Each human nucleus contains two meters of DNA that, amazingly, is packaged into an organelle a mere ~10 μm diameter. Yet, despite this dramatic difference in scale, the three-dimensional organization of the genome is non-random and plays a critical functional role in both health and disease. However, as much of our current view of nuclear organization is derived from ensemble techniques requiring populations of millions or more cells, much less is known about the organization of chromosomes in individual cells and many open questions remain about the mechanisms that shape and structure the genome. Our laboratory uses a combination of computational, molecular, and optical approaches to investigate the causes and consequences of 3D genome organization in single cells.