She is best known for initiating the field of "Ayurgenomics" in partnership with her colleague Dr. Bhavana Prasher (MD Ayurveda) under the mentorship of Prof. Samir K. Brahmachari.
[3] In an interview, Mukerji states one of her most influential mentors has been Dr. Samir Kumar Brahmachari, the former Director General of the Council of Scientific and Industrial Research known for his works in biophysics and pharmacogenetics.
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.
[6] 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.
[8] 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.
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.
Analysis of single nucleotide polymorphisms in Indian and Mexican families show a shared expansion pattern in these two geographically distinct groups, making it possible to understand more about the ancestry of these particular mutations that cause this disease.
Their work helps better explain the mechanisms in play in dyslexia and the association of PCDHG genes with "neural adhesion proteins" that are related to cognitive functionality in primates.
[14] Along with her other projects tracking mutational history and disease evolution, Mukerji also did work studying correlations between polymorphisms in the APOBEC3B gene and malaria susceptibility.
[15] Mukerji actively initiated the field of "Ayurgenomics", integrating the phenotyping Ayurveda principles of Indian medical system with "objective parameters of modern medicine for identifying molecular endophenotypes."
[16] These "Prakriti's" are used for "assessing disease susceptibility and drug responsiveness", a concept that parallels ideas of personalized pharmaceuticals in Western Medicine.
[5] A unique finding of her studies in genomics is "that the ethnically and linguistically diverse Indian population was united by distinct DNA patterns".