2009

Keerthikumar, S., Bhadra, S., Kandasamy, K., Raju, R., Ramachandra, Y. L., Bhattacharyya, C., Imai, K., Ohara, O., Mohan, S. and Pandey, A. Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach. DNA Research. [PubMed].

Parikh, K., Diks, S.H., Tuynman, J.H., Verhaar, A., Lowenberg, M., Hommes, D.W., Joore, J., Pandey, A. and Peppelenbosch, M.P. Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8. PLoS One. 4, e6440. [PubMed].

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

Kandasamy, K., Keerthikumar, S., Raju, R., Prasad, T. S. K., Ramachandra, Y. L., Mohan, S. and Pandey, A. PathBuilder - open source software for annotating and developing pathway resources. Bioinformatics. 25, 2860-2862. [PubMed].

Yang, Y., Chaerkady, R., Beer, M. A., Mendell, J. T. and Pandey, A. Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics. 9, 1374-1384. [PubMed].

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. A compendium of potential biomarkers of pancreatic cancer. PLoS Medicine. 6, e1000046. [PubMed].

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. [PubMed].

Ranganathan, P., Harsha, H. C. and Pandey, A. Molecular alterations in exocrine neoplasms of the pancreas. Archives of Pathology & Laboratory Medicine.133, 405-412. [PubMed]

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

Cooper, E. M., Cutcliffe, C., Kristiansen, T. Z., Pandey, A., Pickart, C. M. and Cohen, R. E. K63-specific deubiquitination by two JAMM/MPN+ complexes: BRISC-associated Brcc36 and proteasomal Poh1. The EMBO Journal. 28, 621-631. [PubMed]

Molina, H., Yang, Y., Ruch, T., Kim, J. W., Mortensen, P., Otto, T., Nalli, A., Tang, Q. Q., Lane, M. D., Chaerkady, R. and Pandey, A. Temporal profiling of the adipocyte proteome during differentiation using a 5-plex SILAC based strategy. Journal of Proteome Research. 8, 48-58. [PubMed]

Li X, Molina H, Huang H, Zhang YY, Liu M, Qian SW, Slawson C, Dias WB, Pandey A, Hart GW, Lane MD, Tang QQ. O-linked N-acetylglucosamine modification on C/EBPbeta: Role during adipocyte differentiation. Journal of Biological Chemistry. 284, 19248-19254. [PubMed].

Ghosh, A. K., Devenport, M., Jethwaney, D., Kalume, D. E., Pandey, A., Anderson, V. E., Sultan, A. A., Kumar, N. and Jacobs-Lorena, M. Malaria parasite invasion of the mosquito salivary gland requires interaction between the Plasmodium TRAP and the Anopheles Saglin proteins. PLoS Pathogens. [PubMed]

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. Human Protein Reference Database - 2009 update. Nucleic Acids Research. 37, D767-D772. [PubMed]

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. Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biology and Therapy. 8, 16-26. [PubMed]

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. RAPID: Resource of Asian Primary Immunodeficiency Diseases. Nucleic Acids Research. 37, D863-D867. [PubMed]

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. Human Proteinpedia: A unified discovery resource for proteomics research. Nucleic Acids Research. 37, D773-D781. [PubMed]

2008

Kristiansen, T. Z., Harsha, H. C., Grønborg, M., Maitra, A. and Pandey, A. Differential membrane proteomics using ¹⁸O-labeling to identify biomarkers for cholangiocarcinoma. Journal of Proteome Research. 8, 4670-4677. [PubMed]

Harsha, H. C., Jimeno, A., Molina, H., Mihalas, A., Goggins, M., Hruban, R., Schulick, R., Kamath, U., Maitra, A., Hidalgo, M. and Pandey, A. Activated epidermal growth factor receptor as a novel target in pancreatic cancer therapy. Journal of Proteome Research. 7, 4651-4658. [PubMed]

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

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. 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. [PubMed]

Guha, U., Chaerkady, R., Marimuthu, A., Patterson, S., Kashyap, M., Harsha, H. C., Bader, J., Lash, A., Pandey, A. and Varmus, H. E. 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 U.S.A. 105, 14112-14117. [PubMed]

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. Antitumor activity and molecular effects of the novel Hsp 90 inhibitor, IPI-504, in pancreatic cancer. Molecular Cancer Therapeutics. 7, 3275-3284. [PubMed]

Mathivanan, S. and Pandey, A. Human Proteinpedia as a resource for clinical proteomics. Molecular and Cellular Proteomics. 7, 2038-2047. [PubMed]

Sarker, R., Grønborg, M., Cha, B., Mohan, S., Chen, Y., Pandey, A., Litchfield, D., Donowitz, M. and Li, X. 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. [PubMed]

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

Amanchy, R., Zhong, J., Molina, H., Chaerkady, R., Iwahori, A., Kalume, D. E., Grønborg, M., Joore, J., Cope, L. and Pandey, A. Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. Journal of Proteome Research. 7, 3900-3910. [PubMed]

Luo, W., Slebos, R. J., Hill, S., Li, M., Brabek, J., Amanchy, R., Chaerkady, R, Pandey, A., Ham, A. J. L. and Hanks, S. Global impact of oncogenic Src on a phosphotyrosine proteome. Journal of Proteome Research. 7, 3447-3460. [PubMed]

Chaerkady, R., Thuluvath, P. J., Nalli, A., Vivekanandan, P., Simmers, J., Torbenson, M. and Pandey, A. ¹⁸O labeling for a quantitative proteomic analysis of glycoproteins in hepatocellular carcinoma. Clinical Proteomics. 9, 1080-1089. [PubMed]

Molina, H., Matthiesen, R., Kandasamy, K. and Pandey, A. Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Analytical Chemistry. 80, 4825-4835. [PubMed]

Chaerkady, R. and Pandey, A. Applications of proteomics to lab diagnosis. Annual Review of Pathology: Mechanisms of Disease. 3, 485-498. [PubMed]

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. New markers of pancreatic cancer identified through differential gene expression analyses: claudin 18 and annexin A8. Am J Surg Pathol. 32, 188-196. [PubMed]

Harsha, H. C., Molina, H. and Pandey, A. Quantitative proteomics using stable isotope labeling with amino acids in cell culture (SILAC). Nature Protocols. 3, 505-516. [PubMed]

Mathivanan, S., Ahmed, M., 157 coauthors and Pandey, A. Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-167. [PubMed]

2007

Zhong, J., Molina, H. and Pandey, A. Phosphoproteomics. Current Protocols in Protein Science. 24, 24.4 [PubMed]

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. Protein pyrophosphorylation by inositol pyrophosphates is a posttranslational event. Proceedings of the National Academy of Sciences, USA. 104, 15305-15310. [PubMed]

Chaerkady, R. and Pandey, A. Quantitative proteomics for identification of cancer biomarkers. Proteomics Clinical Applications. 1, 1080-1089. [PubMed]

Okulate, M., Kalume, D. E., Chaerkady, R., Reddy, R., Kristiansen, K., Bhattacharyya, M., Pandey, A. and Kumar, N. 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. [PubMed]

Sarker, M., Hanumanthu, G. and Pandey, A. 'Plasma Proteome Database' in, Proteomics of human body fluids, pages 129-136 Thongboonkerd, V. Editor (Humana Press, Totowa, New Jersey, USA).[PubMed]

Grønborg, M., Maitra, A. and Pandey, A. 'Proteomics of human pancreatic juice' in, Proteomics of human body fluids, pages 377-397 Thongboonkerd, V. Editor (Humana Press, Totowa, New Jersey, USA).[PubMed]

Kristiansen, T. Z., Maitra, A and Pandey, A. 'Proteomics of human bile' in, Proteomics of human body fluids, pages 399-414 Thongboonkerd, V. Editor (Humana Press, Totowa, New Jersey, USA).[PubMed]

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. Copy-number variants in patients with a strong family history of pancreatic cancer. Cancer Biology & Therapy. 6, 1-8. [PubMed]

Dinglasan, R. R., Kalume, D. E., Kanzok, S. M., Ghosh, A. K., Muratova, O., Pandey, A. and Jacobs-Lorena, M. Disruption of Plasmodium falciparum development by antibodies against a conserved mosquito midgut antigen. Proceedings of the National Academy of Sciences, USA. 104, 13461-13466. [PubMed]

Molina, H., Horn, D. M., Tang, N., Mathivanan, S. and Pandey, A. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proceedings of the National Academy of Sciences, USA. 104, 2199-2204. [PubMed]

Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R., Tattikota, S. G. and Pandey, A. A compendium of curated phosphorylation-based substrate and binding motifs. Nature Biotechnology. 25, 285-286. [PubMed]

Wang, Z., Pandey, A. and Hart, G. W. Dynamic interplay between O-GlcNAcylation and GSK-3-dependent phosphorylation. Molecular and Cellular Proteomics. 6, 1365-1379. [PubMed]

Kim, J. W., Molina, H., Pandey, A. and Lane, M. D. Upstream stimulatory factors regulate the C/EBPalpha gene during differentiation of 3T3-L1 preadipocytes. Biochem. Biophys. Res. Commun. 354, 517-521. [PubMed]

2006

Mathivanan, S., Periaswamy, B., Gandhi, T. K. B., Kandasamy, K., Suresh, S., Mohmood, R., Ramachandra, Y. L. and Pandey, A. An Evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics. 7, S19. [PubMed]

Gandhi, T. K. B., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periyaswamy, B., Mishra, G., Nandakumar, K., Shen, B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J. S. and Pandey, A. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 3, 285-293. [PubMed]

Qiao, Y., Molina, H., Pandey, A., Zhang, J. and Cole, P. A. Chemical rescue of a mutant enzyme in living cells. Science. 311, 1293-1297. [PubMed]

Bose, R., Molina, H., Patterson, A. S., Bitok, J. K., Periaswamy, B., Bader, J. S., Pandey, A. and Cole, P. A. Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proceedings of the National Academy of Sciences, USA. 103, 9773-9778. [PubMed]

Lerin, C., Rodgers, J. T., Kalume, D. E., Kim, S. H., Pandey, A. and Puigserver, P. GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of PGC-1alpha. Cell Metabolism. 3, 429-438. [PubMed]

Wang, D., Kalume, D., Pickart, C., Pandey, A. and Cotter, R. J. Identification of protein ubiquitylation by electrospray ionization tandem mass spectrometric analysis of sulfonated tryptic peptides. Analytical Chemistry. 78, 3681-3687. [PubMed]

Moff, S. L., Clark, D. P., Maitra, A., Pandey, A. and Thuluvath, P. J. Utility of bile duct brushings for the early detection of cholangiocarcinoma in patients with primary sclerosing cholangitis. Journal of Clinical Gastroenterology. 40, 336-341. [PubMed]

Hyland, E. M., Cosgrove, M. S., Molina, H., Wang, D., Pandey, A., Cotter R. J. and Boeke, J. D. Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Molecular and Cellular Biology. 25, 10060-10070. [PubMed]

Liu, B., Molina, H., Kalume, D., Pandey, A., Griffith, J. D. and Englund, P. Role of p38 in replication of Trypanosoma brucei kinetoplast DNA. Molecular and Cellular Biology. 26, 5382-5393. [PubMed]

Grønborg, 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. Biomarker discovery from pancreatic cancer secretome using a differential proteomics approach. Molecular and Cellular Proteomics. 5, 157-171. [PubMed]

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. Human Protein Reference Database - 2006 Update. Nucleic Acids Research. 34, D411-D414. [PubMed]

2005

Rhodes, D. R., Tomlins, S. A., Varambally, S., Mahavisno, V., Barrette, T., Kalyana-Sundaram, S., Ghosh, D., Pandey, A. and Chinnaiyan, A. M. Probabilistic model of the human protein-protein interaction network. Nature Biotechnology. 23, 951-959. [PubMed]

Amanchy, R., Kalume, D. E., Iwahori, A., Zhong, J. and Pandey, A. Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). Journal of Proteome Research. 4, 1661-1671. [PubMed]

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

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., Bala. P., Jithesh, M. K., Rashmi, N. S., Vishnupriya, G., Dhar, K., Reshma, S., Chaerkady, R., Prasad, C. K. Gandhi, T. K. B., Harsha, H. C., Mohan, S. S., Deshpande, K. S., Sarker, M. and Pandey, A. Plasma proteome database as a resource for proteomics research. Proteomics. 5, 3531-3536. [PubMed]

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. 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. [PubMed]

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. A functional annotation of subproteomes in human plasma. Proteomics. 5, 3506-3519. [PubMed]

Harsha, H. C., Suresh, S., Amanchy, R., Deshpande, N., Shanker, K., Yatish, A. J., Muthusamy, B., Vrushabendra, B. M., Rashmi, B. P., Chandrika, K. N., Padma, N., Sharma, S., Badano, J. L, Ramya, M. A., Shivashankar, H. N., Peri, S., Choudhury, D. R., Kavitha, M. P., Saravana, R., Niranjan, V., Gandhi, T. K. B., Ghosh, N., Chandran, S., Menezes, M., Joy, M., Mohan, S. S., Katsanis, N., Deshpande, K. S., Chaerkady, R., Prasad, C. K., and Pandey, A. A manually curated functional annotation of the human X chromosome. Nature Genetics. 37, 322-323. [PubMed]

Tang, Q. Q., Grønborg, M., Huang, H., Kim, J. W., Otto, T. C., Pandey, A. and Lane, M. D. 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. [PubMed]

Molina, H., Bunkenborg, J., Reddy, G. H., Muthusamy, B., Scheel, P. J. and Pandey, A. A proteomic analysis of human hemodialysis fluid. Molecular and Cellular Proteomics. 4, 637-650. [PubMed]

Chaerkady, R., Harsha, H. C., Prasad, C. K. and Pandey, A. Bioinformatics and proteomics approaches for aging research. Biogerontology. 6, 227-232. [PubMed]

Bala, P., Georgantas, R. W., Sudhir, D., Suresh, M., Shanker, K., Vrushbendra, B. M., Civin, C. I., and Pandey, A. TAGmapper: A web-based tool for mapping SAGE tags. Gene. 364, 123-129. [PubMed]

Suresh, S., Mohan, S., Mishra, G., Hanumanthu, G., Suresh, M., Reddy, R. and Pandey, A. Proteomic resources: integrating biomedical information in humans. Gene. 364, 13-18. [PubMed]

Molina, H., Parmigiani, G. and Pandey, A. Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. Analytical Chemistry. 77, 2739-2744. [PubMed]

Gandhi, T. K. B., Chandran, S., Peri, S., Saravana, R., Amanchy, R., Prasad, T. S. K and Pandey, A. A bioinformatics analysis of protein tyrosine phosphatases in humans. DNA Research. 12, 79-89. [PubMed]

Kalume, D. E., Okulate, M., Zhong, J., Reddy, R., Suresh. S., Deshpande, N., Kumar, N. and Pandey, A. A proteomic analysis of salivary glands of female Anopheles gambiae mosquito. Proteomics. 5, 3765-3777. [PubMed]

Amanchy, R., Kalume, D. E. and Pandey A. 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. [PubMed]

2004

Grønborg, M., Bunkenborg, J., Kristiansen, T. Z., Jensen, O. N., Yeo, C. J., Hruban, R. H., Maitra, A., Goggins, M. G. and Pandey A. Comprehensive proteomic analysis of human pancreatic juice. Journal of Proteome Research. 3, 1042-1055. [PubMed]

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. 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. [PubMed]

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. Mac-2-binding protein is a diagnostic marker for biliary tract carcinoma. Cancer. 101, 1609-1615. [PubMed]

Kristiansen, T. Z., Nielsen, M. M., Blagoev, B., Pandey, A. and Mann, M. Mouse embryonic fibroblasts derived from Odin deficient mice display a hyperproliferative phenotype. DNA Research. 11, 285-292. [PubMed]

Kristiansen, T. Z., Bunkenborg, J., Gronborg, M., Molina, H., Thuluvath, P. J., Argani, P., Goggins, M. G., Maitra, A. and Pandey A. A proteomic analysis of human bile. Molecular and Cellular Proteomics. 3, 715-728. [PubMed]

Rhodes, D. R., Yu, J., Shanker, K., Deshpande, N., Varambally, R, Ghosh, D., Barrette, T., Pandey, A. and Chinnaiyan, A. M. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proceedings of the National Academy of Sciences, USA. 101, 9309-9314. [PubMed]

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. BioBuilder as a database development and functional annotation platform for proteins. BMC Bioinformatics. 5, 43. [PubMed]

Ibarrola, N., Chaerkady, R., 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. pp 393-411.

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

Ibarrola, N., Molina, H., Iwahori, A. and Pandey, A. A novel proteomic approach for specific identification of tyrosine kinase substrates using ¹³C-labeled tyrosine. Journal of Biological Chemistry. 279, 15805-15813. [PubMed]

Ibarrola, N., Kratchmarova, I., Nakajima, D., Schiemann, W. P., Moustakas, A., Pandey, A. and Mann, M. Cloning of a novel signaling molecule, AMSH-2, that potentiates transforming growth factor beta signaling. BMC Cell Biology. 5, 2. [PubMed]

Rhodes, D. R., Yu, J., Shanker, K., Deshpande, N., Varambally, R., Ghosh, D., Barrette, T., Pandey, A. and Chinnaiyan, A. M. Oncomine: A cancer microarray database and integrated data-mining platform. Neoplasia. 6, 1-6. [PubMed]

Tewari, M., Hu, P. J., Ahn, J. S., Ayivi-Guedehoussou, N., Vidalain, P. O., 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. Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Molecular Cell. 13, 469-482. [PubMed]

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. The HUPO PSI Molecular Interaction Format - A community standard for the representation of protein interaction data. Nature Biotechnology. 22, 177-183. [PubMed]

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. Human Protein Reference Database as a discovery resource for proteomics. Nucleic Acids Research. 32, D497-D501. [PubMed]

2003

Ibarrola, N., Kalume, D. E., Gronborg, M., Iwahori, A. and Pandey, A. A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture. Analytical Chemistry. 75, 6043-6049. [PubMed]

Chaerkady, R. and Pandey, A. Absolute systems biology - measuring dynamics of protein modifications. Trends in Biotechnology. 21, 467-470.
[PubMed]

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. Development of Human Protein Reference Database as an initial platform for approaching systems biology in humans. Genome Research. 13, 2363-2371. [PubMed]

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

Steen, H., Fernandez, M., Ghaffari, S., Pandey, A. and Mann M. Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanning. Molecular and Cellular Proteomics. 2, 138-145. [PubMed]

Navarro, J. D., Niranjan, V., Peri, S., Jonnalagadda, C. K. and Pandey, A. From biological databases to platforms for biomedical discovery. Trends in Biotechnology. 21, 263-268. [PubMed]

Pandey, A., Peri, S., Thacker, C., Pugh, C. A., Collins, J. J. and Mann, M. Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome. Bioinformatics. 19, 169-172. [PubMed]

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

2002

Pandey, A., Blagoev, B., Kratchmarova, I., Fernandez, M., Nielsen, M., Kristiansen, T., Ohara, O., Podtelejnikov, A., Roche, S., Lodish, H. and Mann, M. Cloning of a novel phosphotyrosine binding domain containing molecule, Odin, involved in signaling by receptor tyrosine kinases. Oncogene. 21, 8029-8036. [PubMed]

Grønborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. A., Ohara, O., Mann, M., Jensen, O. N. and Pandey, A. 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. [PubMed]

Jebanathirajah, J. A., Peri, S. and Pandey, A. Toll and Interleukin-1 Receptor (TIR) domain-containing proteins in plants: a genomic perspective. Trends in Plant Science. 7, 388-391. [PubMed]

Blagoev, B., Kratchmarova, I., Nielsen, M. M., Fernandez, M. M., Voldby, J., Andersen, J. S., Kristiansen, K., Pandey, A. and Mann, M. Inhibition of adipocyte differentiation by Resistin like molecule alpha (RELM alpha): Biochemical characterization of its oligomeric nature. Journal of Biological Chemistry. 277, 42011-42016. [PubMed]

Steen, H. and Pandey, A. Proteomics goes quantitative: measuring protein abundance. Trends in Biotechnology. 20, 361-364. [PubMed]

Ong S-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A. and Mann, M. 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. [PubMed]

Deshpande, N. and Pandey, A. Mining gene expression data for functional annotation of genomes. Trends in Biotechnology. 20, 282.[PubMed]

Shankar, S. H. N. and Pandey, A. A novel mode of activating the JAK-STAT signaling pathway. Trends in Biochemical Sciences. 27, 336.[PubMed]

Kristiansen, T. Z. and Pandey, A. Resources for full-length cDNAs. Trends in Biochemical Sciences. 27, 266-267. [PubMed]

Schiemann, W. P., Blobe, G. C., Kalume, D. E., Pandey, A. and Lodish, H. F. 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. [PubMed]

Dan, I., Watanabe, N. M., Kajikawa, E., Ishida, T., Pandey, A. and Kusumi, A. Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution. Nucleic Acids Research. 30, 2906-2910. [PubMed]

Pandey, A., Dan, I., Kristiansen, T. Z., Watanabe, N. M., Voldby, J., Kajikawa, E., Khosravi-Far, R., Blagoev, B. and Mann, M. 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. [PubMed]

Mann, M., Ong, S. E., Grønborg, M., Steen, H., Jensen, O. N. and Pandey, A. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends in Biotechnology. 20, 261-268. [PubMed]

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. A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes. Molecular and Cellular Proteomics. 1, 213-222. [PubMed]

Pandey, A., Ibarrola, N., Kratchmarova, I., Fernandez, M. M., Constantinescu, S. N, Ohara, O., Sawasdikosol, S., Lodish, H. F. and Mann, M. 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. [PubMed]

Dan, I., Ong, S. E., Watanabe, N. M., Blagoev, B., Nielsen, M. M., Kajikawa, E., Kristiansen, T. Z., Mann, M. and Pandey, A. 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. [PubMed]

Blagoev, B., Nielsen, M. M., Angrist, M., Chakravarti, A. and Pandey, A. Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene. Gene. 284, 161-168. [PubMed]

2001

Peri, S. and Pandey, A. A reassessment of the translation initiation codon in vertebrates. Trends in Genetics. 17, 685-687. [PubMed]

Blagoev, B. and Pandey, A. Microarrays go live - new prospects for proteomics. Trends in Biochemical Sciences. 26, 639-641. [PubMed]

Peri, S., Steen, H. and Pandey, A. GPMAW - a software tool for analyzing proteins and peptides. Trends in Biochemical Sciences. 26, 687-689. [PubMed]

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

Peri, S., Ibarrola, N., Blagoev, B., Mann, M. and Pandey, A. Common pitfalls in bioinformatics based analyses: Look before you leap. Trends in Genetics. 17, 541-545. [PubMed]

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

Mann, M. and Pandey, A. Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. Trends in Biochemical Sciences. 26, 54-61. [PubMed]

Kratchmarova, I., Sosinowski, T., Weiss, A., Witter, K., Vincenz, C. and Pandey, A. Characterization of promoter region and genomic structure of the murine and human genes encoding Src like adapter protein. Gene. 262, 267-273. [PubMed]

2000

Pandey, A., Fernandez, M. M., Steen, H., Blagoev, B., Nielsen, M. M., Mann, M. and Lodish, H. F 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. [PubMed]

Pandey, A. and Mann, M. Proteomics to study genes and genomes. Nature. 405, 837-846. [PubMed]

Pandey, A., Andersen, J. S. and Mann, M. Use of mass spectrometry to study signaling pathways. Science STKE. 2000(37):PL1. [PubMed]

Pandey, A., Ozaki, K., Baumann, H., Levin, S. D., Puel, A., Farr, A. G., Ziegler, S. F., Leonard, W. J. and Lodish, H. F. Cloning of a receptor subunit required for signaling by thymic stromal lymphopoietin. Nature Immunology. 1, 59-64. [PubMed]

Pandey, A., Podtelejnikov, A. V., Blagoev, B., Bustelo, X. R., Mann, M. and Lodish, H. F. 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 U.S.A.. 97, 179-184. [PubMed]

1999

Pandey, A. and Lewitter. F. Nucleotide Sequence Databases: A gold mine for biologists. Trends in Biochemical Sciences. 24, 276-280. [PubMed]