Choli Lee

Dual-patterned pluripotent stem cells self-organize into a human embryo model with extended anterior-posterior patterning

The paper describes a method to generate human embryo-like structures by pre-patterning stem cells and mixing them, resulting in models with extended anterior-posterior organization and neural features.

Chromatin context-dependent regulation and epigenetic manipulation of prime editing

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.

Induction and in silico staging of human gastruloids with neural tube, segmented somites & advanced cell types

This study induces human gastruloids with embryo-like structures using retinoic acid and shows they match E9.5 mouse embryos in developmental stage through single-cell RNA-seq and computational staging.

Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters

This paper develops scQers, single-cell quantitative expression reporters, to measure enhancer activity across multicellular systems with high precision and range.

Multiplex genomic recording of enhancer and signal transduction activity in mammalian cells

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.

A temporally resolved, multiplex molecular recorder based on sequential genome editing

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.

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

The paper integrates single-cell RNA-seq, ATAC-seq, and Hi-C data to study nuclear configuration and gene expression changes during stem cell differentiation and X inactivation, revealing discrete structural changes and delayed chromatin compaction.

TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers

TransMPRA combines CRISPR perturbation and MPRAs to identify trans-acting factors influencing enhancer activity.

Unsupervised manifold alignment for single-cell multi-omics data

This paper applies and extends MMD-MA to align single-cell transcriptome and chromatin accessibility data from ~2000 cells, demonstrating its scalability and accuracy.

Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data

This study uses topic modeling on scHi-C data to identify cell type-specific chromatin structural patterns and compartment structures.

Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells

Sci-Hi-C is a single-cell Hi-C method that maps 3D genome organization in large numbers of single cells, enabling analysis of chromatin interactions and cellular variability.

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

This paper introduces DNase Hi-C and targeted DNase Hi-C methods for high-resolution mapping of chromatin interactions, overcoming limitations of traditional Hi-C techniques.

Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies

This paper introduces THEMIS, a method for analyzing tumor heterogeneity across multiple biopsies, showing improved accuracy over existing methods and applications in tracking cancer progression and treatment resistance.

Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing

This paper introduces sci-RNA-seq, a combinatorial indexing method for single-cell RNA sequencing, and applies it to profile 42,035 C. elegans cells, identifying 27 cell types and their specific genes.

Paired CRISPR/Cas9 guide-RNAs enable high-throughput deletion scanning (ScanDel) of a Mendelian disease locus for functionally critical non-coding elements

This paper introduces ScanDel, a CRISPR-based method to systematically delete non-coding regions of a gene locus, revealing that distal regulatory elements are not critical for HPRT1 function.