Professor Shashidhara specialises in Genetics, Molecular Biology and Evolutionary biology. He started his independent career at CCMB, during which time, he was closely associated with Dr Lalji Singh.

His group has identified key mechanisms that specify organ development and regulate growth control during embryonic development using Drosophila as a model system. They have also expanded their study to examine the status of these evolutionarily conserved mechanisms in epithelial cancers in human. For his contribution to basic and applied biology, Professor Shashidhara is recognized with several Indian national awards including the highest science award the Shanti Swarup Bhatnagar Award. He is a Fellow of all three Science Academies of India. In 2018, Professor Shashidhara was elected as Associate member of European Molecular Biology Organization (EMBO), an international recognition for excellence in research in life sciences.

Professor Shashidhara is one of the founding academic members of Indian Institute of Science Education and Research (IISER) Pune and Ashoka University, contributing to their growth. Professor Shashidhara has served in the past as Vice-President of Indian National Science Academy (INSA) and as Secretary General and President of the International Union of Biological Sciences (IUBS). He is the first Indian to be elected as IUBS President in its 100 years of its history.