INCREDB ID : 158
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Akhilesh Pandey, M.D., Ph.D.
Founder and Director 
 
Institute of Bioinformatics
Discoverer Building, International Tech Park, Whitefield
Bangalore - 560 066   
Karnataka   
 
E-mail: pandey@jhmi.edu
Phone: +91-80-28416140
Fax: +91-80-28416132
 
URL: http://www.ibioinformatics.org/founder.html
 
Positions Held:
Position Affiliation Time Period
Founder and Director Institute of Bioinformatics, Bangalore, India 2002-Present
Professor McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, USA 2010-Present
Associate Professor McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, USA 2006-2010
Assistant Professor McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, USA 2002-2006
Instructor Harvard Medical School, Boston, USA 1998-2002
Visiting Scientist Center for Experimental Bioinformatics, University of Southern Denmark, Odense, Denmark 1999-2002
Resident Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA 1996-1998
 
Area of Specialization:
Genomics
Pathology
Proteomics
Research Summary:
Phosphorylation and signal transduction
Mass spectrometry and proteomics
Bioinformatics and biological databases
Comparative genomics
 
Publications:
1. 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. Phosphoproteome of Cryptococcus neoformans. Journal of Proteomics. 2013. In press.
2. Sreenivasamurthy, S. K., Dey, G., Ramu, M., Kumar, M., Gupta, M. K., Mohanty, A. K., Harsha, H., Sharma, P., Kumar, N., Pandey, A., Kumar, A. and Prasad, T. K.  A compendium of molecules involved in vector-pathogen interactions pertaining to malaria. Malaria Journal. 2013.  12, 216. [PubMed]
3. Hansen, A. M., Chaerkady, R., Sharma, J., Diaz-Mejia, J. J., Tyagi, N., Renuse, S., Jacob, H. K., Pinto, S. M., Sahasrabuddhe, N. A., Kim, M. S., Delanghe, B., Srinivasan, N., Emili, A., Kaper, J. B. and Pandey, A.  The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence. PLoS Pathogens. 2013.  9, e1003403. [PubMed]
4. Chaerkady, R., Shao, H., Scott, S. G., Pandey, A., Jun, A. S. and Chakravarti, S.  The keratoconus corneal proteome: Loss of epithelial integrity and stromal degeneration. Journal of Proteomics. 2013.  87, 122-131. [PubMed]
5. Ambekar, A. S., Nirujogi, R. S., Srikanth, S. M., Chavan, S., Kelkar, D. S., Hinduja, I., Zaveri, K., Prasad, T. S., Harsha, H. C., Pandey, A. and Mukherjee, S.  Proteomic analysis of human follicular fluid: A new perspective towards understanding folliculogenesis. Journal of Proteomics. 2013.  87, 68-77. [PubMed]
6. 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.  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. 2013.  12, 3128-3138. [PubMed]
7. 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.  Identification of head and neck squamous cell carcinoma biomarker candidates through proteomic analysis of cancer cell secretome. Biochimica et Biophysica Acta. 2013.  [PubMed]
8. Nirujogi, R. S., Pawar, H., Renuse, S., Kumar, P., Chavan, S., Sathe, G., Sharma, J., Khobragade, S., Pande, J., Modak, B., Prasad, T. S., Harsha, H. C., Patole, M. S. and Pandey, A.  Moving from unsequenced to sequenced genome: Reanalysis of the proteome of Leishmania donovani. Journal of Proteomics. 2013.  [PubMed]
9. 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.  FAM190A Deficiency Creates a Cell Division Defect. The American Journal of Pathology. 2013.  183, 296-303. [PubMed]
10. 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.  A network map of BDNF/TRKB and BDNF/p75NTR signaling system. 560066, India, sandhya@ibioinformatics.org. Journal of Cell Communication and Signaling. 2013.  [PubMed]
11. Balakrishnan, L., Soman, S., Patil, Y. B., Advani, J., Thomas, J. K., Desai, D. V., Kulkarni-Kale, U., Harsha, H. C., Prasad, T. S., Raju, R., Pandey, A., Dimitriadis, E. and Chatterjee, A.  IL-11/IL11RA receptor mediated signaling: a web accessible knowledgebase. Cell Communication & Adhesion. 2013.  [PubMed]
12. 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.  Construction of human activity-based phosphorylation networks. Molecular Systems Biology. 2013.  9, 655. [PubMed]
13. Venugopal, A. K., Ghantasala, S. S., Selvan, L. D., Mahadevan, A., Renuse, S., Kumar, P., Pawar, H., Sahasrabhuddhe, N. A., Suja, M. S., Ramachandra, Y. L., Prasad, T. S., Madhusudhana, S. N., Hc, H., Chaerkady, R., Satishchandra, P., Pandey, A. and Shankar, S. K.  Quantitative proteomics for identifying biomarkers for Rabies. Clinical Proteomics. 2013.  10, 3. [PubMed]
14. Kashyap, M. K., Pawar, H. A., Keerthikumar, S., Sharma, J., Goel, R., Mahmood, R., Kumar, M. V., Kumar, K. V., Pandey, A., Kumar, R. V., Prasad, T. S. and Harsha, H. C.  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 : Section A of Disease Markers. 2012-2013.  12, 1-9. [PubMed]
15. Soman, S., Raju, R., Sandhya, V. K., Advani, J., Khan, A. A., Harsha, H. C., Prasad, T. S., Sudhakaran, P. R., Pandey, A. and Adishesha, P. K.  A multicellular signal transduction network of AGE/RAGE signaling. Journal of Cell Communication and Signaling. 2013.  7, 19-23. [PubMed]
16. Huang, T. C., Pinto, S. M. and Pandey, A.  Proteomics for understanding miRNA biology. Proteomics. 2013.  13, 558-567. [PubMed]
17. Pawar, H., Maharudraiah, J., Kashyap, M. K., Sharma, J., Srikanth, S. M., Choudhary, R., Chavan, S., Sathe, G., Manju, H. C., Kumar, K. V., Vijayakumar, M., Sirdeshmukh, R., Harsha, H. C., Prasad, T. S., Pandey, A. and Kumar, R. V.  Downregulation of cornulin in esophageal squamous cell carcinoma. Acta Histochemica. 2013.  115, 89-99. [PubMed]
18. 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., Harsha, H. C., Chatterjee, A. and Pandey, A.  SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics. Clinical Applications. 2013.  7, 355-366. [PubMed]
19. 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.  Signaling network of Oncostatin M pathway. Journal of Cell Communication and Signaling. 2013.  7, 103-108. [PubMed]
20. Kumar, G. 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., Shankar, K. and Pandey, A.  Quantitative proteomics for identifying biomarkers for tuberculous meningitis. Clinical Proteomics. 2012.  9, 12. [PubMed]
21. Luo, W., Chang, R., Zhong, J., Pandey, A. and Semenza, G. L.  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 of the United States of America. 2012.  109, E3367-76. [PubMed]
22. 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. Gene expression profiling of tuberculous meningitis co-infected with HIV. Journal of Proteomics and Bioinformatics. 2012. 5, 235-244.
23. van, B., Zhong, J., Kopp, N., Dutta, C., Kim, M. S., Bird, L., Weigert, O., Tyner, J., Pandey, A., Yoda, A. and Weinstock, D. M.  Differences in signaling through the B-cell leukemia oncoprotein CRLF2 in response to TSLP and through mutant JAK2. Blood. 2012.  120, 2853-2863. [PubMed]
24. Ren, Y. R., Chaerkady, R., Hu, S., Wan, J., Qian, J., Zhu, H., Pandey, A. and Kern, S. E.  Unbiased discovery of interactions at a control locus driving expression of the cancer-specific therapeutic and diagnostic target, mesothelin. Journal of Proteome Research. 2012.  11, 5301-5310. [PubMed]
25. Ferrando, I. M., Chaerkady, R., Zhong, J., Molina, H., Jacob, H. K., Herbst-Robinson, K., Dancy, B. M., Katju, V., Bose, R., Zhang, J., Pandey, A. and Cole, P. A.  Identification of targets of c-Src tyrosine kinase by chemical complementation and phosphoproteomics. Molecular & Cellular Proteomics : MCP. 2012.  11, 355-369. [PubMed]
26. Do, V., Gomez-Mendoza, D. P., Kim, M. S., Pandey, A., Ricart, C. A., Ximenes, F. and Sousa, M. V.  Secretome analysis of the fungus Trichoderma harzianum grown on cellulose. Proteomics. 2012.  12, 2716-2728. [PubMed]
27. Kalra, H., Simpson, R. J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V. C., Borras, 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., Inal, J. M., Jenster, G., Kramer-Albers, E. M., Lim, S. K., Llorente, A., Lotvall, J., Marcilla, A., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t, H., Pandey, A., Patel, T., Piper, M. G., Pluchino, S., Prasad, T. S., Rajendran, L., Raposo, G., Record, M., Reid, G. E., Sanchez-Madrid, F., Schiffelers, R. M., Siljander, P., Stensballe, A., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van, B., Vazquez, J., Vidal, M., Wauben, M. H., Yanez-Mo, M., Zoeller, M. and Mathivanan, S.  Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PLoS Biology. 2012.  10, e1001450. [PubMed]
28. Telikicherla, D., Marimuthu, A., Kashyap, M. K., Ramachandra, Y. L., Mohan, S., Roa, J. C., Maharudraiah, J. and Pandey, A.  Overexpression of ribosome binding protein 1 (RRBP1) in breast cancer. Clinical Proteomics. 2012.  9, 7. [PubMed]
29. Bhattacharjee, M., Raju, R., Radhakrishnan, A., Nanjappa, V., Muthusamy, B., Singh, K., Kuppusamy, D., Lingala, B. T., Pan, A., Mathur, P. P., Harsha, H. C., Prasad, T. S., Atkins, G. J., Pandey, A. and Chatterjee, A.  A Bioinformatics Resource for TWEAK-Fn14 Signaling Pathway. Journal of Signal Transduction. 2012.  2012, 376470. [PubMed]
30. Kim, M. S., Kuppireddy, S. V., Sakamuri, S., Singal, M., Getnet, D., Harsha, H. C., Goel, R., Balakrishnan, L., Jacob, H. K., 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.  Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs). Journal of Proteome Research. 2012.  11, 5556-5563. [PubMed]
31. Renuse, S., Harsha, H. C., Kumar, P., Acharya, P. K., Sharma, J., Goel, R., Kumar, G. S., Raju, R., Prasad, T. S., Slotta, T. and Pandey, A.  Proteomic analysis of an unsequenced plant--Mangifera indica. Journal of Proteomics. 2012.  75, 5793-5796. [PubMed]
32. Telikicherla, D., Maharudraiah, J., Pawar, H., Marimuthu, A., Kashyap, M. K., Ramachandra, Y. L., Roa, J. C. and Pandey, A. Overexpression of Kinesin Associated Protein 3 (KIFAP3) in breast cancer. Journal of Proteomics and Bioinformatics. 2012. 5, 122-126.
33. 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., Pandey, A., Shemanko, C. and Chatterjee, A.  A pathway map of prolactin signaling. Journal of Cell Communication and Signaling. 2012.  6, 169-173. [PubMed]
34. 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. Transcriptomic profiling of medial temporal lobe epilepsy. Journal of Proteomics and Bioinformatics. 2012. 5, 31-39. 
35. 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.  TSLP signaling network revealed by SILAC-based phosphoproteomics. Molecular & Cellular Proteomics : MCP. 2012.  11, M112.017764. [PubMed]
36. 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.  Regulation of lipid metabolism by Dicer revealed through SILAC mice. Journal of Proteome Research. 2012.  11, 2193-2205. [PubMed]
37. Agyeman, A. S., Chaerkady, R., Shaw, P. G., Davidson, N. E., Visvanathan, K., Pandey, A. and Kensler, T. W.  Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane-treated human breast epithelial cells reveals common expression profiles. Breast Cancer Research and Treatment. 2012.  132, 175-187. [PubMed]
38. 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.  LC-MS/MS analysis of differentially expressed glioblastoma membrane proteome reveals altered calcium signaling and other protein groups of regulatory functions. Molecular & Cellular Proteomics : MCP. 2012.  11, M111.013565. [PubMed]
39. 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.  Proteomic analysis of the abomasal mucosal response following infection by the nematode, Haemonchus contortus, in genetically resistant and susceptible sheep. Journal of Proteomics. 2012.  75, 2141-2152. [PubMed]
40. Prasad, T. S., Harsha, H. C., Keerthikumar, S., Sekhar, N. R., Selvan, L. D., Kumar, P., Pinto, S. M., Muthusamy, B., Subbannayya, Y., Renuse, S., Chaerkady, R., Mathur, P. P., Ravikumar, R. and Pandey, A.  Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry. Journal of Proteome Research. 2012.  11, 247-260. [PubMed]
41. Goel, R., Harsha, H. C., Pandey, A. and Prasad, T. S.  Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Molecular BioSystems. 2012.  8, 453-463. [PubMed]
42. Pawar, H., Sahasrabuddhe, N. A., Renuse, S., Keerthikumar, S., Sharma, J., Kumar, G. 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.  A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani. Proteomics. 2012.  12, 832-844. [PubMed]
43. Kim, M. S. and Pandey, A.  Electron transfer dissociation mass spectrometry in proteomics. Proteomics. 2012.  12, 530-542. [PubMed]
44. 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. A signaling network of thyroid-stimulating hormone. Journal of Proteomics and Bioinformatics. 2011. 4, 238-241.
45. Kinsinger, C. R., Apffel, J., Baker, M., Bian, X., Borchers, C. H., Bradshaw, R., Brusniak, M. Y., Chan, D. W., 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, S. L., Simpson, R. J., Slotta, D., Smith, R. D., Stein, S. E., Tabb, D. L., Tagle, D., Yates, J. R. and Rodriguez, H.  Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Molecular & Cellular Proteomics : MCP. 2011.  10, O111.015446. [PubMed]
46. Telikicherla, D., Ambekar, A., Palapetta, S. M., Dwivedi, S. B., Raju, R., Sharma, J., Prasad, T. s. K., Ramachandra, Y., Mohan, S. S., Maharudraiah, J., Mukherjee, S. and Pandey, A.  A comprehensive curated resource for follicle stimulating hormone signaling. BMC Research Notes. 2011.  4, 408. [PubMed]
47. 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.  Comprehensive proteomic analysis of human bile. Proteomics. 2011.  11, 4443-4453. [PubMed]
48. 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., Chauhan, D. S., Katoch, K., Katoch, V. M., Kumar, P., Chaerkady, R., Ramachandran, S., Dash, D. and Pandey, A.  Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Molecular & Cellular Proteomics : MCP. 2011.  10, M111.011627. [PubMed]
49. 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. M., Syed, N., Srikanth, M. S., Sathe, G. J., Ahmad, S., Chavan, S. N., Kumar, G. S., Marimuthu, A., Prasad, T. S., Harsha, H. C., Rahiman, B. A., Ohara, O., Bader, G. D., Sujatha, M., Schiemann, W. P. and Pandey, A.  NetSlim: high-confidence curated signaling maps. Database : the Journal of Biological Databases and Curation. 2011.  2011, bar032. [PubMed]
50. 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. A comprehensive curated reaction map of leptin signaling pathway. Journal of Proteomics and Bioinformatics. 2011. 4, 184-189.
51. 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.  An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae. Genes & Development. 2011.  25, 1306-1319. [PubMed]
52. 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., Keshava, P., Okulate, M., Kumar, N. and Pandey, A.  A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Research. 2011.  21, 1872-1881. [PubMed]
53. Chaerkady, R., Letzen, B., Renuse, S., Sahasrabuddhe, N. A., Kumar, P., All, A. H., Thakor, N. V., Delanghe, B., Gearhart, J. D., Pandey, A. and Kerr, C. L.  Quantitative temporal proteomic analysis of human embryonic stem cell differentiation into oligodendrocyte progenitor cells. Proteomics. 2011.  11, 4007-4020. [PubMed]
54. Raju, R., Balakrishnan, L., Nanjappa, V., Bhattacharjee, M., Getnet, D., Muthusamy, B., Kurian, T., Sharma, J., Rahiman, B. A., Harsha, H. C., Shankar, S., Prasad, T. S., Mohan, S. S., Bader, G. D., Wani, M. R. and Pandey, A.  A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway. Database : the Journal of Biological Databases and Curation. 2011.  2011, bar021. [PubMed]
55. 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., Kumar, K. V., Vijayakumar, M., Chaerkady, R., Prasad, T. S., Kumar, R. V., Kumar, R. V. and Pandey, A.  Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biology & Therapy. 2011.  12, 510-522. [PubMed]
56. Shao, H., Chaerkady, R., Chen, S., Pinto, S. M., Sharma, R., Delanghe, B., Birk, D. E., Pandey, A. and Chakravarti, S.  Proteome profiling of wild type and lumican-deficient mouse corneas. Journal of Proteomics. 2011.  74, 1895-1905. [PubMed]
57. Kim, M. S., Zhong, J., Kandasamy, K., Delanghe, B. and Pandey, A.  Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides. Proteomics. 2011.  11, 2568-2572. [PubMed]
58. Marimuthu, A., O'Meally, R. N., 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.  A comprehensive map of the human urinary proteome. Journal of Proteome Research. 2011.  10, 2734-2743. [PubMed]
59. Luo, W., Hu, H., Chang, R., Zhong, J., Knabel, M., O'Meally, R., Cole, R. N., Pandey, A. and Semenza, G. L.  Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1. Cell. 2011.  145, 732-744. [PubMed]
60. Shaw, P. G., Chaerkady, R., Zhang, Z., Davidson, N. E. and Pandey, A.  Monoclonal antibody cocktail as an enrichment tool for acetylome analysis. Analytical Chemistry. 2011.  83, 3623-3626. [PubMed]
61. 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. Gene Expression Profiling of Tuberculous Meningitis. Journal of Proteomics and Bioinformatics. 2011. 4, 98-105.
62. Amanchy, R., Kandasamy, K., Mathivanan, S., Periaswamy, B., Reddy, R., Yoon, W. H., Joore, J., Beer, M. A., Cope, L. and Pandey, A. Identification of novel phosphorylation motifs through an integrative computational and experimental analysis of the human phosphoproteome. Journal of Proteomics and Bioinformatics. 2011. 4, 22-35.
63. 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. Gene expression profiling of gastric cancer. Journal of Proteomics and Bioinformatics. 2011, 4, 74-82.
64. Renuse, S., Chaerkady, R. and Pandey, A.  Proteogenomics. Proteomics. 2011.  11, 620-630. [PubMed]
65. Wang, Q., Chaerkady, R., Wu, J., Hwang, H. J., Papadopoulos, N., Kopelovich, L., Maitra, A., Matthaei, H., Eshleman, J. R., Hruban, R. H., Kinzler, K. W., Pandey, A. and Vogelstein, B.  Mutant proteins as cancer-specific biomarkers. Proceedings of the National Academy of Sciences of the United States of America. 2011.  108, 2444-2449. [PubMed]
66. Zhong, J., Chaerkady, R., Kandasamy, K., Gucek, M., Cole, R. N. and Pandey, A.  The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. Journal of Proteomics. 2011.  74, 294-303. [PubMed]
67. Harsha, H. C. and Pandey, A.  Phosphoproteomics in cancer. Molecular Oncology. 2010.  4, 482-495. [PubMed]
68. Chen, H., Pimienta, G., Gu, Y., Sun, X., Hu, J., Kim, M. S., Chaerkady, R., Gucek, M., Cole, R. N., Sukumar, S. and Pandey, A.  Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 2010.  10, 3800-3810. [PubMed]
69. 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. Comparative proteomic analysis of Candida albicans and Candida glabrata. Clinical Proteomics. 2010. 6, 163-173.
70. Goel, R., Muthusamy, B., Pandey, A. and Prasad, T. S.  Human Protein Reference Database and Human Proteinpedia as Discovery Resources for Molecular Biotechnology. Molecular Biotechnology. 2010.  [PubMed]
71. Zhong, J., Krawczyk, S. A., Chaerkady, R., Huang, H., Goel, R., Bader, J. S., Wong, G. W., Corkey, B. E. and Pandey, A.  Temporal profiling of the secretome during adipogenesis in humans. Journal of Proteome Research. 2010.  9, 5228-5238. [PubMed]
72. Hector, A., Montgomery, E. A., Karikari, C., Canto, M., 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., Eshleman, J. R., Nelkin, B. D., Pandey, A. and Maitra, A.  The Axl receptor tyrosine kinase is an adverse prognostic factor and a therapeutic target in esophageal adenocarcinoma. Cancer Biology & Therapy. 2010.  10, 1009-1018. [PubMed]
73. 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. BioPAX - A community standard for pathway data sharing. Nature Biotechnology. 2010. 28, 935-942.
74. Zachara, N. E., Molina, H., Wong, K. Y., Pandey, A. and Hart, G. W.  The dynamic stress-induced "O-GlcNAc-ome" highlights functions for O-GlcNAc in regulating DNA damage/repair and other cellular pathways. Amino Acids. 2010.  [PubMed]
75. Kashyap, M. K., Harsha, H. C., Renuse, S., Pawar, H., Sahasrabuddhe, N. A., Kim, M. S., Marimuthu, A., Keerthikumar, S., Muthusamy, B., Kandasamy, K., Subbannayya, Y., Prasad, T. S., Mahmood, R., Chaerkady, R., Meltzer, S. J., Kumar, R. V., Rustgi, A. K. and Pandey, A.  SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biology & Therapy. 2010.  10. [PubMed]
76. Yang, Y., Chaerkady, R., Kandasamy, K., Huang, T. C., Selvan, L. D., Dwivedi, S. B., Kent, O. A., Mendell, J. T. and Pandey, A.  Identifying targets of miR-143 using a SILAC-based proteomic approach. Molecular Biosystems. 2010.  6, 1873-1882. [PubMed]
77. Kim, M. S., Kandasamy, K., Chaerkady, R. and Pandey, A.  Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer. Journal of the American Society for Mass Spectrometry. 2010.  21, 1606-1611. [PubMed]
78. Hijikata, A., Raju, R., Keerthikumar, S., Ramabadran, S., Balakrishnan, L., Ramadoss, S. K., Pandey, A., Mohan, S. and Ohara, O.  Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases. DNA Research. 2010.  17, 197-208. [PubMed]
79. Zhong, J. and Pandey, A.  Site-directed mutagenesis reveals a unique requirement for tyrosine residues in IL-7Ralpha and TSLPR cytoplasmic domains in TSLP-dependent cell proliferation. BMC Immunology. 2010.  11, 5. [PubMed]
80. Zhong, J., Liu, X. and Pandey, A.  Effects of transmembrane and juxtamembrane domains on proliferative ability of TSLP receptor. Molecular Immunology. 2010.  47, 1207-1215. [PubMed]
81. 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. Overexpression of periostin and lumican in esophageal squamous cell carcinoma. Cancers. 2010. 2, 133-142.
82. Chaerkady, R., Kerr, C. L., Kandasamy, K., Marimuthu, A., Gearhart, J. D. and Pandey, A.  Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics. 2010.  10, 1359-1373. [PubMed]
83. Kandasamy, K., Mohan, S. S., Raju, R., Keerthikumar, S., Kumar, G. S., Venugopal, A. K., Telikicherla, D., Navarro, J. D., Mathivanan, S., Pecquet, C., Gollapudi, S. K., Tattikota, S. G., Mohan, S., Padhukasahasram, H., Subbannayya, Y., Goel, R., Jacob, H. K., Zhong, J., Sekhar, R., Nanjappa, V., Balakrishnan, L., Subbaiah, R., Ramachandra, Y. L., Rahiman, B. A., Prasad, T. S., Lin, J. X., Houtman, J. C., Desiderio, S., Renauld, J. C., Constantinescu, S. N., Ohara, O., Hirano, T., Kubo, M., Singh, S., Khatri, P., Draghici, S., Bader, G. D., Sander, C., Leonard, W. J. and Pandey, A.  NetPath: a public resource of curated signal transduction pathways. Genome Biology. 2010.  11, R3. [PubMed]
84. Zhou, Q., Chaerkady, R., Shaw, P. G., Kensler, T. W., Pandey, A. and Davidson, N. E.  Screening for therapeutic targets of vorinostat by SILAC-based proteomic analysis in human breast cancer cells. Proteomics. 2010.  10, 1029-1039. [PubMed]
85. Luo, W., Zhong, J., Chang, R., Hu, H., Pandey, A. and Semenza, G. L.  Hsp70 and CHIP selectively mediate ubiquitination and degradation of hypoxia-inducible factor (HIF)-1alpha but Not HIF-2alpha. The Journal of Biological Chemistry. 2010.  285, 3651-3663. [PubMed]
86.. Amanchy, R., Zhong, J., Hong, R., Kim, J. H., Gucek, M., Cole, R. N., Molina, H. and Pandey, A.  Identification of c-Src tyrosine kinase substrates in platelet-derived growth factor receptor signaling. Molecular Oncology. 2009.  3, 439-450. [PubMed]
87. Prasad, T. S., Kandasamy, K. and Pandey, A.  Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods in Molecular Biology. 2009.  577, 67-79. [PubMed]
88. 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. 2009.  16, 345-351. [PubMed]
89. 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. 2009.  4, e6440. [PubMed]
90. 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. 2009.  81, 7170-7180. [PubMed]
91. Kandasamy, K., Keerthikumar, S., Raju, R., Keshava, P., Ramachandra, Y. L., Mohan, S. and Pandey, A.  PathBuilder--open source software for annotating and developing pathway resources. Bioinformatics. 2009.  25, 2860-2862. [PubMed]
92. Yang, Y., Chaerkady, R., Beer, M. A., Mendell, J. T. and Pandey, A.  Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics. 2009.  9, 1374-1384. [PubMed]
93. Harsha, H. C., Kandasamy, K., Ranganathan, P., Rani, S., Ramabadran, S., Gollapudi, S., Balakrishnan, L., Dwivedi, S. B., Telikicherla, D., Selvan, L. D., Goel, R., Mathivanan, S., Marimuthu, A., Kashyap, M., 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. 2009.  6, e1000046. [PubMed]
94. Ranganathan, P., Harsha, H. C. and Pandey, A.  Molecular alterations in exocrine neoplasms of the pancreas. Archives of Pathology & Laboratory Medicine. 2009.  133, 405-412. [PubMed]
95. Chaerkady, R., Kerr, C. L., Marimuthu, A., Kelkar, D. S., Kashyap, M. K., Gucek, M., Gearhart, J. D. and Pandey, A.  Temporal analysis of neural differentiation using quantitative proteomics. Journal of Proteome Research. 2009.  8, 1315-1326. [PubMed]
96. Venugopal, A., Chaerkady, R. and Pandey, A.  Application of mass spectrometry-based proteomics for biomarker discovery in neurological disorders. Annals of Indian Academy of Neurology. 2009.  12, 3-11. [PubMed]
97. 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. 2009.  28, 621-631. [PubMed]
98. Molina, H., Yang, Y., Ruch, T., Kim, J. W., Mortensen, P., Otto, T., Nalli, A., Tang, Q. Q., Lane, M. D., Chaerkady, R. and Pandey, A.  Temporal profiling of the adipocyte proteome during differentiation using a five-plex SILAC based strategy. Journal of Proteome Research. 2009.  8, 48-58. [PubMed]
99. 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.  O-linked N-acetylglucosamine modification on CCAAT enhancer-binding protein beta: role during adipocyte differentiation. The Journal of Biological Chemistry. 2009.  284, 19248-19254. [PubMed]
100. 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. 2009.  5, e1000265. [PubMed]
101. Keshava, P., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A., Balakrishnan, L., Marimuthu, A., Banerjee, S., Somanathan, D. S., Sebastian, A., Rani, S., Ray, S., Harrys, K., Kanth, S., Ahmed, M., Kashyap, M. K., Mohmood, R., Ramachandra, Y. L., Krishna, V., Rahiman, B. A., Mohan, S., Ranganathan, P., Ramabadran, S., Chaerkady, R. and Pandey, A.  Human Protein Reference Database--2009 update. Nucleic Acids Research. 2009.  37, D767-72. [PubMed]
102. Kashyap, M. K., Marimuthu, A., Kishore, C. J., Peri, S., Keerthikumar, S., Prasad, T. S., Mahmood, R., Rao, S., Ranganathan, P., Sanjeeviah, R. C., Vijayakumar, M., Kumar, K. V., Montgomery, E. A., Kumar, R. V. and Pandey, A.  Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biology & Therapy. 2009.  8, 36-46. [PubMed]
103. Keerthikumar, S., Raju, R., Kandasamy, K., Hijikata, A., Ramabadran, S., Balakrishnan, L., Ahmed, M., Rani, S., Selvan, L. D., 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. 2009.  37, D863-7. [PubMed]
104. Kandasamy, K., Keerthikumar, S., Goel, R., Mathivanan, S., Patankar, N., Shafreen, B., Renuse, S., Pawar, H., Ramachandra, Y. L., Acharya, P. K., Ranganathan, P., Chaerkady, R., Keshava, P. and Pandey, A.  Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Research. 2009.  37, D773-81. [PubMed]
105. Kristiansen, T. Z., Harsha, H. C., Gronborg, M., Maitra, A. and Pandey, A.  Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma. Journal of Proteome Research. 2008.  7, 4670-4677. [PubMed]
106. Harsha, H. C., Jimeno, A., Molina, H., Mihalas, A. B., Goggins, M. G., Hruban, R. H., Schulick, R. D., 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. 2008.  7, 4651-4658. [PubMed]
107. Chaerkady, R., Harsha, H. C., Nalli, A., Gucek, M., Vivekanandan, P., Akhtar, J., Cole, R. N., Simmers, J., Schulick, R. D., Singh, S., Torbenson, M., Pandey, A. and Thuluvath, P. J.  A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma. Journal of Proteome Research. 2008.  7, 4289-4298. [PubMed]
108. Dixon, S. J., Fedyshyn, Y., Koh, J. L., Prasad, T. S., Chahwan, C., Chua, G., Toufighi, K., Baryshnikova, A., Hayles, J., Hoe, K. L., Kim, D. U., Park, H. O., Myers, C. L., Pandey, A., Durocher, D., Andrews, B. J. and Boone, C.  Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proceedings of the National Academy of Sciences of the United States of America. 2008.  105, 16653-16658. [PubMed]
109. Guha, U., Chaerkady, R., Marimuthu, A., Patterson, A. S., Kashyap, M. K., Harsha, H. C., Sato, M., Bader, J. S., Lash, A. E., Minna, J. D., Pandey, A. and Varmus, H. E.  Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proceedings of the National Academy of Sciences of the United States of America. 2008.  105, 14112-14117. [PubMed]
110. Song, D., Chaerkady, R., Tan, A. C., Garcia-Garcia, E., Nalli, A., Suarez-Gauthier, A., Lopez-Rios, F., Zhang, X. F., Solomon, A., Tong, J., Read, M., Fritz, C., Jimeno, A., Pandey, A. and Hidalgo, M.  Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer. Molecular Cancer Therapeutics. 2008.  7, 3275-3284. [PubMed]
111. Mathivanan, S. and Pandey, A.  Human Proteinpedia as a resource for clinical proteomics. Molecular & Cellular Proteomics. 2008.  7, 2038-2047. [PubMed]
112. Sarker, R., Gronborg, M., Cha, B., Mohan, S., Chen, Y., Pandey, A., Litchfield, D., Donowitz, M. and Li, X.  Casein kinase 2 binds to the C terminus of Na+/H+ exchanger 3 (NHE3) and stimulates NHE3 basal activity by phosphorylating a separate site in NHE3. Molecular Biology of the Cell. 2008.  19, 3859-3870. [PubMed]
113. Zhong, L., Roybal, J., Chaerkady, R., Zhang, W., Choi, K., Alvarez, C. A., Tran, H., Creighton, C. J., Yan, S., Strieter, R. M., Pandey, A. and Kurie, J. M.  Identification of secreted proteins that mediate cell-cell interactions in an in vitro model of the lung cancer microenvironment. Cancer Research. 2008.  68, 7237-7245. [PubMed]
114. Amanchy, R., Zhong, J., Molina, H., Chaerkady, R., Iwahori, A., Kalume, D. E., Gronborg, M., Joore, J., Cope, L. and Pandey, A.  Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. Journal of Proteome Research. 2008.  7, 3900-3910. [PubMed]
115. Luo, W., Slebos, R. J., Hill, S., Li, M., Brabek, J., Amanchy, R., Chaerkady, R., Pandey, A., Ham, A. J. and Hanks, S. K.  Global impact of oncogenic Src on a phosphotyrosine proteome. Journal of Proteome Research. 2008.  7, 3447-3460. [PubMed]
116. Chaerkady, R., Thuluvath, P. J., Kim, M. S., Nalli, A., Vivekanandan, P., Simmers, J., Torbenson, M. and Pandey, A.  O Labeling for a Quantitative Proteomic Analysis of Glycoproteins in Hepatocellular Carcinoma. Clinical Proteomics. 2008.  4, 137-155. [PubMed]
117. Molina, H., Matthiesen, R., Kandasamy, K. and Pandey, A.  Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Analytical Chemistry. 2008.  80, 4825-4835. [PubMed]
118. Chaerkady, R. and Pandey, A.  Applications of proteomics to lab diagnosis. Annual Review of Pathology. 2008.  3, 485-498. [PubMed]
119. 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. The American Journal of Surgical Pathology. 2008.  32, 188-196. [PubMed]
120. Harsha, H. C., Molina, H. and Pandey, A.  Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nature Protocols. 2008.  3, 505-516. [PubMed]
121. Mathivanan, S., Ahmed, M., Ahn, N. G., Alexandre, H., Amanchy, R., Andrews, P. C., Bader, J. S., Balgley, B. M., Bantscheff, M., Bennett, K. L., Bjorling, E., Blagoev, B., Bose, R., Brahmachari, S. K., Burlingame, A. S., Bustelo, X. R., Cagney, G., Cantin, G. T., Cardasis, H. L., Celis, J. E., Chaerkady, R., Chu, F., Cole, P. A., Costello, C. E., Cotter, R. J., Crockett, D., DeLany, J. P., De, M., DeSouza, L. V., Deutsch, E. W., Dransfield, E., Drewes, G., Droit, A., Dunn, M. J., Elenitoba-Johnson, K., Ewing, R. M., Van, E. y. k., Faca, V., Falkner, J., Fang, X., Fenselau, C., Figeys, D., Gagne, P., Gelfi, C., Gevaert, K., Gimble, J. M., Gnad, F., Goel, R., Gromov, P., Hanash, S. M., Hancock, W. S., Harsha, H. C., Hart, G., Hays, F., He, F., Hebbar, P., Helsens, K., Hermeking, H., Hide, W., Hjerno, K., Hochstrasser, D. F., Hofmann, O., Horn, D. M., Hruban, R. H., Ibarrola, N., James, P., Jensen, O. N., Jensen, P. H., Jung, P., Kandasamy, K., Kheterpal, I., Kikuno, R. F., Korf, U., Korner, R., Kuster, B., Kwon, M. S., Lee, H. J., Lee, Y. J., Lefevre, M., Lehvaslaiho, M., Lescuyer, P., Levander, F., Lim, M. S., Lobke, C., Loo, J. A., Mann, M., Martens, L., Martinez-Heredia, J., McComb, M., McRedmond, J., Mehrle, A., Menon, R., Miller, C. A., Mischak, H., Mohan, S. S., Mohmood, R., Molina, H., Moran, M. F., Morgan, J. D., Moritz, R., Morzel, M., Muddiman, D. C., Nalli, A., Navarro, J. D., Neubert, T. A., Ohara, O., Oliva, R., Omenn, G. S., Oyama, M., Paik, Y. K., Pennington, K., Pepperkok, R., Periaswamy, B., Petricoin, E. F., Poirier, G. G., Prasad, T. S., Purvine, S. O., Rahiman, B. A., Ramachandran, P., Ramachandra, Y. L., Rice, R. H., Rick, J., Ronnholm, R. H., Salonen, J., Sanchez, J. C., Sayd, T., Seshi, B., Shankari, K., Sheng, S. J., Shetty, V., Shivakumar, K., Simpson, R. J., Sirdeshmukh, R., Siu, K. W., Smith, J. C., Smith, R. D., States, D. J., Sugano, S., Sullivan, M., Superti-Furga, G., Takatalo, M., Thongboonkerd, V., Trinidad, J. C., Uhlen, M., Vandekerckhove, J., Vasilescu, J., Veenstra, T. D., Vidal-Taboada, J. M., Vihinen, M., Wait, R., Wang, X., Wiemann, S., Wu, B., Xu, T., Yates, J. R., Zhong, J., Zhou, M., Zhu, Y., Zurbig, P. and Pandey, A.  Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 2008.  26, 164-167. [PubMed]
122. Chaerkady, R. and Pandey, A.  Quantitative proteomics for identification of cancer biomarkers. Proteomics. Clinical Applications. 2007.  1, 1080-1089. [PubMed]
123. 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. 2007.  6, 1592-1599. [PubMed]
124. 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 of the United States of America. 2007.  104, 13461-13466. [PubMed]
125. 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 of the United States of America. 2007.  104, 2199-2204. [PubMed]
126. Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R., Tattikota, S. G. and Pandey, A.  A curated compendium of phosphorylation motifs. Nature Biotechnology. 2007.  25, 285-286. [PubMed]
127. Wang, Z., Pandey, A. and Hart, G. W.  Dynamic interplay between O-linked N-acetylglucosaminylation and glycogen synthase kinase-3-dependent phosphorylation. Molecular & Cellular Proteomics. 2007.  6, 1365-1379. [PubMed]
128. Kim, J. W., Monila, H., Pandey, A. and Lane, M. D.  Upstream stimulatory factors regulate the C/EBP alpha gene during differentiation of 3T3-L1 preadipocytes. Biochemical and Biophysical Research Communications. 2007.  354, 517-521. [PubMed]
129. Mathivanan, S., Periaswamy, B., Gandhi, T. K., 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. 2006.  7 Suppl 5, S19. [PubMed]
130. Gandhi, T. K., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periaswamy, 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. 2006.  38, 285-293. [PubMed]
131. Qiao, Y., Molina, H., Pandey, A., Zhang, J. and Cole, P. A.  Chemical rescue of a mutant enzyme in living cells. Science. 2006.  311, 1293-1297. [PubMed]
132. 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 of the United States of America. 2006.  103, 9773-9778. [PubMed]
133. 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. 2006.  3, 429-438. [PubMed]
134. 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. 2006.  78, 3681-3687. [PubMed]
135. 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. 2006.  40, 336-341. [PubMed]
136. Hyland, E. M., Cosgrove, M. S., Molina, H., Wang, D., Pandey, A., Cottee, 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. 2005.  25, 10060-10070. [PubMed]
137. Liu, B., Molina, H., Kalume, D., Pandey, A., Griffith, J. D. and Englund, P. T.  Role of p38 in replication of Trypanosoma brucei kinetoplast DNA. Molecular and Cellular Biology. 2006.  26, 5382-5393. [PubMed]b
138. 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.  Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Molecular & Cellular Proteomics. 2006.  5, 157-171. [PubMed]
139. Mishra, G. R., Suresh, M., Kumaran, K., Kannabiran, N., Suresh, S., Bala, P., Shivakumar, K., Anuradha, N., Reddy, R., Raghavan, T. M., Menon, S., Hanumanthu, G., Gupta, M., Upendran, S., Gupta, S., Mahesh, M., Jacob, B., Mathew, P., Chatterjee, P., Arun, K. S., Sharma, S., Chandrika, K. N., Deshpande, N., Palvankar, K., Raghavnath, R., Krishnakanth, R., Karathia, H., Rekha, B., Nayak, R., Vishnupriya, G., Kumar, H. G., Nagini, M., Kumar, G. S., Jose, R., Deepthi, P., Mohan, S. S., Gandhi, T. K., Harsha, H. C., Deshpande, K. S., Sarker, M., Prasad, T. S. and Pandey, A.  Human protein reference database--2006 update. Nucleic Acids Research. 2006.  34, D411-4. [PubMed]
140. 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. 2005.  23, 951-959. [PubMed]
141. 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. 2005.  4, 1661-1671. [PubMed]
142. Kalume, D. E., Peri, S., Reddy, R., Zhong, J., Okulate, M., Kumar, N. and Pandey, A.  Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics. 2005.  6, 128. [PubMed]
143. Muthusamy, B., Hanumanthu, G., Suresh, S., Rekha, B., Srinivas, D., Karthick, L., Vrushabendra, B. M., Sharma, S., Mishra, G., Chatterjee, P., Mangala, K. S., Shivashankar, H. N., Chandrika, K. N., Deshpande, N., Suresh, M., Kannabiran, N., Niranjan, V., Nalli, A., Prasad, T. S., Arun, K. S., Reddy, R., Chandran, S., Jadhav, T., Julie, D., Mahesh, M., John, S. L., Palvankar, K., Sudhir, D., Bala, P., Rashmi, N. S., Vishnupriya, G., Dhar, K., Reshma, S., Chaerkady, R., Gandhi, T. K., Harsha, H. C., Mohan, S. S., Deshpande, K. S., Sarker, M. and Pandey, A.  Plasma Proteome Database as a resource for proteomics research. Proteomics. 2005.  5, 3531-3536. [PubMed]
144. 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. 2005.  5, 3226-3245. [PubMed]
145. Ping, P., Vondriska, T. M., Creighton, C. J., Gandhi, T. K., Yang, Z., Menon, R., Kwon, M. S., Cho, S. Y., Drwal, G., Kellmann, M., Peri, S., Suresh, S., Gronborg, M., Molina, H., Chaerkady, R., Rekha, B., Shet, A. S., Gerszten, R. E., Wu, H., Raftery, M., Wasinger, V., Schulz-Knappe, P., Hanash, S. M., Paik, Y. K., Hancock, W. S., States, D. J., Omenn, G. S. and Pandey, A.  A functional annotation of subproteomes in human plasma. Proteomics. 2005.  5, 3506-3519. [PubMed]
146. Harsha, H. C., Suresh, S., Amanchy, R., Deshpande, N., Shanker, K., Yatish, A. J., Muthusamy, B., Vrushabendra, B. M., Rashmi, B. P., Chandrika, K. N., Padma, N., Sharma, S., Badano, J. L., Ramya, M. A., Shivashankar, H. N., Peri, S., Choudhury, D. R., Kavitha, M. P., Saravana, R., Niranjan, V., Gandhi, T. K., Ghosh, N., Chandran, S., Menezes, M., Joy, M., Mohan, S. S., Katsanis, N., Deshpande, K. S., Raghothama, C., Prasad, C. K. and Pandey, A.  A manually curated functional annotation of the human X chromosome. Nature Genetics. 2005.  37, 331-332. [PubMed]
147. Tang, Q. Q., Gronborg, 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 3beta is required for adipogenesis. Proceedings of the National Academy of Sciences of the United States of America. 2005.  102, 9766-9771. [PubMed]
148. Molina, H., Bunkenborg, J., Reddy, G. H., Muthusamy, B., Scheel, P. J. and Pandey, A.  A proteomic analysis of human hemodialysis fluid. Molecular & Cellular Proteomics : MCP. 2005.  4, 637-650. [PubMed]
149. Raghothama, C., Harsha, H. C., Prasad, C. K. and Pandey, A.  Bioinformatics and proteomics approaches for aging research. Biogerontology. 2005.  6, 227-232. [PubMed]
150. Bala, P., Georgantas, R. W., Sudhir, D., Suresh, M., Shanker, K., Vrushabendra, B. M., Civin, C. I. and Pandey, A.  TAGmapper: a web-based tool for mapping SAGE tags. Gene. 2005.  364, 123-129. [PubMed]
151. Suresh, S., Sujatha, M., Mishra, G., Hanumanthu, G. R., Suresh, M., Reddy, R. and Pandey, A.  Proteomic resources: integrating biomedical information in humans. Gene. 2005.  364, 13-18. [PubMed]
152. 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. 2005.  77, 2739-2744. [PubMed]
153. Gandhi, T. K., Chandran, S., Peri, S., Saravana, R., Amanchy, R., Prasad, T. S. and Pandey, A.  A bioinformatics analysis of protein tyrosine phosphatases in humans. DNA Research. 2005.  12, 79-89. [PubMed]
154. 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. 2005.  5, 3765-3777. [PubMed]
155. 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 posttranslational modifications. Science's STKE. 2005.  2005, pl2. [PubMed]
156. 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.  Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Molecular & Cellular Proteomics. 2006.  5, 157-171. [PubMed]
157. Gronborg, 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. 2004.  3, 1042-1055. [PubMed]
158. Hustinx, S. R., Cao, D., Maitra, A., Sato, N., Martin, S. T., 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 & Therapy. 2004.  3, 1254-1261. [PubMed]
159. 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 & Therapy. 2004.  3, 1081-1090. [PubMed]
160. 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.  Mac-2-binding protein is a diagnostic marker for biliary tract carcinoma. Cancer. 2004.  101, 1609-1615. [PubMed]
161. Kristiansen, T. Z., Nielsen, M. M., Blagoev, B., Pandey, A. and Mann, M.  Mouse embryonic fibroblasts derived from Odin deficient mice display a hyperproliiferative phenotype. DNA Research. 2004.  11, 285-292. [PubMed]
162. 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 & Cellular Proteomics. 2004.  3, 715-728. [PubMed]
163. 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 of the United States of America. 2004.  101, 9309-9314. [PubMed]
164. Navarro, J. D., Talreja, N., Peri, S., Vrushabendra, B. M., Rashmi, B. P., Padma, N., Surendranath, V., 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. 2004.  5, 43. [PubMed]
165. Navarro, J. D. and Pandey, A. Unraveling the human interactome: Lessons from the yeast. Drug Discovery Today: Targets. 2004. 3, 79-84.
166. Ibarrola, N., Molina, H., Iwahori, A. and Pandey, A.  A novel proteomic approach for specific identification of tyrosine kinase substrates using [13C]tyrosine. The Journal of Biological Chemistry. 2004.  279, 15805-15813. [PubMed]
167. 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. 2004.  5, 2. [PubMed]
168. 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. 2004.  6, 1-6. [PubMed]
169. 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. 2004.  13, 469-482. [PubMed]
170. Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von, M., 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., 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's molecular interaction format--a community standard for the representation of protein interaction data. Nature Biotechnology. 2004.  22, 177-183. [PubMed]
171. Peri, S., Navarro, J. D., Kristiansen, T. Z., Amanchy, R., Surendranath, V., Muthusamy, B., Gandhi, T. K., 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. 2004.  32, D497-501. [PubMed]
172. 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. 2003.  75, 6043-6049. [PubMed]
173. Raghothama, C. and Pandey, A.  Absolute systems biology--measuring dynamics of protein modifications. Trends in Biotechnology. 2003.  21, 467-470. [PubMed]
174. Peri, S., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T. K., 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., 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. 2003.  13, 2363-2371. [PubMed]
175. Kalume, D. E., Molina, H. and Pandey, A.  Tackling the phosphoproteome: tools and strategies. Current Opinion in Chemical Biology. 2003.  7, 64-69. [PubMed]
176. Steen, H., Fernandez, M., Ghaffari, S., Pandey, A. and Mann, M.  Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanning. Molecular & Cellular Proteomics. 2003.  2, 138-145. [PubMed]
177. Navarro, J. D., Niranjan, V., Peri, S., Jonnalagadda, C. K. and Pandey, A.  From biological databases to platforms for biomedical discovery. Trends in Biotechnology. 2003.  21, 263-268. [PubMed]
178. Pandey, A., Peri, S., Thacker, C., Whipple, C. A., Collins, J. J. and Mann, M.  Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome. Bioinformatics. 2003.  19, 169-172. [PubMed]
179. Deshpande, K. S., Harsha, H. C. and Pandey, A. Microarrays and mass spectrometry: The future of proteomics. Current Genomics. 2003. 4, 605-613.
180. Pandey, A., Blagoev, B., Kratchmarova, I., Fernandez, M., Nielsen, M., Kristiansen, T. Z., Ohara, O., Podtelejnikov, A. V., Roche, S., Lodish, H. F. and Mann, M.  Cloning of a novel phosphotyrosine binding domain containing molecule, Odin, involved in signaling by receptor tyrosine kinases. Oncogene. 2002.  21, 8029-8036. [PubMed]
181. Gronborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. S., 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 & Cellular Proteomics. 2002.  1, 517-527. [PubMed]
182. 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. 2002.  7, 388-391. [PubMed]
183. 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. Biochemical characterization of its oligomeric nature. The Journal of Biological Chemistry. 2002.  277, 42011-42016. [PubMed]
184. Steen, H. and Pandey, A.  Proteomics goes quantitative: measuring protein abundance. Trends in Biotechnology. 2002.  20, 361-364. [PubMed]
185. 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 & Cellular Proteomics. 2002.  1, 376-386. [PubMed]
186. Deshpande, N. and Pandey, A. Mining gene expression data for functional annotation of genomes. Trends in Biotechnology. 2002. 20, 282.
187. Shankar, S. H. N. and Pandey, A. A novel mode of activating the JAK-STAT signaling pathway. Trends in Biochemical Sciences. 2002. 27, 336.
188. Kristiansen, T. Z. and Pandey, A.  Resources for full-length cDNAs. Trends in Biochemical Sciences. 2002.  27, 266-267. [PubMed]
189. 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 transforming growth factor-beta and affects protein kinase cascades. The Journal of Biological Chemistry. 2002.  277, 27367-27377. [PubMed]
190. 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. 2002.  30, 2906-2910. [PubMed]
191. Pandey, A., Dan, I., Kristiansen, T. Z., Watanabe, N. M., Voldby, J., Kajikawa, E., Khosravi-Far, R., Blagoev, B. and Mann, M.  Cloning and characterization of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain. Oncogene. 2002.  21, 3939-3948. [PubMed]
192. Mann, M., Ong, S. E., Gronborg, M., Steen, H., Jensen, O. N. and Pandey, A.  Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends in Biotechnology. 2002.  20, 261-268. [PubMed]
193. 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 & Cellular Proteomics. 2002.  1, 213-222. [PubMed]
194. 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. The Journal of Biological Chemistry. 2002.  277, 19131-19138. [PubMed]
195. 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. The Journal of Biological Chemistry. 2002.  277, 5929-5939. [PubMed]
196. 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. 2002.  284, 161-168. [PubMed]
197. Peri, S. and Pandey, A.  A reassessment of the translation initiation codon in vertebrates. Trends in Genetics. 2001.  17, 685-687. [PubMed]
198. Blagoev, B. and Pandey, A.  Microarrays go live--new prospects for proteomics. Trends in Biochemical Sciences. 2001.  26, 639-641. [PubMed]
199. Peri, S., Steen, H. and Pandey, A.  GPMAW--a software tool for analyzing proteins and peptides. Trends in Biochemical Sciences. 2001.  26, 687-689. [PubMed]
200. Mann, M., Hendrickson, R. C. and Pandey, A.  Analysis of proteins and proteomes by mass spectrometry. Annual Review of Biochemistry. 2001.  70, 437-473. [PubMed]
201. Peri, S., Ibarrola, N., Blagoev, B., Mann, M. and Pandey, A.  Common pitfalls in bioinformatics-based analyses: look before you leap. Trends in Genetics. 2001.  17, 541-545. [PubMed]
202. Ong, S. E. and Pandey, A.  An evaluation of the use of two-dimensional gel electrophoresis in proteomics. Biomolecular Engineering. 2001.  18, 195-205. [PubMed]
203. Mann, M. and Pandey, A.  Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. Trends in Biochemical Sciences. 2001.  26, 54-61. [PubMed]
204. 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. 2001.  262, 267-273. [PubMed]
205. Pandey, A., Fernandez, M. M., Steen, H., Blagoev, B., Nielsen, M. M., Roche, S., Mann, M. and Lodish, H. F.  Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways. The Journal of Biological Chemistry. 2000.  275, 38633-38639. [PubMed]
206. Pandey, A. and Mann, M.  Proteomics to study genes and genomes. Nature. 2000.  405, 837-846. [PubMed]
207. Pandey, A., Andersen, J. S. and Mann, M.  Use of mass spectrometry to study signaling pathways. Science's STKE. 2000.  2000, pl1. [PubMed]
208. 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. 2000.  1, 59-64. [PubMed]
209. 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 of the United States of America. 2000.  97, 179-184. [PubMed]
210. Pandey, A., Fernandez, M. M., Steen, H., Blagoev, B., Nielsen, M. M., Roche, S., Mann, M. and Lodish, H. F.  Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways. The Journal of Biological Chemistry. 2000.  275, 38633-38639. [PubMed]

 
Book Chapters:
Sarker, M., Hanumanthu, G. and Pandey, A. Plasma Proteome Database. In: Proteomics of human body fluids, Thongboonkerd, V. Editor. Humana Press, Totowa, New Jersey, USA. 2007. Part 1. pp 129-136.
Grønborg, M., Maitra, A. and Pandey, A. Proteomics of human pancreatic juice. In: Proteomics of human body fluids, Thongboonkerd, V. Editor. Humana Press, Totowa, New Jersey, USA. 2007. Part 1. pp 377-397.
Kristiansen, T. Z., Maitra, A. and Pandey, A. Proteomics of human bile. In: Proteomics of human body fluids, Thongboonkerd, V. Editor. Humana Press, Totowa, New Jersey, USA. 2007. Part 1.pp 399-414.
Fernandez, L. E. M., Gronborg, M. and Pandey, A. Proteomic strategies for identification of posttranslational modifications. In: Functional Proteomics: Principles and Practical Applications, Ping, P. and Hanash, S. Eds., Humana Press, Totowa, N.J. 2005.
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.
Steen, H. and Pandey, A. Proteomics: A molecular scanner in medicine. In: Encyclopedia of the Human Genome. Volume 4. Cooper, D.N., Editor. John Wiley & Sons, Ltd., Chichester. 2003. pp 879-883.
Steen, H. and Pandey, A. Mass Spectrometry in Protein Characterization. In: Encyclopedia of the Human Genome. Volume 3. Cooper, D.N., Editor. John Wiley & Sons, Ltd., Chichester. 2003. pp 841-844.
Muthusamy, B., Thomas, J. K., Prasad, T. S. K. and Pandey, A. Access guide to Human Proteinpedia. In: Current Protocols in Bioinformatics. Volume 3. 2013. pp 1.21.1-1.21.15.
Harsha, H. C., Pinto, S. M. and Pandey, A. Proteomic strategies to characterize signaling pathways. In: Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology Volume 1007. Matthiesen, R., Editor. Humana Press. 2013. pp 359-377
 
Grant Support:
Project Title Role Funding Agency Sanction Number Sanction Date
Networks and pathways of lysine modification Principal Investigator National Institute of Health, Maryland, USA U54RR020839 2004-2009
Human plasma proteome database (PPD) Principal Investigator Human Proteome Organisation, Montreal, Canada 2005
Proteomic and functional analysis of fibroblasts in breast cancer Principal Investigator Department of Defense, USA 2006-2011
Proteomic characterization of neural differentiation in human embryonic stem cells Principal Investigator Maryland Stem Cell Research Fund, USA 2007-2009
Targeting EGFR and KRAS mutations Principal Investigator National Cancer Institute, National Institute of Health, Maryland, USA P01-129243 NIH/NCI 2007-2012
Program Support on neuroproteomics Co-PI Department of Biotechnology, Government of India BT/01/COE/08/05 2008
DBT multi-institutional research grant: Identification of genes involved in X-linked mental retardation Co-PI Department of Biotechnology, Government of India BT/PR/10345/MED/30/79/2007 2008-2011
DBT multi-institutional coordinated research grant: Establishment of national database on tuberculosis (TB) Co-PI Department of Biotechnology, Government of India BT/PR10485/BID/07/242/2008 2008
Proteomic profiling of squamous cell carcinoma of esophagus Co-PI Department of Biotechnology, Government of India BT/PR12640/MED/30/202|2009 2010-2012

 
 
My CV:   Download
 
Education 
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M.D. in Medicine, Armed Forces Medical College, Pune, India, 1984-1988
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Ph.D. in Pathology, University of Michigan, Ann Arbor, USA, 1990-1995
Honors and Awards
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2006, Era of Hope Scholar Award, Department of Defense
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2004, Beckman Young Investigator Award
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2003, Sidney Kimmel Foundation Scholar
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1997, Howard Temin Award, National Cancer Institute
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1997, Howard Hughes Medical Institute Physician Postdoctoral Fellowship (Declined)
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1996, Experimental Pathologist-in-training Award, American Society for Investigative Pathology
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1988, Second Place overall in Medical School Class
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1986, First in Forensic Medicine, University of Pune
Member
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Editorial Board Member - Molecular and Cellular Proteomics, Proteomics, Clinical Proteomics, Journal of Proteome Research, DNA Research, Journal of Translational Medicine
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Past Editorial Board member - Genome Research and BMC Bioinformatics
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Associate Editor - Journal of Proteomics
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Reviewer - Nature, Science, Cell, Nature Genetics, Nature Biotechnology, Nature Chemical Biology, Science Translational Medicine, Molecular Cell, PNAS, Genome Biology, Journal of Biological Chemistry, Molecular and Cellular Proteomics, Proteomics, Journal of Proteome Research, Analytical Chemistry, Bioinformatics
Type of Neoplasms
Breast
Female
Gastrointestinal tract
Esophagus, Stomach, Pancreas
Hepatobiliary system
Bile ducts, Gallbladder, Liver
  Last modified on : Jul 7, 2013
India Cancer Research Database has been developed by the Institute of Bioinformatics with funding from the Department of Biotechnology, Government of India.