Johnson is an international leader in the development of scientific software. His research is at the interface of experiment and computation and involves developing software and algorithms for the analysis and visualization of scientific data, with a particular emphasis on data from Nuclear Magnetic Resonance (NMR) Spectroscopy. He is the creator of NMRViewJ, one of the leading programs for the processing, analysis and visualization of NMR data from proteins and nucleic acids. He has additionally developed programs for small molecule NMR analysis and for the statistical analysis of collections of NMR spectra used in metabolomics research. Recently he has been involved in the application of data mining algorithms to the prediction of NMR spectra of RNA molecules. As a principal investigator in the Center for HIV RNA Studies (CRNA), he is involved in developing new software tools to be applied to elucidating the structure and function of RNA from the HIV virus.