Roxanne Chiu

Multi-omic identification of key transcriptional regulatory programs during endurance exercise training in rats

The paper identifies tissue-specific transcriptional regulatory programs in rats undergoing endurance exercise training by integrating chromatin accessibility, DNA methylation, and gene expression data.

Polyclonal origins of human premalignant colorectal lesions

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

Single-cell spatial mapping reveals alteration of tissue microenvironment during early colorectal cancer

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

Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis

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

Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue

This study examines how endurance exercise training affects rat subcutaneous white adipose tissue, revealing sex-specific molecular responses and differences in adiposity and metabolism.

Temporal dynamics of the multi-omic response to endurance exercise training across tissues

This study profiles multi-omic changes in multiple tissues of rats during endurance exercise training, identifying molecular adaptations and sex-specific responses across time.

High Resolution Single Cell Maps Reveals Distinct Cell Organization and Function Across Different Regions of the Human Intestine

The paper maps cell organization and function across human intestine regions using single nuclear RNA and open chromatin assays, revealing distinct cell neighborhoods and regulatory differences.

Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

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.