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Akhilesh Pandey Portrait

Akhilesh Pandey
Professor of Biological Chemistry
Johns Hopkins University School of Medicine

527 Broadway Research Building
733 N. Broadway
Baltimore, MD21205
Office Phone: 410-502-6662
Lab Phone: 410-502-6665
Fax: 410-502-7544
Email: pandey@jhmi.edu
Lab Web Site

Click Here for PDF of CV

Global analysis of signal transduction pathways using mass spectrometry; Bioinformatics, sequence databases and annotation

The Pandey Lab is a systems biology lab that integrates molecular and cellular biology, genomics, proteomics and bioinformatics.
 

Signal Transduction and Cancer Biology: 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. Combining molecular biology and quantitative proteomics including SILAC and iTRAQ, our 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, our laboratory has successfully identified potential targets of microRNAs miR-21 and miR-143. We 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: 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, we have 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. We have also initiated a community resource, Human Proteinpedia, to share and integrate protein data in humans.

Recent Publications

Chen H, Pimienta G, Gu Y, Sun X, Hu J, Kim MS, Chaerkady R, Gucek M, Cole RN, Sukumar S, Pandey A. (2010) Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 10, 3800-3810. 
PubMed Reference 

Zhong J, Krawczyk SA, Chaerkady R, Huang H, Goel R, Bader JS, Wong GW, Corkey BE, Pandey A. (2010) Temporal profiling of the secretome during adipogenesis in humans. Journal of Proteome Research. 9, 5228-5238.
PubMed Reference 

Yang Y, Chaerkady R, Kandasamy K, Huang TC, Selvan LD, Dwivedi SB, Kent OA, Mendell JT, Pandey A. (2010) Identifying targets of miR-143 using a SILAC-based proteomic approach. Molecular Biosystems. 6,1873-1882.
PubMed Reference 

Kim MS, Kandasamy K, Chaerkady R, Pandey A.(2010) Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer. Journal of American Society of Mass Spectrometry. 21,1606-1611.
PubMed Reference 

Zhong J, Pandey A. (2010) Site-directed mutagenesis reveals a unique requirement for tyrosine residues in IL-7Ralpha and TSLPR cytoplasmic domains in TSLP-dependent cell proliferation. BMC Immunology. 11, 5.
PubMed Reference 

Chaerkady R, Kerr CL, Kandasamy K, Marimuthu A, Gearhart JD, Pandey A. (2010) Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics. 10,1359-1373.
PubMed Reference 

Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A. (2010) NetPath: a public resource of curated signal transduction pathways. Genome Biology. 11, R3.
PubMed Reference 

Yang Y, Chaerkady R, Beer MA, Mendell JT, Pandey A.(2009) Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics. 9,1374-1384.
PubMed Reference 

Harsha HC, Kandasamy K, Ranganathan P, Rani S, Ramabadran S, Gollapudi S, Balakrishnan L, Dwivedi SB, Telikicherla D, Selvan LDN, Goel R, Mathivanan S, Marimuthu A, Kashyap MK, Vizza RF, Mayer RJ, DeCaprio JA, Srivastava S, Hanash SM, Hruban RH, Pandey A. (2009) A compendium of potential biomarkers of pancreatic cancer. PLoS Medicine. 6, e1000046.
PubMed Reference 

Chaerkady R, Kerr CL, Marimuthu A, Kelkar DS, Kashyap MK, Gucek M, Gearhart JD, Pandey A. (2009) Temporal analysis of neural differentiation using quantitative proteomics. Journal of Proteome Research. 8, 1315-1326.
PubMed Reference 

Molina, H, Yang Y, Ruch T, Kim JW, Mortensen P, Otto T, Nalli A, Tang QQ, Lane MD, Chaerkady R, Pandey A. (2009) Temporal profiling of the adipocyte proteome during differentiation using a 5-plex SILAC based strategy. Journal of Proteome Research. 8, 48-58.
PubMed Reference 

Mathivanan S, 158 coauthors, Pandey A. (2008) Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-167.
PubMed Reference 

Guha U, Chaerkady R, Marimuthu A, Patterson AS, Kashyap MK, Harsha HC, Sato M, Bader JS, Lash AE, Minna JD, Pandey A, Varmus HE. (2008) Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proceedings of National Academy of Sciences of the United States of America. 105, 14112-14117.
PubMed Reference 

Harsha HC, Molina H, Pandey A. (2008) Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nature Protocols. 3, 505-516.
PubMed Reference 

Molina, H., Horn, D. M., Tang, N., Mathivanan, S. and Pandey, A. (2007). Global Proteomic Profiling of Phosphopeptides using Electron Transfer Dissociation Tandem Mass Spectrometry. Proceedings of the National Academy of Sciences, USA. 104, 2199-2204.
PubMed Reference 

Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R., Tattikota, S. G. and Pandey, A. (2007). A compendium of curated phosphorylation-based substrate and binding motifs. Nature Biotechnology. 25, 285-286.
PubMed Reference 

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


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