Jihye Park

Lineage tracing reveals asynchronous fate restriction in mouse embryos and stem cell-derived embryo models

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 structure-informed deep learning framework for modeling TCR-peptide-HLA interactions

StriMap models TCR-peptide-HLA interactions using structural and sequence features, achieving state-of-the-art performance and identifying disease-associated peptides in ankylosing spondylitis.

Time-resolved lineage recording reveals a pre-existing, heritable cell state underlying metastatic potential

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.

Simulation and empirical evaluation of biologically-informed neural network performance

The paper evaluates how dataset characteristics affect biologically-informed neural network performance using simulations and empirical testing with prostate cancer data.

Single-cell epigenetic profiling reveals an interferon response-high program associated with BAP1 deficiency in kidney cancer

The paper identifies an IFN response-high epigenetic program linked to BAP1 deficiency in kidney cancer using single nucleus ATAC sequencing across multiple cohorts.