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CURRICULUM VITAE

AKHILESH PANDEY, M.D., PH.D. January 28, 2014

DEMOGRAPHIC AND PERSONAL INFORMATION Current Appointments Professor, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School

of Medicine Professor, Biological Chemistry, Johns Hopkins University School of Medicine Professor, Department of Oncology, Johns Hopkins University School of Medicine Professor, Department of Pathology, Johns Hopkins University School of Medicine Professor, Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg

School of Public Health Personal Data Broadway Research Building, Room 527 733 N. Broadway, Johns Hopkins University Baltimore, MD 21205 Phone: 410-502-6662 Fax: 410-552-7544 E-mail: pandey@jhmi.edu Education and Training M.D. 1984-1988 Armed Forces Medical College, Pune, India - Medicine Internship 1988-1989 Kilpauk Medical College, Madras, India - Medicine Ph.D. 1990-1995 University of Michigan, Ann Arbor, MI - Pathology Postdoctoral Fellow 1995-1996 Laboratory of Vishva Dixit, University of Michigan, Ann

Arbor, MI - Molecular Biology Resident 1996-1998 Department of Pathology, Brigham and Women’s Hospital,

Boston, MA - Clinical Pathology Postdoctoral Fellow 1996-1999 Laboratory of Harvey Lodish, Whitehead Institute/MIT,

Cambridge, MA - Molecular Biology Visiting Scientist 1999-2002 Laboratory of Matthias Mann, University of Southern

Denmark, Denmark - Mass Spectrometry

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Professional Experience Instructor Department of Pathology, Harvard Medical School, Boston, MA 1998-2002 Assistant Medical Director Clinical Microbiology Laboratory, Department of Pathology,

Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 1998-1999 Assistant Professor McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins

University School of Medicine, Baltimore, MD 2002-2006 Assistant Professor Department of Biological Chemistry, Johns Hopkins University School

of Medicine, Baltimore, MD 2002-2006 Assistant Professor Department of Oncology, Johns Hopkins University School of

Medicine, Baltimore, MD 2004-2006 Assistant Professor Department of Pathology, Johns Hopkins University School of

Medicine, Baltimore, MD 2005-2006 Associate Professor McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins

University School of Medicine, Baltimore, MD 2006-2010 Associate Professor Department of Biological Chemistry, Johns Hopkins University School

of Medicine, Baltimore, MD 2006-2010 Associate Professor Department of Oncology, Johns Hopkins University School of

Medicine, Baltimore, MD 2006-2010 RESEARCH ACTIVITIES Publications i) Peer-reviewed original articles 1. Pandey, A., Tjoelker, L.W. and Thompson, C.B. (1993). Restricted immunoglobulin junctional diversity in neonatal B cells results from developmental selection rather than homology-based V (D) J joining. Journal of Experimental Medicine. 177, 329-337. 2. Pandey, A., Lazar, D.F., Saltiel, A.R. and Dixit, V.M. (1994). Activation of the Eck Receptor Protein Tyrosine Kinase Stimulates Phosphatidylinositol 3-Kinase Activity. Journal of Biological Chemistry. 269, 30154-30157. 3. Shao, H., Lou, L., Pandey, A., Pasquale, E.B. and Dixit, V.M. (1994). cDNA cloning and characterization of a ligand for the Cek5 receptor protein-tyrosine kinase. Journal of Biological Chemistry. 269, 26606-26609. 4. Shao, H., Pandey, A., Seldin, M., O'Shea, K.S. and Dixit, V.M. (1995). Characterization of B61, the ligand for the Eck receptor protein-tyrosine kinase. Journal of Biological Chemistry. 270, 5636-5641. 5. Pandey, A., Duan, H. and Dixit, V.M. (1995). Characterization of a novel Src-like adapter protein that associates with the Eck receptor tyrosine kinase. Journal of Biological Chemistry. 270, 19201-19204.

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6. Pandey, A., Shao, H., Marks, R.M., Polverini, P.J. and Dixit, V.M. (1995). Role of B61, the ligand for the Eck receptor tyrosine kinase, in TNF-α induced angiogenesis. Science. 268, 567-569. 7. Pandey, A., Duan, H., Di Fiore, P. P. and Dixit, V.M. (1995). The Ret receptor protein tyrosine kinase associates with the SH2-containing adapter protein Grb10. Journal of Biological Chemistry. 270, 21461-21463. 8. Angrist, M., Wells, D. E., Chakravarti, A. and Pandey, A. (1995). Chromosomal localization of the mouse Src-like adapter protein (SLAP) gene and its putative human homolog SLA. Genomics. 30, 623-625. 9. Pandey, A., Liu, X., Dixon, J.E., Di Fiore, P. P. and Dixit, V.M. (1996). Direct association between the Ret receptor tyrosine kinase and the Src homology 2-containing adapter protein Grb7. Journal of Biological Chemistry. 271, 10607-10610. 10. Roche, S., Alonso, G., Kazlauskas, A., Dixit, V. M., Courtneidge, S. A. and Pandey, A. (1998). Src-like adaptor protein (Slap) is a negative regulator of mitogenesis. Current Biology. 8, 975-978. 11. Pandey, A., Podtelejnikov, A. V., Blagoev, B., Bustelo, X. R., Mann, M. and Lodish, H. F. (2000). Analysis of receptor signaling pathways by mass spectrometry: Identification of Vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. Proceedings of the National Academy of Sciences. 97, 179-184. 12. Sosinowski T., Pandey, A., Dixit, V. M. and Weiss, A. (2000). Src-like adaptor Protein (SLAP) is a negative regulator of T cell receptor signaling. Journal of Experimental Medicine 191, 463-474. 13. Pandey, A., Ozaki, K., Baumann, H., Levin, S. D., Puel, A., Farr, A. G., Ziegler, S. F., Leonard, W. J. and Lodish, H. F. (2000). Cloning of a receptor subunit required for signaling by thymic stromal lymphopoietin. Nature Immunology 1, 59-64. 14. Pandey, A., Fernandez, M. M., Steen, H., Blagoev, B., Nielsen, M. M., Mann, M. and Lodish, H. F. (2000). Identification of a novel immunoreceptor tyrosine-based activation motif (ITAM) - containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways. Journal of Biological Chemistry. 275, 38633-38639. 15. Kratchmarova, I., Sosinowski, T., Weiss, A., Witter, K., Vincenz, C. and Pandey, A. (2001). Characterization of the promoter region and genomic structure of murine and human Src like adapter protein (SLAP) genes. Gene. 262, 267-273. 16. Peri, S. and Pandey, A. (2001). A reassessment of the translation initiation codon in vertebrates. Trends in Genetics. 17, 685-687.

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17. Steen, H., Küster, B., Fernandez, M., Pandey, A. and Mann, M. (2001). Detection of tyrosine phosphorylated peptides by precursor ion scanning quadrupole TOF mass spectrometry in positive ion mode. Analytical Chemistry. 73, 1440-1448. 18. Steen, H., Kuster, B., Fernandez, M. M., Pandey, A.* and Mann, M. (2002). Tyrosine phosphorylation mapping of the EGF receptor signaling pathway. Journal of Biological Chemistry. 277, 1031-1039. *Corresponding author 19. Pandey, A.,* Ibarrola, N., Kratchmarova, I., Fernandez, M. M., Constantinescu, S. N., Ohara, O., Sawasdikosol, S., Lodish, H. F. and Mann, M. (2002). A novel Src homology 2 domain-containing molecule, Src-like adapter protein-2 (SLAP-2), which negatively regulates T cell receptor signaling. Journal of Biological Chemistry. 277, 19131-19138. *Corresponding author 20. Blagoev, B., Nielsen, M. M., Angrist, M., Chakravarti, A. and Pandey, A. (2002). Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene. Gene. 284, 161-168. 21. Ong S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A.* and Mann, M. (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Molecular and Cellular Proteomics. 1, 376-386. *Corresponding author 22. Pandey, A.,* Dan, I., Kristiansen, T. Z., Watanabe, N. W., Voldby, J., Kajikawa, E., Khosravi-Far, R., Blagoev, B. and Mann, M. (2002). Cloning and characterisation of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain. Oncogene. 21, 3939-3948. *Corresponding author 23. Schiemann, W. P., Blobe, G. C., Kalume, D. E., Pandey, A. and Lodish, H. F. (2002). Context-specific effects of fibulin-5 (DANCE/ EVEC) on cell proliferation, motility, and invasion: Fibulin-5 is induced by TGF-beta and affects protein kinase cascades. Journal of Biological Chemistry. 277, 27367-27377. 24. Dan, I., Watanabe, N. M., Kajikawa, E., Ishida, T., Pandey, A. and Kusumi, A. (2002). Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution. Nucleic Acids Research. 30, 2906-2910. 25. Blagoev, B., Kratchmarova, I., Nielsen, M. M., Fernandez, M. M., Voldby, J., Andersen, J. S., Kristiansen, K. Pandey, A.* and Mann M. (2002). Inhibition of adipocyte differentiation by resistin-like molecule alpha. Biochemical characterization of its oligomeric nature. Journal of Biological Chemistry. 277, 42011-42016. *Corresponding author 26. Blagoev, B., Nielsen, M. M., Angrist, M., Chakravarti, A. and Pandey, A. (2002). Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene. Gene. 284, 161-168.

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27. Dan, I., Ong, S. E., Watanabe, N. M., Blagoev, B., Nielsen, M. M., Kajikawa, E., Kristiansen, T. Z., Mann, M. and Pandey, A. (2002). Cloning of MASK, a novel member of the mammalian germinal center kinase-III subfamily, with apoptosis-inducing properties. Journal of Biological Chemistry. 277, 5929-5939. 28. Kratchmarova, I., Kalume, D. E., Blagoev, B., Scherer, P. E., Podtelejnikov, A. V., Molina, H., Bickel, P. E, Andersen, J. S., Fernandez, M. M., Bunkenborg, J., Roepstorff, P., Kristiansen, K., Lodish, H.F., Mann, M. and Pandey, A. (2002). A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes. Molecular and Cellular Proteomics. 1, 213-222. 29. Gronborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. S., Ohara, O., Mann, M., Jensen, O. N. and Pandey, A. (2002). A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate. Molecular and Cellular Proteomics. 1, 517-527. 30. Pandey, A.,* Blagoev, B., Kratchmarova, I., Fernandez, M., Nielsen, M., Kristiansen, T., Ohara, O., Podtelejnikov, A. V, Roche, S., Lodish, H. and Mann, M. (2002). Cloning of a novel phosphotyrosine binding domain containing molecule, Odin, involved in signaling by receptor tyrosine kinases. Oncogene. 21, 8029-8036. *Corresponding author 31. Pandey, A.,* Peri, S., Thacker, C., Pugh, C. A., Collins, J. J. and Mann, M. (2003). Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome. Bioinformatics. 19, 169-172. *Corresponding author 32. Steen, H., Fernandez, M., Ghaffari, S., Pandey, A.* and Mann, M. (2003). Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanning. Molecular and Cellular Proteomics. 2, 138-145. *Corresponding author 33. Peri, S., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T. K. B., Gronborg, M., Ibarrola, N., Deshpande, N., Shanker, K., Shivashankar, H. N., Rashmi, B. P., Ramya, M. A., Zhao, Z., Chandrika, K. N., Padma, N., Harsha, H. C., Yatish, A. J., Kavitha, M. P., Menezes, M., Choudhury, D. R., Suresh, S., Ghosh, N., Saravana, R., Chandran, S., Krishna, S., Joy, M., Anand, S. K., Madavan, V., Joseph, A., Wong, G. W, Schiemann, W. P., Constantinescu, S. N., Huang, L., Khosravi-Far, R., Steen, H., Tewari, M., Ghaffari, S., Blobe, G. C., Dang, C. V., Garcia, J. G. N., Pevsner, J., Jensen, O. N., Roepstorff, P., Deshpande, K. S., Chinnaiyan, A. M., Hamosh, A., Chakravarti, A. and Pandey, A. (2003). Development of Human Protein Reference Database as an initial platform for approaching systems biology in humans. Genome Research. 13, 2363-2371. 34. Ibarrola, N., Kalume, D. E., Gronborg, M., Iwahori, A. and Pandey, A. (2003). A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture. Analytical Chemistry. 75, 6043-6049.

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35. Peri, S., Navarro, J. D., Kristiansen T. Z., Amanchy, R., Surendranath, V., Muthusamy, B., Gandhi, T. K. B., Chandrika, K. N., Deshpande, N., Suresh, S., Rashmi, B. P., Shanker, K., Padma, N., Niranjan, V., Harsha, H. C., Talreja, N., Vrushabendra, B. M., Ramya, M. A., Yatish, A. J. Joy, M., Shivashankar, H. N., Kavitha, M. P., Menezes, M., Choudhury, D. R., Ghosh, N., Saravana, R., Chandran, S., Mohan, S., Jonnalagadda, C. K., Prasad, C. K., Kumar-Sinha, C., Deshpande, K. S. and Pandey, A. (2004). Human Protein Reference Database as a discovery resource for proteomics. Nucleic Acids Research. 32, D497-501. 36. Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y., Zeng, R., Rana, D., Nikolski, M., Husi, H., Brun, C., Shanker, K., Grant, S. G. N., Sander, C., Bork, P., Zhu, W., Pandey, A., Brazma, A., Jacq, B., Vidal, M., Sherman, D., Legrain, P., Cesareni, G., Xenarios, I., Eisenberg, D., Steipe, B., Hogue, C. and Apweiler, R. (2004). The HUPO PSI Molecular Interaction Format - A community standard for the representation of protein interaction data. Nature Biotechnology. 22, 177-183. 37. Tewari, M., Hu, P. J., Ahn, J. S., Ayivi-Guedehoussou, N., Vidalain, PO., Li, S., Milstein, S., Armstrong, C. M., Boxem, M., Butler, M. D., Busiguina, S, Rual, J-F., Ibarrola, N, Chaklos, S. T., Bertin, N., Vaglio, P., Edgley, M. L., King, K. V., Albert, P. S., Vandenhaute, J., Pandey, A., Riddle, D. L., Ruvkun, G. and Vidal, M. (2004). Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Molecular Cell. 13, 469-482. 38. Ibarrola, N., Kratchmarova, I., Nakajima, D., Schiemann, W. P., Moustakas, A., Pandey, A.* and Mann, M. (2004). Cloning of a novel signaling molecule, AMSH-2, that potentiates transforming growth factor beta signaling. BMC Cell Biology. 5, 2. *Corresponding author 39. Rhodes, D. R., Yu, J., Shanker, K., Deshpande, N., Varambally, R., Ghosh, D., Barrette, T., Pandey, A. and Chinnaiyan, A. M. (2004). Oncomine: A cancer microarray database and integrated data-mining platform. Neoplasia. 6, 1-6. 40. 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. 41. Navarro, J. D., Talreja, N., Peri, S., Vrushabendra, B. M., Rashmi, B.P., Padma, N., Surendranath, S., Jonnalagadda, C.K., Kousthub, P.S., Deshpande, N., Shanker, K. and Pandey, A. (2004). BioBuilder as a database development and functional annotation platform for proteins. BMC Bioinformatics. 5, 43. 42. 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. 43. Rhodes, D. R., Yu, J., Shanker, K., Deshpande, N., Varambally, R., Ghosh, D., Barrette, T., Pandey, A. and Chinnaiyan, A. M. (2004). Large-scale metaanalysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proceedings of the National Academy of Sciences. 101, 9309-9314.

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44. Al-Shami, A., Spolski, R., Kelly, J., Fry, T., Schwartzberg, P. L., Pandey, A., Mackall, C. L. and Leonard, W. J. (2004). A Role for Thymic Stromal Lymphopoietin (TSLP) in CD4+ T cell development. Journal of Experimental Medicine. 200, 159-168. 45. Koopmann, J., Thuluvath, P. J., Zahurak, M. L., Kristiansen, T. Z., Pandey, A., Schulick, R., Argani, P., Hidalgo, M., Iacobelli, S., Goggins, M. and Maitra, A. (2004). Mac-2-binding protein is a diagnostic marker for biliary tract carcinoma. Cancer. 101, 1609-1615. 46. Kristiansen, T. Z., Nielsen, M. M., Blagoev, B., Pandey, A. and Mann, M. (2004) Mouse embryonic fibroblasts derived from Odin deficient mice display a hyperproliferative phenotype. DNA Research.11, 285-292. 47. Cao, D., Hustinx, S. R., Sui, G., Bala, P., Sato, N., Martin, S., Maitra, A., Murphy, K. M., Cameron, J. L., Yeo, C. J., Kern, S. E., Goggins, M., Pandey, A. and Hruban, R. H. (2004). Identification of Novel Highly Expressed Genes in Pancreatic Ductal Adenocarcinomas through a Bioinformatics Analysis of Expressed Sequence Tags. Cancer Biology and Therapy. 3, 1081-1089. 48. Hustinx, S. R., Cao, D., Maitra, A., Sato, N., Martin, S., Sudhir, D., Iacobuzio-Donahue, C., Cameron, J. L., Yeo, C. J., Kern, S. E., Goggins, M., Mollenhauer, J., Pandey, A. and Hruban, R. H. (2004). Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression. Cancer Biology and Therapy, 3, 1254-1261. 49. Gronborg, M., Bunkenborg, J., Kristiansen, T. Z., Jensen, O. N., Yeo, C. J., Hruban, R. H., Maitra, A., Goggins, M. G. and Pandey, A. (2004). Comprehensive Proteomic Analysis of Human Pancreatic Juice. Journal of Proteome Research. 3, 1042-1055. 50. 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., 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, 331-332. 51. Gandhi, T. K. B., Chandran, S., Peri, S., Saravana, R., Yatish, A. J., Amanchy, R., Kumar-Sinha, C., Prasad, T. S. K., Prasad, C. K. and Pandey, A. (2005). A genomic analysis of human protein tyrosine phosphatases. DNA Research. 12, 79-89. 52. 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. 53. Tang, Q. Q., Grønborg, M., Huang, H., Kim, J. W., Otto, T. C., Pandey, A. and Lane, M.D. (2005) Sequential phosphorylation of CCAAT enhancer-binding protein beta by MAPK and glycogen synthase kinase 3beta is required for adipogenesis. Proceedings of the National Academy of Sciences, USA.102, 9766-9771.

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54. Molina, H, Bunkenborg, J., Reddy, G. H., Muthusamy, B., Scheel, P. J. and Pandey, A. (2005). A proteomic analysis of human hemodialysis fluid. Molecular and Cellular Proteomics. 4, 637-650. 55. Kalume, D. E., Okulate, M., Zhong, J., Suresh, S., Deshpande, N., Kumar, N. and Pandey, A. (2005). A proteomic analysis of salivary glands of female Anopheles gambiae mosquito. Proteomics. 5, 3765-3777. 56. Bala, P., Georgantas, R. W., Sudhir, D., Suresh, M., Shanker, K., Vrushbendra, B. M., Civin, C. I., and Pandey, A. (2005) TAGmapper: A web-based tool for mapping SAGE tags. Gene. 364, 123-129. 57. 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. 58. Ping, P., Vondriska, T. M., Creighton, C. J., Gandhi, T. K. B., 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., Muthusamy, 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. (2005). A functional annotation of subproteomes in human plasma. Proteomics. 5, 3506-3519. 59. Rhodes, D. R., Tomlins, S. A., Varambally, R., Mahavisno, V., Barrette, T., Kalyana-Sundaram, S., Ghosh, D., Pandey, A. and Chinnaiyan, A. M. (2005) Integrative prediction of the human protein interaction network and application to cancer biology. Nature Biotechnology. 23, 951-959 60. Hyland, E. M., Cosgrove, M. S., Molina, H., Wang, D., Pandey, A., Cotter R. J. and Boeke, J. D. (2005) Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Molecular Cellular Biology. 25, 10060-10070. 61. Amanchy, R., Kalume, D. E., Iwahori, A., Zhong, J. and Pandey, A. (2005) Phosphoproteome analysis of HeLa cells using stable isotope labeling by amino acids in cell culture (SILAC). Journal of Proteome Research. 4, 1661 -1671. 62. 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.

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63. Mishra, G., Suresh, M., Kumaran, K., Kannabiran, N., Suresh, S., Bala, P., Shivkumar, K., Anuradha, N., Reddy, R., Raghavan, T.M., Menon, S., Hanumanthu, G., Gupta, M., Upendran, S., Gupta, S., Mahesh, M., Jacob, B., Matthew, P., Chatterjee, P., Arun, K. S., Sharma, S., Chandrika, K. N., Deshpande, N., Palvankar, K., Raghavnath, R., Krishnakanth, K., Karathia, H., Rekha, B., Rashmi, N. S., Vishnupriya, G., Kumar, H. G. M., Nagini, M., Kumar, G. S. S., Jose, R., Deepthi, P., Mohan, S. S., Gandhi, T. K. B., Harsha, H. C., Deshpande, K. S., Sarker, M., Prasad, T. S. K. and Pandey, A. (2006). Human Protein Reference Database - 2006 Update. Nucleic Acids Research. 34, D411-D414. 64. 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. 65. Wang, D., Kalume, D., Pickart, C., Pandey, A. and Cotter, R. J. (2006). Identification of protein ubiquitylation by electrospray ionization tandem mass spectrometric analysis of sulfonated tryptic peptides. Analytical Chemistry. 78, 3681-3687. 66. Moff, S. L., Clark, D. P., Maitra, A., Pandey, A. and Thuluvath, P. J. (2006). Utility of bile duct brushings for the early detection of cholangiocarcinoma in patients with primary sclerosing cholangitis. Journal of Clinical Gastroenterology. 40, 336-341. 67. Liu, B., Molina, H., Kalume, D., Pandey, A., Griffith, J. D. and Englund, P (2006). Role of p38 in Replication of Trypanosoma brucei Kinetoplast DNA. Molecular and Cellular Biology. 26, 5382-5393. 68. Gandhi, T. K. B., Zhong, J., Suresh, M., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Shilpa, N., Bala, P., Mishra, G., Kannabiran, N., Shen, B., Deshpande, N., Rashmi, N. S., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J. S., Bader, J. S. and Pandey, A (2006). Analysis of the human protein interactome and its comparison with yeast, worm and fly interaction datasets. Nature Genetics. 38, 285-293. 69. Lerin, C., Rodgers, J. T., Kalume, D. E., Kim, S. H., Pandey, A. and Puigserver, P. (2006). GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of PGC-1alpha. Cell Metabolism. 3, 429-438. 70. Bose, R., Molina, H., Patterson, A. S., Bitok, J. K., Periaswamy, B., Bader, J. S., Pandey, A. and Cole, P. A. (2006). Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proceedings of the National Academy of Sciences, USA. 103, 9773-9778. 71. Mathivanan, S., Periaswamy, B., Gandhi, T. K. B., Kandasamy, K., Suresh, S., Mohmood, R., Ramachandra, Y. L. and Pandey, A. (2006). An Evaluation of Human Protein-Protein Interaction Data in the Public Domain. BMC Bioinformatics. 7, S19. 72. Kim, J. W., Molina, H., Pandey, A. and Lane, M. D. (2007). Upstream stimulatory factors regulate the C/EBPalpha gene during differentiation of 3T3-L1 preadipocytes. Biochemical and Biophysical Research Communications. 354, 517-521.

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73. 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. 74. 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. 5, 285-286. 75. Wang, Z., Pandey, A. and Hart, G. W. (2007) Dynamic interplay between O-GlcNAcylation and GSK-3-dependent phosphorylation. Molecular and Cellular Proteomics. 6, 1365-1379. 76. Lucito, R., Suresh, S., Walter, K., Pandey, A., Lakshmi, B., Krasnitz, A., Sebat, J., Wigler, M., Klein, A. P., Brune, K., Palmisano, E., Maitra, A., Goggins, M. and Hruban, R. H. (2007) Copy-Number Variants in Patients with a Strong Family History of Pancreatic Cancer. Cancer Biology & Therapy. 6, 1592-1599 77. Bhandari, R., Saiardi, A., Ahmadibeni, Y., Snowman, A. M., Resnick, A. C., Kristiansen, T. Z., Molina, H., Pandey, A., Werner, J. K. Jr., Juluri, K. R., Xu, Y., Prestwich, G. D., Parang, K. and Snyder, S. H. (2007) Protein pyrophosphorylation by inositol pyrophosphates is a posttranslational event. Proceedings of the National Academy of Sciences, USA. 104, 15305-15310. 78. Dinglasan, R. R, Kalume, D. E., Kanzok, S. M., Ghosh, A. K., Muratova, O., Pandey, A. and Jacobs-Lorena, M. (2007) Disruption of Plasmodium falciparum development by antibodies against a conserved mosquito midgut antigen. Proceedings of the National Academy of Sciences, USA. 104, 13461-13466. 79. Okulate, M., Kalume, D. E., Chaerkady, R., Reddy, R., Kristiansen, K., Bhattacharyya, M., Pandey, A. and Kumar, N. (2007). Identification and molecular characterization of a novel protein Saglin as a target of monoclonal antibodies affecting salivary gland infectivity of Plasmodium sporozoites. Insect Molecular Biology. 16, 711-722. 80. 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., Björling, 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 Marzo, A. M., DeSouza, L. V., Deutsch, E. W., Dransfield, E., Drewes, G., Droit, A., Dunn, M. J., Elenitoba-Johnson, K., Ewing, R. M., Eyk, J. V., Faca, V., Falkner, J., Fang, X., Fenselau, C., Figeys, D., Gagné, 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., Hjernø, 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., Körner, R., Küster, B., Kwon, M. S., Lee, H. J., Lee, Y. J., Lefevre, M., Lehvaslaiho, M., Lescuyer, P., Levander, F., Lim, M. S., Löbke, C., Loo, J. A., Mann, M., Martens, L., Heredia, J. M., 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,

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R., Periaswamy, B., Petricoin, E. F., Poirier, G. G., Prasad, T. S. K., 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. M., Smith, J. C., Smith, R. D., States, D. J., Sugano, S., Sullivan, M., Furga, G. S., 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., Zuerbig, P. and Pandey, A. (2008). Human Proteinpedia enables sharing of human proteomic data. Nature Biotechnology. 26, 164-167. 81. Karanjawala, Z. E., Illei, P. B., Ashfaq, R., Infante, J. R., Murphy, K., Pandey, A., Schulick, R., Winter, J., Sharma, R., Maitra, A., Goggins, M. and Hruban, R. H. (2008). New markers of pancreatic cancer identified through differential gene expression analyses: claudin 18 and annexin A8. American Journal of Surgical Pathology. 32, 188-196. 82. Molina, H., Matthiesen, R., Kandasamy, K. and Pandey, A. (2008). A comprehensive comparison of collision induced dissociation and electron transfer dissociation. Analytical Chemistry. 80, 4825-4835. 83. Chaerkady, R., Thuluvath, P. J., Nalli, A., Vivekanandan, P., Simmers, J., Torbenson, M. and Pandey, A. (2008). 18O labeling for a quantitative proteomic analysis of glycoproteins in hepatocellular carcinoma. Clinical Proteomics. 9, 1080-1089. 84. Mathivanan, S. and Pandey, A. (2008). Human Proteinpedia as a resource for clinical proteomics. Molecular and Cellular Proteomics. 7, 2038-2047. 85. Luo, W., Slebos, R. J., Hill, S., Li, M., Brabek, J., Amanchy, R., Chaerkady, R., Pandey, A., Ham, A-J. L. and Hanks, S. (2008). Global impact of oncogenic Src on a phosphotyrosine proteome. Journal of Proteome Research. 7, 3447-3460. 86. Amanchy, R., Zhong, J., Molina, H., Chaerkady, R, Iwahori, A., Kalume, D. E., Gronborg, M., Joore, J., Cope, L. and Pandey, A. (2008). Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. Journal of Proteome Research. 7, 3900-3910. 87. 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. (2008). A Quantitative Proteomic Approach for Identification of Potential Biomarkers in Hepatocellular Carcinoma. Journal of Proteome Research. 7, 4289-4298. 88. Kristiansen, T. Z., Harsha, H. C., Grønborg, M., Maitra, A. and Pandey, A. (2008). Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma. Journal of Proteome Research. 7, 4670-4677. 89. Guha, U., Chaerkady, R., Marimuthu, A., Patterson, S., Kashyap, M., Gowda, H., Dowdle, J., Gucek, M., Bader, J. S., Lash, A., Pandey, A. and Varmus, H. (2008). Comparisons of tyrosine-phosphorylated proteins in immortalized human bronchial epithelial cells and lung adenocarcinoma cell lines expressing lung cancer-specific alleles of EGFR and KRAS. Proceedings of the National Academy of Sciences, USA. 105, 14112-14117.

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90. 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 an in vitro model of the lung cancer microenvironment. Cancer Research. 68, 7237-7245. 91. Sarker, R., Grønborg, M., Cha, B., Mohan, S., Chen, Y., Pandey, A., Litchfield, D., Donowitz, M and Li, X. (2008). CK2 Binds to the C-Terminus of NHE3 and Stimulates NHE3 Basal Activity by Phosphorylating a Separate Site in NHE3. Molecular Biology of the Cell. 19, 3859-3870. 92. Dixon, S., Fedyshyn, Y., Koh, J., Prasad, T. S. K., Chahwan, C., Chua, G., Toufighi, K., Baryshnikova, A., Hayles, J., Hoe, K., Kim, D., Park, H., Myers, C., Pandey, A., Durocher, D., Andrews, B. and Boone, C. (2008). Significant conservation of synthetic lethal genetic interaction networks between distantly-related eukaryotes. Proceedings of the National Academy of Sciences U.S.A. 105, 16653-16658. 93. Harsha, H. C., Jimeno, A., Molina, H., Mihalas, A., Goggins, M., Hruban, R., Schulick, R., Kamath, U., Maitra, A., Hidalgo, M. and Pandey, A (2008). Activated epidermal growth factor receptor as a novel target in pancreatic cancer therapy. Journal of Proteome Research. 7, 4651-4658. 94. Song, D., Chaerkady, R., Tan, A., Garcia-Garcia, E., Nalli, A., Gauthier, A., Rios, 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 pancreatic cancer. Molecular Cancer Therapeutics. 7, 3275-3284 95. Ghosh, A. K., Devenport, M., Jethwaney, D., Kalume, D. E., Pandey, A., Anderson, V. E., Sultan, A. A., Kumar, N. and Jacobs-Lorena, M. (2009). Malaria parasite invasion of the mosquito salivary gland requires interaction between the Plasmodium TRAP and the Anopheles Saglin proteins. PLoS Pathogens. 5, e1000265 96. 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. 97. 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, D767-D772. 98. Kandasamy, K., Keerthikumar, S., Mathivanan, S., Patankar, N., Shafreen, B., Renuse, S., Pawar, H., Ramachandra, Y. L., Prasad, T. S. K., Acharya, P. K., Ranganathan, P., Chaerkady, R. and Pandey A. (2009). Human Proteinpedia: A unified discovery resource for proteomics research. Nucleic Acids Research. 37, D773-D781

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99. Keerthikumar, S., Raju, R., Kandasamy, K., Hijikata, A., Ramabadran, S., Balakrishnan, L., Ahmed, M., Rani, S., Selvan, L. N., Somanathan, D. S., Ray, S., Bhattacharjee, M., Gollapudi, S., Ramachandra, Y. L., Bhadra, S., Bhattacharyya, C., Imai, K., Nonoyama, S., Kanegane, H., Miyawaki, T., Pandey, A., Ohara, O. and Mohan, S. (2009). RAPID: Resource of Asian Primary Immunodeficiency Diseases. Nucleic Acids Research. 37, D863-D867 100. Kashyap, M., Marimuthu, A., Kishore, C. J. H., Peri, S., Keerthikumar, S., Prasad, T. S. K., Mahmood, R., Rao, S., Ranganathan, P., Vijayakumar, M., Veerendra Kumar, K. V., Montgomery, E., Vijay Kumar, R. and Pandey A. (2009). Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biology and Therapy. 8, 16-26. 101. Cooper, E. M., Cutcliffe, C., Kristiansen, T. Z., Pandey, A., Pickart, C. M. and Cohen, R. E. (2009) K63-specific deubiquitination by two JAMM/MPN+ complexes: BRISC-associated Brcc36 and proteasomal Poh1. EMBO Journal. 28, 621-631. 102. 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. 103. 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. 104. Harsha, H. C., Kandasamy, K., Ranganathan, P., Rani, S., Ramabadran, S., Gollapudi, S., Balakrishnan, L., Dwivedi, S. B., Telikicherla, D., Selvan, L. D. N., Goel, R., Mathivanan, S., Marimuthu, A., Kashyap, M. K., Vizza, R. F., Mayer, R. J., DeCaprio, J. A., Srivastava, S., Hanash, S. M., Hruban, R. H. and Pandey, A (2009). A compendium of potential biomarkers of pancreatic cancer. PLoS Medicine. 6, e000046.

105. Li, X., Molina, H., Huang, H., Zhang, Y. Y., Liu, M., Qian, S. W., Slawson, C., Dias, W. B., Pandey, A., Hart, G. W., Lane, M. D. and Tang Q. Q. (2009) O-linked N-acetylglucosamine modification on C/EBPbeta: Role during adipocyte differentiation. Journal of Biological Chemistry. 284, 19248-19254.

106. Parikh K, Diks SH, Tuynman JH, Verhaar A, Löwenberg M, Hommes DW, Joore J, Pandey A. and Peppelenbosch MP. (2009) Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8. PLoS One.4:e6440.

107. Kandasamy, K., Pandey, A. and Molina, H. (2009). Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Analytical Chemistry. 81, 7170-7180.

108. Amanchy, R., Zhong, J., Hong, R., Kim, J. H., Gucek, M., Cole, R. N., Molina, H. and Pandey, A. (2009). Identification of c-Src tyrosine kinase substrates in platelet-derived growth factor receptor signaling. Molecular Oncology. 3, 439-450.

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109. Kandasamy, K., Keerthikumar, S., Raju, R., Prasad, T. S. K., Ramachandra, Y. L., Mohan, S. and Pandey, A. (2009). PathBuilder – Open source software for annotating and developing pathway resources. Bioinformatics. 25, 2860-2862.

110. Keerthikumar, S., Bhadra, S., Kandasamy, K., Raju, R., Ramachandra, Y. L., Bhattacharyya, C., Imai, K., Ohara, O., Mohan, S. and Pandey, A. (2009) Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach. DNA Research.16, 345-351.

111. Luo, W., Zhong, J., Chang, R., Hu, H., Pandey, A. and Semenza, G.L. (2009) HSP70 and CHIP selectively mediate Ubiquitination and degradation of hypoxia-inducible factor (HIF)-1α but not HIF-2α. Journal of Biological Chemistry. 285, 3651-3663.

112. 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.

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

113. Zhong, J., Liu, X. and Pandey, A. (2010) Effects of transmembrane and juxtamembrane domains on proliferative ability of TSLP receptor. Molecular Immunology. 47, 1205-1215.

114. Zhou, Q., Chaerkady, R., Shaw, P. G., Kensler, T. W., Pandey, A. and Davidson, N. E. (2010) Screening for therapeutic targets of vorinostat by SILAC-based proteomic analysis in human breast cancer cells. Proteomics. 5, 1029-1039.

115. Kandasamy, K., Mohan, S. S., Raju, R., Keerthikumar, S., Kumar, G. S. S., Venugopal, A. K., Telikicherla, D., Navarro, D. J., Mathivanan, S., Pecquet, C., Gollapudi, S. K., Tattikota, S. G., Mohan, S., Padhukasahasram, H., Subbannayya, Y., Goel, R., Jacob, H. K. C., Zhong, J., Sekhar, R., Nanjappa, V., Balakrishnan, L., Subbaiah, R., Ramachandra, Y. L., Rahiman, B. A., Prasad, T. S. K., Lin, J., Houtman, J. C. D., Desiderio, S., Renauld, J., Constantinescu, S., Ohara, O., Hirano, T., Kubo, M., Singh, S., Khatri, P., Draghici, S., Bader, G. D., Sander, C., Leonard, W. J. and Pandey, A. (2010) NetPath: A public resource of curated signal transduction pathways. Genome Biology. 11, R3.

116. 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. (2010). Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 10, 3800-3810.

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

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

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119. Kashyap MK, Harsha HC, Renuse S, Pawar H, Sahasrabuddhe NA, Kim MS, Marimuthu A, Keerthikumar S, Muthusamy B, Kandasamy K, Subbannayya Y, Prasad TSK, Mahmood R, Chaerkady R, Meltzer SJ, Kumar RV, Rustgi AK and Pandey A. (2010). SILAC based quantitative proteomic approach for identification of potential biomarkers from esophageal squamous cell carcinoma secretome. Cancer Biology and Therapy. 10, 796-810.

120. Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Novere, N. L., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C. and Bader, G. D. (2010). BioPAX - A community standard for pathway data sharing. Nature Biotechnology. 28, 935-942.

121. Zhong J., Krawczyk S., Chaerkady R, Huang H, Goel R, Bader J, Wong WG, Corkey B and Pandey, A. (2010). Temporal profiling of the secretome during adipogenesis in humans. Proteomics. 9, 5228-5238.

122. Kashyap, M. K, Marimuthu, A., Peri, S., Kumar, G. S. S., Jacob, H. C. K., Prasad, T. S. K., Mahmood, R., Veerendra Kumar, K. V., Vijayakumar, M., Meltzer, S. J., Montgomery, E. A., Kumar, R. V. and Pandey, A. (2010). Overexpression of periostin and lumican in esophageal squamous cell carcinoma. Cancers. 2, 133-142.

123. Alvarez, H., Montgomery, E. A., Karikari, C., Canto, M. I., Dunbar, K. B., Wang, J. S., Feldmann, G., Hong , S. M., Haffner, M. C., Meeker, A. K., Holland, S. J., Yu , J., Heckrodt , T. J., Zhang, J., Ding, P., Goff, D., Singh, R., Roa, J. C., Marimuthu, A., Riggins, G. J., Eshelman, J. R., Nelkin, B. D., Pandey, A. and Maitra, A. (2010). The Axl receptor tyrosine kinase is an adverse prognostic factor and a therapeutic target in esophageal adenocarcinoma. Cancer Biology and Therapy. 10, 1009-1018.

124. Prasad, T. S. K., Keerthikumar, S., Chaerkady, R., Kandasamy, K., Renuse, S., Marimuthu, A., Venugopal, A. K., Thomas, J. K., Jacob, H. K. C., Goel, R., Pawar, H., Sahasrabuddhe, N. A., Krishna, V., Nair, B. G., Gucek, M., Cole, R. N., Ravikumar, R., Harsha, H. C. and Pandey, A. (2010). Comparative proteomic analysis of Candida albicans and Candida glabrata. Clinical Proteomics. 6, 163-173.

125. Zhong, J., Chaerkady, R., Kandasamy, K., Gucek, M., Cole, R.N. and Pandey, A. (2011). The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. Journal of Proteomics. 74, 294-303.

126. Wang, Q., Chaerkady, R., Wu, J., Hwang, H., J., Papadopoulos, N., Kopelovich, L., Maitra, A., Matthei, H., Eshleman, J., Hruban, R., Kinzler, K. W., Pandey, A. and Vogelstein, B. (2011).

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Mutant proteins as cancer-specific biomarkers. Proceedings of the National Academy of Sciences U.S.A. 108, 2444-2449.

127. Amanchy, R., Kandasamy, K., Mathivanan, S., Periaswamy, B., Reddy, R., Yoon, W. H., Joore, J., Beer, M. A., Cope, L. and Pandey, A. (2011). Identification of novel phosphorylation motifs through an integrative computational and experimental analysis of the human phosphoproteome. Journal of Proteomics and Bioinformatics. 4, 22-35.

128. Marimuthu, A., Jacob, H. K. C., Jakharia, A., Subbannayya, Y., Keerthikumar, S., Kashyap, M. K., Goel, R., Balakrishnan, L., Dwivedi, S., Pathare, S., Dikshit, J. B., Maharudraiah, J., Singh, S., Kumar, G. S. S., Vijayakumar, M., Veerendra Kumar, K. V., Premalatha, C. S., Tata, P., Hariharan, R., Roa, J. C., Prasad, T. S. K., Chaerkady, R., Kumar, R. V. and Pandey, A. (2011). Gene expression profiling of gastric cancer. Journal of Proteomics and Bioinformatics. 4, 74-82. 129. Marimuthu, A., O’Meally, R, Chaerkady, R., Subbannayya, Y., Nanjappa, V., Kumar, P., Kelkar, D. S., Pinto, S. M., Sharma, R., Renuse, S., Goel, R., Christopher, R., Delanghe, B., Cole, R. N., Harsha, H. C. and Pandey, A. (2011). A comprehensive map of the human urinary proteome. Journal of Proteome Research. 10, 2734-2743. 130. Luo, W., Hu, H., Chang, R., Zhong J., Knabel, M., O'Meally, R., Cole, R. N., Pandey, A. and Semenza, G. L. (2011). Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1. Cell. 145, 732-744. 131. Kim, M. S., Zhong, J., Kandasamy, K., Delanghe, B. and Pandey, A. (2011). Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides. Proteomics. 11, 2568-2572. 132. Kumar, G. S. S., Venugopal, A. K., Selvan, L. D. N., Marimuthu, A., Keerthikumar, S., Pathare, S., Dikshit, J. B., Tata, P., Hariharan, R., Prasad, T. S. K., Harsha, H. C., Ramachandra, Y. L., Mahadevan, A., Chaerkady, R., Shankar, S. K. and Pandey, A. (2011) Gene expression profiling of tuberculous meningitis. Journal of Proteomics and Bioinformatics. 4, 98-105. 133. Zachara, N. E., Molina, H., Wong, K. Y., Pandey, A. and Hart, G. W. (2011). The dynamic stress-induced “O-GlcNAc-ome” highlights functions for O-GlcNAc in regulating DNA damage/repair and other cellular pathways. Amino Acids. 40, 793-808. 134. Raju, R., Balakrishnan, L., Nanjappa, V., Bhattacharjee, M., Getnet, D., Muthusamy, B., Thomas, J. K., Sharma, J., Rahiman, B. A., Harsha, H. C., Shankar, S., Prasad, T. S. K., Mohan, S. S., Bader, G. D., Wani, M. R. and Pandey, A. (2011) A comprehensive manually curated reaction map of RANKL/RANK signaling pathway. Database. 2011:bar021. 135. Shao, H., Chaerkady, R., Chen, S., Pinto, S. M., Sharma, R., Delanghe, B., Birk, D., Pandey, A. and Chakravarti, S. (2011) Proteome profiling of wild type and lumican-deficient mouse corneas. Journal of Proteomics. 74, 1895-1905

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136. Shaw, P., Chaerkady, R., Zhang, Z., Davidson, N. and Pandey, A. (2011) A monoclonal antibody cocktail as an enrichment tool for acetylome analysis. Analytical Chemistry. 83, 3623-3626. 137. Raju, R., Balakrishnan, L., Nanjappa, V., Bhattacharjee, M., Getnet, D., Muthusamy, B., Thomas, J. K., Sharma, J., Rahiman, B. A., Harsha, H. C., Shankar, S., Prasad, T. S. K., Mohan, S. S., Bader, G. D., Wani, M. R. and Pandey, A. (2011). A comprehensive manually curated reaction map of RANKL/RANK signaling pathway. Database. 2011:bar021. 138. Pawar, H., Kashyap, M. K., Sahasrabuddhe, N. A., Renuse, S., Harsha, H. C., Kumar, P., Sharma, J., Kandasamy, K., Marimuthu, A., Nair, B., Rajagopalan, S., Maharudraiah, J., Premalatha, C. S., Veerendra Kumar, K. V., Vijayakumar, M., Chaerkady, R., Prasad, T. S. K., Kumar, R. V. and Pandey, A. (2011). Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biology and Therapy. 12, 510-522. 139. Kinsinger, C. R., Apffel, J., Baker, M., Bian, X., Borchers, C., Bradshaw, R., Brusniak, M-Y., Chan, D., Deutsch, E. W., Domon, B., Gorman, J., Grimm, R., Hancock, W., Hermjakob, H., Horn, D., Hunter, C., Kolar, P., Kraus, H-J., Langen, H., Linding, R., Moritz, R. L., Omenn, G. S., Orlando, R., Pandey, A., Ping, P., Rahbar, A., Rivers, R., Seymour, R. L., Simpson, R. J., Slotta, D., Smith, R. D., Stein, S., Tabb, D. L., Tagle, D., Yates, J. and Rodriguez, H. (2011). Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Molecular and Cellular Proteomics. 10, O111.015446.

140. Chaerkady, R., Kelkar, D. S., Muthusamy, B., Kandasamy, K., Dwivedi, S. B., Sahasrabuddhe, N. A., Kim, M-S., Renuse, S., Pinto, S. M., Sharma, R., Pawar, H., Sekhar, N. R., Mohanty, A. K., Getnet, D., Yang, Y., Zhong, J., Dash, A. P., MacCallum, R. M., Delanghe, B., Mlambo, G., Kumar, A., Prasad, T. S. K., Okulate, M., Kumar, N. and Pandey, A. (2011) A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Research. 21, 1872-1881. 141. Barbhuiya, M. A., Sahasrabuddhe, N. A., Pinto, S. M., Muthusamy, B., Singh, T. D., Nanjappa, V., Keerthikumar, S., Delanghe, B., Harsha, H. C., Chaerkady, R., Jalaj, V., Gupta, S., Shrivastav, B. R., Tiwari, P. K. and Pandey, A. (2011). Comprehensive proteomic analysis of human bile. Proteomics. 11, 4443- 4453. 142. Telikicherla, D., Ambekar, A., Palapetta, S. M., Dwivedi, S. B., Raju, R., Sharma, J., Prasad, T. S. K., Ramachandra, Y. L., Mohan, S. S., Maharudraiah, J., Mukherjee, S. and Pandey, A. (2011). A comprehensive curated resource for Follicle Stimulating Hormone signaling. BMC Research Notes. 4:408 143. Hyland, E. M., Molina, H., Poorey, K., Jie, C., Xie, Z., Dai, J., Qian, J., Bekiranov, S., Auble, D. T., Pandey, A. and Boeke, J. D. (2011). An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae. Genes & Development. 25, 1306-1319. 144. Nanjappa, V., Raju, R., Muthusamy, B., Sharma, J., Thomas, J. K., Nidhina, P. A. H., Harsha, H. C., Pandey, A., Anilkumar G. and Prasad, T. S. K. (2011). A comprehensive curated reaction map of leptin signaling pathway. Journal of Proteomics and Bioinformatics. 4, 184-189.

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145. Raju, R., Nanjappa, V., Balakrishnan, L., Radhakrishnan, A., Thomas, J. K., Sharma, J., Tian, M., Palapetta, S. M., Subbannayya, T., Sekhar, N. R., Muthusamy, B., Goel, R., Subbannayya, Y., Telikicherla, D., Bhattacharjee, M., Pinto, S., Syed, N., Srikanth, M. S., Sathe, G. J., Ahmad, S., Chavan, S. N., Kumar, G. S. S., Marimuthu, A., Prasad, T. S. K., Harsha, H. C., Rahiman, B. A., Ohara, O., Bader, G. D., Mohan, S. S., Schiemann, W. P. and Pandey, A. (2011). Netslim: High-confidence curated signaling maps. Database. 2011:bar032. 146. Kelkar, D. S., Kumar, D., Kumar, P., Balakrishnan, L., Muthusamy, B., Yadav, A. K., Shrivastava, P., Marimuthu, A., Anand, S., Sundaram, H., Kingsbury, R., Harsha, H. C., Nair, B., Prasad, T. S. K., Chauhan, D. S., Katoch, K., Katoch, V. M., Kumar, P., Chaerkady, R., Ramachandran, S., Dash D. and Pandey, A. (2011). Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Molecular and Cellular Proteomics. M111.011627. 147. Goel, R., Raju, R., Maharudraiah, J., Kumar, G. S. S., Ghosh, K., Kumar, A., Lashmi, P. T., Sharma, J., Sharma, R., Balakrishnan, L., Pan, A., Kandasamy, K., Christopher, R., Krishna, V., Mohan, S. S., Harsha, H. C., Mathur, P. P., Pandey, A. and Prasad, T. S. K. (2011). A signaling network of thyroid-stimulating hormone. Journal of Proteomics and Bioinformatics. 4, 238-241. 148. Polisetty, R. V., Gautam, P., Sharma, R., Harsha, H. C., Nair, S. C., Gupta, M. K., Uppin, M. S., Challa, S., Puligopu, A. K., Ankathi, P., Purohit, A. K., Chandak, G. R., Pandey, A. and Sirdeshmukh, R. (2012). LC-MS/MS Analysis of Differentially Expressed Glioblastoma Membrane Proteome Reveals Altered Calcium Signalling and other Protein Groups of Regulatory Functions. Molecular and Cellular Proteomics. 11, M111.013565 149. Pawar, H., Sahasrabuddhe, N. A., Renuse, S., Keerthikumar, S., Sharma, J., Kumar, G. S. S., Venugopal, A., Sekhar, N. R., Kelkar, D. S., Nemade, H., Khobragade, S. N., Muthusamy, B., Kandasamy, K., Harsha, H. C., Chaerkady, R., Patole, M. S. and Pandey, A. (2012). A Proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani. Proteomics. 12, 832-844. 150. Prasad, T. S. K., Harsha, H. C., Keerthikumar, S., Sekhar, N. R., Selvan, L. D. N., Kumar, P., Pinto, S. M., Muthusamy, B., Subbannayya, Y., Renuse, S., Chaerkady, R., Mathur, P. P., Ravikumar, R. and Pandey, A. (2012). Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry. Journal of Proteome Research. 11, 247-260. 151. Nagaraj, S. H., Harsha, H. C., Reverter, A., Colgrave, M. L., Sharma, R., Andronicos, N., Hunt, P., Menzies, M., Lees, M. S., Sekhar, N. R., Pandey, A. and Ingham, A. (2012). Proteomic analysis of the abomasal mucosal response following infection by the nematode, Haemonchus contortus, in genetically resistant and susceptible sheep. Journal of Proteomics. 75, 2141-2152. 152. Agyeman, A. S., Chaerkady, R., Shaw, P. G., Davidson, N. E., Visvanathan, K., Pandey, A. and Kensler, T. W. (2012) Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane treated human breast epithelial cells reveals common expression profiles. Breast Cancer Research and Treatment. 132, 175-187. 153. Huang, T. C., Sahasrabuddhe, N. A., Kim, M. S., Getnet, D., Yang, Y., Peterson, J. M., Ghosh, B., Chaerkady, R., Leach, S. D., Marchionni, L., Wong, G. W. and Pandey A. (2012).

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Regulation of Lipid Metabolism by Dicer Revealed through SILAC Mice. Journal of Proteome Research. 11, 2193-2205. 154. Zhong, J., Kim, M. S., Chaerkady, R., Wu, X., Huang, T. C., Getnet, D., Mitchell, C. J., Palapetta, S. M., Sharma, J., O'Meally, R. N., Cole, R. N., Yoda, A., Moritz, A., Loriaux, M. M., Rush, J., Weinstock, D. M., Tyner, J. W. and Pandey, A. (2012). TSLP signaling network revealed by SILAC-based phosphoproteomics. Molecular and Cellular Proteomics. 11, M112.017764. 155. Venugopal, A. K., Kumar, G. S. S., Mahadevan, A., Selvan, L. D. N., Marimuthu, A., Dikshit, J. B., Tata, P., Ramachandra, Y. L., Chaerkady, R., Sinha, S., Chandramouli, B. A., Arivazhagan, A., Satishchandra, P., Shankar, S. K. and Pandey, A. (2012). Transcriptomic Profiling of Medial Temporal Lobe Epilepsy. Journal of Proteomics and Bioinformatics. 5, 31-39. 156. Radhakrishnan, A., Raju, R., Tuladhar, N., Subbannayya, T., Thomas, J. K., Goel, R., Telikicherla, D., Palapetta, S. M., Rahiman, B. A., Venkatesh, D. D., Urmila, K. K., Harsha, H. C., Mathur, P. P., Prasad, T. S. K., Pandey, A., Shemanko, C. and Chatterjee, A. (2012). A pathway map of prolactin signaling. Journal of Cell Communication and Signaling. 11, 355-369. 157. Telikicherla, D., Maharudraiah, J., Pawar, H., Marimuthu, A., Kashyap, M. K., Ramachandra, Y. L., Roa, J. C. and Pandey, A. (2012). Overexpression of Kinesin Associated Protein 3 (KIFAP3) in Breast Cancer. Journal of Proteomics and Bioinformatics. 5, 122-126. 158. Renuse, S., Harsha, H. C., Kumar, P., Acharya, P. K., Sharma, J., Goel, R., Kumar, G. S. S., Raju, R., Prasad, T. S. K., Slotta, T. and Pandey, A. (2012). Proteomic analysis of an unsequenced plant - Mangifera indica. Journal of Proteomics. 75, 5793-5796.

159. Kim, M. S., Kuppireddy, S. V., Sakamuri, S., Singal, M., Getnet, D., Harsha, H. C., Goel, R., Balakrishnan, L., Jacob, H. K. C., Kashyap, M. K., Tankala, S. G., Maitra, A., Iacobuzio-Donahue, C. A., Jaffee, E., Goggins, M. G., Velculescu, V. E., Hruban, R. H. and Pandey, A. (2012). Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs). Journal of Proteome Research. 11,5556-5563. 160. Bhattacharjee, M., Raju, R., Radhakrishnan, A., Nanjappa, V., Muthusamy, B., Singh, K., Kuppusaami, D., Lingala, B. T., Pan, A., Mathur, P. P., Harsha, H. C., Prasad, T. S. K., Atkins, G. J., Pandey, A. and Chatterjee, A. (2012). A bioinformatics resource for TWEAK-Fn14 signaling pathway. Journal of Signal Transduction. 2012:376470. 161. Telikicherla, D., Marimuthu, A., Kashyap, M. K., Ramachandra, Y. L., Mohan, S., Roa, J. C., Maharudraiah, J., and Pandey, A. (2012). Overexpression of Ribosome Binding Protein 1 (RRBP1) in breast cancer. Clinical Proteomics. 2012, 9:7. 162. Vidal M, Chan DW, Gerstein M, Mann M, Omenn GS, Tagle D, Sechi S, Apweiler R, Bader J, Barnes S, Bettauer R, Chan MM, Coon J, Dolinski K, Dowell BL, Edmonds CG, Gaudet S, Gerszten R, Kagan J, Mazurchuk R, McShane L, Moritz RL, Palmer-Toy D, Pandey A, Polanski M, Quackenbush J, Sheeley D, Skates S, Srivastava S, Wang W, Weng Z, White F. (2012). The human proteome-a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. Clinical Proteomics. 9, 6.

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163. Kalra, H., Simpson, R. J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V. C., Borràs, F. E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton, A., Cocucci, E., Falcon-Perez, J. M., Gabrielsson, S., Gho, Y. S., Gupta, D., Harsha, H. C., Hendrix, A., Hill, A. F., Inaal, J. M., Jenster, G., Kiang, L. S., Krämer-Albers, E-M., Llorente, A., Lötvall, J., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t Hoen, E. N. M., Pandey, A., Patel, T., Piper, M. G., Pluchino, S., Prasad, T. S. K., Rajendran, L., Raposo, G., Record, M., Reid, G. E., Sánchez-Madrid, F., Schiffelers, R. M., Siljander, P., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B. W. M., Vázquez, J., Vidal, M., Yáñez-Mó, M., Zoeller, M. and Mathivanan, S. (2012). Vesiclepedia: A compendium for extracellular vesicles with continuous community annotation. PLoS Biology. 10, e1001450. 164. Do Vale L, H., Gómez-Mendoza, D. P., Kim, M. S., Pandey, A., Ricart, C. A., Ximenes-Filho, E, Sousa, M. V. (2012). Secretome analysis of the fungus Trichoderma harzianum grown on cellulose. Proteomics. 12, 2716-2728. 165. Martinez-Ferrando, I., Chaerkady, R., Zhong, J., Molina, H., Kishore, H., Herbst-Robinson, K., Dancy, B. M., Katju, V., Bose, R., Zhang, J., Pandey, A. and Cole, P. A. (2012). Identification of targets of c-Src tyrosine kinase by chemical complementation and phosphoproteomics. Molecular and Cellular Proteomics. 11, 355-369. 166. Ren, Y. R., Chaerkady, R., Hu, S., Wan, J., Qian, J., Zhu, H., Pandey, A. and Kern, S. E. (2012). Unbiased discovery of interactions at a control locus driving expression of the cancer-specific therapeutic and diagnostic target, mesothelin. Journal of Proteome Research. 11, 5301-5310. 167. van Bodegom, D., Zhong, J., Kopp, N., Dutta, C., Kim, M. S., Bird, L., Weigert, O., Tyner, J., Pandey, A., Yoda, A. and Weinstock, D. M. (2012). Differences in signaling through the B-cell leukemia oncoprotein CRLF2 in response to TSLP and through mutant JAK2. Blood. 120, 2853-2863. 168. Kumar, G. S. S., Venugopal, A. K., Kashyap, M. K., Raju, R., Marimuthu, A., Palapetta, S. M., Subbannayya, Y., Goel, R., Chawla, A., Dikshit, J. B., Tata, P., Harsha, H. C., Maharudraiah, J., Ramachandra, Y. L., Satishchandra, P., Prasad, T. S. K., Pandey, A., Mahadevan, A. and Shankar, S. K. (2012).Gene expression profiling of tuberculous meningitis co-infected with HIV. Journal of Proteomics and Bioinformatics. 5, 235-244. 169. Luo, W., Chang, R., Zhong, J., Pandey, A. and Semenza, G. L. (2012). The histone demethylase JMJD2C is a coactivator for hypoxia-inducible factor 1 that is required for breast cancer progression. Proceedings of the National Academy of Sciences U.S.A. 109, 19889–19890. 170. Kumar, G. S. S., Venugopal, A. K., Mahadevan, A., Renuse, S., Harsha, H. C., Sahasrabuddhe, N. A., Pawar, H., Sharma, R., Kumar, P., Rajagopalan, S., Waddell, K., Ramachandra, Y. L., Satishchandra, P., Chaerkady, R., Prasad, T. S. K., Shankar, S. K. and Pandey, A. (2012). Quantitative proteomics for identifying biomarkers for tuberculous meningitis. Clinical Proteomics. 9, 12-24.

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171. Marimuthu, A., Subbannayya, Y., Sahasrabuddhe, N. A., Balakrishnan, L., Syed, N., Sekhar, N. R., Katte, T. V., Pinto, S. M., Srikanth, S. M., Kumar, P., Pawar, H., Kashyap, M. K., Maharudraiah, J., Ashktorab, H., Smoot, D. T., Ramaswamy, G., Kumar, R. V., Cheng, Y., Meltzer, S. J., Roa, J. C., Chaerkady, R., Prasad, T. S. K., Harsha, H. C., Chatterjee, A. and Pandey, A. (2012). SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics - Clinical Applications. In press 172. Dey, G., Radhakrishnan, A., Syed, N., Thomas, J. K., Nadig, A., Srikumar, K., Mathur, P. P., Pandey, A., Lin, S. K., Raju, R. and Prasad, T. S. K. (2013). Signaling network of Oncostatin M pathway. Journal of Cell Communication and Signaling. 7, 103-108. 173. Venugopal, A. K., Kumar, G. S. S., Selvan, L. D. N., Mahadevan, A., Renuse, S., Kumar, P., Pawar, H., Sahasrabuddhe, N. A., Suja, M. S., Ramachandra, Y. L., Prasad, T. S. K., Madhusudhana, S. N., Harsha, H. C., Chaerkady, R., Satishchandra, P., Pandey, A. and Shankar, S. K. (2013). Quantitative proteomics for identifying biomarkers for Rabies. Clinical Proteomics. 10, 3. 174. Kashyap, M. K., Pawar, H., Keerthikumar, S., Sharma, J., Goel, R., Mahmood, R., Vijaya Kumar, M., Veerendra Kumar, K. V., Pandey, A., Kumar, R. V., Prasad, T. S. K. and Harsha, H. C. (2013). Evaluation of protein expression pattern of stanniocalcin 2, insulin-like growth factor-binding protein 7, inhibin beta A and four and a half LIM domains 1 in esophageal squamous cell carcinoma. Cancer Biomarkers. 12, 1-9. 175. Soman, S., Raju, R., Sandhya, V. K., Advani, J., Khan, A. A., Harsha, H. C., Prasad, T. S. K., Sudhakaran, P. R., Pandey, A. and Adishesha, P. K. (2013). A multicellular signal transduction network of AGE/RAGE signaling. Journal of Cell Communication and Signaling. 7, 19-23. 176. Pawar, H., Maharudraiah, J., Kashyap, M. K., Sharma, J., Srikanth, M. S., Choudhary, R., Chavan, S., Sathe, G., Manju, H .C., Veerendra Kumar, K. V., Vijayakumar, M., Sirdeshmukh, R., Harsha, H. C., Prasad, T. S. K., Pandey, A. and Kumar, R. V. (2013). Downregulation of cornulin in esophageal squamous cell carcinoma. Acta Histochemica. 115, 89-99. 177. Newman, R. H., Hu, J., Rho, H. S., Xie, Z., Woodard, C., Neiswinger, J., Cooper, C., Shirley, M., Clark, H. M., Hu, S., Hwang, W., Jeong, J. S., Wu, G., Lin, J., Gao, X., Ni, Q., Goel, R., Xia, S., Ji, H., Dalby, K. N., Birnbaum, M. J., Cole, P. A., Knapp, S., Ryazanov, A. G, Zack, D. J., Blackshaw, S., Pawson, T., Gingras, A. C., Desiderio, S., Pandey, A., Turk, B. E, Zhang, J., Zhu, H. and Qian, J. (2013). Construction of human activity-based phosphorylation networks. Molecular Systems Biology. 9:655. 178. Balakrishnan, L., Soman, S., Patil, Y. B., Advani, J., Thomas, J. K., Venkatesh, D. D., Urmila, K. K., Harsha, H. C., Prasad, T. S. K., Raju, R., Pandey, A., Dimitriadis, E., and Chatterjee, A. (2013). IL-11/IL11RA receptor mediated signaling: a web accessible knowledgebase. Cell Communication and Adhesion. 20, 81-86. 179. Sandhya, V. K., Raju, R., Verma, R., Advani, J., Sharma, R., Radhakrishnan, A., Nanjappa, V., Narayana, J., Somani, B. L., Mukherjee, K. K., Pandey, A., Christopher, R. and Prasad, T. S.

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K. (2013). A network map of BDNF/TRKB and BDNF/p75NTR signaling system. Journal of Cell Communication and Signaling. 4, 301-307. 180. Patel, K., Scrimieri, F., Ghosh, S., Zhong, J., Kim, M. S., Ren, Y. R., Morgan, R. A., Iacobuzio-Donahue, C. A., Pandey, A. and Kern, S. E. (2013). FAM190A deficiency creates a cell division defect. American Journal of Pathology. 183, 296-303. 181. Nirujogi, R. S., Pawar, H., Renuse, S., Kumar, P., Chavan, S., Sathe, G., Sharma, J., Khobragade, S., Pande, J., Modak, B., Prasad, T. S. K., Harsha, H. C., Patole, M. S. and Pandey, A. (2013). Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani. Journal of Proteomics. 13, 210-218. 182. Marimuthu, A., Chavan, S., Sathe, G., Sahasrabuddhe, N. A., Srikanth, S. M., Renuse, S., Ahmad, S., Radhakrishnan, A., Barbhuiya, M. A., Kumar, R. V., Harsha, H. C., Sidransky, D., Califano, J., Pandey, A. and Chatterjee, A. (2013). Identification of head and neck squamous cell carcinoma biomarker candidates through proteomic analysis of cancer cell secretome. BBA - Proteins and Proteomics. 1834, 2308-231. 183. Hansen, A. M., Chaerkady, R., Sharma, J., Díaz-Mejía, J. J., Tyagi, N., Renuse, S., Jacob, H. K. C., Pinto, S. M., Sahasrabuddhe, N. A., Kim, M. S., Delange, B., Srinivasan, N., Emili, A., Kaper, J. and Pandey, A. (2013). The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathogens. 9, e1003403. 184. Polisetty, R. V., Gautam, P., Gupta, M. K., Sharma, R., Uppin, M. S., Challa, S., Ankathi, P., Purohit, A. K., Renu, D., Harsha, H. C., Pandey, A. and Sirdeshmukh, R. (2013). Heterogeneous nuclear ribonucleoproteins and their interactors are a major class of deregulated proteins in anaplastic astrocytoma – a Grade III malignant glioma. Journal of Proteome Research. 12, 3128-3138. 185. Ambekar, S. A., Nirujogi, R. S., Srikanth, S. M., Chavan, S., Kelkar, D. S., Hinduja, I., Zaveri, K., Prasad, T. S. K., Harsha, H. C., Pandey, A. and Mukherjee, S. (2013). Proteomic analysis of human follicular fluid: A new perspective towards understanding folliculogenesis. Journal of Proteomics. 87, 68-77. 186. Chaerkady, R., Shao, H., Scott, S. G., Pandey, A., Jun A. S. and Chakravarti, S. (2013). The keratoconus corneal proteome: loss of epithelial integrity and stromal degeneration. Journal of Proteomics. 87, 122-131. 187. Puttamallesh, V. N., Sreenivasamurthy, S. K., Singh, P. K., Harsha, H. C., Ganjiwale, A., Broor, S., Pandey, A., Narayana, J. and Prasad, T. S. K. (2013). Proteomic profiling of serum samples from chikungunya infected patients provides insights into host response. Clinical Proteomics. 10, 14. 188. Bhattacharjee, M., Sharma, R., Goel, R., Balakrishnan, L., Renuse, S., Advani, J., Shantal, T. G., Verma, R., Pinto, S. M., Nirujogi, R. S., Nair, B., Prasad, T. S. K., Harsha, H. C., Jois, R., Shankar, S. and Pandey, A. (2013). A Multilectin affinity approach for comparative glycoprotein profiling of rheumatoid arthritis and spondyloarthropathy. Clinical Proteomics. 10, 11.

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189. Goel, R., Murthy, K., Srikanth, S. M., Pinto, S. M., Bhattacharjee, M., Kelkar, D. S., Madugundu, A. K., Dey, G., Mohan, S. S., Krishna, V., Prasad, T. S. K., Chakravarti, S., Harsha, H. C. and Pandey, A. (2013). Characterizing the normal proteome of human ciliary body. Clinical Proteomics. 10, 9. 190. Selvan, L. D. N., Renuse, S., Jyothi, E. K., Sharma, J., Pinto, S. M., Yelamanchi, S. D., Puttamallesh, V. N., Ravikumar, R., Pandey, A., Prasad, T. S. K. and Harsha, H. C. (2013). Phosphoproteome of Cryptococcus neoformans. Journal of Proteomics. In press. 191. Prasad, T. S. K., Verma, R., Kumar, S., Nirujogi, R. S., Sathe, G. J., Madugundu, A. K., Sharma, J., Puttamallesh, V. N., Ganjiwale, A., Myneedu, V. P., Chatterjee, A., Pandey, A., Harsha, H. C. and Narayana, J. (2013). Proteomic analysis of purified protein derivative of Mycobacterium tuberculosis. Clinical Proteomics. 10, 8. 192. Sreenivasamurthy, S. K., Dey, G., Ramu, M., Kumar, M., Gupta, M. K., Mohanty, A. K., Harsha, H. C., Sharma, P., Kumar, N., Pandey, A., Kumar, A. and Prasad, T. S. K. (2013). A compendium of molecules involved in vector-pathogen interactions pertaining to malaria. Malaria Journal. 12, 216. 193. Selvan, L. D. N., Kaviyil, J. E., Nirujogi, R. S., Muthusamy, B., Puttamallesh, V. N., Subbannayya, T., Syed, N., Radhakrishnan, A., Kelkar, D. S., Ahmad, S., Pinto, S. M., Kumar, P., Madugundu, A. K., Nair, B., Chatterjee, A., Pandey, A., Ravikumar, R., Gowda, H. and Prasad, T. S. K. (2014). Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry. Clinical Proteomics. In press. 194. Zhong, J., Sharma, J., Raju, R., Palapetta, S. M., Prasad, T. S. K., Huang, T. C., Yoda, A., Tyner, J. W., van Bodegom, D., Weinstock, D. M., Ziegler, S. F. and Pandey, A. (2014). TSLP signaling pathway map: A platform for analysis of TSLP mediated signaling. Database. In press. Balakrishnan, L., Nirujogi, R. S., Ahmad, S., Bhattacharjee, M., Srikanth, S. M., Renuse, S., Kelkar, D. S., Subbannayya, Y., Raju, R., Goel, R., Thomas, J. K., Kaur, N., Dhillon, M., Tankala, S. G., Jois, R., Vasudev, V., Ramachandra, Y. L., Sahasrabuddhe, N. A., Prasad, T. S. K., Mohan, S., Gowda, H., Shankar, S. and Pandey, A. (2014). Proteomic analysis of human osteoarthritis synovial fluid. Clinical Proteomics. In press. 195. Balakrishnan, L., Bhattacharjee, M., Ahmad, S., Nirujogi, R. S., Renuse, S., Subbannayya, Y., Marimuthu, A., Srikanth, S. M., Raju, R., Dhillon, M., Kaur, N., Jois, R., Vasudev, V., Ramachandra, Y. L., Sahasrabuddhe, N. A., Prasad, T. S. K., Mohan, S., Gowda, H., Shankar, S. and Pandey, A. (2014). Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients. Clinical Proteomics. In press. 196. Nanjappa, V., Thomas, J. K., Marimuthu, A., Muthusamy, B., Radhakrishnan, A., Sharma, R., Khan, A. A., Balakrishnan, L., Sahasrabuddhe, N., Kumar, S., Jhaveri, B. N., Sheth, K. V., Khatana, R. K., Shaw, P. G., Srikanth, S. M., Mathur, P. P., Shankar, S., Nagaraja, D., Christopher, R., Mathivanan, S., Raju, R., Sirdeshmukh, R., Chatterjee, A., Simpson, R. J., Harsha, H. C., Pandey, A. and Prasad, T. S. K. (2014). Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic Acids Research. 42, D959-D965.

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197. Vega-Rodríguez, J., Ghosh, A. K., Kanzok, S. M., Dinglasan, R. R., Wang, S., Bongio, N. J., Kalume, D. E., Miura, K., Long, C. A., Pandey, A. and Jacobs-Lorena M. (2014). Multiple pathways for Plasmodium ookinete invasion of the mosquito midgut. Proceeding of the National Academy of Sciences, USA. In press. 198. Haeusler, A. R., Donnelly, C. J., Periz, G., Simko, E. A. J., Shaw, P. J., Kim, M. S., Maragakis, N. J., Troncoso, J. C., Pandey, A., Sattler, R., Rothstein, J. D. and Wang, J. (2014). C9orf72 Nucleotide-Repeat Structures Initiate Molecular Cascades of Disease. Nature. In press. Martin, I., Kim, J. W., Lee, B. D., Kang, H. C., Xu, J. C., Jia, H., Stankowski, J., Kim, M. S., Zhong, J., Kumar, M., Andrabi, S. A., Xiong, Y., Dickson, D. W., Wszolek, Z. W., Pandey, A., Dawson, T. M. and Dawson, V. L. (2014). Ribosomal protein phosphorylation mediates LRRK2 neurodegeneration in Parkinson’s disease. Cell. In press. ii) Review articles 1. Pandey, A., Lindberg, R. A. and Dixit, V. M. (1995). Cell signalling: Receptor orphans find a family. Current Biology. 5, 986-989. 2. Pandey, A. and Lewitter. F. (1999). Nucleotide Sequence Databases: A gold mine for biologists. Trends in Biochemical Sciences. 24, 276-280. 3. Pandey, A. and Mann, M. (2000). Proteomics to study genes and genomes. Nature. 405, 837-846. 4. Pandey, A., Andersen, J. S. and Mann, M. (2000). Use of mass spectrometry to study signaling pathways. Science's STKE. 37, pl1. 5. Mann, M. and Pandey, A. (2001). Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. Trends in Biochemical Sciences. 26, 54-61. 6. Mann, M., Hendrickson, R. C. and Pandey, A. (2001). Analysis of proteins and proteomes by mass spectrometry. Annual Review of Biochemistry. 70, 437-473. 7. Peri, S., Ibarrola, N., Blagoev, B., Mann, M. and Pandey, A. (2001). Common pitfalls in bioinformatics based analyses: Look before you leap. Trends in Genetics. 17, 541-545. 8. Ong, S. E. and Pandey, A. (2001). An evaluation of the use of two dimensional gel electrophoresis in proteomics. Biomolecular Engineering. 18, 195-205. 9. Kristiansen, T. Z. and Pandey, A. (2002). Resources for full-length cDNAs. Trends in Biochemical Sciences. 27, 266-267. 10. Mann, M., Ong, S. E., Gronborg, M., Steen, H., Jensen, O. N. and Pandey, A. (2002). Analysis of protein phosphorylation using mass spectrometry: Deciphering the phosphoproteome. Trends in Biotechnology. 20, 261-268. 11. Steen, H. and Pandey, A. (2002). ‘Proteomics goes quantitative: Measuring protein abundance.’ Trends in Biotechnology. 20, 361-364.

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12. Jebanathirajah, J. A., Peri, S. and Pandey, A. (2002). Toll and Interleukin-1 receptor (TIR) domain-containing proteins in plants: A genomic perspective. Trends in Plant Sciences. 7, 388-391. 13. Steen, H., Pandey, A., Andersen, J. S. and Mann, M. (2002). Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion (PSI) scanning method. Science’s STKE. 154: pl16. 14. Kalume, D. E., Molina, H. and Pandey, A. (2003). Tackling the phosphoproteome: tools and strategies. Current Opinion in Chemical Biology. 7, 64-69. 15. Navarro, J. D., Niranjan, V., Peri, S., Jonnalagadda, C. K. and Pandey, A. (2003). From biological databases to platforms for biomedical discovery. Trends in Biotechnology. 21, 263-268. 16. Deshpande, K. S., Harsha, H. C. and Pandey, A. (2003). Microarrays and mass spectrometry: The future of proteomics. Current Genomics. 4, 605-613. 17. Raghothama, C. and Pandey A. (2003). Absolute systems biology-measuring dynamics of protein modifications. Trends in Biotechnology. 21, 467-470. 18. Navarro, J. D. and Pandey, A. (2004). Unraveling the human interactome: Lessons from the yeast. Drug Discovery Today: Targets. 3, 79-84. 19. 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. 267, pl2. 20. Raghothama, C., Harsha, H. C., Prasad, C. K. and Pandey, A. (2005). Bioinformatics and proteomics approaches for proteomics research. Biogerontology. 6, 227-232. 21.Suresh, S., Sujatha Mohan, S., Mishra, G., Hanumanthu, G. R., Suresh, M., Reddy, R. and Pandey, A. (2005) Proteomic resources: Integrating biomedical information in humans. Gene. 364, 13-18. 22. Raghothama, C. and Pandey, A. (2007). Quantitative proteomics for identification of cancer biomarkers. Proteomics Clinical Applications. 1, 1080-1089. 23. Harsha, H. C. and Pandey, A. (2008). Quantitative proteomics using stable isotope labeling with amino acids in cell culture (SILAC). Nature Protocols. 3, 505-516. 24. Raghothama, C. and Pandey, A. (2008). Application of proteomics to lab diagnosis. Annual Review of Pathology. 3, 485-498. 25. Venugopal, A. K., Chaerkady, R. and Pandey, A. (2009). Application of mass spectrometry-based proteomics for biomarker discovery in neurological disorders. Annals of Indian Academy of Neurology. 12, 3-11.

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26. Ranganathan, P, Harsha, H. C. and Pandey, A. (2009). Molecular alterations in exocrine neoplasms of the pancreas. Archives of Pathology and Laboratory Medicine. 133, 405-412. 27. Harsha, H. C. and Pandey, A. (2010). Phosphoproteomics in Cancer. Molecular Oncology. 4, 482-495. 28. Renuse, S., Chaerkady, R. and Pandey, A. (2011). Proteogenomics. Proteomics. 11, 620-630. 29. Goel, R., Harsha, H. C., Pandey, A. and Prasad, T. S. K. (2011). Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Molecular Biosystems. In press. 30. Kim, M. S. and Pandey, A. (2012). Electron transfer dissociation mass spectrometry in proteomics. Proteomics. 12, 530-542. 31. Huang, T. C., Pinto, S. M. and Pandey, A. (2013). Proteomics for understanding microRNA biology. Proteomics. 13, 558-567. iii) Book chapters 1. Pandey, A., Toso, R., Bartley, T. D., Lindberg, R. A. and Dixit, V. M., ‘LERK-1,’ in, Human Cytokines: Handbook for Basic and Clinical Research, Vol. 3, Aggarwal, B. B. Ed. (Blackwell Scientific Publications, Inc., 1998). pp 490-504. 2. Steen, H. and Pandey, A. ‘Mass Spectrometry in Protein Characterization,’ in, Encyclopedia of the Human Genome, Volume 3, Cooper, D. N. Ed. (John Wiley & Sons, Ltd., Chichester, 2003). pp 841-844. 3. Steen, H. and Pandey, A. ‘Proteomics: A molecular scanner in medicine,’ in, Encyclopedia of the Human Genome, Volume 4, Cooper, D. N. Ed. (John Wiley & Sons, Ltd., Chichester, 2003). pp 879-883. 4. Ibarrola, N., Raghothama, C., and Pandey, A. ‘Proteomic analysis of the adipocyte secretome,’ in, Genomics and Proteomics in Nutrition, Berdanier C. D. and Moustaid-Moussa, N. Eds., (Marcel Dekker, Inc. New York, 2004). pp 393-411. 5. Ping, P., Vondriska, T. M., Creighton, C. J., Gandhi, T. K. B., 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., Muthusamy, 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. (2006). “A functional annotation of subproteomes in human plasma” in Exploring the Human Plasma Proteome, Gilbert S. Omenn, Ed., Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. pp 329-351

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6. Sarker, M., Hanumanthu, G. R. and Pandey, A. (2006). ‘Plasma Proteome Database’ in ‘Proteomics of human body fluids, Thongboonkerd, V. Ed. Humana Press, Totowa, N.J. pp 129-136 7. Gronborg, M., Maitra, A. and Pandey, A. (2006). ‘Proteomics of Human Pancreatic Juice’ in ‘Proteomics of human body fluids, Thongboonkerd, V. Ed. Humana Press, Totowa, N.J. pp 377-398 8. Kristiansen, T. Z., Maitra, A. and Pandey, A. (2006). ‘Proteomics of Human Bile’ in ‘Proteomics of human body fluids, Thongboonkerd, V. Ed. Humana Press, Totowa, N.J. pp 399-414. 9. Zhong, J., Molina, H. and Pandey, A. (2007) Phosphoproteomics, in Current Protocols in Protein Science. John Wiley & Sons, Ltd., Chichester. 50: 24.4.1-24.4.21. 10. Pimienta, G. and Pandey, A. (2009) SILAC for Global Phosphoproteomic Analysis, in Phospho-Proteomics, Methods and Protocols, de Graauw, M. Ed., Humana Press, New York, vol. 527. pp107-116. 11. Prasad, T. S. K., Kandasamy, K. and Pandey, A. (2009) Human Protein Reference Database and Human Proteinpedia as Discovery Tools for Systems Biology, Methods in Molecular Biology. 577, 67-79. 12. Muthusamy, B., Thomas, J. K., Prasad, T. S. K. and Pandey, A. (2013). Access guide to Human Proteinpedia in Current Protocols in Bioinformatics. 41:1.21.1-1.21.15. 13. Harsha, H. C., Pinto, S. M. and Pandey, A. (2013). Proteomic strategies to characterize signaling pathways. Methods in Molecular Biology. 1007, 359-377. Inventions, patents and copyrights 1. Thymic Stromal Lymphopoietin Receptor molecules and uses thereof: U.S. Patent No. 6,955,895

2. Methods for use of TSLP and agonists and antagonists thereof: U.S. Patent No. 7,731,953

3. Thymic Stromal Lymphopoietin Receptor molecules and uses thereof: U.S. Patent No. 7,402,659 4. Human Protein Reference Database, Copyright 2003-2009 with Johns Hopkins University Extramural Sponsorship i) Current Grants N00024-13-D-6400 (Pandey, PI) 06/01/13-09/30/14

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DOD/DTRA Title: A Comprehensive Systems Biology Approach to Host-Toxicant Response Total annual direct costs: $229,000 Role: Principal Investigator Effort: 15% HHSN261201200050C (Nevo-Robin) 09/28/12–09/27/14 NIH/NCI/Robin Biomedical (Subcontract to JHU) Development of tools for cryogenic biopsy of soft tissues Title: Assessment of a cryogenic device to preserve biopsy tissues. Total annual direct costs: $57,997 Role: Co-investigator Effort: 5% U54GM103520 (Boeke, PI) 09/01/09-08/31/14 NIH/NCRR Title: Networks and Pathways of Lysine Modification Total annual direct costs: $116,000 Role: Co-investigator Effort: 20% R01AI099280 (Rathod, PI) 05/01/12–04/30/17 NIH/NIAID; Subcontract (Pandey, PI) Total annual direct costs: $64,723 Title: Chemical Genomics for Antimalarial Targets Role: Co-investigator Effort: 10% HHSN268201000032C (Van Eyk, PI) 08/15/10-08/14/15 NIH/NHLBI Total annual direct costs: $112,000 Title: Proteomics of Adaptation to Ischemia/Hypoxia in Heart, Lung and Blood. Major Goals: Technology development for post-translational modifications Role: Co-Investigator Effort: 10% U24 CA160036 (Chan, Zhang, H. Zhang Z, PI) 04/01/11–03/31/16 NIH/NCI Title: Proteome Characterization Center: A genoproteomics pipeline for cancer biomarkers Major goals: The major goal of this Center is the proteomic characterization of cancer tissues and plasma samples. Total annual direct costs: $67,000 Effort: 15% Investigator-initiated project (Dawson, PI) 06/01/13-05/31/16 Maryland Stem Cell Research Fund Title: Parkinson’s disease causing mutations in LRRK2 lead to neuronal dysfunction in neurons Total annual direct costs: $40,000

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Role: Co-investigator Effort: 1% Foundation Award (Dawson, PI) 06/01/13-05/31/14 Diana Helis Henry Medical Research Foundation Title: Identifying Parkinson's Disease Biomarkers Using Mass Spectrometry Total annual direct costs: $69,042 Role: Co-investigator Effort: 10% P50CA062924 (Kern) 09/19/12-08/31/17 NCI Title: SPORE in Gastrointestinal Cancer Total annual direct costs: $22,000 Major Goals: Identification of biomarkers Role: Co-Investigator Effort: 10% Subaward from Dana Farber Cancer Institute (Weinstock, PI) 04/01/13-09/30/13 William Lawrence and Blanche Hughes Foundation Title: Proteomic Analysis of CRLF2 Signaling Total annual direct costs: $25,000 Role: Co-investigator Effort: 2% 223996 Career Catalyst Award (Wu, PI) 9/1/10-9/18/14 Susan G. Komen Breast Cancer Foundation Total annual direct costs: $120,000 Title: Proteomic analysis of triple negative breast cancer Role: Mentor/Collaborator Effort: 0% R37 CA043460 (Vogelstein, PI) 02/01/12-11/30/16 NIH/NCI Total annual direct costs: $30,000 Molecular genetic analysis of colorectal cancer Major Goals: Signaling pathways activated by mutant PI3-Kinase Role: Co-investigator Effort: 0% Funding for Postdoc (Pandey, PI) 06/01/13-05/31/14 Agilent Technologies Title: Agilent Mass Spectrometer and Integrated Biology Collaboration Total annual direct costs: $60,000 Role: Principal Investigator Effort: 0% ii) Previous

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Grants Services Agreement (Pandey, PI) 05/01/12-04/30/13 Janssen Pharmaceuticals Total annual direct costs: $101,441 Title: Phosphoproteomics analysis Role: Principal Investigator Effort: 10% Avon Foundation for Women 01/01/13–12/31/13 Title: Proteomic analysis of hormone refractory breast cancer Total annual direct costs: $50,000 Role: Principal Investigator Effort: 1% Exploratory Award (Chaerkady, PI) 07/01/11–06/30/13 Maryland Stem Cell Research Fund Total annual direct costs: $60,000 Title: Signaling mechanisms specifying oligodendrocyte development Role: Mentor/Collaborator Effort: 0% DOD Era of Hope Scholar Award (Pandey, PI) 04/17/06-04/16/12 Department of Defense Total Direct Costs: $2,500,000 Title: Proteomic and Functional Analysis of Fibroblasts in Breast Cancer Role: PI Effort: 33% P01 CA129243 (Varmus, PI) 07/01/07-06/30/12 NIH/NCI/ Memorial Sloan-Kettering Cancer Center (Subcontract) Total Direct Costs: $86,450 Novel targets for therapy of adenocarcinoma Major Goals: Quantitative proteomic analysis of signaling pathways in lung cancer Role: Co-investigator Effort: 1% Pancreatic Cancer Pilot Project (Pandey, PI) 01/01/12-12/31/12 Sol Goldman Foundation for Pancreatic Cancer Research Total annual direct costs: $50,000 Title: EphB4 as a therapeutic target in pancreatic cancer Role: Principal Investigator Effort: 10% R01 CA106424 (Pandey, PI) 03/11/05-03/10/09 NIH/NCI Total Direct Costs: $711,000 Title: Molecular Dissection of Growth Factor Receptor Signaling.

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Role: PI Effort: 20% R01DK080750 (Civin, PI) 4/1/08-3/31/11 NIH/NIDDK Total Direct Costs: $27,369 MicroRNAs regulating erythroid development Role: Co-investigator Effort: 2% KG081288 (Gabrielson, PI) 9/19/08-9/18/11 Susan G. Komen Breast Cancer Foundation Total Direct Costs: $122,580 Unrecognized mechanisms of docetaxel activity in breast cancer Role: Co-investigator Effort: 8% R01DE016887 (Elisseeff, PI) 7/1/06-5/31/11 NIH/NIDCR Total Direct Costs: $101,422 Tissue engineering for congenital craniofacial defects Role: Co-investigator Effort: 5% 1S10RR027469 (Pandey, PI) 4/1/10 to 3/31/11 NCCR/NIH Total Direct Costs: $495,330 Title: Quadrupole Time-of Flight Mass Spectrometer Role: Principal Investigator 1S10RR025419 (Cotter, PI) 5/1/09 to 4/30/10 NCCR/NIH Total Direct Costs: $413,070 Title: Triple Quadrupole Mass Spectrometer for Multiple Reaction Monitoring Role: Co-investigator 1S10RR023025 (Cotter, PI) 5/1/07 to 4/30/08 NCCR/NIH Total Direct Costs: $928,365 Title: Linear Ion Trap/Fourier Transform Mass Spectrometer Role: Co-investigator Exploratory Grant (Pandey, PI) 010/1/07–09/30/09 Maryland Stem Cell Research Fund Total Direct Costs: $200,000 Proteomic characterization of neural differentiation in human embryonic stem cells Major Goals: Quantitative proteomic analysis of hES-derived neural cells during differentiation Role: Principal Investigator

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Effort: 5% Beckman Young Investigator Award (Pandey, PI) 06/01/04-05/31/07 Arnold and Beckman Mabel Foundation Title: A Combined Proteomic and Bioinformatic Approach to Study EGF Receptor Signal Transduction Pathway Total Direct Costs: $240,000 Role: PI Effort: 10% Kimmel Scholar Award (Pandey, PI) 07/01/03-06/30/05 Sidney Kimmel Foundation for Cancer Research Title: Proteomic analysis of EGF receptor signaling pathway Total Direct Costs: $200,000 Role: PI Effort: 10% R01 GM076570-01 (Hlavacek, PI) 04/01/07-03/31/10 NIH/ University of New Mexico (Subcontract) Total Direct Costs: $39,309 Computational Tools for Rule-based Modeling of Biochemical Systems Major Goals: Modeling of signal transduction pathways Role: Co-investigator Effort: 1% R01 DK066627-02 (Lane, PI) 09/16/03-08/31/07 NIH/NIDDK Title: Factors and Genes Responsible for Adipocyte Commitment Total Direct Costs: $402, 056 Role: Co-investigator Effort: 13% Career Development Award (Pandey, PI) 01/01/03-02/28/05 JHU Breast Cancer SPORE Title: Characterization of tyrosine kinase signaling pathways using mass spectrometry. Total Direct Costs: $100,000 Role: PI Effort: 20% Malaria Pilot Project (Pandey, PI) 11/15/02-11/14/04 Johns Hopkins Malaria Research Institute Title: Proteomic analysis of salivary glands of Anopheles gambiae mosquito Total Direct Costs: $100,000 Role: PI Effort: 10% Pilot Project, (Pandey, PI) 04/01/03-03/31/04 Alexander and Margaret Stewart Trust Grant and Johns Hopkins GI Cancer SPORE

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Title: Identification of Novel Biomarkers in Biliary Tract Cancers Total Direct Costs: $40,000 Role: PI Effort: 10% K01 CA 75447 (Pandey, PI) 08/19/97-07/31/02 NIH/NCI Howard Temin Award Title: Signal transduction through the erythropoietin receptor Total Direct Costs: $741,250 Role: PI Effort: 100% Contracts Human Database Project (Pandey, PI) 09/04/04-09/03/08 NIH/NCBI Title: Human Protein Reference Database Total Direct Costs: $2,250,000 Role: PI Other Academic Educational Grant (Pandey, PI) 12/1/03-11/30/04 Sun Microsystems Title: Mass Spectrometry Data Analysis $130,000 award in equipment Role: PI Effort: 1% Academic Educational Grant (Pandey, PI) 2/1/03-3/31/04 Sun Microsystems Title: Comparative genomic analysis of the human X chromosome $95,000 award in equipment Role: PI Effort: 1% DOD Predoctoral Traineeship Award (Zhong, PI) 03/21/05 - 04/20/08 Department of Defense Title: Characterization of Odin, a Novel Inhibitory Molecule, in EGF Receptor Signaling Total Direct Costs: $87,918 Annual Direct Costs: $29,306 Role: Mentor Effort: 0% Malaria Pilot Project (Pandey, PI) 09/01/04-08/31/06 Johns Hopkins Malaria Research Institute Title: Proteomic Analysis of Anopheles gambiae mosquito Total Direct Costs: $100,000

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Current Year Direct Costs: $50,000 Role: PI Effort: 10% RESEARCH PROGRAMME BUILDING/LEADERSHIP 2002-Present, Institute of Bioinformatics, Bangalore, India, Founder (Director since 2007). This Institute has a current staff of 60 scientists, which includes software engineers, molecular biologists and bioinformaticians. This Institute has evolved into a leading research institute in India performing cutting edge research in genomics and proteomics. Achievements of the institute for the past few years has been well recognized by the community and greatly appreciated by the Indian government, which has recently awarded the Institute with a $2.1 million support to establishing a Center for Neuroproteomics. It is affiliated to several Universities for award of Ph.D. degrees. EDUCATIONAL ACTIVITIES Teaching i) Classroom instruction Course Title: Molecules and Cells, Section: Metabolism, Johns Hopkins University SOM (Course # 580.221), Fall 2003. Role: Instructor Course Title: Molecules and Cells, Section: Metabolism, Johns Hopkins University SOM (Course # 580.221), Fall 2004. Role: Instructor Course Title: Bioinformatics Course, Biological Databases and Distributed Computing, Johns Hopkins University Bloomberg School of Public Health (Course # 140.637). Winter 2004. Role: Co-Director Course Title: Topics in Biological Chemistry, Department of Biological Chemistry, Johns Hopkins University. Winter 2005. Role: Discussion Leader. Course Title: Protein Bioinformatics, Johns Hopkins University Bloomberg School of Public Health, Spring 2005. Role: Instructor. Course Title: Biological Database and Distributed Computing Fall 2005. Role: Co-Director. Course Title: Protein Bioinformatics, Bloomberg School of Public Health, Johns Hopkins University, Winter 2006. Role: Instructor Course Title: Human Genetics (Roger Reeves), McKusick Nathan’s Institute of Genetic Medicine, Johns Hopkins University, Winter 2007. Role: Instructor. Course Title: Human Genetics (Roger Reeves), McKusick Nathan’s Institute of Genetic Medicine, Johns Hopkins University, Winter 2009. Role: Instructor.

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Course Title: Human Genetics (Roger Reeves), McKusick Nathan’s Institute of Genetic Medicine, Johns Hopkins University, Winter 2012. Role: Instructor. Course Title: Human Genetics (Roger Reeves), McKusick Nathan’s Institute of Genetic Medicine, Johns Hopkins University, Winter 2013. Role: Instructor. ii) CME instruction Course Title: ‘New Paradigms for Tyrosine Kinase Specificity: Molecular Biology to the Clinic.’ July 11, 2003. Washington, DC. Role: Instructor, Lecture: ‘Proteomic Approaches to Studying Tyrosine Kinase Signaling Pathways.’ American Association for Cancer Research. Course Title: Application of the new biology to the diagnosis and treatment of hematologic malignancies’ December 7, 2001. Orlando, FL. Role: Instructor, Plenary lecture ‘Proteomic approaches to studying signaling pathways in leukemias and lymphomas,’ The Leukemia and Lymphoma Society. American Society of Hematology. Course Title: ‘Recharting ancient pathways: Proteomics, the next frontier of inflammation research’ May 26, 2004. Orlando, FL. Role: Instructor, Lecture ‘Phosphoproteomics: Fresh insights into tyrosine phosphorylation events in the EGF receptor signaling pathway.’ American Thoracic Society. Course Title: ‘Bioinformatics for Proteomics’, Role: Instructor, Washington, D.C. March, 2005. Course Title: Proteomics, Role: Instructor, Cold Spring Harbor Labs, July, 2005. Course Title: ‘Bioinformatics for Proteomics’, Role: Course Leader, 2nd Annual Symposium, U.S. Human Proteome Organization (U.S. HUPO), March 2006. Course Title: Proteomics, Role: Instructor, Cold Spring Harbor Labs, July, 2006. Course Title: ‘Quantitative Proteomics’ Role: Course leader, Workshop at the Association for Biomolecular Research Facilities, Tampa, Florida, March 2007 Mentoring (pre- and post-doctoral) i) Advisees 1. Irina Kratchmarova, Ph.D., 6/1/99-2/1/02, Current Position: Postdoctoral Fellow, Laboratory of Matthias Mann, University of Southern Denmark, Odense, Denmark. Received Ph.D. degree 2. Blagoy Blagoev, Ph.D., 6/1/99-2/1/02, Current Position: Assistant Professor, University of Southern Denmark, Odense, Denmark: Received Ph.D. degree 3. Minerva Fernandez, M.Sc, 1/1/00-2/1/02, Current Position: Research Assistant, Sainte Justine Hospital, Montreal, Canada. 4. Suraj Peri, Ph.D., 1/1/03- 09/01/05, Current Position: Research Scientist, Fox Chase Cancer Centre

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5. Mads Gronborg, Ph.D., 1/1/03- 2/27/06, Current Position: Post Doctoral Fellow, Max Planck Institute for Biophysical Chemistry 6. Troels Kristiansen, Ph.D., Graduate Student: 1/1/03- 11/15/05, Current Position: McKinsey Consulting, Denmark 7. Suresh Mathivanan, Ph.D., 07/11/05- 06/30/08, Current Position: Postdoctoral Fellow, WEHI, Melbourne, Australia 8. Shubha Suresh, M.Sc., Graduate Student: 09/27/05- 11/15/06 9. Salil Sharma, M.Sc., Graduate Student: 9/13/04- 05/20/06, Current Position: Ph.D. Student, University of Miami, Florida. 10. Raghunath Reddy, M.Sc., Graduate Student: 9/30/04- 07/31/06, Current position: Ph.D. student, The FIRC Institute of Molecular Oncology, Milan, Italy 11. T.K.B. Gandhi, M.Sc., Graduate Student: 06/13/05-9/26/06, Current position: Ph.D. Student, Tubingen, Germany 12. Balamurugan Periaswamy, M.Sc., Ph.D. student 1/30/06–6/30/07 Current Position: Ph.D. student, Swiss Federal Institute of Technology, Zürich 13. Jun Zhong, M.Sc., Graduate Student, Biological Chemistry Program: 6/10/04-Present. Received Department of Defense Predoctoral Traineeship Award 14. Wan-Hee Yoon, M.Sc., Rotation Student, Biological Chemistry Program: 8/16/04-12/07/04 15. Zihao Wang, M.Sc., Rotation Student, Biological Chemistry Program: 9/1/04-12/07/04 16. Beiyi Shen, M.Sc., Rotation Student, Biological Chemistry Program: 12/8/04-3/10/05 17. Vikas Kumar, M.Sc., Rotation student: 2/17/05-08/17/05 Current Position: Ph.D. Student, University of Otago Christchurch, Christchurch, New Zealand. 18. Danny Navarro, M.Sc., Student: 05/01/02-06/30/04, Current Position: Bioinformatician, Netherlands Proteomic Centre. 19. Harsha Gowda, M.Sc. (from Institute of Bioinformatics, Bangalore, India) – Student, 2/24/06-2/1/09, Current position: Research Associate, Scripps Center for Metabolomics and Mass Spectrometry, La Jolla, California 20. Min-Sik Kim, M.Sc., Graduate Student, Biological Chemistry Program: 6/17/08-12/12/12 21. Kumaran Kandasamy, M.Sc. (from Institute of Bioinformatics, Bangalore, India) – Student, 3/19/07-3/26/11, Current position: Postdoctoral Fellow, Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna, Austria 22. Manoj Kashyap, M.Sc. (from Institute of Bioinformatics, Bangalore, India) – Student, 11/5/07-3/2/11. 23. Arivusudar Marimuthu, M.Sc. (from Institute of Bioinformatics, Bangalore, India): Student, 11/5/07-3/1/12. Current position: Faculty Scientist, Institute of Bioinformatics, Bangalore, India 24. Qing Wang, M.Sc., Graduate Student, Pharmacology and Molecular Sciences, (Laboratory of Bert Vogelstein), 01/05/09- Present 25. Charles Jacob Harrys Kishore, M.Sc. (from Institute of Bioinformatics, Bangalore, India): Student, 11/05/07 – 06/30/12, Current position: Postdoctoral Fellow, Centro Nacional de Investigaciones Oncologicas, Madrid, Spain. 26. Abhilash K. Venugopal, M.Sc. (from Institute of Bioinformatics, Bangalore, India): Student, 2009 - 2012 27. Nandini Sahasrabuddhe, M.Sc. (from Institute of Bioinformatics, Bangalore, India): Student, 2009 - 2012 28. Santosh S. Renuse, M.Sc. (from Institute of Bioinformatics, Bangalore, India): Student, 2009 – 2012 29 Tai-Chung Huang, M.D. Graduate Student, Human Genetics Program, 2010 – Present

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30. Raja Sekhar Nirujogi, M.Sc. (from Institute of Bioinformatics, Bangalore, India): Student, 2010 – Present 31. Sneha M. Pinto, M.Sc (from Institute of Bioinformatics, Bangalore, India): Student, 2010 - Present 32. Chris Mitchell, B.S. Graduate Student, BCMB Program, 2011 – Present 33. Saddiq Zahari, B.S. Graduate Student, Biological Chemistry, 2011 – Present 34. Srikanth Manda, M.Sc. (from Institute of Bioinformatics, Bangalore, India): Student, 2010 – Present 35. Anjun Bose, B.S. Graduate Student, Biomedical Engineering, 2013- Present Postdoctoral fellows: 1. Dario Kalume, Ph.D., Postdoctoral Fellow: 7/1/02-8/30/05, Current Position: Associate Professor, Department of Tropical Medicine, Oswaldo Cruz Institute, Rio de Janeiro, Brazil 2. Ramars Amanchy, Ph.D., Postdoctoral Fellow: 7/1/02-5/31/07, Current Position: Postdoctoral Fellow, University of Cincinnati, OH 3. Anuradha Nalli, Ph.D., Postdoctoral Fellow: 3/21/07-3/31/08 4. Henrik Molina, Ph.D., Postdoctoral Fellow: 1/20/07-7/31/08, Current Position: Research Assistant Professor, Rockefeller University 5. Mobolaji Okulate, Ph.D., Postdoctoral Fellow (laboratory of N. Kumar): 1/1/04-10/01/04, Current Position: Assistant Professor, University of Maryland, MD 6. Jakob Bunkenborg, Ph.D., Postdoctoral Fellow, 4/29/03-1/31/04; Current Position: Postdoctoral Fellow, University of Southern Denmark, Odense, Denmark. Received a Postdoctoral Fellowship award from the Danish Natural Science Research Council. 7. Nieves Ibarrola, Ph.D., Postdoctoral Fellow: 5/1/02-1/31/04; Current Position: Proteomics Head, University of Salamanca, Spain. 8. Genaro Pimienta, Ph.D., Postdoctoral Fellow. 10/15/07 - 12/31/08, Current Position: Postdoctoral Fellow, Yale University 8. Raghothama Chaerkady, Ph.D., Postdoctoral Fellow: 3/15/06-10/31/11, Current Position, Research Associate, Johns Hopkins Mass Spectrometry Core Facility 9. Yi Yang, M.D., Ph.D., Postdoctoral Fellow: 3/15/07-6/30/10, Current Position: Physician Assistant, Mercy Medical Center, Baltimore, MD 10. Xinyan Wu, Ph.D., Instructor, 2/15/09 –Present 11. Derese Getnet, Ph.D., Postdoctoral Fellow – 7/15/10-5/3/13, Current Position: US Army 12. Min-Sik Kim, Ph.D., Postdoctoral Fellow – 12/12/12-Present 13. Pamela Leal-Rojas, Ph.D., Postdoctoral Fellow – 1/7/13-Present 14. Chan-Hyun Na, PhD., Postdoctoral Fellow – 8/8/13-Present 15. Mustafa Barbhuiya, Ph.D., Postdoctoral Fellow – 8/15/13-Present ii) Thesis committees 1. Soo Hee Lee (Laboratory of Paul Englund, Dept. of Biological Chemistry, Johns Hopkins), 2002-2006, Member 2. Yingfeng Qiao (Laboratory of Phil Cole, Dept. of Pharmacology, Johns Hopkins), 2004-2006, Member 3. Jessica LaRusch (Laboratory of Garry Cutting, Institute of Genetic Medicine, Johns Hopkins), 2002-2007, Member 4. Rebekah Gundry (Laboratory of Robert Cotter, Dept. of Pharmacology, Johns Hopkins), 2004-2007, Member

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5. Chris Frank (Laboratory of Carol Grieder, Molecular Biology and Genetics, Johns Hopkins), 2003-2005, Member 6. Geoffrey Hesketh (Laboratory of Jennifer van Eyk, Dept. of Medicine, Johns Hopkins), 2005-2008, Member 7. Zihao Wang (Laboratory of Jerry Hart, Dept. of Biological Chemistry, Johns Hopkins), 2005-2008, Member 8. Liangfeng Han (Laboratory of Sara Sukumar, Dept. of Oncology, Johns Hopkins), 2005-2009, Member 9. Elisha Roberson (Laboratory of Jonathan Pevsner, Kennedy Krieger Institute), 2007-2009, Member. 10. Bjorn Kafsack (Laboratory of Vern Carruthers, Bloomberg School of Public Health), 2005-2009, Member) 11. Patrick Shaw (Laboratory of Nancy Davidson, Dept of Oncology, Johns Hopkins), 2007-2011, Member 12. Shino Shimoji (Laboraty of Gerald Hart, Dept. of Biological Chemistry, Johns Hopkins), 2007-2011, Member 13. Abena Agyeman (Laboratory of Thomas Kensler, Bloomberg School of Public Health), 2009-2011, Member 14. Darshil Jhaveri (Laboratory of Liz Jaffee, Dept of Oncology, Johns Hopkins), 2010-Present, Member Editorial activities Editorial board appointments Genome Research (2003- 2006), Editorial board member Journal of Proteome Research (2006- Present), Editorial Advisory board member Clinical Proteomics (2006- Present), Editorial board member DNA Research (2008- Present), Editor Molecular and Cellular Proteomics (2009-Present), Editorial board member Proteomics (2009-Present), Editorial board member BMC Bioinformatics (2009-2011) Associate Editor Journal of Proteomics (2011-Present) Associate Editor Journal of Translational Medicine (2011-Present), Editorial board member ii) Journal peer review activities Ad hoc reviewer for: Nature, Nature Biotechnology, Nature Genetics, Nature Methods, Science, Science Translational Medicine, Cell, Molecular Cell, Proceeding of the National Academy of Sciences, USA, Cancer Research, Genome Biology, Genome Research, Journal of Biological Chemistry, Molecular and Cellular Proteomics, Proteomics, Journal of Proteome Research, Analytical Chemistry, Trends in Genetics, Drug Discovery Today, Bioinformatics, Nucleic Acids Research, BMC Genomics, BMC Bioinformatics, Journal of Neuroscience, Proteins, Gene CLINICAL ACTIVITIES

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None ORGANIZATIONAL ACTIVITIES Institutional Administrative Appointments Scientific Advisory Board, ABI Mass Spectrometry/Proteomics Facility, Johns Hopkins

University, 2003-Present Advisory Board, Malaria Research Institute Grants Program, Johns Hopkins University, 2004-

2008 Biostatistics/Oncology Faculty Search Committee, Johns Hopkins University, 2004-2009 Biological Chemistry Faculty Search Committee, 2004-12 Biological Chemistry Graduate Student Admissions Committee, 2003-Present BCMB Oral Examination Committee, 2003-Present Professional Societies American Society for Biochemistry and Molecular Biology, 1998-Present, Member American Society of Investigative Pathology, 1995-Present, Member American Society for Mass Spectrometry, 2000-Present, Member American Association for Cancer Research, 2003-Present, Member Human Proteome Organization, 2003-Present, Member US Human Proteome Organization, 2004- Present, Member American Chemical Society, 2004- Present, Member Conference Organizer, Session Chair U.S. Human Proteome Organization, 1st Annual Symposium, March 2005, Role: Session Chair,

Post-translational Modifications U.S. Human Proteome Organization, 1st Annual Symposium, March 2005, Role: Course Leader,

Workshop entitled: ‘Bioinformatics for Proteomics’ Association for Biomolecular Research Facilities, Annual Meeting, April 2007, ‘Bioinformatics

Role: Session chair, Protein Complexes HUGO Human Genome Organization, 13th Human Genome meeting, September 28, 2008, Role:

Role: Session Chair, Disease Proteomics American Society for Investigative Pathology, FASEB April 18, 2009, Role: Session Chair,

Minisymposium: Cancer Genetics, Epigenetics, and Biomarkers Annual Meeting of the American Society for Mass Spectrometry, Vancouver, May 22, 2012,

Role: Session Chair: Systems Biology U.S. Human Proteome Organization, 9th Annual Conference, March 10-13, 2013, Role:

Organizing Committee Advisory Committees, Review Groups National Institutes of Health, USA: Proteomics Special Emphasis Panel; 2004, Grant Reviewer National Institutes of Health, USA: Biodata Management and Analysis Panel, 2005, Grant Reviewer National Institutes of Health, USA: EDRN Biomarker Panel, 2005, Grant Reviewer

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National Science Foundation, USA, CAREER Award Program, 2004, Grant Reviewer Science Foundation Ireland, Ireland, 2003, Grant Reviewer Genome British Columbia, Canada, Grant Reviewer Netherlands Organization for Scientific Research, 2003, Grant Reviewer Italian Association for Cancer Research, 2004, Grant Reviewer BBVA Foundation, Bioinformatics Grants Program, Spain, 2004, Grant Reviewer Michael J. Fox Foundation for Parkinson’s Research, 2004, Grant Reviewer Bioinformatics Faculty Search Committee, University of Southern Denmark, 2003, Role: Member Ph.D. Steering Committee, Odense University Hospital, University of Southern Denmark. Odense, Denmark. 2003-Present. Role: Member Department of Defense, USA, Breast Cancer Research Program, 2007, Grant Reviewer Netherlands Genomics Initiative, 2009, Grant Reviewer Wellcome Trust/ DBT India Alliance, 2009, Grant Reviewer National Institutes of Health, USA: NIDDK Chronic Pancreatitis Panel; 2009, Grant Reviewer National Institutes of Health, USA: NIA Adhoc panel; 2009, Grant Reviewer Department of Defense, USA, Breast Cancer Research Program, 2009, Integration Panel member (ad hoc) Department of Biotechnology, India: Cancer Biology, 2009-Present, Task Force Member Department of Biotechnology, India: Human Genetics & Genome Analysis, 2009-Present, Task Force Member RECOGNITION Awards and Honors Experimental Pathologist-in-training Award, 1996, American Society for Investigative

Pathology, USA Physician Postdoctoral Fellowship, 1997 (Declined), Howard Hughes Medical Institute Howard Temin Award, 1997, National Cancer Institute Sidney Kimmel Foundation Scholar, 2003, Sidney Kimmel Foundation Beckman Young Investigator Award, 2004, Arnold and Mabel Beckman Foundation Era of Hope Scholar Award, 2006, Department of Defense Invited Talks and Panels 1. Invited Speaker. Talk title: ‘Unraveling breast cancer signaling pathways using

phosphoproteomics’ at the 5th Annual meeting of Proteomics Society of India, National Chemical Laboratories, Pune, India, November 28, 2013.

2. Invited Speaker. Talk title ‘Insights from a multi-omic analysis of a single human cell type’ at 12th Annual HUPO Conference, Yokohama, Japan, September 16, 2013.

3. Invited Speaker, Talk Title: ‘Cancer Databases’ workshop organized by Early Detection Research Network, NCI at Caltech, Pasadena, CA, April 29, 2013.

4. Plenary Speaker, Talk title: ‘A draft map of the human proteome and integrating multi-Omics dataset for human genome annotation’ at KHUPO 13th Annual International Proteomic Conference, Seoul, Korea, March 28, 2013.

5. Invited Speaker, Talk Title: ‘Annotation of the Zebrafish genome through an integrated transcriptomic and proteomic analysis ‘at Agilent Symposium, Baltimore, MD, March 14, 2013.

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6. Invited Speaker. Talk title ‘A draft map of the human proteome’ at 9th Annual US HUPO Conference, Baltimore, MD, March 11, 2013.

7. Invited Speaker. Talk title: ‘A draft map of the human proteome and integrating multi-Omics dataset for human genome annotation’ at the 4th Annual meeting of Proteomics Society of India, National Chemical Laboratories, Pune, India, November 23, 2012.

8. Invited Speaker. Talk title: ‘A draft map of the human proteome’ at HUPO 11th Annual World Congress Meeting, Boston, MA, September 10, 2012.

9. Invited Speaker, Talk title: ‘Dissection of the Nrf2/Keap1 pathway using a multi-Omics approach’ Korean Society of Toxicology, Seoul, June 1, 2012.

10. Invited Speaker, Talk title: ‘A Systems Approach to Dissecting Pathways in Health and Disease’ Janssen Pharmaceuticals (Johnson & Johnson), May 2, 2012.

11. Invited Speaker, ‘Interrogating a single cell type - From the genome to the proteome and everything else in between’ Canadian Proteomics Research Network, April 24, 2012.

12. Invited Speaker, Talk title: ‘Phosphoproteomics in cancer and integration of multi-Omics datasets’ AACR, Chicago, April 1, 2012.

13. Invited Speaker, Talk title: ‘Interrogating a single cell type - From the genome to the proteome and everything else in between’ Genentech, March 29, 2012.

14. Invited Speaker, Talk title: ‘Phosphoproteomics for Elucidating Signaling Pathways in Health and Disease’ University of Maryland, March 26, 2012.

15. Plenary Speaker, Talk title: ‘Interrogating a single cell type - From the genome to the proteome and everything else in between’ University of South Florida, Tampa, Bioinformatics Symposium, March 14, 2012.

16. Invited Webinar Speaker, Talk title: ‘Establishing candidate biomarkers to determine the pharmacodynamic action of sulforaphane in the breast’ on Illuminating Pathways for Disease Research Webinar, organized by Genetic Engineering and Technology News, March 7, 2012.

17. Plenary Speaker, Talk title: ‘Proteogenomics and Integration of multi-Omics datasets’ at the International workshop on Proteomics and Structural Biology, National Dairy Research Institute, Karnal, India, February 27, 2012.

18. Plenary Speaker. Talk title: ‘Proteomics and its Applications in Biological Research’ the International workshop on Proteomics and Structural Biology, National Dairy Research Institute, Karnal, India, February 29, 2012.

19. Invited Speaker. Talk title: ‘Proteomics: From Genome Annotation to Understanding Bacterial Pathogenesis’ at the International Conference On Open Source for Computer-Aided Translational Medicine, IMTECH, Chandigarh, India, February 23, 2012.

20. Invited Speaker. Talk title: ‘Unraveling cancer signaling pathways using global phosphoproteomic approaches’ January, 29, 2012 at 31st Annual Convention of the Indian Association for Cancer Research. Mumbai, India.

21. Invited Speaker. Talk title: ‘Integrating Omics Data: From the genome to the proteome’ November, 15, 2011 at 9th Functional Proteomics Center Symposium on Multi-Omics, Korean Proteomics Society, Seoul, South Korea.

22. Plenary Speaker. Talk title: ‘The promise of personalized medicine’ August 13, 2011, Golden Jubilee Symposium, Armed Forces Medical College, Pune, India.

23. Invited Speaker. Talk title: ‘Proteomics and its Application to Pancreatic Cancer Research’ June 19, 2011, Workshop on Foundations of Pancreatic Cancer, Cold Spring Harbor Laboratory, NY.

24. Invited Speaker. Talk title: ‘Use of biomarkers in other areas of medicine. Case studies in Alzheimer’s, ovarian cancer and cardiovascular diseases’ April 29, 2011, Association for Research in Vision and Ophthalmology Symposium, Ft. Lauderdale, FL.

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25. Workshop Session Chair and Speaker. Talk title: ‘Databases and Resources for Sequences, PTMs and Pathways’ March 21, 2011 at Annual US HUPO Meeting, Raleigh, NC.

26. Invited Speaker. Talk title: ‘Proteogenomic Analysis of Zebrafish ’ March 12, 2011, RECOMB Satellite Conference on Computational Proteomics, University of California, San Diego, CA.

27. Invited Speaker. Talk title: ‘Unraveling cancer signaling pathways using global phosphoproteomic approaches’ March 9, 2011, University of California, Los Angeles, CA.

28. Invited Speaker. Talk title: ‘Quantitative mass spectrometry to study proteomes and signaling pathways’ February 24, 2011 at Systems Biology of Connective Tissue Disorders meeting, National Institutes of Health, Bethesda, MD.

29. Invited Speaker. Talk title: ‘Unraveling cancer signaling pathways using global phosphoproteomic approaches’ February 8, 2011 at the 4th Congress of the Spanish Proteomics Society, Segovia, Spain.

30. Invited Speaker, Talk Title: ‘Proteogenomics’ September 22, 2010 at the Human Proteome Organization Annual Meeting, Sydney, Australia.

31. .Invited Speaker, Talk Title: ‘Proteogenomics – from unsequenced genomes to the unsequenced’ February 23-25, 2010. Center for Cellular and Molecular Biology, Hyderabad, India.

32. Invited Speaker and Session Chair, Talk Title: ‘Proteomics for identification of biomarkers and therapeutic targets’ at 29th Annual Meeting of the Indian Association of Cancer Research February 21, 2010.

33. Invited Speaker, May 7, 2009. Mount Sinai School of Medicine, New York, Talk Title: Proteomics to study signal transduction and stem cell biology.

34. Invited Speaker. American Society for Physiology, Experimental Biology 2009. April 22, 2009, Role: Session on Proteomics Techniques in Physiology and Cell Biology. Talk Title: Quantitative proteomics: Identification of miRNA-regulated gene products and drug targets.

35. Session Chair and Invited Speaker, American Society for Investigative Pathology, Experimental Biology 2009. April 18, 2009, in Minisymposium: Cancer Genetics, Epigenetics, and Biomarkers. Talk Title: Identification of diagnostic and therapeutic targets of pancreatic cancer using proteomic approaches.

36. Invited Speaker. Sigma-Aldrich, St. Louis, MO. April 16, 2008. Talk Title: Leveraging Technology and Bioinformatics for Systems Biology.

37. Invited Speaker. Agilent Technologies, Santa Clara, CA. March 30, 2009. Talk Title: Leveraging Technology and Bioinformatics for Systems Biology.

38. Invited Speaker. Talk title: ‘Phosphoproteomics: From signaling pathways to therapeutic targets’ March 14, 2009 at Proteomics 2009 Symposium, Children’s Hospital, Boston.

39. Invited Speaker. Talk title: ‘Cancer Proteomics: From signal transduction to therapeutic targets’ March 3-4, 2009 at the Functional Phosphoproteomics and Cell Signaling Workshop, Ramon Areces Foundation, Madrid, Spain.

40. Keynote speaker. Talk title: “Proteinpedia.” January 26, 2009, at the “Netherlands Proteomics initiative meeting” held at Utrecht, Netherlands.

41. Webinar on ‘Systems Biology: New Approaches, New Tools, and Implications for Human Healthcare’ on October 30, 2008. Title of talk: “Systems biology not reverse engineering.”

42. .“Biomarkers for Pancreatic Cancer and Chronic Pancreatitis.” November 8, 2008, ‘The chronic pancreatitis and pancreatic cancer continuum’ Symposium organized by the American Pancreatic Association/Lustgarten Foundation, Chicago, USA.

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43. “Annotation of Anopheles gambiae mosquito using mass spectrometry-derived data.” November 8, 2008, Invited Lecture in ‘Bioinformatics and Statistical Genomics’ section at Human Genome Organization (HUGO) international meeting, Hyderabad, India.

44. “Proteomics for annotation of genomes.” September 28, 2008, Human Genome Organization (HUGO) international meeting, Hyderabad, India.

45. “Opportunities in Bioinformatics and Biotechnology for Cancer Research in India.” April 25, 2008. Invited Lecture at session organized by Bangalore BIO on ‘IT and Informatics in Biotechnology - New Solutions for Life Sciences’ at National Centre for Biological Sciences, Bangalore, India.

46. Invited Lecture “Proteomic approaches to studying signaling in cancer.” , February 23-25, 2008, at International Symposium on ‘Model Organisms and Stem Cells in Development, Regeneration and Disease at National Centre for Biological Sciences, Bangalore, India.

47. “Data analysis and dissemination in proteomics: Are we doing enough?”, February 17, 2008, Current Trends in Proteomics at Centre for Cellular and Molecular Biology, Hyderabad, India.

48. Plenary lecture “Proteomics for functional annotation of genomes.” at Applications of Bioinformatics in Genome Research Symposium, February 13, 2008, University of Pondicherry, India.

49. Invited Lecture “Quantitative proteomics for studying signaling pathways and identifying cancer biomarkers.” Institute of Life Sciences, January 31, 2008, Bhubaneshwar, India.

50. “Global quantitative proteomic profiling in cancer.” Invited Lecture at the 5th Biannual Kuningas Foundation GIST Symposium on January 18, 2008, Helsinki, Finland.

51. ‘Human Proteinpedia: A portal for sharing and integration of human proteomic data.’ October 12, 2007. Kazusa DNA Research Institute, Chiba, Japan.

52. ‘Human Proteinpedia: A portal for sharing and integration of human proteomic data.’ October 6-10, 2007. 6th Annual Human Proteome Organization (HUPO) Meeting. Seoul, South Korea.

53. ‘Proteomic approaches to identify cancer biomarkers and therapeutic targets in pancreatic cancer.’ October 6-10, 2007. 6th Annual Human Proteome Organization (HUPO) Meeting. Seoul, South Korea.

54. “Use of Stable Isotope Labeling for Unraveling Signaling Pathways and Identifying Cancer Biomarkers.” April 28, 2007, Biological Mass Spectrometry Symposium at Experimental Biology (FASEB), Washington, D. C.

55. “Human Proteinpedia: A portal for sharing and integration of human protein data.” April 19, 2007, 9th Annual NHLBI 10 Center Proteomic Investigators Meeting, Boston, MA.

56. ‘Human Proteinpedia: A portal for sharing and integration of human proteomic data.’ March 7, 2007, 3rd Annual U.S. Human Proteome Organization (US HUPO) Meeting. Seattle.

57. ‘Proteomic approaches to identify cancer biomarkers and therapeutic targets in pancreatic cancer.’ March 7, 2007. 3rd Annual U.S. Human Proteome Organization (US HUPO) Meeting. Seattle.

58. ‘Integrating genomic and proteomic approaches to study signal transduction.’ December 21, 2007. Indian Institute of Technology, Kanpur, India.

59. ‘Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) for Elucidation of Protein Complexes and Protein Dynamics.’ at the workshop on Quantitative Proteomics, Association for Biomolecular Research Facilities, March 31, 2007 held at Tampa, Florida.

60. Special lecture: “Approaching Systems Biology: Vignettes from an Indo-US Collaboration”, Dec 18-20, 2006, New Delhi, International Conference on Bioinformatics, 2006.

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61. Invited Lecture. ‘Proteomic approaches to study tyrosine kinase signaling pathways.’ October 3, 2005. Memorial Sloan-Kettering Cancer Center. New York.

62. American Association of Cancer Research Symposium, Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications. September 21-25, 2005, San Diego, CA. ‘Proteomic and Bioinformatics Analysis of Signal Transduction Pathways’.

63. ‘Annotation of genomes using mass spectrometry-derived data,’ May 19, 2005, Bethesda, MD.

64. ‘Stable isotope labeling with amino acids in cell culture (SILAC) for studying signal transduction.’ February 7, 2005, Savannah, Georgia. Association of Biomolecular Research Facilities (ABRF) Annual Meeting.

65. Proteomic approaches to study signal transduction pathways, February 4, 2005. NIH, Bethesda, MD.

66. Panelist: Proteomic Technologies Informatics Workshop, February 8-9, 2005, Seattle, WA. National Cancer Institute, NIH.

67. ‘Stable isotope labeling with amino acids in cell culture (SILAC) for studying signal transduction.’ February 7, 2005, Savannah, Georgia. Association of Biomolecular Research Facilities (ABRF) Annual Meeting.

68. Proteomic approaches to study signal transduction pathways, February 4, 2005. NIH, Bethesda, MD.

69. Panelist: Drosophila Encyclopedia of DNA Elements, NIH. December 5-6, 2004. Bethesda, Maryland. NIH. Proteomic approaches to study signal transduction pathways.

70. ‘Proteomic databases for systems biology,’ October 29, 2004, Chiba, Japan. BITS 2004, Kazusa DNA Research Institute.

71. ‘Building Tools for Integrating Genomic, Transcriptomic and Proteomic Information for Systems Biology’ October 28, 2004, Hangzhou, China. Indo-China Science and Technology Forum.

72. ‘Plasma Proteome Database,’ October 25-27, 2004. Beijing, China. HUPO 3rd Annual World Congress.

73. ‘Integrating genomics, proteomics and bioinformatics data for systems biology’ at the ‘Functional Genomics and Proteomics as Applied to Metabolic Diseases Workshop’ September 27-28, 2004. Odense, Denmark. Metabolism Ph.D. Program’s Summer School. Odense University Hospital, University of Southern Denmark.

74. ‘Proteomics and protein databases,’ September 27, 2004. Odense, Denmark. Metabolism Ph.D. Program’s Summer School. Odense University Hospital, University of Southern Denmark.

75. ‘Mass spectrometry for functional annotation of genomes,’ September 22-24, 2004. Hinxton, U.K. Fourth Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics.

76. Plenary lecture: ‘Integrating Bioinformatics and Proteomics to Tackle the Anopheles Genome,’ January 6-10, 2004, Bangalore, India. Indo-US Symposium on Infectious Disease Research and Development, U.S. Delegate.

77. ‘Bioinformatics and Database Issues in the Annotation of the Human Genome and Proteome.’ December 22, 2003, Chiba, Japan. Beyond Identification of Transcribed Sequences (BITS 2003), Kazusa DNA Research Institute.

78. ‘Proteomic Approaches to Study Signal Transduction Pathways,’ December 9, 2003, Nashville, TN. Vanderbilt Cancer Center Seminar Series.

79. ‘Proteomic Approaches for Studying Signal Transduction Pathways,’ November 3-5, 2003. Madrid, Spain. 4th Workshop on Molecular Medicine, BBVA Foundation.

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80. ‘Bioinformatics issues with database searching with genomic and proteomic data,’ October 16, 2003, Ann Arbor, Michigan. Michigan Bioinformatics Seminar Series, University of Michigan, Ann Arbor.

81. Human Protein Reference Database as a Platform for Systems Biology. October 10, 2003. Montreal Canada. Human Proteome Organization (HUPO) 2nd Annual & IUBMB XIX Joint World Congress.

82. ‘Mass Spectrometry-based Proteomics for a Global Analysis of Signal Transduction Pathways’ October 2-3, 2003, Burlington Vermont. Vermont Cancer Center Research Symposium ‘Translational Cancer Research: From Basic Science to Patient Care.’

83. ‘Database Searching with Mass Spectrometry-Derived Data,’ September 22, 2003. Princeton, New Jersey. The 6th Annual Symposium on Chemical and Pharmaceutical Structural Analysis, From Proteomics to Pills: New Initiatives in Proteomics, Drug Discovery and Development.

84. ‘Integrating genomics, proteomics and bioinformatics-based data’ September 9, 2003, Bangalore, India. Indo-US Science and Technology Forum, U.S. Delegate.

85. ‘Integrating Molecular Biology, Proteomics and Bioinformatics to Study Signaling and Cancer.’ August 31, 2003. Odense, Denmark. Summer School 2003. ‘Functional Genomics and Proteomics as Applied to Metabolic Diseases,’ Odense University Hospital, University of Southern Denmark.

86. ‘Protein Databases and Annotation Issues,’ March 28-29, 2003. Workshop at 16th Course in Medical Genetics, European School of Genetic Medicine.

87. ‘Use of proteomics for functional annotation of genomes,’ Bertinoro, Italy. March 29, 2003. 16th course in Medical Genetics, European School of Genetic Medicine.

88. ‘Bioinformatics challenges for annotation of the human genome.’ Feb. 22-24, 2003, Proteomics Symposium, Center for Cellular and Molecular Biology, Hyderabad, India.

89. ‘Human Protein Reference Database.’ Translating Biology Using Proteomics and Functional Genomics. Feb 10-13, 2003. Denver, CO, USA. Association for Biomolecular Research Facilities.

90. ‘Bioinformatics and proteomics approaches for studying signal transduction,’ Pathology bioinformatics: Tools and Techniques – Workshop. November 12, 2002, University of Michigan, Ann Arbor, MI. University of Michigan Bioinformatics Program.

91. ‘Proteomic approaches for studying phosphorylation,’ November 5, 2002, University of Maryland, College Park, MD. Proteome Society.

92. ‘Integrating bioinformatics, molecular biology and proteomic approaches for studying signal transduction,’ October 3, 2002, Beverly MA. Cell Signaling Technology, Beverly, MA.

93. ‘Use of mass spectrometry-based proteomic approaches for studying signal transduction,’ October 1, 2002. University of Maryland, College Park, MD.

94. ‘Proteomic approaches for studying signal transduction,’ August 18, 2002, Bangalore, India. Indian Institute of Science, Bangalore, India.

95. ‘Proteomic approaches for studying signal transduction,’ August 13, 2002, National Center for Biological Sciences, Bangalore, India.

OTHER PROFESSIONAL ACCOMPLISHMENTS Significantly contributed towards scientific data management and sharing of scientific data among research community. Human Protein Reference database (HPRD) which was developed by my group is one among several initiatives, which to a great deal serve the scientific community in providing easy access to all available published data on human proteins. This is

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evident by the fact that HPRD gets 2 million hits per month and it has been cited in data published in Nature Biotechnology, Nature Genetics, Nucleic Acids Research, Genome Research, Genome Biology and BMC Bioinformatics among others. Another major initiative towards public sharing of scientific data is the development of Human Proteinpedia, which serves as a model for data dissemination among researchers. With the huge volume of data generated from proteomics experiments using all kinds of platforms, Proteinpedia has made it simpler for researchers to make their data available and usable by others.