Dennis J. Hazelett

ELMER v.2 reconstructs gene regulatory networks from DNA methylation and transcriptome data to identify Master Regulators in diseases like breast cancer.

The paper uses transcriptomic and epigenomic profiling to show that high-grade serous ovarian cancers predominantly originate from fallopian tube secretory epithelial cells, with distinct transcription factors driving tumorigenesis based on cell-of-origin.

HiCAGE provides an R package for annotating and visualizing 3C-based genomic data, integrating with RNA-seq and gene ontologies.

The paper introduces StateHub and StatePaintR to provide rapid, reproducible chromatin state annotations for genome annotation, supporting variant prioritization and analysis.