Prior to his PhD training, Welles worked in two different labs studying cancer biology and neuroscience. He studied various isoforms of p63 (p53 family member) and their function in metabolism, stem cell biology, mouse embryonic development and cancer. He also worked on dissecting signalling pathways that are involved in remyelination of axons after physical trauma to the brain and spinal cord. Currently, Welles is studying epigenetics and evolution of gene expression. He uses C. elegans as a model to study how parental environment shapes the phenotypes of their descendants. He is particularly interested in understanding how epigenetic information is transmitted from one generation to the next, and how parental sex and genetic variation can influence gene expression in offspring. His research interests are in genetics, genomics, evolution, metabolism and developmental biology.