Christian J. Stoeckert

The paper describes the development of a beta cell genomics application ontology (BCGO) based on the Ontology for Biomedical Investigations, validated through data annotation, queries, and automated classification.

The paper introduces GenomicsDB, a public knowledgebase for Alzheimer's disease genetic datasets and annotations, enabling data sharing and discovery through harmonized GWAS summary statistics and functional annotations.

The paper describes how the OBO Foundry formalized its principles into operational rules and implemented automated checks to evaluate ontology compliance, improving interoperability and quality.

The paper analyzes transcriptomics data availability and reusability between microarray and RNA-seq experiments published between 2009 and 2013, and provides recommendations to improve RNA-seq data sharing.

The paper introduces a tool for standardizing clinical data using a realism-based common data model and semantic technologies.

iterativeWGCNA improves module detection in WGCNA by iteratively refining gene clusters and minimizing information loss.