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Evaluation of Gene Expression and Phenotypic Profiling Data as Quantitative Descriptors for Predicting Drug Targets and Mechanisms of Action

https://doi.org/10.1101/580654
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s12551-018-0490-8openalex-snapshot
Mining data and metadata from the gene expression omnibus
inferredcites →https://doi.org/10.1016/j.cell.2017.10.049openalex-snapshot
A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles
inferredcites →https://doi.org/10.1016/j.chembiol.2018.01.015openalex-snapshot
Repurposing High-Throughput Image Assays Enables Biological Activity Prediction for Drug Discovery
inferredcites →https://doi.org/10.1016/j.copbio.2016.04.003openalex-snapshot
Applications in image-based profiling of perturbations
inferredcites →https://doi.org/10.1021/acs.jcim.8b00670openalex-snapshot
Accurate Prediction of Biological Assays with High-Throughput Microscopy Images and Convolutional Networks
inferredcites →https://doi.org/10.1021/acs.molpharmaceut.6b00248openalex-snapshot
Deep Learning Applications for Predicting Pharmacological Properties of Drugs and Drug Repurposing Using Transcriptomic Data
inferredcites →https://doi.org/10.1021/tx4004038openalex-snapshot
Quantitative High Content Imaging of Cellular Adaptive Stress Response Pathways in Toxicity for Chemical Safety Assessment
inferredcites →https://doi.org/10.1038/nm.4306openalex-snapshot
The Drug Repurposing Hub: a next-generation drug library and information resource
inferredcites →https://doi.org/10.1038/nprot.2016.105openalex-snapshot
Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes
inferredcites →https://doi.org/10.1038/s41467-019-10154-8openalex-snapshot
Capturing single-cell heterogeneity via data fusion improves image-based profiling
inferredcites →https://doi.org/10.1093/bib/bbw112openalex-snapshot
A review of connectivity map and computational approaches in pharmacogenomics
inferredcites →https://doi.org/10.1093/gigascience/giw014openalex-snapshot
A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay
inferredcites →https://doi.org/10.1093/gigascience/giw015openalex-snapshot
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
inferredcites →https://doi.org/10.1093/nar/gku476openalex-snapshot
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures
inferredcites →https://doi.org/10.1126/science.1132939openalex-snapshot
The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease
inferredcites →https://doi.org/10.1177/1087057113503553openalex-snapshot
Comparison of Methods for Image-Based Profiling of Cellular Morphological Responses to Small-Molecule Treatment
inferredcites →https://doi.org/10.1177/2472555218818756openalex-snapshot
Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological Changes
inferredcites →https://doi.org/10.1177/2472555218820805openalex-snapshot
Evaluation of Machine Learning Classifiers to Predict Compound Mechanism of Action When Transferred across Distinct Cell Lines
inferredcites →https://doi.org/10.1186/gb-2006-7-10-r100openalex-snapshot
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
inferredcites →https://doi.org/10.1371/journal.pone.0080999openalex-snapshot
Multiplex Cytological Profiling Assay to Measure Diverse Cellular States
inferredcites →https://doi.org/10.18637/jss.v018.i05openalex-snapshot
Chemical Informatics Functionality in R

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Transcriptomics and cell painting analysis reveals molecular and morphological features associated with fed‐batch production performance in CHO recombinant clones
inferred← citeshttps://doi.org/10.1016/j.ailsci.2023.100060openalex-snapshot
Combining molecular and cell painting image data for mechanism of action prediction
inferred← citeshttps://doi.org/10.1016/j.cbpa.2021.04.001openalex-snapshot
Image-based cell phenotyping with deep learning
inferred← citeshttps://doi.org/10.1016/j.cels.2022.08.003openalex-snapshot
Virtual screening for small-molecule pathway regulators by image-profile matching
inferred← citeshttps://doi.org/10.1016/j.cels.2022.10.001openalex-snapshot
Morphology and gene expression profiling provide complementary information for mapping cell state
inferred← citeshttps://doi.org/10.1016/j.csbj.2024.07.012openalex-snapshot
Systematic data analysis pipeline for quantitative morphological cell phenotyping
inferred← citeshttps://doi.org/10.1016/j.slasd.2022.12.003openalex-snapshot
Using chemical and biological data to predict drug toxicity
inferred← citeshttps://doi.org/10.1016/j.taap.2022.116032openalex-snapshot
Combining phenotypic profiling and targeted RNA-Seq reveals linkages between transcriptional perturbations and chemical effects on cell morphology: Retinoic acid as an example
inferred← citeshttps://doi.org/10.1021/acs.chemrestox.0c00303openalex-snapshot
Comparison of Cellular Morphological Descriptors and Molecular Fingerprints for the Prediction of Cytotoxicity- and Proliferation-Related Assays
inferred← citeshttps://doi.org/10.1021/acs.chemrestox.2c00381openalex-snapshot
Assessment of Drug-Induced Liver Injury through Cell Morphology and Gene Expression Analysis
inferred← citeshttps://doi.org/10.1021/acs.chemrestox.4c00169openalex-snapshot
Cell Painting and Chemical Structure Read-Across Can Complement Each Other for Rat Acute Oral Toxicity Prediction in Chemical Early Derisking
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00864openalex-snapshot
Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01855openalex-snapshot
Compound Activity Prediction with Dose-Dependent Transcriptomic Profiles and Deep Learning
inferred← citeshttps://doi.org/10.1038/s41467-023-37570-1openalex-snapshot
Predicting compound activity from phenotypic profiles and chemical structures
inferred← citeshttps://doi.org/10.1038/s41540-024-00397-7openalex-snapshot
A comprehensive review of computational cell cycle models in guiding cancer treatment strategies
inferred← citeshttps://doi.org/10.1038/s41573-020-00117-wopenalex-snapshot
Image-based profiling for drug discovery: due for a machine-learning upgrade?
inferred← citeshttps://doi.org/10.1038/s41592-022-01667-0openalex-snapshot
High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations
inferred← citeshttps://doi.org/10.1038/s41592-024-02528-8openalex-snapshot
Cell Painting: a decade of discovery and innovation in cellular imaging
inferred← citeshttps://doi.org/10.1038/s41598-020-69354-8openalex-snapshot
Tales of 1,008 small molecules: phenomic profiling through live-cell imaging in a panel of reporter cell lines
inferred← citeshttps://doi.org/10.1038/s42003-022-03763-5openalex-snapshot
Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection
inferred← citeshttps://doi.org/10.1091/mbc.e23-08-0298openalex-snapshot
From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability
inferred← citeshttps://doi.org/10.1093/bib/bbae284openalex-snapshot
Morphological profiling for drug discovery in the era of deep learning
inferred← citeshttps://doi.org/10.1101/2022.08.11.503624openalex-snapshot
Merging Bioactivity Predictions from Cell Morphology and Chemical Fingerprint Models Using Similarity to Training Data
inferred← citeshttps://doi.org/10.1186/s13321-023-00723-xopenalex-snapshot
Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data
inferred← citeshttps://doi.org/10.14232/phd.11423openalex-snapshot
Application of deep learning algorithms to single-cell segmentation and phenotypic profiling
inferred← citeshttps://doi.org/10.26434/chemrxiv.12571241openalex-snapshot
Multitask Bioactivity Predictions Using Structural Chemical and Cell Morphology Information
inferred← citeshttps://doi.org/10.3389/fchem.2020.00296openalex-snapshot
Exploring the Use of Compound-Induced Transcriptomic Data Generated From Cell Lines to Predict Compound Activity Toward Molecular Targets
inferred← citeshttps://doi.org/10.3389/ftox.2024.1401036openalex-snapshot
Unleashing the potential of cell painting assays for compound activities and hazards prediction
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