ChangHee Lee

Molecule-resolved inference reveals the spatial organization of transcriptional programs

The paper introduces FICTURE2, a statistical model that infers transcriptional programs from individual RNA molecules in spatial transcriptomics data, revealing spatial organization and cellular identity without segmentation.

Creation of a High-Resolution, Continually Evolvable Lineage Tracer

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

Shifts in embryonic oxygen levels cue heterochrony in limb initiation

The paper identifies differential oxygen levels as a driver of heterochrony in limb development between avian and mammalian embryos.

Integration of in situ hybridization and scRNA-seq data provides a 2D topographical map of the developing retina across species

The paper integrates in situ hybridization and scRNA-seq data to create 2D topographic maps of the developing retina across species, revealing conserved and divergent patterning programs.

Convergent flow-mediated mesenchymal force drives embryonic foregut constriction and splitting

This study identifies a biomechanical mechanism involving mesenchymal forces and SHH signaling that drives epithelial tube splitting during tracheal-esophageal separation in embryos.

Integration of sexual dimorphism and left-right asymmetry in the development of the duck syrinx

The paper investigates how sexual dimorphism and left-right asymmetry interact in duck syrinx development, showing that PITX2 and estrogen signaling regulate asymmetric growth differently in males and females.

Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics

This paper describes a protocol to repurpose Illumina sequencing flow cells for high-resolution spatial transcriptomics, enabling detailed spatial gene expression analysis with improved resolution and cost efficiency.

FICTURE: Scalable segmentation-free analysis of submicron resolution spatial transcriptomics

FICTURE provides a scalable segmentation-free method for analyzing high-resolution spatial transcriptomics data, revealing detailed tissue architecture in complex regions.

Hox genes modulate physical forces to differentially shape small and large intestinal epithelia

This study shows Hoxd13 regulates hindgut morphogenesis through the TGFβ pathway by altering mesenchymal biomechanics.

Direct Reprogramming of Non-limb Fibroblasts toCells with Properties of Limb Progenitors

This study reprograms non-limb fibroblasts into cells with limb progenitor properties using Prdm16, Zbtb16, Lin28, and Lin41.

Otx2 and Oc1 directly regulate the transcriptional program of cone photoreceptor development

The paper identifies cis-regulatory modules regulated by Otx2 and Oc1 in cone photoreceptor development and shows Otx2 autoregulation.