicology and applied pharmacology · 2024Article
- Cell identity revealed by precise cell cycle state mapping links data modalities.bioRxiv : the preprint server for biology · 2024Article
- Evaluating batch correction methods for image-based cell profiling.Nature communications · 2024Article
- A Decade in a Systematic Review: The Evolution and Impact of Cell Painting.bioRxiv : the preprint server for biology · 2024Article
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- The Genomic Intersection of Oligodendrocyte Dynamics in Schizophrenia and Aging Unravels Novel Pathological Mechanisms and Therapeutic Potentials.International journal of molecular sciences · 2024Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
Abstract
Cell morphological phenotypes, including shape, size, intensity, and texture of cellular compartments have been shown to change in response to perturbation with small molecule compounds. Image-based cell profiling or cell morphological profiling has been used to associate changes of cell morphological features with alterations in cellular function and to infer molecular mechanisms of action. Recently, the Library of Integrated Network-based Cellular Signatures (LINCS) Project has measured gene expression and performed image-based cell profiling on cell lines treated with 9515 unique compounds. These data provide an opportunity to study the interdependence between transcription and cell morphology. Previous methods to investigate cell phenotypes have focused on targeting candidate genes as components of known pathways, RNAi morphological profiling, and cataloging morphological defects; however, these methods do not provide an explicit model to link transcriptomic changes with corresponding alterations in morphology. To address this, we propose a cell morphology enrichment analysis to assess the association between transcriptomic alterations and changes in cell morphology. Additionally, for a new transcriptomic query, our approach can be used to predict associated changes in cellular morphology. We demonstrate the utility of our method by applying it to cell morphological changes in a human bone osteosarcoma cell line.
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Registered trials
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