Hani Jieun Kim

This study uses single-cell RNA-sequencing and spatial transcriptomics to analyze epithelial and fibroblast states in hormone therapy-naive prostate cancer, identifying novel phenotypes and molecular perturbations.

Refate identifies chemical compounds targeting trans-regulatory networks to enable cellular conversion by integrating single-cell data and drug databases.

The paper identifies mesendoderm progenitor cells in mouse embryos and shows their contribution to endoderm and mesoderm lineages through lineage tracing and analysis of Mixl1 function.

This study benchmarks single-cell multimodal omics integration methods across multiple tasks to guide method selection based on data characteristics and study goals.

This study evaluates blastoid models of early human development by comparing them to a reference map of human blastocysts, identifying their lineage coverage and differentiation progression.

This study evaluates spatially variable gene detection methods across multiple spatial transcriptomics datasets to assess their performance, reliability, and practicality.

This study benchmarks retinal organoid protocols by comparing their cellular and molecular fidelity to fetal and adult human retinal tissues.

Cepo identifies cell identity by analyzing differentially stable genes from scRNA-seq data, improving cell-type characterization and spatial mapping.

The paper shows LSD1 associates with RNA polymerase II pausing at gene promoters in mouse ESCs and influences gene expression patterns.

scClassify improves cell type classification in scRNA-seq data by using ensemble learning, achieving more accurate and fine-grained results than original publications.

CiteFuse is a tool for analyzing CITE-seq data, integrating RNA and protein data, and offering clustering, differential expression, and visualization features.

PhosR provides tools for processing and analyzing phosphoproteomic data, enabling data imputation, normalization, and functional analysis of kinase activity and signaling pathways.