Kiet T. Phong

Spatial transcriptomics resolves ductal TREM2+ and stromal FOLR2+ macrophages in the normal human breast at microanatomical resolution

The paper uses spatial transcriptomics to identify and characterize two distinct macrophage populations in the normal human breast at microanatomical resolution.

Longitudinal single cell RNA-sequencing of Pik3caH1047R-driven mammary tumorigenesis reveals coordinated transformation of epithelial and fibroblast transcriptional states

This study uses single-cell RNA-sequencing to track how Pik3caH1047R mutation drives mammary tumor progression by altering epithelial and fibroblast transcriptional states.

Single cell RNA-sequencing reveals an association between testosterone treatment and reduced hormone signaling in the human mammary gland

This study uses single-cell RNA sequencing to show that testosterone treatment reduces estrogen signaling in mammary gland cells of transgender men compared to cisgender women.

Benchmarking Cell Type and Gene Set Annotation by Large Language Models with AnnDictionary

The paper benchmarks large language models for cell-type and gene set annotation using AnnDictionary, finding high accuracy in cell-type annotation and strong functional gene set recovery.

Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC

The paper introduces MULTI-ATAC, a method to reduce batch effects in scATAC-seq by pooling samples before transposition, enabling scalable and batch-free experiments.

Microfluidics-free single-cell genomics with templated emulsification

The paper introduces PIP-seq, a microfluidics-free method for single-cell RNA sequencing that enables high-throughput, scalable, and flexible processing of samples.

Changes in epithelial proportions and transcriptional state underlie major premenopausal breast cancer risks

This study identifies how changes in epithelial proportions and transcriptional states influenced by pregnancy and BMI affect hormone signaling and breast cancer risk in premenopausal women.