@article {Park2021-rd,
	title = {CoCoA-diff: counterfactual inference for single-cell gene expression analysis},
	journal = {Genome Biol.},
	volume = {22},
	number = {1},
	year = {2021},
	pages = {1{\textendash}23},
	publisher = {BioMed Central},
	abstract = {Finding a causal gene is a fundamental problem in genomic medicine. We present a causal inference framework, CoCoA-diff, that prioritizes disease genes by adjusting confounders without prior knowledge of control variables in single-cell RNA-seq data. We demonstrate that our method substantially improves statistical power in simulations and real-world data analysis of 70k brain cells collected for dissecting Alzheimer{\textquoteright}s disease. We identify 215 differentially regulated causal genes in various cell types, including highly relevant genes with a proper cell type context. Genes found in different types enrich distinctive pathways, implicating the importance of cell types in understanding multifaceted disease mechanisms.},
	author = {Park, Yongjin P and Kellis, Manolis}
}
