Joy Linyue Fan

Joint representation and visualization of derailed cell states with Decipher

Decipher is a deep generative model that integrates single-cell RNA-seq data to visualize and characterize transitions between normal and perturbed cell states across different diseases.

Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease

This study uses spatiotemporal single-cell analysis to track T cell clonal dynamics and phenotypic plasticity in GVHD, revealing links between TCR features, clonal expansion, and disease severity.

Echidna: A Bayesian framework for quantifying gene dosage effect impacting phenotypic plasticity

Echidna quantifies gene dosage effects on phenotypic plasticity by integrating scRNA-seq and WGS data to separate genetic from cell non-autonomous mechanisms.

Starfysh reveals heterogeneous spatial dynamics in the breast tumor microenvironment

Starfysh integrates spatial transcriptomics and histology to analyze tumor microenvironments, identifying disease-specific spatial hubs and immune interactions in breast cancers.

Multi-modal single-cell and whole-genome sequencing of minute, frozen specimens to propel clinical applications

This study develops a method for single-cell and whole-genome sequencing of frozen clinical specimens, demonstrating its utility in analyzing tumor evolution and rare disease biospecimens.