ArticleNature methods2025
A genome-wide atlas of human cell morphology.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Nuclear mechanotransduction: tools for mechanical perturbation and chromatin characterization.Nucleus (Austin, Tex.) · 2026Review
- Testing the Transferability of Perturbational Similarity Maps Across Species, Cell Systems, and Assay Modalities.Neuroinformatics · 2026Article
- Development of a universal imaging "phenome" using shape, appearance and motion (SAM) features and the SAM Phenotype Observation Tool (SPOT).Nature communications · 2026Article
- Cell Painting in activated cells illuminates phenotypic dark space and drug mechanisms of action.Nature communications · 2026Article
- Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.Cell · 2026Article
- Causal effect estimation from trans-regulatory single-cell CRISPR screens.Cell genomics · 2026Review
- Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation.Nature biotechnology · 2026Article
- Genome-wide CRISPR interference screen identifies Clip2 as a novel regulator of osteocyte maturation and morphology.The Journal of biological chemistry · 2026Article
- Brieflow: an integrated computational pipeline for high-throughput analysis of optical pooled screening data.Nature communications · 2026Article
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.PLoS computational biology · 2026Article
- A microscopy-based CRISPR screening platform enables organellar functional genomics and illuminates ciliary biology.Developmental cell · 2026Article
- Deep learning-based in silico labeling for analyzing morphological features of MSCs to predict immunomodulatory capacity.Communications biology · 2026Article
- Bridging the variant-to-function gap in type 2 diabetes: advances and challenges.Diabetologia · 2026Review
- A pooled Cell Painting CRISPR screening platform enables de novo inference of gene function by self-supervised deep learning.Nature communications · 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
- SubCell: Proteome-aware vision foundation models for microscopy capture single-cell biology.bioRxiv : the preprint server for biology · 2025Article
- Integrated spatial morpho-transcriptomics predicts functional traits in pancreatic cancer.Science advances · 2025Article
- Computational prediction of mutagenicity through comprehensive cell painting analysis.Mutagenesis · 2025Article
- Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting.bioRxiv : the preprint server for biology · 2025Article
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22 authors.
Funding
Abstract
A key challenge of the modern genomics era is developing empirical data-driven representations of gene function. Here we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-wide genotype-phenotype maps comprising CRISPR-Cas9-based knockouts of >20,000 genes in >30 million cells. Our optical pooled cell profiling platform (PERISCOPE) combines a destainable high-dimensional phenotyping panel (based on Cell Painting) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries. This perturbation atlas comprises high-dimensional phenotypic profiles of individual cells with sufficient resolution to cluster thousands of human genes, reconstruct known pathways and protein-protein interaction networks, interrogate subcellular processes and identify culture media-specific responses. Using this atlas, we identify the poorly characterized disease-associated TMEM251/LYSET as a Golgi-resident transmembrane protein essential for mannose-6-phosphate-dependent trafficking of lysosomal enzymes. In sum, this perturbation atlas and screening platform represents a rich and accessible resource for connecting genes to cellular functions at scale.
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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.