Junhong Choi

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.

The paper uses lineage tracing to show that fate restriction in mouse embryos and stem cell-derived models is asynchronous and not solely determined by cell identity.

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

Ordered lineage recording in lung cancer xenografts shows pre-transplant glycolytic and lineage-heritable expression states predict metastatic colonization, while ENO1 alone predicts onward spread.

SciPhy estimates time-scaled phylogenies and cell population parameters from sequential genetic lineage tracing data using a Bayesian framework, showing improved accuracy over existing methods.

The paper develops monoclonal gastruloids from single mouse embryonic stem cells and uses DNA Typewriter to reveal heritable lineage biases in early development.

This paper introduces P3 editing, a method that links protein-protein proximity to CRISPR-Cas9 dual-component guide RNA formation, enabling genome editing triggered by molecular interactions in human cells.

The paper designs and characterizes diverse genomic parts for precise genome editing and molecular recording in mammalian cells.

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.

This paper introduces ENGRAM, a method to genomically record enhancer and signal transduction activity in mammalian cells, demonstrating its ability to track multiple transcriptional reporters with high fidelity.

This paper introduces DNA Ticker Tape, a system for in vivo molecular recording that sequentially records events using CRISPR-Cas9 and prime editing, demonstrating its ability to record complex event histories and cell lineage.

The paper shows that a short translational ramp in mRNA's first 5 codons significantly affects protein synthesis efficiency, independent of tRNA abundance or initiation efficiency.