In cells, communication between a gene and sequences that regulate the gene occurs through physical contact. Our goal is to understand how this communication occurs within the nucleus. To do so, we leverage 3D genome mapping technologies to capture the dynamic chromatin interactions and study gene regulation in the context of developmental biology. Interpreting these high-throughput sequencing data probing the (3D) genome, epigenome, and transcriptome requires sophisticated algorithms and computational tools, which we develop by using ideas from signal processing, graph theory, information theory, and coding theory.