ArticleGenome biology2024
Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- A high-throughput co-culture CRISPR array for rapid fitness hypothesis testing and growth engineering in CHO cells.iScience · 2026Article
- Integration of cell-specific gene expression and chromatin accessibility facilitates localization of neurodegenerative risk in microglia.bioRxiv : the preprint server for biology · 2026Article
- Canon enables causal inference of downstream genes in single-cell CRISPR studies via instrumental variable analysis.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Dual-line Genome-scale CRISPR Screening Enables Robust Target Gene Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Region-Level Design and Analysis of CRISPR Perturbation Screens with FRACTEL.bioRxiv : the preprint server for biology · 2026Article
- Causal effect estimation from trans-regulatory single-cell CRISPR screens.Cell genomics · 2026Review
- Targeted single-cell RNA and perturbation sequencing with TAP-seq.Nature protocols · 2026Review
- PerturbPlan: An analytical framework for designing Perturb-seq experiments.bioRxiv : the preprint server for biology · 2026Article
- Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells.bioRxiv : the preprint server for biology · 2026Article
- AI-driven CRISPR screening: optimizing gene editing through automation and intelligent decision support.Journal of translational medicine · 2026Review
- Predicting the unseen: A diffusion-based debiasing framework for transcriptional response prediction at single-cell resolution.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Interrogating the Regulatory Function of HAQERs during Human Cortical Development.bioRxiv : the preprint server for biology · 2025Article
- Genetic drivers of Chinese hamster ovary cell proliferation revealed by functional genomics.iScience · 2025Article
- Large-scale discovery of neural enhancers for cis-regulation therapies.bioRxiv : the preprint server for biology · 2025Article
- GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density.Genome biology · 2025Article
- Predicting the unseen: a diffusion-based debiasing framework for transcriptional response prediction at single-cell resolution.bioRxiv : the preprint server for biology · 2025Article
- Enhancer-targeting CRISPR screens at coronary artery disease loci suggest shared mechanisms of disease risk.medRxiv : the preprint server for health sciences · 2025Article
- Simultaneous inference for generalized linear models with unmeasured confounders.Journal of the American Statistical Association · 2025Article
- GWAS-Informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density.bioRxiv : the preprint server for biology · 2024Article
- A scalable, high-throughput neural development platform identifies shared impact of ASD genes on cell fate and differentiation.bioRxiv : the preprint server for biology · 2024Article
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4 authors.
Funding
Abstract
Single-cell CRISPR screens (perturb-seq) link genetic perturbations to phenotypic changes in individual cells. The most fundamental task in perturb-seq analysis is to test for association between a perturbation and a count outcome, such as gene expression. We conduct the first-ever comprehensive benchmarking study of association testing methods for low multiplicity-of-infection (MOI) perturb-seq data, finding that existing methods produce excess false positives. We conduct an extensive empirical investigation of the data, identifying three core analysis challenges: sparsity, confounding, and model misspecification. Finally, we develop an association testing method - SCEPTRE low-MOI - that resolves these analysis challenges and demonstrates improved calibration and power.
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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.