Single-cell sequencing technologies have revolutionized human biological research, giving scientists an arsenal of tools to probe the cellular mechanisms of health and disease. However, these technologies have been limited by their sample preparation requirements and the ability to scale to a large number of cells and many individuals, resulting in the loss of valuable information or the lack of statical power, limiting biological insight. Here I describe the recent developments of single-cell multiplexing techniques and antibody oligonucleotide conjugates, their variations, and the novel application of genetic multiplexing and surface protein sequencing to study the cellular mechanisms of COVID-19, systemic lupus erythematosus, and juvenile dermatomyositis. I then describe two novel techniques which address the limitations of single-cell technologies, and discuss their use in immunological studies of disease. These techniques are 1) XYZeq, a method for unbiased mRNA capture from solid tissues with spatial resolution and single-cell transcriptomic resolution, and 2) clue, a framework for encoding multiplexed single-cell sequencing experiments that eliminates the need for reference genotypes and orthogonal barcoding, offering a more efficient method for demultiplexing samples. The XYZeq method was used to study the tumor microenvironment in a liver metastasis mouse model, while the clue method was used to study the effects on mRNA and surface protein expression of stimulation with immunomodulatory molecules on peripheral blood mononuclear cells. The results of these studies demonstrate the power of single-cell sequencing and establish the utility of new single-cell techniques for uncovering the cellular mechanisms of disease.