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Akhilesh Pandey, M.D., Ph.D.

Photo of Dr. Akhilesh Pandey, M.D., Ph.D.

Professor of Biological Chemistry

Research Interests: Comparative genomics; Bioinformatics and biological databases; Mass spectrometry and proteomics; Phosphorylation and signal transduction


Dr. Akhilesh Pandey is a professor of biological chemistry, oncology and pathology at the Johns Hopkins University School of Medicine. He is also a professor of molecular microbiology and immunology at Johns Hopkins Bloomberg School of Public Health. Dr. Pandey’s research focuses on global analysis of signal transduction pathways using mass spectrometry as well as bioinformatics, sequence databases and annotation.

Dr. Pandey earned his medical degree from Armed Forces Medical College and completed his residency in pathology at the Brigham and Women's Hospital (Harvard Medical School). He obtained his Ph.D. from the University of Michigan in molecular biology. He was a postdoctoral fellow in the laboratory of Dr. Harvey Lodish at the Massachusetts Institute of Technology’s Whitehead Institute for Biomedical Research.

Dr. Pandey developed the SILAC method for quantitative proteomics and methods to characterize signaling pathways in a global fashion using mass spectrometry-based proteomic methods. Dr. Pandey''s laboratory is known for taking a systems biology approach by combining many “-omics” technologies.

He has received numerous prestigious awards including the Experimental Pathologist-In-Training Award by the American Society for Investigative Pathology, Howard Temin Award from the National Cancer Institute, and the Sidney Kimmel Scholar Award by the Sidney Kimmel Foundation for Cancer Research. He has also received the Era of Hope Scholar Award by the United States Department of Defense.

Dr. Pandey serves as an editorial board member of Molecular and Cellular Proteomics, and the Journals of Proteome Research, Proteomics, Clinical Proteomics, Clinical and Translational Medicine and DNA Research. more


  • Professor of Biological Chemistry
  • Professor of Oncology
  • Professor of Pathology



  • M.D., Armed Forces Medical College - University of Pune - Pune - Maharashtra - (India) (1988)
  • Ph.D., University of Michigan (Michigan) (1995)

Additional Training

Brigham and Women's Hospital, Boston, MA, 1998, Residency in Clinical Pathology; University of Michigan, Ann Arbor, MI, 1996, Molecular Biology; Whitehead Institute/MIT, Cambridge, MA, 1999, Molecular Biology

Research & Publications

Research Summary

Dr. Pandy’s work includes:

Signal transduction and cancer biology - Cell surface receptors transmit signals to the interior of the cell upon binding to a ligand. He and his team have cloned a number of signaling molecules that are involved in signal transduction through receptor tyrosine kinases and cytokine receptors. Combining molecular biology and quantitative proteomics including SILAC and iTRAQ, the laboratory is dissecting these signaling pathways in various malignancies including lung cancer, breast cancer, pancreatic cancer, gastric cancer, cholangiocarcinoma and leukemias.

MiRNA biology: microRNAs have been shown to be critical for post-transcriptional regulation of the genome. By binding to mRNAs, miRNAs can modulate translation through mechanisms that are not yet fully elucidated. Using quantitative proteomics, his laboratory has successfully identified potential targets of microRNAs miR-21 and miR-143. They also generated SILAC mice to study the function of Dicer and its impact on global proteomic changes.

Mass spectrometry: High-resolution mass spectrometry has become a core technology for large scale analysis of the proteome, lipidome and metabolome. Targeted analysis of molecules of interest is an emerging technology for accurate quantitative analyses by applying MRM (multiple reaction monitoring) on triple quadrupole mass spectrometer. The Pandey Lab has a special interest in developing mass spectrometric methods for highly sensitive and accurate detection of molecules.

Human genome analysis and bioinformatics: His research in bioinformatics mainly involves functional annotation of genomes, creation of databases, comparative genomics and experimental approaches for validating computational predictions. In collaboration with the Institute of Bioinformatics in Bangalore, India, the Pandey Lab has developed several resources focusing on human proteins and pathways: Human Protein Reference Database catalogs all human proteins, their modular domain structures and interaction partners. NetPath is a curated resource of signal transduction pathways in humans. They have also initiated a community resource, Human Proteinpedia, to share and integrate protein data in humans.


The Pandey Lab is a systems biology lab that combines molecular biology, analytical chemistry and computational biology with various "-omics" technologies, including genomics and proteomics, to understand signaling pathways and to identify therapeutic targets and biomarkers in a number of cancers.

Lab Website: Pandey Lab

Selected Publications

View all on Pubmed

Nanjappa, V., Thomas, J. K., Marimuthu, A., Muthusamy, B., Radhakrishnan, A., Sharma, R., Khan, A. A., Balakrishnan, L., Sahasrabuddhe, N., Kumar, S., Jhaveri, B. N., Sheth, K. V., Khatana, R. K., Shaw, P. G., Srikanth, S. M., Mathur, P. P., Shankar, S., Nagaraja, D., Christopher, R., Mathivanan, S., Raju, R., Sirdeshmukh, R., Chatterjee, A., Simpson, R. J., Harsha, H. C., Pandey, A. and Prasad, T. S. K. "Plasma Proteome Database as a resource for proteomics research: 2014 update." Nucleic Acids Research, 2014, 42, D959-D965.

Balakrishnan, L., Bhattacharjee, M., Ahmad, S., Nirujogi, R. S., Renuse, S., Subbannayya, Y., Marimuthu, A., Srikanth, S. M., Raju, R., Dhillon, M., Kaur, N., Jois, R., Vasudev, V., Ramachandra, Y. L., Sahasrabuddhe, N. A., Prasad, T. S. K., Mohan, S., Gowda, H., Shankar, S. and Pandey, A. "Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients." Clinical Proteomics, 2014. In press.

Zhong, J., Sharma, J., Raju, R., Palapetta, S. M., Prasad, T. S. K., Huang, T. C., Yoda, A., Tyner, J. W., van Bodegom, D., Weinstock, D. M., Ziegler, S. F. and Pandey, A. "TSLP signaling pathway map: A platform for analysis of TSLP mediated signaling." Database, 2014. In press.

Selvan, L. D. N., Kaviyil, J. E., Nirujogi, R. S., Muthusamy, B., Puttamallesh, V. N., Subbannayya, T., Syed, N., Radhakrishnan, A., Kelkar, D. S., Ahmad, S., Pinto, S. M., Kumar, P., Madugundu, A. K., Nair, B., Chatterjee, A., Pandey, A., Ravikumar, R., Gowda, H. and Prasad, T. S. K. "Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry." Clinical Proteomics, 2014. In press.

Sreenivasamurthy, S. K., Dey, G., Ramu, M., Kumar, M., Gupta, M. K., Mohanty, A. K., Harsha, H. C., Sharma, P., Kumar, N., Pandey, A., Kumar, A. and Prasad, T. S. K. "A compendium of molecules involved in vector-pathogen interactions pertaining to malaria." Malaria Journal, 2013, 12, 216.

Academic Affiliations & Courses

Graduate Program Affiliation

Graduate Program in Biological Chemistry

Activities & Honors


  • Experimental Pathologist-in-training Award, American Society for Investigative Pathology, 1996
  • Era of Hope Scholar Award, Department of Defense, 2006
  • Howard Temin Award, National Cancer Institute, 1997
  • Kimmel Scholar Award, Sidney Kimmel Foundation for Cancer Research, 2003
  • Era of Hope Scholar Award, DOD, 2006
  • Beckman Young Investigator Award, 2004


  • American Association for Cancer Research, 2003
  • American Chemical Society, 2004
  • American Society for Biochemistry and Molecular Biology, 1998
  • American Society for Mass Spectrometry, 2000
  • American Society of Investigative Pathology, 1995
  • Human Proteome Organization, 2003
  • U.S. Human Proteome Organization, 2004

Professional Activities

  • American Society for Biochemistry and Molecular Biology
  • American Association for Cancer Research
  • American Society for Mass Spectrometry
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