Jeanne Shen

SCOPE improves AI triage in 3D pathology by using morphology-aware prototypes to identify high-risk 2D slices for pathologist review.

The paper identifies OLFM4 as a marker of high-risk gastric intestinal metaplasia, showing its restricted localization to epithelial glands and focal expansion with disease severity.

This study shows that many premalignant colorectal polyps contain multiple genetic lineages, indicating polyclonal origins rather than single-cell expansion.

This study identifies the immunosuppressive cellular and genomic features of colorectal cancer brain metastases and their mechanisms of adaptation.

The paper uses spatial CODEX experiments to show early colorectal cancer microenvironment changes in FAP, including CAFs, immune suppression, and beta-catenin nuclear translocation.

This study shows that early colorectal cancer loses promoter-enhancer connectivity, leading to gene expression changes and a two-phase model of transcriptional regulation.

This paper introduces RNA-GAN, a deep generative model that creates synthetic whole-slide image tiles using gene expression profiles, outperforming traditional GANs and showing imputation capabilities.

This paper introduces RNA-Cascaded-Diffusion-Model to generate synthetic whole-slide image tiles from RNA-Seq data, improving machine learning model performance in low-data settings.

The paper uses single-cell data to show a continuum of cell state and composition changes from polyps to colorectal cancer, identifying stem-like cells and regulatory markers.