Allen has been following the coronavirus outbreak closely. He also is involved in surveillance for influenza-related hospital admissions through the FluCAN system, based at 17 hospitals nationally.

His research covers a diverse area within infectious diseases, including sepsis and severe melioidosis, tropical medicine, influenza and vaccine effectiveness, hospital infection prevention and control, antibiotic pharmacokinetics, antimicrobial drug policy and clinical infectious diseases. He has published over 280 peer-reviewed scientific publications (as well as >50 letters/editorials and 17 book chapters).