Shiqi Xie

This paper improves Perturb-seq by analyzing guide multiplets, reducing costs and maintaining signal recovery.

This paper develops inducible CRISPR/Cas9 systems with improved dynamic range and reduced off-target effects for precise gene perturbation.

Epiregulon infers single-cell TF activity using ATAC-seq and RNA-seq to predict drug response and identify drivers of cell state.

The paper uses single-cell CRISPRi screens to show variant-associated enhancers regulate cancer genes in breast cancer, revealing network motifs and subtype-specific functions.

The paper identifies regulators of inflammatory macrophage states and shows that TNF mRNA m6A modification controls its stability and contributes to disease.

The paper identifies enhancers linked to congenital heart defects that, when repressed, impair human cardiomyocyte differentiation.

The paper develops Reprogram-Seq to screen TF cocktails for reprogramming cell states, identifying a 3-TF combination that reprograms MEFs to epicardial-like cells.

The paper identifies SUOX as a vitiligo-associated gene by integrating GWAS data with tissue-specific gene expression prediction and experimental validation of an enhancer.

The paper identifies frequent recombination between sgRNA and barcode in single-cell CRISPR assays, reducing signal-to-noise ratio and suggesting improved methods.