Qiuyue Yuan

Detection of Spatially Aberrant Cells in Spatial Transcriptomics Data by Conformal Prediction

The paper introduces SPADE, a framework that detects spatially aberrant cells in spatial transcriptomics data using variational autoencoders and conformal prediction.

Epiregulon: Inference of single-cell transcription factor activity to predict drug response and drivers of cell state

Epiregulon infers single-cell TF activity using ATAC-seq and RNA-seq to predict drug response and identify drivers of cell state.

Integrated Single-Cell Multiomic Profiling of Caudate Nucleus Suggests Key Mechanisms in Alcohol Use Disorder

The paper uses multiomic profiling of the caudate nucleus to identify gene expression and chromatin changes in AUD, linking them to risk genes through QTL analysis.

Continuous lifelong learning for modeling of gene regulation from single cell multiome data by leveraging atlas-scale external data

LINGER improves GRN inference from single-cell multiome data by integrating atlas-scale bulk data and TF motif knowledge, achieving 2-3 fold higher accuracy.

Heritability enrichment in context-specific regulatory networks improves phenotype-relevant tissue identification

SpecVar improves heritability enrichment by integrating regulatory networks with GWAS data to identify relevant tissues and shared heritability.