Huaiyu Mi

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.

This paper develops a probabilistic model using phylogenetic trees and Gene Ontology annotations to predict gene functions, showing scalability and agreement with biological intuition.

The paper identifies a multiscale temporal regulatory network involving genes that regulate circadian, cell cycle, and aging processes, enriched for signal transduction, metabolism, and stress response genes.

BDQC identifies data outliers and anomalies in large-scale genomic pipelines without domain knowledge, improving data quality and enabling new insights.