David Alan Young

The paper develops a low-annotation-budget classifier using active learning and PubMedBERT to identify chondrogenesis regulators from PubMed abstracts, achieving high performance with fewer annotations.

The paper develops an automated pipeline using large language models to generate a gene perturbation transcriptomic atlas from public data, achieving high precision and recall in identifying perturbation groups.

This study quantifies DNA methylation changes during human articular cartilage development and identifies epigenomic mediators of osteoarthritis risk in prenatal joint tissues.

The paper identifies miR-199a/b-5p as pro-chondrogenic regulators and constructs a multi-miRNA kinetic model of chondrogenesis.

The paper identifies and functionally validates dynamically accessible chromatin regions in response to IL-1 stimulation using ATAC-seq and CRISPR/Cas9.

The paper identifies miR-140-3p as more abundant in human cartilage and shows its isomiRs have distinct functional targets.

The paper uses histone ChIP-seq and DNA methylation data to identify enhancer usage changes during chondrocyte differentiation and their regulation by SOX9.

The paper identifies DNA hypomethylation during MSC chondrogenesis, particularly at enhancer regions, and links these changes to the chondrocyte phenotype and cartilage disease.

This study compares DNA methylation measurements from two Illumina arrays in cartilage and finds high overall correlation but poor correlation for CpG sites with low variance.

This study identifies CASC20 and KIF26B as genetic loci associated with heterotopic ossification through genome-wide association and functional analyses.