Zhuorui Xie

The CFDE Workbench integrates metadata and processed data from Common Fund programs to enable FAIR and AI-ready cross-program knowledge discovery.

The paper introduces a knowledge graph framework for integrating and querying biomedical data across domains, demonstrating its utility in eight use cases.

The paper introduces a web-based platform for building bioinformatics workflows using APIs, enabling hypothesis generation across multiple data sources.

Rummagene extracts and provides access to gene sets from PMC publications for search and analysis, revealing trends and enabling functional predictions.

The paper presents a LINCS Microenvironment perturbation dataset cataloging transcriptional, proteomic, epigenomic, and phenotypic responses of MCF10A cells to six ligands, enabling integrative analysis of molecular and phenotypic changes.

The paper constructs a reproductive toxicity knowledge graph (ReproTox-KG) to link birth defects, drugs, and genes, identifying potential molecular mechanisms for drug-induced birth defects.

Elysium provides a cloud-based RNA-seq alignment service with a GUI, allowing users to upload FASTQ files and obtain aligned results without needing programming skills or Amazon credentials.