Bernstein’s research focuses on epigenetics and specifically how modifications to the protein scaffold called chromatin contribute to mammalian development and human cancer. His work is notable for the identification of specialized chromatin structures that underlie stem cell pluripotency and aberrant epigenetic mechanisms that drive tumor initiation and drug resistance. Current work in the Bernstein lab spans a range of projects from technology development to cancer biology and therapeutic strategies. Key themes include: developing new technologies for mapping gene expression and chromatin modifications at the single cell and single molecule level; understanding cell fate decisions at fine resolution in development and disease; and investigating how genome and chromatin organization is aberrantly altered in cancer, and importantly, how these changes contribute to tumor biology.