J. Keith Joung

The paper identifies HECTD4 as a tumor and metastasis suppressor that targets COX-2 for degradation, with COX-2 stabilization driving pro-tumorigenic effects in breast cancer.

This study shows that gene editing of HSCs without ex vivo culture reduces genotoxicity while maintaining therapeutic efficacy for beta-hemoglobinopathy treatment.

This study identifies pegRNA misfolding as a factor limiting CRISPR prime editing efficiency and shows refolding and point mutations can significantly improve it in zebrafish embryos.

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.

The paper uses high-resolution CTCF MNase HiChIP data to analyze chromatin loop structures and introduces FactorFinder, finding that fully extruded CTCF-CTCF loops are rare and that chromatin state affects cohesin extrusion dynamics.

This paper designs synthetic gene regulatory programs for human cells that can be controlled by FDA-approved drugs and demonstrate therapeutic applications in immune cells.

ONE-seq identifies population-specific off-target effects of CRISPR gene editors using global human genome sequence diversity.

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.

This paper optimizes AsCas12a for combinatorial genetic screens in human cells by improving on-target and off-target activity and enabling higher-order multiplexing.

This study shows that disrupting the kringle 1 domain of prothrombin in zebrafish causes late-onset mortality due to impaired clot formation, revealing its role in thrombin biosynthesis and activation.

The paper describes SECURE-ABE and -CBE base editors with reduced RNA off-target activities and improved DNA editing precision.

This study shows that zebrafish dscaml1 is crucial for retinal patterning and oculomotor circuit function, with mutations causing deficits in gaze stabilization and saccade fatigue similar to human ocular motor apraxia.

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.

The paper introduces VIVO, a method to detect off-target mutations from in vivo CRISPR-Cas editing, showing that well-designed gRNAs can edit efficiently without detectable off-targets.

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 evaluates CRISPR-Cas9 base editors to minimize bystander and off-target mutations while improving precision in C-to-T DNA editing.

This study demonstrates allele-specific CRISPR/Cas9 editing of the P23H mutation in Rho-P23H mice, reducing mutant allele expression and delaying photoreceptor degeneration.

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