National Health & Medical Research Council (NHMRC), Australia (Jan 2019 – Dec 2022) VITAL: Vaccine Immunomodulation Throughout the Ageing Lifespan (Project Grant APP1141840) CIA Prof Magdalena Plebanski, RMIT, Melbourne. Katie Flanagan - Chief Investigator B (CIB).

National Health & Medical Research Council (NHMRC), Australia (Jan 2019-Dec 2022) Characterisation of mobile antimicrobial resistance in the human gastrointestinal microbiota (Project Grant APP115633) CIA Dr Sam Forster, Hudson Institute, Melbourne. Katie Flanagan - Associate Investigator (AI).

National Health & Medical Research Council (NHMRC), Australia (Jan 2019-Dec 2021) Epigenetic reprogramming of monocytes by BCG vaccination (Project Grant APP1157556) CIA Boris Novakovic, Murdoch Children’s Research Institute, Melbourne.
Katie Flanagan - Associate Investigator (AI).

Clifford Craig Foundation, Tasmania, Australia (Jan-Dec 2019)

Understanding immunity to influenza in children. Katie Flanagan - Chief Investigator (CIA).

Clifford Craig Foundation, Tasmania, Australia (Jan 2018 – Dec 2019)
Heterologous effect of diphtheria-tetanus-acellular pertussis vaccination on influenza vaccine challenge in the elderly
Katie Flanagan - Chief Investigator (CIA).

Bill and Melinda Gates Foundation (BMGF), USA (Jan 2018 – 2021)  

Immunology sub-study in a phase II novel neonatal rotavirus vaccine (RV3-BB) trial based in Blantyre, Malawi. CIA Prof Julie Bines, Murdoch. Children’s Research Institute, Melbourne. Katie Flanagan – Chief Investigator.

National Health and Medical Research Council (NHMRC), Australia (Jan 2016 – Dec 2019)​​​​​​. A systems biology approach to understanding the beneficial heterologous effects
of neonatal BCG vaccination in a Melbourne-based randomised controlled trial (Project Grant APP1099680). CIA Prof Nigel Curtis, Murdoch Children’s Research Institute, Melbourne. Katie Flanagan - Chief Investigator (CIB).

National Health & Medical Research Council (NHMRC), Australia (Jan 2016 – Dec 2020). Extending the MIS BAIR randomised trial of BCG to prevent childhood allergy and infection (Project Grant APP1082205). CIA Prof Nigel Curtis, Murdoch Children’s Research Institute, Melbourne. Katie Flanagan - Chief Investigator (CID).

Clifford Craig Foundation, Tasmania, Australia (Jan – Dec 2018). Defining the gut microbiota in Tasmanian older adults
Katie Flanagan - Chief Investigator (CIA).

Clifford Craig Medical Research Trust, Tasmania, Australia (Jan 2016 – Dec 2017). Heterologous effect of diphtheria-tetanus-acellular pertussis vaccination on influenza vaccine challenge in the elderly. Katie Flanagan – Chief Investigator (CIA).

National Health & Medical Research Council (NHMRC), Australia (Jan 2013 – Dec 2016). BCG immunisation to prevent the development of allergy in infants: a randomised trial (Project Grant APP1051228). CIA Prof Nigel Curtis, Murdoch Children’s Research Institute, Melbourne. Katie Flanagan - Chief Investigator (CIE).