Tianyi Li

Highly resolved tumor architecture via matched spatial and nucleus transcriptomics from a single tissue section

SIMPlex generates matched spatial and single-nucleus transcriptomic profiles from the same tissue section to resolve cell states with spatial signatures in mouse and human cancer tissues.

In vivo validation of predicted fitness effects at single-base resolution in a Brachypodium distachyon mutant population

The paper validates variant effect predictions in a Brachypodium distachyon mutant population using burden and purging tests, showing ESM outperforms SIFT and PlantCAD for missense variants.

Genomic language models improve cross-species gene expression prediction and accurately capture regulatory variant effects in Brachypodium mutant lines

The paper develops deep learning models to predict gene expression across species and assesses their ability to capture regulatory variant effects in Brachypodium mutant lines, showing improved accuracy over existing methods.

Acute high-dose irradiation of human primary ovarian cells reveals a shift in transcriptomics profile and impairment in cell-cell adhesion

This study examines how human ovarian cortical and medullary cells respond to acute X-ray exposure, finding transcriptomic shifts and impaired cell-cell adhesion.

Epigenetic Reprogramming Alters Intestinal Stem Cell Fate in Pouchitis

This study shows that inflammation in pouchitis alters intestinal stem cell fate through epigenetic changes, which can be reversed by JAK/STAT therapies.