We are developing bioinformatic tools and resources to help understand the epigenomic regulatory mechanisms that function during early maize endosperm development. The recent completion of the maize genome has facilitated understanding the epigenetic regulation of endosperm development and the molecular mechanisms underlying gene imprinting at a genomic level. Although application of next-generation sequencing technology for epigenome and transcriptome profiling has allowed accumulation of significant amount of sequence data, bioinformatic approaches are still needed to properly analyze these large datasets. Three main objectives of the ongoing projects in our Lab are to develop computational tools and resources to: 1) Improve maize gene models using active transcription-associated histone modifications, 2) Develop algorithms to screen for core TFs and build regulatory networks using nucleosome-positioning dynamics, and 3) Identify epigenetically modified, imprinted genes at the genome level. Our work will fundamentally advance our understanding of transcriptional and epigenetic regulation, genomic imprinting, and the molecular mechanisms involved in maize endosperm development.