Shih-Yu Chen

BioTrajX: evaluating biological plausibility in single-cell trajectory inference

BioTrajX evaluates biological plausibility of single-cell trajectories using three metrics to compare different trajectory inference results.

Oxidative Stress-Induced Microglial CD22 Upregulation Impairs Phagocytosis and Exacerbates Huntingtons Disease

This study identifies CD22 upregulation in microglia due to oxidative stress in HD, which impairs phagocytosis and worsens disease progression.

A multi-omics map of diabetic nephropathy links c-Jun activation to tubular injury and metabolic stress

This study integrates multi-omics data to identify c-Jun as a key driver of tubular injury and fibrosis in diabetic nephropathy.

Natural Killer Cell Receptor Signaling and Activation Depend on Cell Cycle Stages

This study shows that NK cell receptor signaling and activation vary with cell cycle stages, with some proteins showing non-monotonic abundance changes.

Subcellular localization of drug distribution by super-resolution ion beam imaging

The paper introduces srIBI, a super-resolution imaging technique, to visualize subcellular localization of biomolecules and drugs at the nanometer scale.

Ion beam subcellular tomography

This paper introduces ion beam tomography (IBT), a 3D subcellular imaging technique, and demonstrates its ability to visualize genomic regions, RNA transcripts, and protein factors with high resolution.

Evolutionary Origin of the Mammalian Hematopoietic System Found in a Colonial Chordate

The paper identifies hematopoietic stem cells and related lineages in Botryllus schlosseri, suggesting their evolutionary origin in a common ancestor of tunicates and vertebrates.