Dr. Dandekar's research program is focused on the molecular pathogenesis of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) infections with special emphasis on gastrointestinal mucosal lymphoid tissue (GALT) as a major target organ of the viral infection and as a viral reservoir.

Current studies have been focused on determining the molecular mechanisms of the disruption of gut mucosal immune system in HIV infection and restoration during anti-retroviral therapy. Her research has utilized the SIV infected rhesus macaque model to investigate the pathologic effects of viral infection on the gut mucosal immune system and function.