ArticleNature protocols2022
Pooled genetic perturbation screens with image-based phenotypes.
Article in Nature protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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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
47 citing papers in PubMed.
- De novo design of miniproteins targeting GPCRs.Nature · 2026Article
- A one-week automated genome-wide optical pooled screen using OttoSeq.Genome biology · 2026Article
- Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.Cell · 2026Article
- The one-week automated genome-wide optical pooled screen.bioRxiv : the preprint server for biology · 2026Article
- STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.PLoS computational biology · 2026Article
- Toward trustworthy virtual cells: a roadmap for perturbation-resolved, context-aware, and experimentally validated cell models.Frontiers in cell and developmental biology · 2026Review
- Physiologically Relevant 3D CRISPR Screening Enhances Mechanistic Insight into Chemical Toxicity Compared to 2D Screening.bioRxiv : the preprint server for biology · 2025Article
- Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy.PLoS computational biology · 2025Article
- STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.bioRxiv : the preprint server for biology · 2025Article
- Optical pooled screening for the discovery of regulators of the alternative lengthening of telomeres pathway.Methods (San Diego, Calif.) · 2025Article
- Pathogenic morphological signatures of perturbations in mitochondrial-related genes revealed by pooled imaging assay.Npj imaging · 2025Article
- Single-cell image-based screens identify host regulators of Ebola virus infection dynamics.Nature microbiology · 2025Article
- High-content image-based pooled screens reveal regulators of synaptogenesis.Cell reports · 2025Article
- CROPseq-multi: a universal solution for multiplexed perturbation in high-content pooled CRISPR screens.bioRxiv : the preprint server for biology · 2025Article
- MORPH Predicts the Single-Cell Outcome of Genetic Perturbations Across Conditions and Data Modalities.bioRxiv : the preprint server for biology · 2025Article
- Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.Nature biotechnology · 2025Article
- Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq.Nature methods · 2025Article
- Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap.Nature biotechnology · 2025Article
- Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens.Cell systems · 2025Article
- Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Discovery of the genetic components underpinning fundamental and disease-related processes is being rapidly accelerated by combining efficient, programmable genetic engineering with phenotypic readouts of high spatial, temporal and/or molecular resolution. Microscopy is a fundamental tool for studying cell biology, but its lack of high-throughput sequence readouts hinders integration in large-scale genetic screens. Optical pooled screens using in situ sequencing provide massively scalable integration of barcoded lentiviral libraries (e.g., CRISPR perturbation libraries) with high-content imaging assays, including dynamic processes in live cells. The protocol uses standard lentiviral vectors and molecular biology, providing single-cell resolution of phenotype and engineered genotype, scalability to millions of cells and accurate sequence reads sufficient to distinguish >10
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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.