Ferguson works on nutritional genomics, mutagenesis and the causes and control of chronic diseases such as inflammatory bowel disease. She has also worked on genes associated with satiety, the feeling of fullness after eating.

For ten years, Ferguson led Nutrigenomics New Zealand, which was a partnership between the University of Auckland, and three Crown Research Institutes: Crop & Food Research, AgResearch and HortResearch. Research focused on the genetics of inflammatory bowel disease and how personalised dietary changes could influence disease. This led to the first international conference on nutrigenomics and gut health, in 2006.