Genome-wide transcriptome studies such as FANTOM and ENCODE have shown that mammalian genomes are pervasively transcribed, generating a wide variety of transcript isoforms. Most transcripts do not code for proteins, but are thought to have regulatory roles as non-coding RNAs. However, in most cases the specific biological function of non-coding RNAs is unknown. The Laboratory for Applied Computational Genomics develops and applies bioinformatics methods to analyze genome-wide data generated using next-generation sequencers for the purpose of categorizing and functionally understanding RNA molecules. We are particularly interested in the 3D conformation of mammalian genomes, and the secondary and tertiary structure of RNA molecules.