Universities play a vital role in transmission and generation of new discoveries and knowledge. In this paper, we study how research input and research output are related in these institutions. We focus on two types of research input: research funding and human resources, and employ various forms of publication to measure research output, namely books, book chapters, journal articles and conference papers. More importantly, we examine the recent trend of switching to a performance-based funding system by both developed and developing countries alike to support university research. We study these issues by exploring research activities carried out by Australian universities from 1992 to 2010. Australia first adopted a performance-based funding system in 1995 and further strengthened it in 2002. We find that research funding plays an important role in generating research output, particularly journal articles. On average, a one percent increase in the total research income brought about a 0.1074 percent increase in a measure of the total research publication and led to a 0.1753 percent increase in journal article publication. Among various sources of research income, competitive grants promoted all forms of publication while research income secured from industries and private sources posed a drag to research publication. Such effects were more visible in well-established, elite universities than those with a shorter history. On the other hand, the effects of human resources were stronger on these new, small and regional universities than on their elite counterparts. Exploring more closely, we find that academic staff was a key factor in journal article publication and its impact was more pronounced on the new, small and regional universities. Lastly, the adoption of a performance-based funding system appeared to boost research output.