Yuqiu Yang

Spatial Topology Reveals Biologically Distinct Recurrent Motifs in Colorectal Cancer

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: Bayesian Rank Aggregation in Genomics with Extended Ranking Schemes

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

eTRex Reveals Oncogenic Transcriptional Regulatory Programs Across Human Cancers

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: Missegmented Transcript Inference Correction for Improved Spatial Transcriptomics Analysis

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

Unified Probabilistic Analysis of CyTOF: A Deep Generative Approach using CytoOne

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

MetaNorm: Incorporating Meta-analytic Priors into Normalization of NanoString nCounter Data

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

Cytomulate: accurate and efficient simulation of CyTOF data

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

Comparative Analysis of Dimension Reduction Methods for Cytometry by Time-of-Flight Data

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