Bryan Queme

This paper introduces an annotation-based gene-peak linkage method that improves gene expression prediction from chromatin accessibility in human kidney multi-omics data.

The paper introduces MANGO, a network-based method to detect gene set clustering by conditioning on network topology and gene degree, showing improved performance over existing approaches.

SNPWay provides a streamlined workflow for SNP-to-function and pathway over-representation analysis using integrated tools and a web server.

The paper benchmarks SNP annotation tools and gene models across the genome, showing discrepancies in annotation and their impact on pathway analysis.

The paper introduces pathway-based polygenic risk scores (pPRS) to detect gene-environment interactions, finding a significant interaction between NSAIDs and the TGF-β/GRHR pathway in colorectal cancer.

The paper introduces qHTSWaterfall, a 3D visualization tool for qHTS data, enabling the plotting of concentration-response curves with EC50 and Hill slope parameters.