Singer's career has been focused on the cell biology of RNA, its isolation, detection, expression, and translation. A patent in situ hybridization technique his lab developed for detecting RNA in morphologically preserved cells revealed that messenger RNA can localize in specific cellular compartments. This work has given rise to the field of RNA transport and localization, enhanced by Singer's and his colleagues’ development of imaging technology and RNA reporters. His lab has shown that the dynamics of RNA transcription on a single gene can be interrogated by live cell imaging, as well as by multiplexed fluorescent probes.
Singer's laboratories at Einstein and Janelia have been instrumental in developing rapid and sensitive microscopy that can study single molecules of RNA in living cells and in devising methods to track them through their life cycle. This technology has implications for understanding the role of RNA in such disease processes as cancer metastasis and intellectual disability. He holds 12 patents on his work.