After completing her doctoral degree, Mukerji joined the Institute of Genomics and Integrative Biology in New Delhi in 1997. She has since worked in the field of population genetics and evolutionary genomics and has also had a particular interest in personalized medicine and the integration of Western Medicine and Ayurvedic medical practices. One of her most notable works was deciphering the functions of Alu regions, the most abundant transposon found in primate populations. Her and her team concluded that these sequences code for RNA that serve as transcription factors, regulating a multitude of cell functions, including heat shock stress responses. Mukerji's publications on Alu sequences provide evidence of its involvement in homeostatic maintenance in humans, as well as the functions of miRNA as regulatory pathways specific to humans. Mukerji has since continued to work in trying to understand the mechanisms behind heat shock response systems and the functions of satellite non-coding RNA as a transcriptional repressor. She took an active role in establishing the Indian Genome Variation Consortium. Created in 2003, this database collects information on the genetic variations between the multiple subpopulations in India in an effort to improve personalized pharmaceuticals and understand genetic predisposition to disease. She established that genomic data could be adopted to decipher "signatures of natural selection and tracing mutational histories", and has used her studies to track migration patterns of many Asian populations and disease origins. Data from this initiative was used in a publication Mukerji was a contributor on, linking the genetic ancestry of the Siddi people from the Western region of India to Bantu-speaking East African tribes. Another study in which Mukerji used the IGV database is in studying keratinization genes, associated with waterproofing epidermal layers and being a contributor to different skin phenotypes for populations living in different climates. She wanted to see whether or not this gene responds to environmental stresses and how intensely or rapidly. Using an analysis of copy number variants and DNA and protein sequence differences amongst diverse Indian populations from varying climates, Mukerji makes conclusions about the changes within this area of skin-related genes and the role it plays in adaptations in response to environmental stimuli. Mukerji has also done significant work towards bettering clinical diagnostics processes of disorders in India. She worked particularly with a group of neurodegenerative diseases known as Cerebellar ataxias, a heritable condition in which the cerebellum portion of the brain becomes damaged. This condition is known to arise from a combination of many mutations, and so establishing a clear genetic correlation is difficult, making clinical screening difficult as well.