Sha Sun

Cell-level random splits leak group-owned answers in single-cell benchmarks

The paper identifies and quantifies leakage in single-cell benchmarks caused by group-owned answers and introduces a tool to assess this leakage before model training.

XIST Is a Key Modulator Associated with the Adhesome Network

This study shows XIST modulates the adhesome network and cell stemness by altering adhesion pathways and gene expression in ovarian cancer cells and across tissues.

Single-cell foundation modeling with species-nativeprotein tokens links regenerative competence across frog and mouse

This paper develops a species-native representation for Xenopus laevis to compare regenerative competence across species and identifies a vector competence ruler that distinguishes regenerative from fibrotic repair in mice.

Xist expression in male Peromyscus leucopus is associated with restricted chromatin repression and incomplete X-to-autosome dosage compensation

This study identifies robust Xist expression in male Peromyscus leucopus somatic cells, showing gene-selective repression rather than global X-chromosome inactivation.

Gateway analysis reveals transient molecular programs at cell-fate transitions

The paper introduces gateway analysis to identify rare transient cell states at fate transitions in single-cell atlases and finds it detects previously missed molecular programs.

A continuum reaction-diffusion model for spread of gene silencing in chromosomal inactivation

This paper develops a reaction-diffusion model to explain the spatial control of gene silencing during X chromosome inactivation, showing how feedback loops and chromatin modifications regulate the spread of silencing.

DistortCorrect Stitcher: Microscopy Image Stitching with Integrated Optical Distortion Correction

DistortCorrect Stitcher improves microscopy image stitching by integrating optical distortion correction, enhancing alignment accuracy for spatial transcriptomics data.

Functional conservation of lncRNA JPX despite sequence and structural divergence

The paper investigates the functional conservation of lncRNA JPX across species despite sequence and structural divergence, showing it can functionally complement Jpx in mouse cells.