ArticleCell2022
Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq.
Article in Cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 446 papers.
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Who cites it
446 citing papers in PubMed, 598 citations in OpenAlex.
- Single-cell Transcriptomics in Autoimmune Diseases: Mechanistic Insights, Cross-disease Convergence, and Translational Challenges in Rheumatoid Arthritis, Systemic Lupus Erythematosus, Type 1 Diabetes, and Multiple Sclerosis.Clinical reviews in allergy & immunology · 2026Review
- Latent causal diffusions for single-cell perturbation modeling.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Testing the Transferability of Perturbational Similarity Maps Across Species, Cell Systems, and Assay Modalities.Neuroinformatics · 2026Article
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- Deep learning perturbation models can outperform baselines on calibrated metrics.Nature biotechnology · 2026Article
- Pop-Corn: Predicting Perturbation Phenotype Effects Across Single-Cell and Spatial Contexts.bioRxiv : the preprint server for biology · 2026Article
- Review
- An atlas of transcription factor cooperation reveals how motif readers shape regulatory output.bioRxiv : the preprint server for biology · 2026Article
- Integration of cell-specific gene expression and chromatin accessibility facilitates localization of neurodegenerative risk in microglia.bioRxiv : the preprint server for biology · 2026Article
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- A stress-adaptive lipid kinase axis defines metabolic vulnerabilities in neuroendocrine prostate cancer.Cancer cell · 2026Article
- A systematic comparison of single-cell perturbation response prediction models.Science advances · 2026Article
- A transcription factor regulatory atlas for activity inference and perturbation prediction.Nucleic acids research · 2026Article
- Systematic CRISPRi perturbation of 1,408 autism risk genes maps multilevel transcriptional convergence in human cortical neurons.bioRxiv : the preprint server for biology · 2026Article
- Evolving conservation: The role of unconventional approaches to restore contemporary vertebrate populations and genomic biodiversity.The Journal of heredity · 2026Review
- Characterizing and mitigating cross-library PCR chimeras in Perturb-seq using Perturb-Audit.Blood science (Baltimore, Md.) · 2026Article
- A systematic assessment of single-cell language model configurations.NAR genomics and bioinformatics · 2026Article
- Benchmarking methods for inferring single-cell transcription factor activity using large-scale perturbation sequencing data.Briefings in bioinformatics · 2026Article
- From Cluster to Claim: Calibrating Interpretation in Single-Cell Transcriptomics.Advanced genetics (Hoboken, N.J.) · 2026Article
386 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors at 6 institutions in 1 country.
Funding
Abstract
A central goal of genetics is to define the relationships between genotypes and phenotypes. High-content phenotypic screens such as Perturb-seq (CRISPR-based screens with single-cell RNA-sequencing readouts) enable massively parallel functional genomic mapping but, to date, have been used at limited scales. Here, we perform genome-scale Perturb-seq targeting all expressed genes with CRISPR interference (CRISPRi) across >2.5 million human cells. We use transcriptional phenotypes to predict the function of poorly characterized genes, uncovering new regulators of ribosome biogenesis (including CCDC86, ZNF236, and SPATA5L1), transcription (C7orf26), and mitochondrial respiration (TMEM242). In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena-from RNA processing to differentiation. We leverage this ability to systematically identify genetic drivers and consequences of aneuploidy and to discover an unanticipated layer of stress-specific regulation of the mitochondrial genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait of gene and cellular function.
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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.