Name: Dr. Raghothama Chaerkady

Designation: Faculty Scientist

Department/Institute/University: Institute of Bioinformatics, Bangalore

Date of Birth: 21 July 1967 Sex (M/F): M SC/ST: No

Education (Post-Graduation onwards & Professional Career)

Institution
Place / Degree
Awarded / Year / Field of Study
1. / Kasturba Medical College, Manipal University, India. / M.Sc. / 1991 / Biochemistry
2. / Manipal University, India. / Ph.D. / 1999 / Biochemistry

I. Positions and Employment (Starting with the most recent employment)

2003-Present Faculty scientist, Institute of Bioinformatics, Bangalore, India

2001-2003 Postdoctoral Fellow, Mason Eye Institute, Missouri University, Columbia, MO

2000-2001 Assistant Professor, Biochemistry, Kasturba Medical College, Manipal, India.

1998-1999 Senior Lecturer, Biochemistry, Kasturba Medical College, Manipal, India.

1991-1998 Lecturer, Biochemistry, Kasturba Medical College, Manipal, India.

Other Experience and Professional Memberships

2003-2004 Visiting scientist, (Proteomics), (2003-2004), NCBS, Bangalore, India

Honors

2004 Young Investigator Award, Human Proteome Organization (HUPO), Beijing, China.

1993 Dr Pai Gold medal for best research papers published in 1993 and 1996 – KMC Manipal

Reviewer for journals

Proteomics , Journal of Proteome Research and Trends in Analytical Chemistry

II. PUBLICATIONS (Numbers only): 41

Research Papers: 30; Review Articles: 7, Book Chapters: 2

a) Six recent publications relevant to the proposed area of work

Chaerkady, R. and Pandey, A. (2007). *Quantitative proteomics for identification of cancerbiomarkers. Proteomics - Clinical Applications. 1, 1080-1089.* “Most accessed” article during2007-2008.

Chaerkady, R., Thuluvath, P.J., Kim, M., Nalli, A., Vivekanandan, P., Simmers, J., Torbenson, M.and Pandey, A. (2008). 18O labeling for a quantitative proteomic analysis of glycoproteins inhepatocellular carcinoma. Clinical Proteomics. 9, 1080-1089.

Chaerkady, R., Harsha, H. C., Nalli, A., Gucek, M., Vivekanandan, P., Akhtar, J., Cole, R.N.,Simmers, J., Schulick, R., Singh, S., Torbenson, M., Pandey, A. and Thuluvath, P. J. (2008). A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma.Journal of Proteome Research. 7, 4289-4298.

Song, D., Chaerkady, R., Tan, A. C., García-García, E., Nalli, A., Suárez-Gauthier, A., López-Ríos,F., Zhang, X., Solomon, A., Tong, J., Read, M., Fritz, C., Jimeno, A., Pandey, A. and Hidalgo, M.(2008). Antitumor activity and molecular effects of the novel Hsp 90 inhibitor, IPI-504, in pancreaticcancer. Molecular Cancer Therapeutics. 7, 3275-3284.

Zhong, L., Roybal, J., Chaerkady, R., Zhang, W., Choi, K., Tran, H., Yan, S., Strieter, R. M., Pandey,A. and Kurie, J. M. (2008). Identification of secreted proteins that mediate cell-cell interactions in anin vitro model of the lung cancer microenvironment. Cancer Research. 68, 7237-7245.

Chaerkady, R*., Kerr, C. L., Kandasamy, K., Marimuthu, A., Gearhart, J. D. and Pandey, A. (2010).Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics,10, 1359-1373. “Most accessed” article during 2010.

b) Ten additional recent publications

Chaerkady, R. and Pandey, A. (2003). Absolute systems biology--measuring dynamics ofprotein modifications. Trends in Biotechnology. 21, 467-470.

Chaerkady, R., Harsha, H. C., Prasad, C. K. and Pandey, A. (2005). Bioinformatics andproteomicsapproaches for aging research. Biogerontology. 6, 1–6.

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., Chaerkady, R., Prasad, C. K. and Pandey, A. (2005). A manually curated functional annotation of the human X chromosome. Nature Genetics. 37, 331-332.

Chaerkady, R.* and Pandey, A. (2008). Applications of proteomics to lab diagnosis. Annual Review of Pathology. 3, 485-498.* Corresponding author

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., Prasad, T. S. K. and Pandey, A. (2009). Human Proteinpedia: A unified discovery resource for proteomics research. Nucleic Acids Research. 37, D767-D772.

Prasad, T. S. K., 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., Kishore, C. J. H., Kanth, S., Ahmed, M., Kashyap, M., Mohmood, R., Ramachandra, Y. L., Krishna, V., Rahiman, A. B., Mohan, S., Ranganathan, P., Ramabadran, S., Chaerkady, R. and Pandey, A. (2009). Human Protein Reference Database – 2009 update. Nucleic Acids Research. 37, D773-D781.

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. (2009). Temporal profiling of the adipocyte proteome during differentiation using a 5-plex SILAC based strategy. Journal of Proteome Research. 8, 48-58.

Yang, Y., Chaerkady, R., Beer, M. A., Mendell, J. T. and Pandey, A. (2009). Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics. 9, 1374-1384. “Most accessed” article during 2009-2010.

Chaerkady, R., Kerr, C. L., Marimuthu, A., Kelkar, D. S., Kashyap, M. K., Gucek, M., Gearhart, J. D. and Pandey, A. (2009). Temporal analysis of neural differentiation using quantitative proteomics. Journal of Proteome Research. 8, 1315–1326.

Pimienta, G., Chaerkady, R., Pandey, A. (2009). SILAC for Global Phosphoproteomic Analysis.Methods in Molecular Biology. 527,107-116.

III. Research Support
Ongoing Research Projects
Sl No. / Title of Project / Funding Agency / Amount / Date of sanction and Duration
1 / Program Support on
neuroproteomics / DBT / 8.68 crores
(INR) / 26/12/2008
5 years
2 / Netpath: Signaling pathway project / MSKCC / $ 40,000 / 01/01/2006; one time
3 / Plasma Proteome Database project / HUPO / $ 30,000 / 03/09/2004;
one time
4 / Human Protein Reference Database project / NCBI & JHU / $ 200,000 / 01/10/2004;
4 years

Completed Research Projects (State only major projects of last 3 years)

Sl No. / Title of Project / Funding Agency / Amount / Date of completion
1 / Protein Tyrosine Phosphatase project / Internal funding / NA / July 2005

Place: Bangalore Signature of Investigator
Date: May 10, 2010

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