In the past decade, the main strategy for genome-wide mapping of chromatin modifications, histone marks and interactions between DNA and proteins, has been ChIP followed by microarray analysis (ChIP-chip). Recent improvements in the efficiency, quality, and cost of genome-wide sequencing prompted biologists to abandon microarrays in favor of next-generation sequencing, a method referred to as ChIP-Seq. Functional annotation of the noncoding sequences, which account for more than 95% of the genome, is difficult however due to the inherent lack of statistical and computational biology methods and tools available to agnostically interrogate epigenomic changes in humans.

The main goal of our research program is to build new computational tools to comprehensively characterize and functionally annotate the human epigenome. This research programs builds on the power of next- generation sequencing (NGS) coupled with chromatin immunoprecipitation (ChIP), an approach called ChIP-Seq to detect epigenetic variations at an unprecedented level of resolution.