To produce the right complements of proteins that enable cell type-specific behaviors, cells interpret the instructions in DNA through gene "transcription" or "expression." Proper gene expression depends on complex rules and physical interactions between a multitude of components. Improper transcription of genes or proper transcription of broken genes is central to many human diseases.

The Abraham lab studies how gene transcription is controlled, including how the genome is organized in the nucleus and how specific genes are regulated by environmental cues. We also study how transcriptional processes are altered in disease to either understand the disease or to suggest treatments. We develop and deploy computational pipelines to synthesize and distill complicated transcriptional processes and how they go awry in diseased cells. Much of our work centers on the study of super-enhancers, arrangements of transcription-regulating DNA elements that allow genes especially important for a cell's identity to be tightly controlled by the cell's environment. These super-enhancers have proven useful for identifying regulators of cell identity, regulation of genes by signaling pathways, genes required for tumor cell survival, targetable protein nodes in cancers, and important mutations in tumor genomes. Super-enhancers and their associated genes can be aggregated to computationally model the core regulatory circuitry dictating the identities of specific cell types.