Yuqiu Yang

The paper introduces STORM, a method to identify recurrent spatial motifs in colorectal cancer without cell-type labels, finding a fibroblast barrier linked to immune exclusion and prognosis.

BiGER is a Bayesian rank aggregation method for meta-analysis of gene lists, handling mixed rankings and missing data with high accuracy.

The paper develops eTRex, a variational Bayesian model, to analyze 4,819 ATAC-seq datasets and create a pan-cancer atlas of transcriptional regulator profiles, revealing common and context-specific regulators.

MisTIC corrects transcript misassignment in spatial transcriptomics data, improving cell type identification, differential expression analysis, and RNA localization.

CytoOne is a probabilistic framework for CyTOF data that integrates batch correction, differential analysis, and visualization, effectively modeling sparse and noisy data.

This study shows ZNF397 loss leads to TET2-driven epigenetic changes, lineage plasticity, and resistance to AR-targeted therapies in AR-dependent cancers, with TET2 inhibitors reversing resistance.

MetaNorm improves normalization of NanoString nCounter data by incorporating meta-analytic priors, enhancing stability and computational efficiency.

This paper develops pMTnet-omni, an AI system predicting TCR-pMHC binding across species and MHC classes, achieving high accuracy and showing clinical utility in predicting immune-related adverse events.

Cytomulate simulates CyTOF data accurately and efficiently, outperforming existing methods in capturing data characteristics and learning distributions.

This paper benchmarks 21 dimension reduction methods on CyTOF data, finding SAUCIE, SQuaD-MDS, and scvis as top performers with different strengths.