Jonathan Y. Hsu

The paper introduces PERSIST-On, a CRISPR-based method for stable and tunable gene activation by recruiting endogenous transcription factors to target promoters.

MOSAIC enables high-throughput in situ saturation mutagenesis and CRISPR prime editing guide RNA optimization in human cells, identifying optimized pegRNAs and drug resistance variants.

PrimeDesign is a tool for designing prime editing guide RNAs, enabling single and combination edits, and it supports the creation of a database for over 68,500 pathogenic variants.

STREAM is an interactive pipeline for reconstructing and visualizing complex branching trajectories from single-cell transcriptomic and epigenomic data.

CRISPResso2 is a software tool for analyzing genome editing data, providing allele-specific quantification and scalable alignment to assess editing efficiency and safety.

CRISPR-SURF deconvolves CRISPR tiling screen data to identify functional regulatory elements across CRISPR-Cas, CRISPRi, and CRISPRa experiments.

BrainImageR associates gene sets with postmortem brain expression data to identify spatial and temporal associations in human brain development.

The paper challenges the claim that CRISPR-Cas9 induces off-target mutations by showing that the observed variants are likely pre-existing genetic differences between treated mice and the control.

This paper demonstrates CRISPR-Cpf1-based transcription factors for inducible and tunable regulation of human gene expression, enabling combinatorial gene activation.