Akhilesh Pandey, M.D., Ph.D. Associate Professor Institute Of

BIOGRAPHICAL SKETCH

NAME POSITION TITLE

Akhilesh Pandey, M.D., Ph.D. Associate Professor Institute of Genetic Medicine, Biological Chemistry, Oncology and Pathology EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)

INSTITUTION AND LOCATION DEGREE YEAR(s) FIELD OF STUDY (if applicable) Armed Forces Medical College, Pune, India M.D. 1988 Medicine University of Michigan, Ann Arbor, MI Ph.D. 1995 Pathology

PROFESSIONAL EXPERIENCE

Associate Professor 2006-Present McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Oncology and Pathology, Johns Hopkins University, Baltimore, MD Assistant Professor 2002-2006 McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Oncology and Pathology, Johns Hopkins University, Baltimore, MD Instructor 1998-2002 Department of Pathology, Harvard Medical School, Boston, MA Visiting Scientist 1999-2002 Laboratory of Matthias Mann, Center for Experimental Bioinformatics, University of Southern Denmark, Odense, Denmark Postdoctoral Fellow 1996-1999 Laboratory of Harvey Lodish, Whitehead Institute for Biomedical Research, Cambridge, MA Postdoctoral Fellow 1995-1996 Laboratory of Vishva Dixit, University of Michigan, Ann Arbor, MI Residency 1996-1998 Department of Pathology, Brigham and Women’s Hospital, Harvard (Clinical Pathology) Medical School, Boston, MA Internship 1989-1990 Kilpauk Medical College, Madras, India

PROFESSIONAL SOCIETIES

American Society for Biochemistry and Molecular Biology American Society for Mass Spectrometry American Association for Cancer Research

AWARDS AND HONORS

First in Forensic Medicine, University of Pune, 1986 Second Place overall in Medical School Class of 1988 Experimental Pathologist-in-training Award, American Society for Investigative Pathology, 1996 Howard Hughes Medical Institute Physician Postdoctoral Fellowship, 1997 (Declined) Howard Temin Award, National Cancer Institute, 1997 Sidney Kimmel Foundation Scholar, 2003 Beckman Young Investigator Award, 2004 Era of Hope Scholar Award, Department of Defense, 2006

GRANT REVIEWER

National Institutes of Health, USA: Proteomics Special Emphasis Panel; 2004, Biodata Management and Analysis Panel, 2005; EDRN Biomarker Panel, 2005 National Science Foundation, USA Science Foundation Ireland, Ireland Netherlands Organization for Scientific Research BBVA Foundation, Bioinformatics Grants Program, Spain Michael J. Fox Foundation for Parkinson’s Research

EDITORIAL BOARD/REVIEWER:

Editorial Board Member: Genome Research, Clinical Proteomics, Journal of Proteome Research Reviewer: Nature, Nature Genetics, Nature Biotechnology, Cell, Molecular Cell, PNAS, Genome Biology, Journal of Biological Chemistry, Molecular and Cellular Proteomics, Proteomics, Journal of Proteome Research, Analytical Chemistry, Trends in Genetics, Bioinformatics, Nucleic Acids Research

Peer-Reviewed Scientific Articles:

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Peri, S. and Pandey, A. (2001). A reassessment of the translation initiation codon in vertebrates. Trends in Genetics. 17, 685-687.

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.

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

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

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.

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

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

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.

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. 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

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.

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.

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.

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

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

Steen H, Fernandez M, Ghaffari S, Pandey A.* Mann M. (2003). Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanning. Molecular and Cellular Proteomics. 2, 138-145. *Corresponding author

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

Koopmann, J., Thuluvath, P. J., Zahurak, M. L., Kristiansen, T. Z., Pandey, A., Richard Schulick, R., Argani, P., Hidalgo, M., Iacobelli, S., Michael Goggins, M. and Anirban Maitra. (2004). Mac-2-binding protein is a diagnostic marker for biliary tract carcinoma. Cancer. 101, 1609-1615.

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. *Corresponding author

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.

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. Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression. Cancer Biology and Therapy, 3, 1254-1261.

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.

Tang, Q. Q., Gronborg, 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 3 beta is required for adipogenesis. Proceedings of the National Academy of Sciences. U.S.A. 102, 9766-9771.

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.

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.

Kalume, D.E., Peri, S., Zhong, J., Okulate, M., Surendranath, V., Kumar, N. and Pandey, A. (2005). A proteomic analysis of salivary glands of female Anopheles gambiae mosquito. Proteomics. 5, 3765-3777.

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.

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.

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.

Omenn, G. S., States, D. J., Adamski, M., Blackwell, T. W., Menon, R., Hermjakob, H., Apweiler, R., Haab, B. B., Simpson, R. J., Eddes, J. S., Kapp, E. A., Moritz, R. L., Chan, D. W., Rai, A. J., Admon, A., Aebersold, R., Eng, J., Hancock, W. S., Hefta, S. A., Meyer, H., Paik, Y. K., Yoo, J. S., Ping, P., Pounds, J., Adkins, J., Qian, X., Wang, R., Wasinger, V., Wu, C. Y., Zhao, X., Zeng, R., Archakov, A., Tsugita, A., Beer, I., Pandey, A., Pisano, M., Andrews, P., Tammen, H., Speicher, D. W. and Hanash, S. M. (2005) Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 5, 3226-3245.

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.

Muthusamy, B., Hanumanthu, G., Reshmi, R., Sriranjini, S., Rekha, B., Srinivas, D., Vani, K. V., Padma, N., Suresh, S., Talreja, N., Karthick, L., Vrushabendra, B.M., Sharma, S., Ghosh, N., Rashmi, B.P., Kavitha, M.P., Kadekar, S., Chatterjee, P., Sushma, B. R., Mangala, K. S., Shivashankar, H.N., Ramya, M.A., Chandrika, K.N., Mohan, S. S., Deshpande, N., Niranjan, V., Nalli, A., Prasad, T. S. K., Arun, K. S., Reddy, R., Mishra, G., Shibani, P., Chandran, S., Stanley, L. A., Jadhav, T., Julie, D., Mahesh, M., John, S. L., Palvankar, K., Gopika, B., Annapurna, E., Sudhir, D., P. Bala., Jithesh, M. K., Rashmi, N. S., Vishnupriya, G., Dhar, K., Reshma, S., Gandhi, T.K.B., Saravana, R., Shilpa, N., Pallavi, R., Jiwan, D., Khan, I., Harsha, H.C., Deshpande, K.S., Raghothama, C., Prasad, C.K. and Pandey, A. (2005). Plasma proteome database as a resource for proteomics. Proteomics. 5, 3531-3536.

Ping, P., Vondriska, T. M., Creighton, C. J., Gandhi, T. K., B., Yang, Z., Menon, R., Kwon, M.S., 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.

Kalume, D. E., Peri, S., Zhong, J., Okulate, M., Reddy, R., Kumar, N. and Pandey, A. (2005). Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics. 6:128.

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.

Bala, P., Georgantas, R. W., Sudhir, D., Suresh, M., Civin, C. I. and Pandey, A. (2005). TAGmapper: A web- based tool for mapping SAGE tags. Gene. 364, 123-129.

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.

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.

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.

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.

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.

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.

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.

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 comparison with yeast, worm and fly interaction datasets. Nature Genetics.38, 285-293.

Reviews, Analyses and Book Chapters:

Pandey, A., Lindberg, R. A. and Dixit, V. M. (1995). Cell signalling: Receptor orphans find a family. Current Biology. 5, 986-989.

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, Aggarwal, B. B. Ed. (Blackwell Scientific Publications, Inc.,1998). Vol. 3. 490-504.

Pandey, A. and Lewitter. F. (1999). Nucleotide Sequence Databases: A gold mine for biologists. Trends in Biochemical Sciences. 24, 276-280.

Pandey, A. and Mann, M. (2000). Proteomics to study genes and genomes. Nature. 405, 837-846.

Pandey, A., Andersen, J. S. and Mann, M. (2000). Use of mass spectrometry to study signaling pathways. Science's STKE. http://stke.sciencemag.org/cgi/content/full/sigtrans;2000/37/pl1

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.

Mann, M., Hendrickson, R. C. and Pandey, A. (2001). Analysis of proteins and proteomes by mass spectrometry. Annual Review of Biochemistry. 70, 437-473.

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.

Ong, S. E. and Pandey, A. (2001). An evaluation of the use of two dimensional gel electrophoresis in proteomics. Biomolecular Engineering. 18, 195-205.

Kristiansen, T. Z. and Pandey, A. (2002). Resources for full-length cDNAs. Trends in Biochemical Sciences. 27, 266-267.

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.

Steen, H. and Pandey, A. (2002) ‘Proteomics goes quantitative: Measuring protein abundance.’ Trends in Biotechnology. 20, 361-364.

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.

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. http://stke.sciencemag.org/cgi/content/full/sigtrans;2002/154/pl16.

Kalume, D. E., Molina, H. and Pandey, A. (2003). Tackling the phosphoproteome: tools and strategies. Current Opinion in Chemical Biology. 7, 64-69.

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.

Deshpande, K. S., Harsha, H. C. and Pandey, A. (2003). Microarrays and mass spectrometry: The future of proteomics. Current Genomics. 4, 605-613.

Raghothama, C. and Pandey A. (2003). Absolute systems biology-measuring dynamics of protein modifications. Trends in Biotechnology. 21, 467-470.

Steen, H. and Pandey, A. (2003) ‘Mass Spectrometry in Protein Characterization,’ in, Encyclopedia of the Human Genome, Volume 3, Ed. Cooper, DN (John Wiley & Sons, Ltd., Chichester, 2003). pp841-844.

Steen, H. and Pandey, A. (2003) ‘Proteomics: A molecular scanner in medicine,’ in, Encyclopedia of the Human Genome, Volume 4, Ed. Cooper, DN (John Wiley & Sons, Ltd., Chichester, 2003). pp879-883.

Ibarrola, N., Raghothama, C., and Pandey, A. (2004). 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. pp 393-411.

Navarro, J. D. and Pandey, A. (2004). Unraveling the human interactome: Lessons from the yeast. Drug Discovery Today: Targets. 3, 79-84.

Amanchy, R., Kalume, D. E. and Pandey, A. (2005). Stable isotope labeling with amino acids in cell culture (SILAC) for studying dynamics of protein abundance and post-translational modifications. Science's STKE 2005. pl2.

Fernandez, L. E. M., Gronborg, M. and Pandey, A. (2005). ‘Proteomic strategies for identification of post- translational modifications,’ in, Functional Proteomics: Principles and Practical Applications, Ping, P. and Hanash, S. Eds. (Humana Press, Totowa, N.J). In Press.

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). In Press.

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). In Press.

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). In Press.