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Vijay Khonde has a diverse work experience spanning multiple industries. Vijay started their career as a Research Scholar at the Interactive Research School of Health Affairs, Bharati Vidyapeeth Deemed University in 2011. In 2010, they worked as an R&D Officer at Godavari Biorefineries Ltd, focusing on molecular diagnosis kit development. Vijay then joined Praj Industries in 2011 as a Senior Research Technologist in their Molecular Biology, Genetic Engineering and Biochemistry Centre of Excellence. Vijay held various roles at Praj Industries including Associate Staff Technologist, Staff Scientist, and Senior Staff Scientist. In 2014, they worked as a Specialization Student at VIB-Department of Molecular Biology.

Vijay Khonde obtained their M.Sc. degree in Biotechnology from the School of Life Sciences at Swami Ramanand Teerth Marathwada University in Nanded. Vijay completed their studies at this institution from 2004 to 2006.