Epigenetic processes which modulate gene expression are critical for the development, plasticity, and degeneration of neural circuits throughout the lifespan. For example, disruption of normal DNA methylation patterns plays a major role in neurodevelopmental disorders and age-related decline in learning and memory. However, the normal development of methylation patterns and their effect on gene expression in brain cells is largely unknown. In the 15 years since completing the human genome project, many individual labs and large-scale consortia have focused on mapping the epigenomic landscape of coding and non-coding DNA elements. Advances in sequencing techniques have accelerated the growth of substantial genomic and epigenomic databases. Our lab seeks to exploit the full potential of these resources for elucidating developmental and regulatory processes, by creating computational analysis tools and theoretical models which are tailored to the scope and resolution of the data.