David S. Lee

The paper introduces OPTIMuS PRIME-Del, a CRISPR-based method for multiplexed, precise deletion of cis-regulatory elements, validated through molecular tagging and scRNA-seq analysis.

Conditioning RFdiffusion on edge beta-strand pairing yields specific binders to polar targets, with in silico success above 9.2% versus 0.98% for hotspot-only conditioning.

This study identifies lesion-remote astrocytes (LRAs) that drive microglia-mediated white matter repair after spinal cord injury through Ccn1-dependent mechanisms.

This paper designs synthetic insulin receptor agonists that modulate receptor conformation and signaling, showing improved potency and activity in disease mutants.

The paper develops a method to discover new effector handles for proteome editing by combining de novo protein design with multiplex screening, identifying handles for degradation and stabilization of target proteins.

The paper designs de novo proteins called NeoNectins that specifically bind integrin α5β1, enhancing cell attachment and tissue integration in biomaterials.

The paper designs TrkA agonists that activate neuronal differentiation and neurite outgrowth without triggering pain-related gene expression.

This paper introduces Genome-Shuffle-seq, a method for generating and mapping structural variants in mammalian genomes, and demonstrates its application in mouse embryonic stem cells.

This paper introduces SNIPR, a synthetic receptor that responds to soluble ligands, enabling targeted CAR T-cell therapy and synthetic cell signaling.

This paper designs high-affinity proteins that bind to convex protein sites using geometrically matching concave scaffolds, achieving low nanomolar to picomolar affinities.

This paper identifies epigenetic features affecting prime editing efficiency and shows how chromatin state can be manipulated to enhance or reduce editing efficiency at specific genomic loci.

The paper introduces clue, a reference-free framework for multiplexed single-cell sequencing to identify genetic modifiers of immune responses using SNP-based clustering and eQTL mapping.

The paper introduces memento, a method for differential expression analysis of scRNA-seq data, and shows it identifies significant differences in mean, variability, and gene correlation across experimental conditions.

SCITO-seq enables cost-effective profiling of over 10^5 cells using combinatorial indexing with dsc-seq, demonstrating feasibility in mixed cell lines and human lymphocytes.

The paper uses CRISPR perturbations and single-cell transcriptomics to identify gene regulators and interactions in CD4+ T cells, revealing 134 regulators and 194 regulator pairs.