Dr Varghese studied physics and mathematics at the Universities of Queensland and Western Australia. His early career comprised post doctoral fellowships at the University of Western Australia and CSIRO's Division of Protein Chemistry and a research appointment at the University of Sussex, UK.

He was appointed Principal Research Scientist in CSIRO in 1984 and has worked with protein structures since that time. He was seconded to the Biomolecular Research Institute from 1990 to 2000 then returned to CSIRO to head the Structural Biology Program.

His current interests are investigating the structure and function of cell receptors, viral antigens and drug resistance in pathogenic organisms. The facilities he runs include an X-ray diffraction laboratory, drug design facility, virology and parasitology laboratories and a proteomics facility.

Dr Varghese is the author of numerous scientific papers and several patents. The development of the anti-influenza drug Relenza TM was based on his crystallographic studies, and more recently, he was responsible for the construction of the 64-node Caduceus Beowulf Cluster, a dedicated in silico drug design facility.