INCREDB ID : 173
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Raghothama Chaerkady, Ph.D.
Faculty Scientist 
 
Institute of Bioinformatics
Discoverer Building, International Tech Park, Whitefield
Bangalore - 560 066    
Karnataka   
 
E-mail: raghothama@ibioinformatics.org
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:
Genomics
Proteomics
Bioinformatics and Databases
Publications:
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
 
Education 
::
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
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1993 and 1996, Dr. Pai Gold medal for best research papers published, KMC Manipal
Member
::
Reviewer - Journal of Proteome Research, Proteomics,Trends in Analytical Chemistry
  Last modified on : Mar 4, 2011
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