Professor Hoy has made significant contributions to the HIV research effort nationally and internationally. She has been Principal Investigator (PI) for over 200 clinical studies at the Alfred Hospital (Fairfeld Hospital) and has collaborated widely on investigator-initiated pathogenesis studies. Her main research interest is in the evaluation of the causes of co-morbidity and mortality in people living with HIV infection and the effect of Antiretroviral Therapy. Her current research interests include the comorbidities associated with Aging and HIV, in particular bone disease and cardiovascular disease, and the impact of residual immune activation and chronic inflammation.  Her other passion is ensuring the quality of care provided to PLHIV, and quality of life experienced by PLHIV.

She has mentored over 10 postgraduate students (MPH, PhD, postdoctoral fellows). Her research productivity is evidenced by over 200 peer-reviewed publications, and the editing/authorship of 8 books. She was a member of the Australian Antiretroviral Guidelines Panel for over 10 years, and has been a productive member of the international IAS-USA Antiretroviral Guidelines panel since 2012.