Rupert's main research interest is the study of messenger RNA (mRNA) methylation in plants and other eukaryotes. His group studies the enzymes involved in the synthesis of N6 methyladenosine, the mRNAs that are targeted for methylation, the consequences of this methylation and the proteins that recognise the modified nucleotide.

He also has a long standing interest in synthetic biology approaches to crop improvement with research areas including the manipulation of plant-microbe interactions through "quorum sensing", chloroplast transformation systems and the production of taxanes in heterologous plant systems.