Keller's research focuses on using computer-assisted methods to analyze RNAs. One area of research is on the regulatory mechanisms of non-coding RNAs, as well as the effect of various influencing factors on the single-cell transcriptome, which is resolved in both time and space. Based on his experience in modeling regulatory influences, Keller has dedicated his HIPS department to studying the interaction of bacteria with humans. In this research, he explores the exchange of information and material between commensal and pathogenic bacteria, as well as their host. The goal is to find new producers of natural products and identify new natural products, which can serve as a starting point for the development of new active substances. From a medical point of view, his research aims to better understand and influence the aging process, as well as neurodegenerative diseases such as Alzheimer's and Parkinson's.