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Raghothama Chaerkady, Ph.D.
Faculty Scientist 
Institute of Bioinformatics
Discoverer Building, International Tech Park, Whitefield
Bangalore - 560 066    
Phone: +91-80-28416140
Fax: +91-80-28416132
Positions Held:
Position Affiliation Time Period
Faculty Scientist Institute of Bioinformatics, Bangalore, India 2003-Present
Visiting Scientist National Centre for Biological Sciences, Tata Institute of Fundemental Research, Bangalore, India 2003-2004
Assistant Professor Kasturba Medical College, Manipal, India 2000-2001
Senior Lecturer Kasturba Medical College, Manipal, India 1998-1999
Lecturer Kasturba Medical College, Manipal, India 1991-1998
Area of Specialization:
Bioinformatics and Databases
1. Wang, Q., Chaerkady, R., Wu, J., Hwang, H. J., Papadopoulos, N., Kopelovich, L., Maitra, A., Matthaei, H., Eshleman, J. R., Hruban, R. H., Kinzler, K. W., Pandey, A. and Vogelstein, B.  Mutant proteins as cancer-specific biomarkers. Proceedings of the National Academy of Sciences of the United States of America. 2011. [PubMed]
2. Renuse, S., Chaerkady, R. and Pandey, A.  Proteogenomics. Proteomics. 2010. [PubMed]
3. Zhong, J., Chaerkady, R., Kandasamy, K., Gucek, M., Cole, R. N. and Pandey, A.  The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. Journal of Proteomics. 2011. 74, 294-303. [PubMed]
4. Chen, H., Pimienta, G., Gu, Y., Sun, X., Hu, J., Kim, M. S., Chaerkady, R., Gucek, M., Cole, R. N., Sukumar, S. and Pandey, A.  Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 2010. 10, 3800-10. [PubMed]
5. Zhong, J., Krawczyk, S. A., Chaerkady, R., Huang, H., Goel, R., Bader, J. S., Wong, G. W., Corkey, B. E. and Pandey, A.  Temporal profiling of the secretome during adipogenesis in humans. Journal of Proteome Research. 2010. 9, 5228-38. [PubMed]
6. Kashyap, M. K., Harsha, H. C., Renuse, S., Pawar, H., Sahasrabuddhe, N. A., Kim, M. S., Marimuthu, A., Keerthikumar, S., Muthusamy, B., Kandasamy, K., Subbannayya, Y., Prasad, T. S., Mahmood, R., Chaerkady, R., Meltzer, S. J., Kumar, R. V., Rustgi, A. K. and Pandey, A.  SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biology & Therapy. 2010. 10. [PubMed]
7. Yang, Y., Chaerkady, R., Kandasamy, K., Huang, T. C., Selvan, L. D., Dwivedi, S. B., Kent, O. A., Mendell, J. T. and Pandey, A.  Identifying targets of miR-143 using a SILAC-based proteomic approach. Molecular BioSystems. 2010. 6, 1873-82. [PubMed]
8. Kim, M. S., Kandasamy, K., Chaerkady, R. and Pandey, A.  Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer. Journal of the American Society for Mass Spectrometry. 2010. 21, 1606-11. [PubMed]
9. Venugopal, A., Chaerkady, R. and Pandey, A.  Application of mass spectrometry-based proteomics for biomarker discovery in neurological disorders. Annals of Indian Academy of Neurology. 2009. 12, 3-11. [PubMed]
10. Chaerkady, R., Kerr, C. L., Kandasamy, K., Marimuthu, A., Gearhart, J. D. and Pandey, A.  Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics. 2010. 10, 1359-73. [PubMed]
11. Zhou, Q., Chaerkady, R., Shaw, P. G., Kensler, T. W., Pandey, A. and Davidson, N. E.  Screening for therapeutic targets of vorinostat by SILAC-based proteomic analysis in human breast cancer cells. Proteomics. 2010. 10, 1029-39. [PubMed]
12. Yang, Y., Chaerkady, R., Beer, M. A., Mendell, J. T. and Pandey, A.  Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics. 2009. 9, 1374-84. [PubMed]
13. Pimienta, G., Chaerkady, R. and Pandey, A.  SILAC for global phosphoproteomic analysis. Methods in Molecular Biology. 2009. 527, 107-16, x. [PubMed]
14. Chaerkady, R., Kerr, C. L., Marimuthu, A., Kelkar, D. S., Kashyap, M. K., Gucek, M., Gearhart, J. D. and Pandey, A.  Temporal analysis of neural differentiation using quantitative proteomics. Journal of Proteome Research. 2009. 8, 1315-26. [PubMed]
15. Keshava, P., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A., Balakrishnan, L., Marimuthu, A., Banerjee, S., Somanathan, D. S., Sebastian, A., Rani, S., Ray, S., Harrys, K., Kanth, S., Ahmed, M., Kashyap, M. K., Mohmood, R., Ramachandra, Y. L., Krishna, V., Rahiman, B. A., Mohan, S., Ranganathan, P., Ramabadran, S., Chaerkady, R. and Pandey, A.  Human Protein Reference Database--2009 update. Nucleic Acids Research. 2009. 37, D767-72. [PubMed]
16. Kandasamy, K., Keerthikumar, S., Goel, R., Mathivanan, S., Patankar, N., Shafreen, B., Renuse, S., Pawar, H., Ramachandra, Y. L., Acharya, P. K., Ranganathan, P., Chaerkady, R., Keshava, P. and Pandey, A.  Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Research. 2009. 37, D773-81. [PubMed]
17. Molina, H., Yang, Y., Ruch, T., Kim, J. W., Mortensen, P., Otto, T., Nalli, A., Tang, Q. Q., Lane, M. D., Chaerkady, R. and Pandey, A.  Temporal profiling of the adipocyte proteome during differentiation using a five-plex SILAC based strategy. Journal of Proteome Research. 2009. 8, 48-58. [PubMed]
18. Song, D., Chaerkady, R., Tan, A. C., Garcia-Garcia, E., Nalli, A., Suarez-Gauthier, A., Lopez-Rios, F., Zhang, X. F., Solomon, A., Tong, J., Read, M., Fritz, C., Jimeno, A., Pandey, A. and Hidalgo, M.  Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer. Molecular Cancer Therapeutics. 2008. 7, 3275-84. [PubMed]
19. Guha, U., Chaerkady, R., Marimuthu, A., Patterson, A. S., Kashyap, M. K., Harsha, H. C., Sato, M., Bader, J. S., Lash, A. E., Minna, J. D., Pandey, A. and Varmus, H. E.  Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proceedings of the National Academy of Sciences of the United States of America. 2008. 105, 14112-7. [PubMed]
20. Zhong, L., Roybal, J., Chaerkady, R., Zhang, W., Choi, K., Alvarez, C. A., Tran, H., Creighton, C. J., Yan, S., Strieter, R. M., Pandey, A. and Kurie, J. M.  Identification of secreted proteins that mediate cell-cell interactions in an in vitro model of the lung cancer microenvironment. Cancer Research. 2008. 68, 7237-45. [PubMed]
21. Chaerkady, R., Harsha, H. C., Nalli, A., Gucek, M., Vivekanandan, P., Akhtar, J., Cole, R. N., Simmers, J., Schulick, R. D., Singh, S., Torbenson, M., Pandey, A. and Thuluvath, P. J.  A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma. Journal of Proteome Research. 2008. 7, 4289-98. [PubMed]
22. Amanchy, R., Zhong, J., Molina, H., Chaerkady, R., Iwahori, A., Kalume, D. E., Gronborg, M., Joore, J., Cope, L. and Pandey, A.  Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. Journal of Proteome Research. 2008. 7, 3900-10. [PubMed]
23. Chaerkady, R., Thuluvath, P. J., Kim, M. S., Nalli, A., Vivekanandan, P., Simmers, J., Torbenson, M. and Pandey, A.  O Labeling for a Quantitative Proteomic Analysis of Glycoproteins in Hepatocellular Carcinoma. Clinical Proteomics. 2008. 4, 137-155. [PubMed]
24. Luo, W., Slebos, R. J., Hill, S., Li, M., Brabek, J., Amanchy, R., Chaerkady, R., Pandey, A., Ham, A. J. and Hanks, S. K.  Global impact of oncogenic Src on a phosphotyrosine proteome. Journal of Proteome Research. 2008. 7, 3447-60. [PubMed]
25. Basu, B., Desai, R., Balaji, J., Chaerkady, R., Sriram, V., Maiti, S. and Panicker, M. M.  Serotonin in pre-implantation mouse embryos is localized to the mitochondria and can modulate mitochondrial potential. Reproduction. 2008. 135, 657-69. [PubMed]
26. Mathivanan, S., Ahmed, M., Ahn, N. G., Alexandre, H., Amanchy, R., Andrews, P. C., Bader, J. S., Balgley, B. M., Bantscheff, M., Bennett, K. L., Bjorling, E., Blagoev, B., Bose, R., Brahmachari, S. K., Burlingame, A. S., Bustelo, X. R., Cagney, G., Cantin, G. T., Cardasis, H. L., Celis, J. E., Chaerkady, R., Chu, F., Cole, P. A., Costello, C. E., Cotter, R. J., Crockett, D., DeLany, J. P., De, M., DeSouza, L. V., Deutsch, E. W., Dransfield, E., Drewes, G., Droit, A., Dunn, M. J., Elenitoba-Johnson, K., Ewing, R. M., Van, E. y. k., Faca, V., Falkner, J., Fang, X., Fenselau, C., Figeys, D., Gagne, P., Gelfi, C., Gevaert, K., Gimble, J. M., Gnad, F., Goel, R., Gromov, P., Hanash, S. M., Hancock, W. S., Harsha, H. C., Hart, G., Hays, F., He, F., Hebbar, P., Helsens, K., Hermeking, H., Hide, W., Hjerno, K., Hochstrasser, D. F., Hofmann, O., Horn, D. M., Hruban, R. H., Ibarrola, N., James, P., Jensen, O. N., Jensen, P. H., Jung, P., Kandasamy, K., Kheterpal, I., Kikuno, R. F., Korf, U., Korner, R., Kuster, B., Kwon, M. S., Lee, H. J., Lee, Y. J., Lefevre, M., Lehvaslaiho, M., Lescuyer, P., Levander, F., Lim, M. S., Lobke, C., Loo, J. A., Mann, M., Martens, L., Martinez-Heredia, J., McComb, M., McRedmond, J., Mehrle, A., Menon, R., Miller, C. A., Mischak, H., Mohan, S. S., Mohmood, R., Molina, H., Moran, M. F., Morgan, J. D., Moritz, R., Morzel, M., Muddiman, D. C., Nalli, A., Navarro, J. D., Neubert, T. A., Ohara, O., Oliva, R., Omenn, G. S., Oyama, M., Paik, Y. K., Pennington, K., Pepperkok, R., Periaswamy, B., Petricoin, E. F., Poirier, G. G., Prasad, T. S., Purvine, S. O., Rahiman, B. A., Ramachandran, P., Ramachandra, Y. L., Rice, R. H., Rick, J., Ronnholm, R. H., Salonen, J., Sanchez, J. C., Sayd, T., Seshi, B., Shankari, K., Sheng, S. J., Shetty, V., Shivakumar, K., Simpson, R. J., Sirdeshmukh, R., Siu, K. W., Smith, J. C., Smith, R. D., States, D. J., Sugano, S., Sullivan, M., Superti-Furga, G., Takatalo, M., Thongboonkerd, V., Trinidad, J. C., Uhlen, M., Vandekerckhove, J., Vasilescu, J., Veenstra, T. D., Vidal-Taboada, J. M., Vihinen, M., Wait, R., Wang, X., Wiemann, S., Wu, B., Xu, T., Yates, J. R., Zhong, J., Zhou, M., Zhu, Y., Zurbig, P. and Pandey, A.  Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 2008. 26, 164-7. [PubMed]
27. Chaerkady, R. and Pandey, A.  Applications of proteomics to lab diagnosis. Annual Review of Pathology. 2008. 3, 485-98. [PubMed]
28. Chaerkady, R. and Pandey, A.  Quantitative proteomics for identification of cancer biomarkers. Proteomics. Clinical Applications. 2007. 1, 1080-9. [PubMed]
29. Raghothama, C., Harsha, H. C., Prasad, C. K. and Pandey, A.  Bioinformatics and proteomics approaches for aging research. Biogerontology. 2005. 6, 227-32. [PubMed]
30. Ping, P., Vondriska, T. M., Creighton, C. J., Gandhi, T. K., Yang, Z., Menon, R., Kwon, M. S., Cho, S. Y., Drwal, G., Kellmann, M., Peri, S., Suresh, S., Gronborg, M., Molina, H., Chaerkady, R., Rekha, B., Shet, A. S., Gerszten, R. E., Wu, H., Raftery, M., Wasinger, V., Schulz-Knappe, P., Hanash, S. M., Paik, Y. K., Hancock, W. S., States, D. J., Omenn, G. S. and Pandey, A.  A functional annotation of subproteomes in human plasma. Proteomics. 2005. 5, 3506-19. [PubMed]
31. Muthusamy, B., Hanumanthu, G., Suresh, S., Rekha, B., Srinivas, D., Karthick, L., Vrushabendra, B. M., Sharma, S., Mishra, G., Chatterjee, P., Mangala, K. S., Shivashankar, H. N., Chandrika, K. N., Deshpande, N., Suresh, M., Kannabiran, N., Niranjan, V., Nalli, A., Prasad, T. S., Arun, K. S., Reddy, R., Chandran, S., Jadhav, T., Julie, D., Mahesh, M., John, S. L., Palvankar, K., Sudhir, D., Bala, P., Rashmi, N. S., Vishnupriya, G., Dhar, K., Reshma, S., Chaerkady, R., Gandhi, T. K., Harsha, H. C., Mohan, S. S., Deshpande, K. S., Sarker, M. and Pandey, A.  Plasma Proteome Database as a resource for proteomics research. Proteomics. 2005. 5, 3531-6. [PubMed]
32. 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., Ghosh, N., Chandran, S., Menezes, M., Joy, M., Mohan, S. S., Katsanis, N., Deshpande, K. S., Raghothama, C., Prasad, C. K. and Pandey, A.  A manually curated functional annotation of the human X chromosome. Nature Genetics. 2005. 37, 331-2. [PubMed]
33. Chaerkady, R. and Sharma, K. K.  Characterization of a bradykinin-hydrolyzing protease from the bovine lens. Investigative Ophthalmology & Visual Science. 2004. 45, 1214-23. [PubMed]
34. Raghothama, C. and Pandey, A.  Absolute systems biology--measuring dynamics of protein modifications. Trends in Biotechnology. 2003. 21, 467-70. [PubMed]
35. Senthilkumar, R., Chaerkady, R. and Sharma, K. K.  Identification and properties of anti-chaperone-like peptides derived from oxidized bovine lens betaL-crystallins. The Journal of Biological Chemistry. 2002. 277, 39136-43. [PubMed]


Grant Support:
Project Title Role Funding Agency Sanction Number Sanction Date
Program Support on Neuroproteomics Department of Biotechnology, Government of India 2008-2013
Netpath: Signaling pathway project Memorial Sloan-Kettering Cancer Center, New York, USA 2006-2007
Plasma Proteome Database project Human Proteome Organisation, Montreal, Canada 2004-2005
Human Protein Reference Database project National Center for Biotechnology Information, National Institute of Health, Maryland, USA & Johns Hopkins University, Baltimore, USA 2004-2008
Protein Tyrosine Phosphatase project 2005


My CV:   Download
M.Sc. in Biochemistry, Kasturba Medical College, Manipal, India
Ph.D. in Biochemistry, Manipal University, Manipal, India
Honors and Awards
2004, Young Investigator Award, Human Proteome Organization, Beijing, China
1993 and 1996, Dr. Pai Gold medal for best research papers published, KMC Manipal
Reviewer - Journal of Proteome Research, Proteomics,Trends in Analytical Chemistry
  Last modified on : Mar 4, 2011
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