Jeff Chen has developed an innovative research program to study molecular mechanisms for gene expression changes and evolutionary consequences in hybrids (formed between strains of the same or different species) and allopolyploids (formed between two or more related species) relative to the parents. His research employs Arabidopsis (a weedy plant in the mustard family) and cotton as experimental systems and uses genomic, proteomic, and systems biology approaches, as well as molecular biology and genetic methodologies. Dosage changes and novel interactions between parental genomes and alleles in hybrids and polyploids may induce epigenetic and epigenomic changes, leading to hybrid incompatibility, heterosis in plants, and diseases and cancers in animals. He and his colleagues have found that epigenetic changes in gene expression in plant hybrids and allopolyploids are associated with altered circadian rhythms and hybrid vigor, seed size, enhanced resistance to biotic and abiotic stresses, and fiber cell and trichome development. Moreover, the results have significant implications, not only for the field of genetics and epigenetics, but also for the ultimate success of biotechnological efforts to safely and effectively manipulate gene expression associated with growth vigor in plants and crops that produce food, feed, and biofuels.