Malcolm Perry's indexed work centers on computational genomics of developmental gene regulation, with a doctoral thesis addressing how regulatory elements shape developmental programmes. His broader output is anchored in the Ensembl resource: he contributes to the Ensembl genome annotation releases spanning 2022–2025, whose citation counts (1915, 1023, 782, 702) reflect their role as reference infrastructure for comparative and regulatory genomics. A related thread examines ancient topologically associating domains coinciding with Metazoan clusters of extreme noncoding conservation, linking chromatin architecture to deep evolutionary conservation. Beyond these, Perry contributed to amphioxus functional genomics and the origins of vertebrate gene regulation, a comparative study of regulatory evolution, and to work on horizontally acquired genes in vertebrate and invertebrate genomes