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Delighted to share a landmark preprint from our lab, using genome language models and AI agents for biological discovery and genome mining! The stretches of DNA between protein-coding genes are often called the genome’s “dark matter,” but they are far from empty. They encode RNA molecules that sense metabolites, regulate genes, and control some of molecular biology's most important tools (such as programmable genome editors e.g. CRISPR/bridge) Much of this biology is unexplored. One reason is that RNAs can retain similar structures and functions even as their DNA sequences change dramatically, making their relationships difficult to recognize with conventional computational tools