| Associate Professor, Departments of Biological Chemistry, Pathology and Oncology |  |
Education and Training: - M.D., Armed Forces Medical College, Pune, India, 1988
- Intern in Medicine, Kilpauk Medical College, Madras, India, 1990
- Ph.D. in Pathology, University of Michigan, 1995
- Postdoc in Pathology, University of Michigan, 1996
- Resident in Clinical Pathology, Harvard, 1998
- Postdoc, Whitehead Institute for Biomedical Research, 2000
- Visiting Scientist, University of Southern Denmark, 2001
Main Interests:
The Pandey Lab is comprised of an interdisciplinary group of molecular biologists, mass spectrometrists, and computational biologists who are interested in systems biology.
Signal Transduction: Cell-surface receptors transmit signals to the interior of the cell upon binding to a ligand. We have cloned a number of signaling molecules that are involved in signal transduction through receptor tyrosine kinases and cytokine receptors. Using a combination of molecular biology and proteomics-based approaches including mass spectrometry, our laboratory is dissecting these signaling pathways further. We are also using peptide and protein microarrays as well as computational methods for identification of tyrosine kinase substrates and phosphorylation sites.
Mass Spectrometry: We are using state-of-the-art mass spectrometric methods for identification of proteins, for characterizing post-translational modifications in signal transduction pathways and in the analysis of different cancers. Techniques that help us quantitate levels of protein as well as post-translational modifications are being applied to various biological projects. Computational methods that allow researchers to extract annotated information from existing databases, including genomic databases, while performing searches using mass spectrometry-derived data are being developed.
Bioinformatics: Our 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 ( http://www.ibioinformatics.org), we have recently developed a Human Protein Reference Database (http://www.hprd.org ). Our other interests include analysis of protein interactions networks and application of signaling networks in the context of microarray data.
Cancer Biomarkers: We are using proteomic approaches to identify potential biomarkers for early diagnosis of cancers. We are using body fluids (e.g. nipple aspirate, bile, pancreatic juice, serum) as well as tissue for identification of differentially expressed proteins by mass spectrometry. We use immunohistochemistry on tissue microarrays and ELISA assays on serum for validation of the biomarkers identified using mass spectrometry.
- Phosphorylation and signal transduction
- Proteomics and mass spectrometry
- Bioinformatics
- Databases
- Preceptor, Biological Chemistry, BCMB and Human Genetics
- Editorial Board Member: Genome Research, Clinical Proteomics, Journal of Proteome Research
- Howard Temin Award, National Cancer Institute, 1997
- Sidney Kimmel Foundation scholar, 2003
- Beckman Young Investigator Award, 2004
- Era of Hope Scholar Award, Department of Defense, 2006
Publications: Gandhi, T. K. B., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periyaswamy, B., Mishra, G., Nandakumar, K., Shen, B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J. S. and Pandey, A. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 3, 285-293. PubMed Reference
Qiao, Y., Molina, H., Pandey, A., Zhang, J. and Cole, P. A. (2006). Chemical rescue of a mutant enzyme in living cells. Science. 311, 1293-1297. PubMed Reference
Gronborg, M. Kristiansen, T. Z., Iwahori, A., Chang, R., Reddy, R., Sato, N., Molina, H., Jensen, O. N., Hruban, R. H., Goggins, M. G., Maitra, A. and Pandey, A. (2006). Biomarker discovery from pancreatic cancer secretome using a differential proteomics approach. Molecular and Cellular Proteomics. 5, 157-171. PubMed Reference
Harsha, H. C., Suresh, S., Amanchy, R., Deshpande, N., Shanker, K., Yatish, A. J., Muthusamy, B., Vrushabendra, B. M., Rashmi, B. P., Chandrika, K. N., Padma, N., Sharma, S., Badano, J. L, Ramya, M. A., Shivashankar, H.N., Peri, S., Choudhury, D. R., Kavitha, M. P., Saravana, R., Niranjan, V., Gandhi, T. K. B., Ghosh, N., Chandran, S., Menezes, M., Joy, M., Mohan, S. S., Katsanis, N., Deshpande, K. S., Raghothama, C., Prasad, C. K., and Pandey, A. (2005) A manually curated functional annotation of the human X chromosome. Nature Genetics. 37, 322-323. PubMed Reference
Amanchy, R., Kalume, D. E., Iwahori, A., Zhong, J. and Pandey, A. (2005) Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). Journal of Proteome Research. 4, 1661-1671. PubMed Reference
Amanchy, R., Kalume, D. E. and Pandey A. (2005) Stable isotope labeling with amino acids in cell culture (SILAC) for studying dynamics of protein abundance and post-translational modifications. Science's STKE 2005. pl2. PubMed Reference
Molina, H., Parmigiani, G. and Pandey, A. (2005). Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. Analytical Chemistry. 77, 2739-2744. PubMed Reference
Kalume, D. E., Peri, S., Zhong, J., Okulate, M., Reddy, R., Kumar, N. and Pandey, A. (2005) Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics. 6:128. PubMed Reference
Muthusamy, B., Hanumanthu, G., Reshmi, R., Sriranjini, S., Suresh, S., Rekha, B., Srinivas, D., Karthick, L., Vrushabendra, B. M., Sharma, S., Mishra, G., Rashmi, B. P., Kadekar, S., Chatterjee, P., Mangala, K. S., Shivashankar, H. N., Chandrika, K. N., Deshpande, N., Suresh, M., Kannabiran, N., Niranjan, V., Nalli, A., Prasad, T. S. K., Arun, K. S., Reddy, R., Chandran, S., Jadhav, T., Julie, D., Mahesh, M., John, S. L., Palvankar, K., Sudhir, D., P. Bala., Jithesh, M. K., Rashmi, N. S., Vishnupriya, G., Dhar, K., Reshma, S., Raghothama, C., Prasad, C. K. Gandhi, T. K. B., Harsha, H. C., Mohan, S. S., Deshpande, K. S., Sarker, M. and Pandey, A. (2005) Plasma proteome database as a resource for proteomics research. Proteomics. 5, 3531-3536. PubMed Reference
Rhodes, D. R., Tomlins, S. A., Varambally, S., Mahavisno, V., Barrette, T., Kalyana-Sundaram, S., Ghosh, D., Pandey, A. and Chinnaiyan, A. M. (2005) Probabilistic model of the human protein-protein interaction network. Nature Biotechnology. 23, 951-959. PubMed Reference
Ibarrola, N., Molina, H., Iwahori, A. and Pandey, A. (2004) A novel proteomic approach for specific identification of tyrosine kinase substrates using 13C-labeled tyrosine. Journal of Biological Chemistry. 279, 15805-15813. PubMed Reference
Kristiansen, T. Z., Bunkenborg, J., Gronborg, M., Molina, H., Thuluvath, P. J., Argani, P., Goggins, M. G., Maitra, A. and Pandey, A. (2004). A proteomic analysis of human bile. Molecular and Cellular Proteomics. 3, 715-728. PubMed Reference
Akhilesh Pandey, MD, PhD Johns Hopkins School of Medicine
733 N Broadway
Breadway Research Building, Rm 569
Baltimore, MD 21205
Phone: (410) 502-6662
Fax: (410) 502-7544
E-Mail: pandey@jhmi.edu Visit the Pandey Lab
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