Mukhopadhyay joined Biocomplexity Institute following his postdoctoral training in the laboratory of Prof. Ralph S. Wolfe at the University of Illinois. Prior to his graduate training in the Prof. Lacy Daniels' laboratory at the University of Iowa, he worked as a biochemical engineer for Hindustan Antibiotics Limited in India. Mukhopadhyay's group studies the biochemical mechanisms used by microorganisms to survive under extreme conditions with specific focus on the methanogenic archaea, natural gas production and tuberculosis. They also examine the structure-function relationships of two CO2-fixing enzymes (PEPCK and PEPC) with relevance in type 2 diabetes and production of chemicals and food crop.