David R. Liu

This study identifies genomic subtypes and immune features of mucosal melanoma, linking CD163+ macrophages to immune resistance and suggesting TIM-3 blockade as a therapeutic target.

The paper introduces SCRIBBLE, a lineage tracing tool that enables high-resolution, multigenerational lineage tracking in embryonic mouse retina.

This study demonstrates in vivo gene therapy for hemoglobinopathies using EPOR editing to enhance the expansion of gene-corrected erythroid cells without drug selection.

This paper develops a virus-like particle-based system for CRISPR gene editing and screening in primary human myeloid cells, identifying TNFAIP3 as a key regulator of inflammatory polarization.

ESCAPE identifies covalent ligand-protein interactions by using prime editing to disrupt cysteine residues and assesses their impact on cellular phenotypes.

This paper demonstrates a method using CD117-blocking antibody and epitope-engineered HSPCs to treat β-thalassemia without myeloablative conditioning.

This paper designs a protein family that binds and senses small molecules using deep learning and physics-based methods, achieving nanomolar sensitivity for cortisol.

OptiPrime predicts prime editing outcomes with high accuracy, enabling efficient therapeutic applications in human and mouse cells.

The paper introduces two ultrasmall chemogenetic tags, mgTag and cTag, which enable group-transfer reactions to append moieties to proteins, demonstrating their utility in cell signaling and proximity induction.

The paper evaluates base editing efficiency for USH2A mutations using in vitro screening and a mouse model, showing high correction rates and comparing methods.

The paper uses CRISPR editing and multimodal single-cell sequencing to identify the functional effects of disease variants in primary human cells.

This study evaluates the functional impact of genetic variants using a high-throughput prime editing sensor strategy, identifying both known and novel TP53 variants with diverse effects on p53 function.

The paper uses base editor screens to assess phosphorylation site functionality in T cell activation, identifying novel sites that modulate transcriptional activity and signaling pathways.

The paper uses base editing to assess the functional impact of cysteine mutations in cancer dependency genes, identifying essential and ligandable cysteines for drug development.

This study demonstrates the use of protecting oligos to enhance crRNA stability and potency for in vivo genome editing via AAV co-delivery in mice.

This paper demonstrates nonviral base editing of a KCNJ13 mutation in a mouse model of retinal degeneration, preserving vision through functional rescue of Kir7.1 channels.

The paper evaluates CRISPR base editors for correcting a KCNJ13 mutation causing LCA16, finding high on-target efficiency but negligible channel function due to bystander edits and mRNA structural issues.

The paper identifies causal genetic variants in autoimmune diseases by combining allele-specific reporter assays with chromatin accessibility data, showing their impact on gene expression and T cell function.

This paper introduces twin prime editing (twinPE) and its combination with site-specific recombinases to enable precise DNA deletion, replacement, integration, and inversion in human cells without double-strand breaks.

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

This paper compares CRISPR-mediated HDR and PE2 systems in mice to show PE2's higher fidelity in editing a TFBS, leading to more effective tissue-specific gene inactivation.

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 uses CRISPR-Cas9 base editors in pooled screens to assess the functional impact of human variants, identifying loss-of-function mutations and drug sensitivity/resistance mutations.

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