Xiaoqing Yu

Ploidy shapes gemcitabine response through altered potency and delayed cell death

This study shows that higher ploidy reduces gemcitabine potency and delays cell death by altering drug exposure kinetics and response timing.

circPMS1-mediated LIM protein scaffolding promotes cytoskeletal remodeling and melanoma metastasis

This study identifies circPMS1 as a pro-metastatic circRNA in melanoma that promotes cytoskeletal remodeling and metastasis by scaffolding LIM proteins.

The small MAF transcription factor MAFG co-opts MITF to promote melanoma progression

This study identifies MAFG as a driver of melanoma progression by interacting with MITF to alter gene expression and promote a dedifferentiated melanoma phenotype.

TAp73 mediates anti-tumor immunity through regulation of lipid metabolism in the lung tumor microenvironment

This study shows TAp73 regulates lipid metabolism in lung tumor microenvironment to enhance anti-tumor immunity through T-cell activation.

A multi-step immune-competent genetic mouse model reveals phenotypic plasticity in uveal melanoma

This paper develops a genetically engineered mouse model of uveal melanoma that recapitulates human disease progression and immune microenvironment features, revealing phenotypic plasticity and cooperative genetic drivers.

A longitudinal data framework for context-specific genotype-to-phenotype mapping

The paper introduces CLONEID, a framework for organizing clone-resolved data to enable longitudinal genotype-to-phenotype mapping in experiments with repeated molecular and phenotypic measurements.

Utility of cellular imaging modality in subcellular spatial transcriptomic profiling of tumor tissues

The paper develops ROICellTrack, a deep learning framework that integrates cellular imaging with spatial transcriptomics to analyze tumor tissues, revealing cancer-immune mixtures and spatial clustering patterns.

spatialGE: A user-friendly web application to democratize spatial transcriptomics analysis

spatialGE simplifies spatial transcriptomics analysis by providing a user-friendly web interface for non-programmers, enabling tasks like quality control, domain detection, and spatial analysis.

Differential gene expression analysis of spatial transcriptomic experiments using spatial mixed models

This study applies spatial mixed models to differential gene expression analysis in spatial transcriptomics, showing they reduce type-I error and improve model fit compared to non-spatial methods.

Unveiling targeted cell-free DNA methylation regions through paired methylome analysis of tumor and normal tissues

The paper identifies differentially methylated regions in cfDNA from tumor and normal tissues using paired-sample analysis to discover potential biomarkers for head and neck cancers.

Wide and Deep Learning for Automatic Cell Type Identification

This paper applies wide deep learning to cell type classification, showing improved accuracy when models are trained on one cancer type and tested on another.

Multiple-kernel learning for genomic data mining and prediction

This paper introduces an R package for multiple kernel learning, showing improved classification by combining multiple data sources in ovarian cancer.

lncDIFF: a novel distribution-free method for differential expression analysis of long non-coding RNA

lncDIFF detects differentially expressed long non-coding RNAs with higher power and lower false discovery rate compared to existing methods.

DNA methylation-based immune cell deconvolution in solid tumors

This study uses DNA methylation data to accurately predict immune cell infiltration in solid tumors, particularly in melanoma, and provides a simple model for clinical application.