A single human cell contains about 6 picograms of DNA. Nonetheless, recent advances in DNA sequencing technologies have made it possible to sequence the genome of thousands of individual single cells. In addition to the DNA bases present, DNA sequencing libraries can contain information on RNA transcripts as well as epigenetic features central to cellular identity like DNA methylation (5mC), DNA hydroxymethylation (5hmC), and DNA accessibility. Connecting these epigenetic features to gene expression is challenging, particularly in complex heterogeneous systems. To resolve this, my work involves developing techniques to capture the mentioned features simultaneously from a single cell and then applied them to key areas of human development and health.