Barkan's research is focused on how nucleus-encoded proteins affect chloroplast gene expression.[8][9][10] Experiments from her lab use mutants, primarily in maize (Zea mays) but also Arabidopsis thaliana, to investigate chloroplast mRNA translation and stability, as well as many aspects of RNA maturation, including splicing and editing.[11][12][13] Barkan and her colleagues have discovered and studied dozens of plant nuclear genes that encode chloroplast RNA binding proteins that directly affect multiple aspects of RNA metabolism (processing, splicing, translation, stability).[14] The majority of the nucleus-encoded proteins that Barkan has characterized contain pentatricopeptide repeats (PPR).[15] Barkan has also discovered and named the CRM (chloroplast RNA splicing and ribosome maturation) domain, which is found in nucleus-encoded proteins required for chloroplast RNA splicing.[16][17] In 2019, Barkan and colleagues successfully constructed PPR proteins that bound specific RNA sequences in vivo, thus establishing a system for creating targeted protein-RNA interactions.[18][19]