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PUBLICATIONS
     
  Following is a partial list of relevant publications by the Founder and Director and/or the staff at the Institute of Bioinformatics from 2002 onward.

 
 

Total number of publications - 210

 
   
 201420132012201120102009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002
   
 

2014 (Number of publications - 35)

 
 
Kim, M. S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., Thomas, J. K., Muthusamy, B., Leal-Rojas, P., Kumar, P., Sahasrabuddhe, N. A., Balakrishnan, L., Advani, J., George, B., Renuse, S., Selvan, L. D. N., Patil, A. H., Nanjappa, V., Radhakrishnan, A., Prasad, S., Subbannayya, T., Raju, R., Kumar, M., Sreenivasamurthy, S. K., Marimuthu, A., Sathe, G. J., Chavan, S., Datta, K. K., Subbannayya, Y., Sahu, A., Yelamanchi, S. D., Jayaram, S., Rajagopalan, P., Sharma, J., Murthy, K. R., Syed, N., Goel, R., Khan, A. A., Ahmad, S., Dey, G., Mudgal, K., Chatterjee, A., Huang, T. C., Zhong, J., Wu, X., Shaw, P. G., Freed, D., Zahari, M. S., Mukherjee, K. K., Shankar, S., Mahadevan, A., Lam, H., Mitchell, C. J., Shankar, S. K., Satishchandra, P., Schroeder, J. T., Sirdeshmukh, R., Maitra, A., Leach, S. D., Drake, C. G., Halushka, M. K., Prasad, T. S. K., Hruban, R. H., Kerr, C. L., Bader, G. D., Iacobuzio-Donahue, C. A., Gowda, H. and Pandey, A. (2014). A draft map of the human proteome. Nature. 509, 575-581.  [PubMed]

 
 
Wu, X., Renuse, S., Sahasrabuddhe, N. A., Zahari, M. S., Chaerkady, R., Kim, M. S., Nirujogi, R. S., Mohseni, M., Kumar, P., Raju, R., Zhong, J., Yang, J., Neiswinger, J., Jeong, J. S., Newman, R., Powers, M. A., Somani, B. L., Gabrielson, E., Sukumar, S., Stearns, V., Qian, J., Zhu, H., Vogelstein, B., Park, B. H. and Pandey, A. (2014). Activation of diverse signaling pathways by oncogenic PIK3CA mutations. Nature Communications. In press.
 
 
 
Kim, M. S., Zhong, Y., Yachida, S., Rajeshkumar, N. V., Abel, M., Marimuthu, A., Mudgal, K., Hruban, R. H., Tyner, J. W., Maitra, A., Iacobuzio-Donahue, C. A. and Pandey, A. (2014). Heterogeneity of pancreatic cancer metastases in a single patient revealed by quantitative proteomics.  Molecular and Cellular Proteomics.  [PubMed]

 
 
Kelkar, D. S., Provost. E., Chaerkady, R., Muthusamy, B., Manda, S. S., Subbannayya, T., Selvan, L. D. N., Wang, C. H., Datta, K. K., Woo, S., Dwivedi, S. B., Renuse, S., Getnet, D., Huang, T. C., Kim, M. S., Pinto, S. M., Mitchell, C. J., Madugundu, A. K., Kumar, P., Sharma, J. Advani, J., Dey, G., Balakrishnan, L., Syed, N., Nanjappa, V., Subbannayya, Y., Goel, R., Prasad, T. S. K., Bafna, V., Sirdeshmukh, R., Gowda, H., Wang, C., Leach, S. D. and Pandey, A. (2014). Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Molecular and Cellular Proteomics. [PubMed]

 
 
Renuse, S., Madugundu, A. K., Kumar, P., Nair, B., Gowda, H., Prasad, T. S. K., and Pandey, A. (2014). Proteomic analysis and genome annotation of Pichia pastoris, a recombinant protein expression host. Proteomics.  In Press

 
 
Syed, N., Chavan, S., Sahasrabuddhe, N. A., Renuse, S., Sathe, G., Nanjappa, V., Radhakrishnan, A., Raja, R., Pinto, S. M., Srinivasan, A., Prasad, T. S. K., Srikumar, K., Gowda, H., Santosh, V., Sidransky, D., Califano, J. A., Pandey, A and Chatterjee, A. (2014). Silencing of high-mobility group box 2 (HMGB2) modulates cisplatin and 5-fluorouracil sensitivity in head and neck squamous cell carcinoma. Proteomics.  In Press

 
 
Sahu, A., Kumar, S., Sreenivasamurthy, S. K., Selvan, L. D. N., Madugundu, A. K., Yelamanchi, S. D., Puttamallesh, V. N., Dey, G., Anil, A. K., Srinivasan, A., Mukherjee, K. K., Gowda, H., Satishchandra, P., Mahadevan, A., Pandey, A., Prasad, T. S. K. and Shankar, S. K. (2014). Host response profile of human brain proteome in toxoplasma encephalitis co-infected with HIV. Clinical Proteomics.  In Press

 
 
Subbannayya, Y., Syed, N., Barbhuiya, M. A., Raja, R., Marimuthu, A., Sahasrabuddhe, N. A., Pinto, S. M., Manda, S. S., Renuse, S., Manju, H. C., Zameer, M. A. L., Sharma, J., Brait, M., Srikumar, K., Roa, J. C., Vijaya Kumar, M., Veerendra Kumar, K. V., Prasad, T. S. K., Ramaswamy, G., Kumar, R. V., Pandey, A., Gowda, H., Chatterjee, A. (2014). Calcium calmodulin dependent kinase kinase 2 - a novel therapeutic target for gastric adenocarcinoma. Cancer Biology and Therapy. In Press. 

 
 
Wu, X., Zahari, M. S., Renuse, S., Sakamuri, S., Singal, M., Gabrielson, E., Sukumar, S. and Pandey, A. (2014). A breast cancer cell microarray (CMA) as a rapid method to characterize candidate biomarkers.  Cancer Biology and Therapy. In Press  

 
 
Huang, T. C., Renuse, S., Pinto, S., Kumar, P., Yang, Y., Chaerkady, R., Godsey, B., Mendell, J. T., Halushka, M. K., Civin, C. I., Marchionni, L. and Pandey, A. (2014). Identification of miR-145 targets through an integrated omics analysis. Molecular Biosystems. In Press  

 
 
Khan, A. A., Sandhya, V. K., Singh, P., Parthasarathy, D., Kumar, A., Advani, J., Gattu, R., Ranjit, D. V., Vaidyanathan, R., Mathur, P. P., Prasad, T. S. K., Gabhann, F. M., Pandey, A., Raju, R. and Gowda, H. (2014). Signaling network map of endothelial TEK tyrosine kinase.   Journal of Signal Transduction. In Press  

 
 
Sahasrabuddhe, N. A., Huang, T. C., Ahmad, S., Kim, M. S., Yang, Y., Ghosh, B., Leach, S. D., Gowda, H., Somani, B. L., Chaerkady, R. and Pandey, A. (2014). Regulation of PPAR-alpha pathway by Dicer revealed through Proteomic analysis. Journal of Proteomics. 108, 306-315.  [PubMed]

 
 
Nanjappa, V., Thomas, J. K., Marimuthu, A., Muthusamy, B., Radhakrishnan, A., Sharma, R., Khan, A. A., Balakrishnan, L., Sahasrabuddhe, N., Kumar, S., Jhaveri, B. N., Sheth, K. V., Khatana, R. K., Shaw, P. G., Srikanth, S. M., Mathur, P. P., Shankar, S., Nagaraja, D., Christopher, R., Mathivanan, S., Raju, R., Sirdeshmukh, R., Chatterjee, A., Simpson, R. J., Harsha, H. C., Pandey, A. and Prasad, T. S. K. (2014). Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic Acids Research. 42, D959-D965. [PubMed]

 
 
Thomas, J. K., Kim, M. S., Balakrishnan, L., Nanjappa, V., Raju, R., Marimuthu, A., Radhakrishnan, A., Muthusamy, B., Khan, A. A., Sakamuri, S., Tankala, S. G., Singal, M., Nair, B., Sirdeshmukh, R., Chatterjee, A., Prasad, T. S. K., Maitra, A., Gowda, H., Hruban, R. H. and Pandey, A. (2014). Pancreatic Cancer Database: An integrative resource for pancreatic cancer. Cancer Biology and Therapy. 15, 8. [PubMed]

 
 
Jayaram, S., Gupta, M. K., Polisetty, R. V., Cho, W. C. and Sirdeshmukh, R. (2014). Towards developing biomarkers for Glioblastoma Multiforme: a proteomics view. Expert Review of Proteomics [PubMed]

 
 
Marimuthu, A., Huang, T. C., Selvan, L. D. N., Renuse, S., Nirujogi, R. S., Kumar, P., Rajagopalan, S., Pandey, A., Harsha, H. C. and Chatterjee, A. (2014). Identification of targets of miR-200b by a SILAC-based quantitative proteomic approach. EuPA Open Proteomics. 4, 10-17. [PubMed]

 
 
Pawar, H., Renuse, S., Khobragade, S. N., Chavan, S., Sathe, G., Kumar, P., Mahale, K. N., Gore, K., Kulkarni, A., Dixit, T., Raju, R., Prasad, T. S. K., Harsha, H. C., Patole, M. S. and Pandey, A. (2014). Neglected tropical diseases and omics science: Proteogenomics analysis of the promastigote stage of Leishmania major parasite. OMICS: A Journal of Integrative Biology. 18, 499-512. [PubMed]

 
 
Manda, S. S., Nirujogi, R. S., Pinto, S., Kim, M. S., Datta, K. K., Sirdeshmukh, R., Prasad, T. S. K., Thongboonkerd, V., Pandey, A. and Gowda, H. (2014). Identification and characterization of proteins encoded by chromosome 12 as part of Chromosome-centric Human Proteome Project. Journal of Proteome Research. 13, 3166-3177. [PubMed]

 
 
Gupta, M. K., Jayaram, S., Madugundu, A. K., Chavan, S., Advani, J., Pandey, A., Thongboonkerd, V., Sirdeshmukh, R. (2014). Chromosome-Centric Human Proteome Project: Deciphering Proteins Associated with Glioma and Neurodegenerative Disorders on Chromosome 12. Journal of Proteome Research. 13, 3178-3190. [PubMed]

 
 
Pinto, S. M., Manda, S. S., Kim, M. S., Taylor, K., Selvan, L. D. N., Balakrishnan, L., Subbannayya, T., Yan, F., Prasad, T. S. K., Gowda, H., Lee, C., Hancock, W. S. and Pandey, A. (2014). Functional annotation of proteome encoded by human chromosome 22. Journal of Proteome Research. 13, 2749-2760. [PubMed]

 
 
Gowda, H., Ivanisevic, J., Johnson, C. H., Kurczy, M. E., Benton, H. P., Rinehart, D., Nguyen, T., Ray, J., Kuehl, J., Arevalo, B., Westenskow, P. D., Wang, J., Arkin, A. P., Deutschbauer, A. M., Patti, G. J. and Siuzdak, G. (2014). Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses. Analytical Chemistry.  86, 6931-6939. [PubMed]

 
 
Kagohara, L. T., Schussel, J., Subbannayya, T., Sahasrabuddhe, N., Lebron, C., Brait, M., Maldonado, L., Valle, V. B., Pirini, F., Jahuira, M., Lopez, J., Letelier, P., Brebi-Mieville, P., Ili, C., Pandey, A., Chatterjee, A., Sidransky, D. and Guerrero-Preston, R. (2014). Global and gene-specific DNA methylation pattern discriminates cholecystitis from gallbladder cancer patients in Chile. Future Oncology. [PubMed]

 
 
Soni, B. L., Marimuthu, A., Pawar, H., Sawant, S. S., Borges, A., Kannan, R., Pandey, A., Ingle, A. D., Harsha, H. C., Vaidya, M. M.(2014). Quantitative proteomic analysis of different stages of rat lingual carcinogenesis. Clinical Communications Oncology. 1, 2. [PubMed]

 
 
Murthy, K. R., Goel, R., Subbannayya, Y., Jacob, H. K. C., Murthy, P. R., Srikanth, S. M., Patil, A. H., Sharma, R., Sahasrabuddhe, N. A., Parashar, A., Nair, B. G., Krishna V., Prasad, T. S. K., Gowda, H. and Pandey, A. (2014). Proteomic analysis of human vitreous humor. Clinical Proteomics. 11, 29. [PubMed]

 
 
Dwivedi, S. B., Muthusamy, B., Kumar, P., Kim, M. S., Nirujogi, R. S., Getnet, D., Ahiakonu, P., Dey, G., Nair, B., Gowda, H., Prasad, T. S. K., Kumar, N., Pandey, A. and Okulate, M. (2014). Brain proteomics of Anopheles gambiae. OMICS: A Journal of Integrative Biology. 18, 421-37. [PubMed]

 
 
Raju, R., Palappetta, S. M., Sandhya, V. K., Sahu, A., Alipoor, A., Balakrishnan, L., Advani, J., George, B., Kini, K. R., Prashanth, G. N., Prakash, H. S., Prasad, T. S. K., Chang, Y., Chen, L., Pandey, A. and Gowda, H. (2014).  A network map of FGF-1/FGFR signaling system. Journal of Signal Transduction. 8, 165-170.[PubMed]

 
 
Sahasrabuddhe, N. A., Barbhuiya, M. A., Bhunia, S., Subbannayya, T., Gowda, H., Advani, J., Shrivastav, B. R., Navani, S., Leal, P., Roa, J. C., Chaerkady, R., Gupta, S., Chatterjee, A., Pandey, A. and Tiwari, P. K. (2014). Identification of Prosaposin and Transgelin as potential biomarkers for gallbladder cancer using quantitative proteomics. Biochemical and Biophysical Research Communications. 446, 863-869.  [PubMed]

 
 
Subbannayya, Y., Anuja, K., Advani, J., Ojha, U. K., Nanjappa, V., George, B., Sonawane, A., Kumar, R. V., Ramaswamy, G., Pandey, A., Somani, B. L. and Raju, R. (2014). A network map of the Gastrin signaling pathway. Journal of Cell Communication and Signaling. 8, 165-170. [PubMed]

 
 
Zhong, J., Sharma, J., Raju, R., Palapetta, S. M., Prasad, T. S. K., Huang, T. C., Yoda, A.,  Tyner, J. W., van Bodegom, D., Weinstock, D. M., Ziegler, S. F. and Pandey, A. (2014). TSLP signaling pathway map: A platform for analysis of TSLP mediated signaling. Database. bau007. [PubMed]

 
 
Balakrishnan, L., Nirujogi, R. S., Ahmad, S., Bhattacharjee, M.,  Srikanth, S. M., Renuse, S., Kelkar, D. S., Subbannayya, Y.,  Raju, R.,  Goel, R., Thomas, J. K., Kaur, N., Dhillon, M., Tankala, S. G., Jois, R., Vasudev, V., Ramachandra, Y. L., Sahasrabuddhe, N. A., Prasad, T. S. K., Mohan, S., Gowda, H., Shankar, S. and Pandey, A. (2014). Proteomic analysis of human osteoarthritis synovial fluid. Clinical Proteomics. 11, 6. [PubMed]

 
 
Selvan, L. D. N., Kaviyil, J. E., Nirujogi, R. S., Muthusamy, B., Puttamallesh, V. N., Subbannayya, T., Syed, N., Radhakrishnan, A., Kelkar, D. S., Ahmad, S., Pinto, S. M., Kumar, P., Madugundu, A. K., Nair, B., Chatterjee, A., Pandey, A., Ravikumar, R., Gowda, H. and Prasad, T. S. K. (2014). Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry. Clinical Proteomics. 11, 5. [PubMed]

 
 
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. (2014). Phosphoproteome of Cryptococcus neoformans. Journal of Proteomics. 97, 287-295. [PubMed]

 
Nirujogi, R. S., Pawar, H., Renuse, S., Kumar, P., Chavan, S., Sathe, G. J., Sharma, J., Khobragade, S., Pande, J., Modak, B., Prasad, T. S. K., Harsha, H. C., Patole, M. S. and Pandey, A. (2014). Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani. Journal of Proteomics. 97, 48-61. [PubMed]

 
Balakrishnan, L., Bhattacharjee, M., Ahmad, S., Nirujogi, R. S., Renuse, S., Subbannayya, Y., Marimuthu, A., Srikanth, S. M., Raju, R., Dhillon, M., Kaur, N., Jois, R., Vasudev, V., Ramachandra, Y. L., Sahasrabuddhe, N. A., Prasad, T. S. K., Mohan, S., Gowda, H., Shankar, S. and Pandey, A. (2014). Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients. Clinical Proteomics. 11, 1. [PubMed]

 
 
Ramadasan-Nair, R., Gayathri, N., Mishra, S., Sunitha, B., Mythri, R., Nalini, A., Subbannayya, Y., Harsha, H. C., Kolthur-Seetharam, U. and Bharath, M. M. (2014). Mitochondrial alterations and oxidative stress in an acute transient mouse model of muscle degeneration: Implications for muscular dystrophy and related muscle pathologies. Journal of Biological Chemistry. 289, 485-509. [PubMed]

 
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2013 (Number of publications - 24)

 
     
 
Varghese A. M., Sharma A., Mishra P., Vijayalakshmi K., Harsha H. C., Sathyaprabha T. N., Bharath S. M., Nalini A., Alladi P. A., Raju T. R. (2013). Chitotriosidase - a putative biomarker for sporadic amyotrophic lateral sclerosis. Clinical Proteomics. 10, 19. [PubMed]

 
Puttamallesh, V. N., Sreenivasamurthy, S. K., Singh, P. K., Harsha, H. C., Ganjiwale, A., Broor, S., Pandey, A., Narayana, J. and Prasad, T. S. K. (2013). Proteomic profiling of serum samples from chikungunya infected patients provides insights into host response. Clinical Proteomics. 10, 14. [PubMed]

 
Bhattacharjee, M., Sharma, R., Goel, R., Balakrishnan, L., Renuse, S., Advani, J.,  Shantal, T. G., Verma, R., Pinto, S. M., Nirujogi, R. S., Nair, B., Prasad, T. S. K., Harsha, H. C., Jois, R., Shankar, S. and Pandey, A. (2013). A Multilectin affinity approach for  comparative glycoprotein profiling of rheumatoid arthritis and spondyloarthropathy. Clinical Proteomics. 10, 11. [PubMed]

 
Goel, R., Murthy, K., Srikanth, S. M., Pinto, S. M., Bhattacharjee, M., Kelkar, D. S., Madugundu, A. K., Dey, G., Mohan, S. S., Krishna, V., Prasad, T. S. K., Chakravarti, S., Harsha, H. C. and Pandey, A. (2013). Characterizing the normal proteome of human ciliary body. Clinical Proteomics. 10, 9. [PubMed] 

 
Prasad, T. S. K., Verma, R., Kumar, S., Nirujogi, R. S., Sathe, G. J., Madugundu, A. K., Sharma, J., Puttamallesh, V. N., Ganjiwale, A., Myneedu, V. P., Chatterjee, A., Pandey, A., Harsha, H. C. and Narayana, J. (2013). Proteomic analysis of purified protein derivative of Mycobacterium tuberculosis. Clinical Proteomics. 10, 8. [PubMed]

 
Sreenivasamurthy, S. K., Dey, G., Ramu, M., Kumar, M., Gupta, M. K., Mohanty, A. K., Harsha, H. C., Sharma, P., Kumar, N., Pandey, A., Kumar, A. and Prasad, T. S. K. (2013). A compendium of molecules involved in vector-pathogen interactions pertaining to malaria. Malaria Journal. 12, 216. [PubMed]

 
Hansen, A. M., Chaerkady, R., Sharma, J., Díaz-Mejía, J. J., Tyagi, N., Renuse, S., Jacob, H. K. C., Pinto, S. M., Sahasrabuddhe, N. A., Kim, M. S., Delange, B., Srinivasan, N., Emili, A., Kaper, J. and Pandey, A. (2013). The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathogens. 9, e1003403. [PubMed]

 
Chaerkady, R., Shao, H., Scott, S. G., Pandey, A., Jun A. S. and Chakravarti, S. (2013). The keratoconus corneal proteome: loss of epithelial integrity and stromal degeneration. Journal of Proteomics. 87, 122-131. [PubMed]

 
Ambekar, S. A., Nirujogi, R. S., Srikanth, S. M., Chavan, S., Kelkar, D. S., Hinduja, I., Zaveri, K., Prasad, T. S. K., Harsha, H. C., Pandey, A. and Mukherjee, S. (2013). Proteomic analysis of human follicular fluid: A new perspective towards understanding folliculogenesis. Journal of Proteomics. 87, 68-77. [PubMed]

 
Polisetty, R. V., Gautam, P., Gupta, M. K., Sharma, R., Uppin, M. S., Challa, S., Ankathi, P., Purohit, A. K., Renu, D., Harsha, H. C., Pandey, A. and Sirdeshmukh, R. (2013). Heterogeneous nuclear ribonucleoproteins and their interactors are a major class of deregulated proteins in anaplastic astrocytoma – a Grade III malignant glioma. Journal of Proteome Research. 12, 3128-3138. [PubMed]

 
Marimuthu, A., Chavan, S., Sathe, G. J., Sahasrabuddhe, N. A., Srikanth, S. M., Renuse, S., Ahmad, S., Radhakrishnan, A., Barbhuiya, M. A., Kumar, R. V., Harsha, H. C., Sidransky, D., Califano, J., Pandey, A. and Chatterjee, A. (2013). Identification of head and neck squamous cell carcinoma biomarker candidates through proteomic analysis of cancer cell secretome. BBA - Proteins and Proteomics. 1834, 2308-2316. [PubMed]

 

 

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. K. (2013). A network map of BDNF/TRKB and BDNF/p75NTR signaling system. Journal of Cell Communication and Signaling. 4, 301-307. [PubMed]

 
Subbannayya, T., Balakrishnan, L., Sudarshan, G., Advani, J., Kumar, S., Mahmood, R., Nair, B., Sirdeshmukh, R., Mukherjee, K. K., Umathe, S. N., Raju, R. and Prasad, T. S. K. (2013). An integrated map of corticotropin-releasing hormone signaling pathway. Journal of Cell Communication and Signaling. 4, 295-300. [PubMed]

 
Balakrishnan, L., Soman, S., Patil, Y. B., Advani, J., Thomas, J. K., Venkatesh, D. D., Urmila, K. K., Harsha, H. C., Prasad, T. S. K., Raju, R., Pandey, A., Dimitriadis, E., and Chatterjee, A. (2013). IL-11/IL11RA receptor mediated signaling: a web accessible knowledgebase. Cell Communication and Adhesion. 20, 81-86. [PubMed]

 
Venugopal, A. K., Kumar, G. S. S., Selvan, L. D. N., Mahadevan, A., Renuse, S., Kumar, P., Pawar, H., Sahasrabuddhe, N. A., Suja, M. S., Ramachandra, Y. L., Prasad, T. S. K., Madhusudhana, S. N., Harsha, H. C., Chaerkady, R., Satishchandra, P., Pandey, A. and Shankar, S. K. (2013). Quantitative proteomics for identifying biomarkers for Rabies. Clinical Proteomics. 10, 3. [PubMed]

 
 
Newman, R. H., Hu, J., Rho, H. S., Xie, Z., Woodard, C., Neiswinger, J., Cooper, C., Shirley, M., Clark, H. M., Hu, S., Hwang, W., Jeong, J. S., Wu, G., Lin, J., Gao, X., Ni, Q., Goel, R., Xia, S., Ji, H., Dalby, K. N., Birnbaum, M. J., Cole, P. A., Knapp, S., Ryazanov, A. G, Zack, D. J., Blackshaw, S., Pawson, T., Gingras, A. C., Desiderio, S., Pandey, A., Turk, B. E, Zhang, J., Zhu, H. and Qian, J. (2013). Construction of human activity-based phosphorylation networks. Molecular Systems Biology. 9, 655. [PubMed]

 
Harsha, H. C., Pinto, S. M. and Pandey, A. (2013). Proteomic strategies to characterize signaling pathways. Methods in Molecular Biology. 1007, 359-377. [PubMed]

 
 
Gupta, M. K., Polisetty, R. V., Ramamoorthy, K., Tiwary, S., Kaur, N., Shiras, A. and Sirdeshmukh, R. (2013). Secretome analysis of Glioblastoma cell line - HNGC-2. Molecular BioSystems. 9, 1390-1400. [PubMed]

 
 
Muthusamy, B., Thomas, J. K., Prasad, T. S. K. and Pandey, A. (2013). Access guide to Human Proteinpedia. Current Protocols in Bioinformatics. 41, 1.21.1-1.21.15. [PubMed]

 
 
Mushahary, D., Gautam, P., Sundaram, C. S. and Sirdeshmukh, R. (2013). Expanded protein expression profile of human placenta using two-dimensional gel electrophoresis. Placenta. 34, 193-196. [PubMed]

 
 
Kashyap, M. K., Pawar, H., Keerthikumar, S., Sharma, J., Goel, R., Mahmood, R., Vijaya Kumar, M., Veerendra Kumar, K. V., Pandey, A., Kumar, R. V., Prasad, T. S. K. and Harsha, H. C. (2013). Evaluation of protein expression pattern of stanniocalcin 2, insulin-like growth factor-binding protein 7, inhibin beta A and four and a half LIM domains 1 in esophageal squamous cell carcinoma. Cancer Biomarkers. 12, 1-9. [PubMed]

 
 
Huang, T. C., Pinto, S. M. and Pandey, A. (2013). Proteomics for understanding microRNA biology. Proteomics. 13, 558-567. [PubMed]

 
 
Soman, S., Raju, R., Sandhya, V. K., Advani, J., Khan, A. A., Harsha, H. C., Prasad, T. S. K., Sudhakaran, P. R., Pandey, A. and Adishesha, P. K. (2013). A multicellular signal transduction network of AGE/RAGE signaling. Journal of Cell Communication and Signaling. 7, 19-23. [PubMed]

 
 
Pawar, H., Maharudraiah, J., Kashyap, M. K., Sharma, J., Srikanth, M. S., Choudhary, R., Chavan, S., Sathe, G. J., Manju, H .C., Veerendra Kumar, K. V., Vijayakumar, M., Sirdeshmukh, R., Harsha, H. C., Prasad, T. S. K., Pandey, A. and Kumar, R. V. (2013). Downregulation of cornulin in esophageal squamous cell carcinoma. Acta Histochemica. 115, 89-99. [PubMed]

 
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2012 (Number of publications -22)


 
 
Marimuthu, A., Subbannayya, Y., Sahasrabuddhe, N. A., Balakrishnan, L., Syed, N., Sekhar, N. R., Katte, T. V., Pinto, S. M., Srikanth, S. M., Kumar, P., Pawar, H., Kashyap, M. K., Maharudraiah, J., Ashktorab, H., Smoot, D. T., Ramaswamy, G., Kumar, R. V., Cheng, Y., Meltzer, S. J., Roa, J. C., Chaerkady, R., Prasad, T. S. K., Harsha, H. C., Chatterjee, A. and Pandey, A. (2012). SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics - Clinical Applications. 7, 355-366. [PubMed]

 
 
Dey, G., Radhakrishnan, A., Syed, N., Thomas, J. K., Nadig, A., Srikumar, K., Mathur, P. P., Pandey, A., Lin, S. K., Raju, R. and Prasad, T. S. K. (2012). Signaling network of Oncostatin M pathway. Journal of Cell Communication and Signaling. 7, 103-108. [PubMed]

 
 
Kumar, G. S. S., Venugopal, A. K., Mahadevan, A., Renuse, S., Harsha, H. C., Sahasrabuddhe, N. A., Pawar, H., Sharma, R., Kumar, P., Rajagopalan, S., Waddell, K., Ramachandra, Y. L., Satishchandra, P., Chaerkady, R., Prasad, T. S. K., Shankar, S. K. and Pandey, A. (2012). Quantitative proteomics for identifying biomarkers for tuberculous meningitis. Clinical Proteomics. 9, 12-24  [PubMed]

 
 
Kumar, G. S. S., Venugopal, A. K., Kashyap, M. K., Raju, R., Marimuthu, A., Palapetta, S. M., Subbannayya, Y., Goel, R., Chawla, A., Dikshit, J. B., Tata, P., Harsha, H. C., Maharudraiah, J., Ramachandra, Y. L., Satishchandra, P., Prasad, T. S. K., Pandey, A., Mahadevan, A. and Shankar, S. K. (2012). Gene expression profiling of tuberculous meningitis co-infected with HIV. Journal of Proteomics and Bioinformatics. 5, 235-244.  [PubMed]

 
 
Gautam, P., Nair, S. C., Gupta, M. K., Sharma, R., Polisetty, R. V., Uppin, M. S., Challa, S., Puligopu, A. K., Ankathi, P., Purohit, A. K., Chandak, G. R., Harsha, H. C. and Sirdeshmukh, R. (2012). Proteins with altered levels in plasma from glioblastoma patients as revealed by iTRAQ-based quantitative proteomic analysis. PLOS ONE. 7, e46153. [PubMed]

 
 
Telikicherla, D., Marimuthu, A., Kashyap, M. K., Ramachandra, Y. L., Mohan, S., Roa, J. C., Maharudraiah, J., and Pandey, A. (2012). Overexpression of Ribosome Binding Protein 1 (RRBP1) in breast cancer. Clinical Proteomics. 2012, 9, 7. [PubMed]

 
 
Bhattacharjee, M., Raju, R., Radhakrishnan, A., Nanjappa, V., Muthusamy, B., Singh, K., Kuppusaami, D., Lingala, B. T., Pan, A., Mathur, P. P., Harsha, H. C., Prasad, T. S. K., Atkins, G. J., Pandey, A. and Chatterjee, A. (2012). A bioinformatics resource for TWEAK-Fn14 signaling pathway. Journal of Signal Transduction. Article ID 376470. [PubMed]

 
 
Kalra, H., Simpson, R. J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V. C., Borràs, F. E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton, A., Cocucci, E., Falcon-Perez, J. M., Gabrielsson, S., Gho, Y. S., Gupta, D., Harsha, H. C., Hendrix, A., Hill, A. F., Inaal, J. M., Jenster, G., Kiang, L. S., Krämer-Albers, E-M., Llorente, A., Lötvall, J., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t Hoen, E. N. M., Pandey, A., Patel, T., Piper, M. G., Pluchino, S., Prasad, T. S. K., Rajendran, L., Raposo, G., Record, M., Reid, G. E., Sánchez-Madrid, F., Schiffelers, R. M., Siljander, P., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B. W. M., Vázquez, J., Vidal, M., Yáñez-Mó, M., Zoeller, M. and Mathivanan, S. (2012). Vesiclepedia: A compendium for extracellular vesicles with continuous community annotation. PLoS Biology. 10, e1001450. [PubMed]

 
 
Kim, M. S., Kuppireddy, S. V., Sakamuri, S., Singal, M., Getnet, D., Harsha, H. C., Goel, R., Balakrishnan, L., Jacob, H. K. C., Kashyap, M. K., Tankala, S. G., Maitra, A., Iacobuzio-Donahue, C. A., Jaffee, E., Goggins, M. G., Velculescu, V. E., Hruban, R. H. and Pandey, A. (2012). Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs). Journal of Proteome Research. 11, 5556-5563. [PubMed]

 
 
Renuse, S., Harsha, H. C., Kumar, P., Acharya, P. K., Sharma, J., Goel, R., Kumar, G. S. S., Raju, R., Prasad, T. S. K., Slotta, T. and Pandey, A. (2012). Proteomic analysis of an unsequenced plant - Mangifera indica. Journal of Proteomics. 75, 5793-5796. [PubMed]

 
 
 
 
Telikicherla, D., Maharudraiah, J., Pawar, H., Marimuthu, A., Kashyap, M. K., Ramachandra, Y. L., Roa, J. C. and Pandey, A. (2012). Overexpression of Kinesin Associated Protein 3 (KIFAP3) in Breast Cancer. Journal of Proteomics and Bioinformatics. 5, 122-126. [PubMed]

 
 
Martinez-Ferrando, I., Chaerkady, R., Zhong, J., Molina, H., Kishore, H., Herbst-Robinson, K., Dancy, B. M., Katju, V., Bose, R., Zhang, J., Pandey, A. and Cole, P. A. (2012). Identification of targets of c-Src tyrosine kinase by chemical complementation and phosphoproteomics. Molecular and Cellular Proteomics. 11, 355-369. [PubMed]

 
 
Radhakrishnan, A., Raju, R., Tuladhar, N., Subbannayya, T., Thomas, J. K., Goel, R., Telikicherla, D., Palapetta, S. M., Rahiman, B. A., Venkatesh, D. D., Urmila, K. K., Harsha, H. C., Mathur, P. P., Prasad, T. S. K., Pandey, A., Shemanko, C. and Chatterjee, A. (2012). A pathway map of prolactin signaling. Journal of Cell Communication and Signaling. 6, 169-173. [PubMed]

 
 
 
 
 
Venugopal, A. K., Kumar, G. S. S., Mahadevan, A., Selvan, L. D. N., Marimuthu, A., Dikshit, J. B., Tata, P., Ramachandra, Y. L., Chaerkady, R., Sinha, S., Chandramouli, B. A., Arivazhagan, A., Satishchandra, P., Shankar, S. K. and Pandey, A. (2012). Transcriptomic profiling of medial temporal lobe epilepsy. Journal of Proteomics and Bioinformatics. 5, 31-39. [PubMed]

 
 
Agyeman, A. S., Chaerkady, R., Shaw, P. G., Davidson, N. E., Visvanathan, K., Pandey, A. and Kensler, T. W. (2012). Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane treated human breast epithelial cells reveals common expression profiles. Breast Cancer Research and Treatment. 132, 175-187. [PubMed]

 
 
Zhong, J., Kim, M. S., Chaerkady, R., Wu, X., Huang, T. C., Getnet, D., Mitchell, C. J., Palapetta, S. M., Sharma, J., O'Meally, R. N., Cole, R. N., Yoda, A., Moritz, A., Loriaux, M. M., Rush, J., Weinstock, D. M., Tyner, J. W. and Pandey, A. (2012). TSLP signaling network revealed by SILAC-based phosphoproteomics. Molecular and Cellular Proteomics. 11, M112.017764. [PubMed]

 
 
Huang, T. C., Sahasrabuddhe, N. A., Kim, M. S., Getnet, D., Yang, Y., Peterson, J. M., Ghosh, B., Chaerkady, R., Leach, S. D., Marchionni, L., Wong, G. W. and Pandey A. (2012). Regulation of lipid metabolism by Dicer revealed through SILAC Mice. Journal of Proteome Research. 11, 2193-2205. [PubMed]

 
 
Polisetty, R. V., Gautam, P., Sharma, R., Harsha, H. C., Nair, S. C., Gupta, M. K., Uppin, M. S., Challa, S., Puligopu, A. K., Ankathi, P., Purohit, A. K., Chandak, G. R., Pandey, A. and Sirdeshmukh, R. (2012). LC-MS/MS analysis of differentially expressed glioblastoma membrane proteome reveals altered calcium signalling and other protein groups of regulatory functions. Molecular and Cellular Proteomics. 11, M111.013565. [PubMed]

 
 
Nagaraj, S. H., Harsha, H. C., Reverter, A., Colgrave, M. L., Sharma, R., Andronicos, N., Hunt, P., Menzies, M., Lees, M. S., Sekhar, N. R., Pandey, A. and Ingham, A. (2012). Proteomic analysis of the abomasal mucosal response following infection by the nematode, Haemonchus contortus, in genetically resistant and susceptible sheep. Journal of Proteomics. 75, 2141-2152. [PubMed]

 
 
Prasad, T. S. K., Harsha, H. C., Keerthikumar, S., Sekhar, N. R., Selvan, L. D. N., Kumar, P., Pinto, S. M., Muthusamy, B., Subbannayya, Y., Renuse, S., Chaerkady, R., Mathur, P. P., Ravikumar, R. and Pandey, A. (2012). Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry. Journal of Proteome Research. 11, 247-260. [PubMed]

 
 
Goel, R., Harsha, H. C., Pandey, A. and Prasad, T. S. K. (2012). Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Molecular Biosystems. 8, 453-463. [PubMed]

 
 
Pawar, H., Sahasrabuddhe, N. A., Renuse, S., Keerthikumar, S., Sharma, J., Kumar, G. S. S., Venugopal, A., Sekhar, N. R., Kelkar, D. S., Nemade, H., Khobragade, S. N., Muthusamy, B., Kandasamy, K., Harsha, H. C., Chaerkady, R., Patole, M. S. and Pandey, A. (2012). A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani. Proteomics. 12, 832-844. [PubMed]

 
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2011 (Number of publications -22)

 
 
Goel, R., Raju, R., Maharudraiah, J., Kumar, G. S. S., Ghosh, K., Kumar, A., Lashmi, P. T., Sharma, J., Sharma, R., Balakrishnan, L., Pan, A., Kandasamy, K., Christopher, R., Krishna, V., Mohan, S. S., Harsha, H. C., Mathur, P. P., Pandey, A. and Prasad, T. S. K. (2011). A signaling network of thyroid-stimulating hormone. Journal of Proteomics and Bioinformatics. 4, 238-241. [PubMed]

 
 
Barbhuiya, M. A., Sahasrabuddhe, N. A., Pinto, S. M., Muthusamy, B., Singh, T. D., Nanjappa, V., Keerthikumar, S., Delanghe, B., Harsha, H. C., Chaerkady, R., Jalaj, V., Gupta, S., Shrivastav, B. R., Tiwari, P. K. and Pandey, A. (2011). Comprehensive proteomic analysis of human bile. Proteomics. 11, 4443- 4453. [PubMed]

 
 
Kinsinger, C. R., Apffel, J., Baker, M., Bian, X., Borchers, C. H., Bradshaw, R. A., 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. L., Slotta, D., Smith, R. D., Stein, S. E., Tabb, D. L., Tagle, D., Yates, J. R. 3rd. and Rodriguez, H. (2011). Recommendations for mass apectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Molecular and Cellular Proteomics. 10, O111.015446. [PubMed]

 
 
Telikicherla, D., Ambekar, A., Palapetta, S. M., Dwivedi, S. B., Raju, R., Sharma, J., Prasad, T. S. K., Ramachandra, Y. L., Mohan, S. S., Maharudraiah, J., Mukherjee, S. and Pandey, A. (2011). A comprehensive curated resource for Follicle Stimulating Hormone signaling. BMC Research Notes. 4, 408. [PubMed]

 
 
Kelkar, D. S., Kumar, D., Kumar, P., Balakrishnan, L., Muthusamy, B., Yadav, A. K., Shrivastava, P., Marimuthu, A., Anand, S., Sundaram, H., Kingsbury, R., Harsha, H. C., Nair, B., Prasad, T. S. K., Chauhan, D. S., Katoch, K., Katoch, V. M., Kumar, P., Chaerkady, R., Ramachandran, S., Dash D. and Pandey, A. (2011). Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Molecular and Cellular Proteomics. 10, M111.011627. [PubMed]

 
 
Raju, R., Nanjappa, V., Balakrishnan, L., Radhakrishnan, A., Thomas, J. K., Sharma, J., Tian, M., Palapetta, S. M., Subbannayya, T., Sekhar, N. R., Muthusamy, B., Goel, R., Subbannayya, Y., Telikicherla, D., Bhattacharjee, M., Pinto, S., Syed, N., Srikanth, M. S., Sathe, G. J., Ahmad, S., Chavan, S. N., Kumar, G. S. S., Marimuthu, A., Prasad, T. S. K., Harsha, H. C., Rahiman, B. A., Ohara, O., Bader, G. D., Mohan, S. S., Schiemann, W. P. and Pandey, A. (2011). NetSlim: High-confidence curated signaling maps. Database. 2011, bar032. [PubMed]

 
 
Nanjappa, V., Raju, R., Muthusamy, B., Sharma, J., Thomas, J. K., Nidhina, P. A. H., Harsha, H. C., Pandey, A., Anilkumar G. and Prasad, T. S. K. (2011). A comprehensive curated reaction map of leptin signaling pathway. Journal of Proteomics and Bioinformatics. 4, 184-189. [PubMed]

 
 
Chaerkady, R., Kelkar, D. S., Muthusamy, B., Kandasamy, K., Dwivedi, S. B., Sahasrabuddhe, N. A., Kim, M-S., Renuse, S., Pinto, S. M., Sharma, R., Pawar, H., Sekhar, N. R., Mohanty, A. K., Getnet, D., Yang, Y., Zhong, J., Dash, A. P., MacCallum, R. M., Delanghe, B., Mlambo, G., Kumar, A., Prasad, T. S. K., Okulate, M., Kumar, N. and Pandey, A. (2011). A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Research. 21, 1872-1881. [PubMed]

 
 
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. (2011). Quantitative temporal proteomic analysis of human embryonic stem cell differentiation into oligodendrocyte progenitor cells. Proteomics. 11, 4007-4020. [PubMed]

 
 
Raju, R., Balakrishnan, L., Nanjappa, V., Bhattacharjee, M., Getnet, D., Muthusamy, B., Thomas, J. K., Sharma, J., Rahiman, B. A., Harsha, H. C., Shankar, S., Prasad, T. S. K., Mohan, S. S., Bader, G. D., Wani, M. R. and Pandey, A. (2011). A comprehensive manually curated reaction map of RANKL/RANK signaling pathway. Database. 2110, bar021. [PubMed]

 
 
Pawar, H., Kashyap, M. K., Sahasrabuddhe, N. A., Renuse, S., Harsha, H. C., Kumar, P., Sharma, J., Kandasamy, K., Marimuthu, A., Nair, B., Rajagopalan, S., Maharudraiah, J., Premalatha, C. S., Veerendra Kumar, K. V., Vijayakumar, M., Chaerkady, R., Prasad, T. S. K., Kumar, R. V. and Pandey, A. (2011). Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biology and Therapy. 12, 510-522. [PubMed]

 
 
Shao, H., Chaerkady, R., Chen, S., Pinto, S. M., Sharma, R., Delanghe, B., Birk, D., Pandey, A. and Chakravarti, S. (2011). Proteome profiling of wild type and lumican-deficient mouse corneas. Journal of Proteomics. 74, 1895-1905. [PubMed]

 
 
Kim, M. S., Zhong, J., Kandasamy, K., Delanghe, B. and Pandey, A (2011). Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides. Proteomics. 11, 2568-2572. [PubMed]

 
 
Marimuthu, A., O'Meally, R., Chaerkady, R., Subbannayya, Y., Nanjappa, V., Kumar, P., Kelkar, D., Pinto, S., Sharma, R., Renuse, S., Goel, R., Christopher, R., Delanghe, B., Cole, R. N., Harsha, H. C. and Pandey, A. (2011). A comprehensive map of the human urinary proteome. Journal of Proteome Research. 10, 2734-2743. [PubMed]

 
 
Shaw, P., Chaerkady, R., Zhang, Z., Davidson, N. and Pandey, A (2011). A monoclonal antibody cocktail as an enrichment tool for acetylome analysis. Analytical Chemistry.83, 3623-3626. [PubMed]

 
 
Kumar, G. S. S., Venugopal, A. K., Selvan, L. D. N., Marimuthu, A., Keerthikumar, S., Pathare, S., Dikshit, J. B., Tata, P., Hariharan, R., Prasad, T. S. K., Harsha, H. C., Ramachandra, Y. L., Mahadevan, A., Chaerkady, R., Shankar, S. K. and Pandey, A (2011). Gene expression profiling of tuberculous meningitis. Journal of Proteomics and Bioinformatics. 4, 98-105. [PubMed]

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

 
 
Prasad, T. S. K. and Chaerkady, R. (2011). 'Application of Quantitative Proteomic Approaches to Toxicology' In: Handbook of Systems Toxicology. Daniel A. Casciano and Saura C. Sahu Editors. John Wiley & Sons Limited. pp 217-226 .

 
 
Marimuthu, A., Jacob, H. K. C., Jakharia, A., Subbannayya, Y., Keerthikumar, S., Kashyap, M. K., Goel, R., Balakrishnan, L., Dwivedi, S., Pathare, S., Dikshit, J. B., Maharudraiah, J., Singh, S., Kumar, G. S. S., Vijayakumar, M., Veerendra Kumar, K. V., Premalatha, C. S., Tata, P., Hariharan, R., Roa, J. C., Prasad, T. S. K., Chaerkady, R., Kumar, R. V. and Pandey, A.. (2011). Gene expression profiling of gastric cancer. Journal of Proteomics and Bioinformatics. 4, 74-82. [PubMed]

 
 
Wang, Q., Chaerkady, R., Wu, J., Hwang, H., J., Papadopoulos, N., Kopelovich, L., Maitra, A., Matthei, H., Eshleman, J., Hruban, R., Kinzler, K. W., Pandey, A. and Vogelstein, B. (2011). Mutant proteins as cancer-specific biomarkers. Proceedings of the National Academy of Sciences U.S.A. 108, 2444-2449. [PubMed]

 
 
Renuse, S., Chaerkady, R. and Pandey, A. (2011). Proteogenomics. Proteomics. 11, 620-630. [PubMed]

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

 
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2010 (Number of publications -16)

 
 
Harsha, H. C. and Pandey, A. (2010). Phosphoproteomics in Cancer. Molecular Oncology. 4, 482-495. [PubMed]

 
 
Chen, H., Pimienta, G., Gu, Y., Sun, X., Hu, J., Kim, M. S., Chaerkady, R., Gucek, M., Cole, R. N., Sukumar, S. and Pandey, A. (2010). Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 10, 3800-3810. [PubMed]

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

 
 
Goel, R., Muthusamy, B., Pandey, A. and Prasad, T. S. K. (2010). Human Protein Reference Database and Human Proteinpedia as discovery resources for molecular biotechnology. Molecular Biotechnology. 48, 87-95. [PubMed]

 
 
Zhong, J., Krawczyk, S. A., Chaerkady, R., Huang, H., Goel, R., Bader, J. S., Wong, G. W., Corkey, B. E. and Pandey, A. (2010). Temporal profiling of the secretome during adipogenesis in humans. Journal of Proteome Research. 9, 5228-5238. [PubMed]

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

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

 
 
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. K., Mahmood, R., Chaerkady, R., Meltzer, S. J., Kumar, R. V., Rustgi, A. K. and Pandey, A. (2010). SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biology and Therapy. 10, 796-810. [PubMed]

 
 
Yang, Y., Chaerkady, R., Kandasamy, K., Huang, T. C., Selvan, L. D. N., Dwivedi, S. B., Kent, O. A., Mendell, J. T. and Pandey, A. (2010). Identifying targets of miR-143 using a SILAC-based proteomic approach. Molecular Biosystems. 6, 1873-1882 . [PubMed]

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

 
 
Hijikata, A., Raju, R., Keerthikumar, S., Ramabadran, S., Balakrishnan, L., Ramadoss, S. K., Pandey, A., Mohan, S. and Ohara, O. (2010). Mutation@A Glance: An integrative web application for analysing mutations from human genetic diseases. DNA Research. 17, 197-208. [PubMed]

 
 
Chaerkady, R., Kerr, C. L., Kandasamy, K., Marimuthu, A., Gearhart, J. D. and Pandey, A. (2010). Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics. 10, 1359-1373. [PubMed]

 
 
Kandasamy, K., Mohan, S. S., Raju, R., Keerthikumar, S., Kumar, G. S. 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. C., Zhong, J., Sekhar, R., Nanjappa, V., Balakrishnan, L., Subbaiah, R., Ramachandra, Y. L., Rahiman, B. A., Prasad, T. S. K., Lin, J., Houtman, J. C. D., Desiderio, S., Renauld, J., Constantinescu, S. N., Ohara, O., Hirano, T., Kubo, M., Singh, S., Khatri, P., Draghici, S., Bader, G. D., Sander, C., Leonard, W. J. and Pandey, A. (2010). NetPath: A public resource of curated signal transduction pathways. Genome Biology. 11, R3. [PubMed]

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

 
 
Zhou, Q., Chaerkady, R., Shaw, P. G., Kensler, T. W., Pandey, A. and Davidson, N. E. (2010). Screening for therapeutic targets of vorinostat by SILAC-based proteomic analysis in human breast cancer cells. Proteomics. 10, 1029-1039. [PubMed]

 
 
Luo, W., Zhong, J., Chang, R., Hu, H., Pandey, A. and Semenza, G. L. (2010). HSP70 and CHIP selectively mediate ubiquitination and degradation of hypoxia-inducible factor (HIF)-1α but not HIF-2α. Journal of Biological Chemistry. 285, 3651-3663. [PubMed]

 
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2009 (Number of publications -16)

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

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

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

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

 
 
Prasad, T. S. K., Kandasamy, K. and Pandey, A. (2009). 'Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology' In: Reverse Chemical Genetics: Methods and Protocols. Hisashi Koga, Editor. (Humana Press, Totowa, New Jersey, USA) Methods in Molecular Biology . 577, 67-79. [PubMed]

 
 
Venugopal, A., Chaerkady, R., Pandey, A. (2009). Application of mass spectrometry-based proteomics for biomarker discovery in neurological disorders. Annals of Indian Academy of Neurology. 12, 3-11. [PubMed]

 
 
Yang, Y., Chaerkady, R., Beer, M. A., Mendell, J. T. and Pandey, A. (2009). Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics. 9, 1374-1384. [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. (2009). A compendium of potential biomarkers of pancreatic cancer. PLoS Medicine. 6, e1000046. [PubMed]

 
 
Ranganathan, P., Harsha, H. C. and Pandey, A. (2009). 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. (2009). Temporal analysis of neural differentiation using quantitative proteomics. Journal of Proteome Research. 8, 1315-1326. [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. (2009). Temporal profiling of the adipocyte proteome during differentiation using a 5-plex SILAC based strategy. Journal of Proteome Research. 8, 48-58. [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. (2009). Malaria parasite invasion of the mosquito salivary gland requires interaction between the Plasmodium TRAP and the Anopheles Saglin proteins. PLoS Pathogens. 5, e1000265. [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. (2009). 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., Kumar, R.V. and Pandey, A. (2009). 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. (2009). RAPID: Resource of Asian Primary Immunodeficiency Diseases. Nucleic Acids Research. 37, D863-D867. [PubMed]

 
 
Kandasamy, K., Keerthikumar, S., Goel, R., Mathivanan, S., Patankar, N., Shafreen, B., Renuse, S., Pawar, H., Ramachandra, Y. L., Acharya, P. K., Ranganathan, P., Chaerkady, R., Prasad, T. S. K. and Pandey, A. (2009). Human Proteinpedia: A unified discovery resource for proteomics research. Nucleic Acids Research. 37, D773-D781. [PubMed]

 
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2008 (Number of publications -17)

 
 
Kristiansen, T. Z., Harsha, H. C., Grønborg, M., Maitra, A. and Pandey, A. (2008). Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma. Journal of Proteome Research. 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. (2008). 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. (2008). 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. (2008). Significant conservation of synthetic lethal genetic interaction networks between distantly-related eukaryotes. Proceedings of the National Academy of Sciences U.S.A. 105, 16653-16658. [PubMed]

 
 
Guha, U., Chaerkady, R., Marimuthu, A., Patterson, S., Kashyap, M., Harsha, H. C., Bader, J., Lash, A., Pandey, A. and Varmus, H. E. (2008). Comparisons of tyrosine-phosphorylated proteins in immortalized human bronchial epithelial cells and lung adenocarcinoma cell lines expressing lung cancer-specific alleles of EGFR and KRAS. Proceedings of the National Academy of Sciences 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. (2008). 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. (2008). 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. (2008). CK2 binds to the C-Terminus of NHE3 and stimulates NHE3 basal activity by phosphorylating a separate site in NHE3. Molecular Biology of the Cell. 19, 3859-3870. [PubMed]

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

 
 
Amanchy, R., Zhong, J., Molina, H., Chaerkady, R., Iwahori, A., Kalume, D. E., Grønborg, M., Joore, J., Cope, L. and Pandey, A. (2008). Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. Journal of Proteome Research. 7, 3900-3910. [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. (2008). 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. (2008). 18O labeling for a quantitative proteomic analysis of glycoproteins in hepatocellular carcinoma. Clinical Proteomics. 4, 137-155 [PubMed]

 
 
Molina, H., Matthiesen, R., Kandasamy, K. and Pandey, A. (2008). Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Analytical Chemistry. 80, 4825-4835. [PubMed]

 
 
Chaerkady, R. and Pandey, A. (2008). Applications of proteomics to lab diagnosis. Annual Review of Pathology: Mechanisms of Disease. 3, 485-498. [PubMed]

 
 
Basu, B., Desai, R., Balaji, J., Chaerkady, R., Sriram, V., Maiti, S. and Panicker, M. (2008). Serotonin in pre-implantation mouse embryos is localized to the mitochondria and can modulate mitochondrial potential. Reproduction. 135, 657-669. [PubMed]

 
 
Harsha, H. C., Molina, H. and Pandey, A. (2008). 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. (2008). Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-167. [PubMed]

 
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2007 (Number of publications - 6)

 
 
Chaerkady, R. and Pandey, A. (2007). Quantitative proteomics for identification of cancer biomarkers. Proteomics Clinical Applications. 1, 1080-1089. [PubMed]

 
 
Sarker, M., Hanumanthu, G. and Pandey, A. (2007). 'Plasma Proteome Database' in, Proteomics of human body fluids, pages 129-136 Thongboonkerd, V. Editor (Humana Press, Totowa, New Jersey, USA). [PubMed]

 
 
Okulate, M., Kalume, D. E., Chaerkady, R., Reddy, R., Kristiansen, K., Bhattacharyya, M., Pandey, A. and Kumar, N. (2007). Identification and molecular characterization of a novel protein Saglin as a target of monoclonal antibodies affecting salivary gland infectivity of Plasmodium sporozoites. Insect Molecular Biology. 16, 711-722. [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. (2007). Copy-number variants in patients with a strong family history of pancreatic cancer. Cancer Biology & Therapy. 6, 1-8. [PubMed]

 
 
Molina, H., Horn, D. M., Tang, N., Mathivanan, S. and Pandey, A. (2007). Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proceedings of the National Academy of Sciences, USA. 104, 2199-2204. [PubMed]

 
 
Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R., Tattikota, S. G. and Pandey, A. (2007). A compendium of curated phosphorylation-based substrate and binding motifs. Nature Biotechnology. 25, 285-286. [PubMed]

 
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2006 (Number of publications - 4)

 
 
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. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 3, 285-293. [PubMed]

 
 
Bose, R., Molina, H., Patterson, A. S., Bitok, J. K., Periaswamy, B., Bader, J. S., Pandey, A. and Cole, P. A. (2006). Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proceedings of the National Academy of Sciences, USA . 103, 9773-9778. [PubMed]

 
 
Mathivanan, S., Periaswamy, B., Gandhi, T. K. B., Kandasamy, K., Suresh, S., Mohmood, R., Ramachandra, Y. L. and Pandey, A. (2006). An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics. 7, S19. [PubMed]

 
 
Mishra, G., 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., Matthew, P., Chatterjee, P., Arun, K. S., Sharma, S., Chandrika, K. N., Deshpande, N., Palvankar, K., Raghavnath, R., Krishnakanth, K., Karathia, H., Rekha, B., Rashmi, N. S., Vishnupriya, G., Kumar, H. G. M., Nagini, M., Kumar, G. S. S., Jose, R., Deepthi, P., Mohan, S. S., Gandhi, T. K. B., Harsha, H. C., Deshpande, K. S., Sarker, M., Prasad, T. S. K. and Pandey, A. (2006). Human Protein Reference Database - 2006 update. Nucleic Acids Research. 34, D411-D414. [PubMed]

 
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2005 (Number of publications - 13)

 
 
Chaerkady, R., Harsha, H. C., Prasad, C. K. and Pandey, A. (2005). Bioinformatics and proteomics approaches for aging research. Biogerontology. 6, 227-232. [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. (2005). Biomarker discovery from pancreatic cancer secretome using a differential proteomics approach. Molecular and Cellular Proteomics. 5, 157-171. [PubMed]

 
 
Rhodes, D. R., Tomlins, S. A., Varambally, S., Mahavisno, V., Barrette, T., Kalyana-Sundaram, S., Ghosh, D., Pandey, A. and Chinnaiyan, A. M. (2005). Probabilistic model of the human protein-protein interaction network. Nature Biotechnology. 23, 951-959. [PubMed]

 
 
Haab, B. B., Geierstanger, B. H., Michailidis, G., Vitzthum, F., Forrester, S., Okon, R., Saviranta, P., Brinker, A., Sorette, M., Perlee, L., Suresh, S., Drwal, G., Adkins, J. N. and Omenn, G. S. (2005). Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: Systematic variation between sample types and calibration of mass spectrometry data. Proteomics. 5, 3278-3291. [PubMed]

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

 
 
Suresh, S., Mohan, S., Mishra, G., Hanumanthu, G., Suresh, M., Reddy, R. and Pandey, A. (2005). Proteomic resources: Integrating biomedical information in humans. Gene. 364, 13-18. [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. (2005). Plasma Proteome Database as a resource for proteomics research. Proteomics. 5, 3531-3536. [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., Grønborg, M., Molina, H., Chaerkady, R., Rekha, B., Muthusamy, B., Shet, A. S., Gerszten, R. E., Wu, H., Raftery, M., Wasinger, V., Schulz-Knappe, P., Hanash, S. M., Paik, Y. K., Hancock, W. S., States, D. J., Omenn, G. S. and Pandey, A. (2005). A functional annotation of subproteomes in human plasma. Proteomics. 5, 3506-3519. [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. (2005). A manually curated functional annotation of the human X chromosome. Nature Genetics. 37, 331-332. [PubMed]

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

 
 
Gandhi, T. K. B., Chandran, S., Peri, S., Saravana, R., Amanchy, R., Prasad, T. S. K and Pandey, A. (2005). 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. (2005). A proteomic analysis of salivary glands of female Anopheles gambiae mosquito. Proteomics. 5, 3765-3777. [PubMed]

 
 
Molina, H., Bunkenborg, J., Reddy, G. H., Muthusamy, B., Scheel, P. J. and Pandey, A. (2005). A proteomic analysis of human hemodialysis fluid. Molecular and Cellular Proteomics. 4, 637-650. [PubMed]

 
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2004 (Number of publications - 8)

 
 
Hustinx, S. R., Cao, D., Maitra, A., Sato, N., Martin, S., Sudhir, D., Iacobuzio-Donahue, C., Cameron, J. L., Yeo, C. J., Kern, S. E., Goggins, M., Mollenhauer, J., Pandey, A. and Hruban, R. H. (2004). Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression. Cancer Biology and Therapy, 3. 1254-1261. [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. (2004). Identification of novel highly expressed genes in pancreatic ductal adenocarcinomas through a bioinformatics analysis of expressed sequence tags. Cancer Biology and Therapy. 3, 1081-1089. [PubMed]

 
 
Rhodes, D. R., Yu, J., Shanker, K., Deshpande, N., Varambally, R, Ghosh, D., Barrette, T., Pandey, A. and Chinnaiyan, A. M. (2004). 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. (2004). 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.

 
 
Rhodes, D. R., Yu, J., Shanker, K., Deshpande, N., Varambally, R, Ghosh, D., Barrette, T., Pandey, A. and Chinnaiyan, A. M. (2004). Oncomine: A cancer microarray database and integrated data-mining platform. Neoplasia. 6, 1-6. [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. (2004). 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. (2004). Human Protein Reference Database as a discovery resource for proteomics. Nucleic Acids Research. 32, 497-501. [PubMed]

 
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2003 (Number of publications - 6)

 
 
Chaerkady, R. and Pandey, A. (2003). 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., Grønborg, 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., Poovaiah, K. M., Menezes, M., Choudhury, D. R., Suresh, S., Ghosh, N., Saravana, R., Chandran, S., Krishna, S., Joy, M., Anand, S. K., Madavan, V., Joseph, A., Wong, G. W., Schiemann, W. P., Constantinescu, S. N., Huang, L., Khosravi-Far, R., Steen, H., Tewari, M., Ghaffari, S., Blobe, G. C., Dang, C. V., Garcia, J. G. N., Pevsner, J., Jensen, O. N., Roepstorff, P., Deshpande, K. S., Chinnaiyan, A. M., Hamosh, A., Chakravarti, A. and Pandey, A. (2003). Development of Human Protein Reference Database as an initial platform for approaching systems biology in humans. Genome Research. 13, 2363-2371.[PubMed]

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

 
 
Navarro, J. D., Niranjan, V., Peri, S., Jonnalagadda, C. K. and Pandey, A. (2003). From biological databases to platforms for biomedical discovery. Trends in Biotechnology. 21, 263-268. [PubMed]

 
 
Pandey, A., Peri, S., Thacker, C., Whipple, C. A., Collins, J. J. and Mann, M. (2003). Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome. Bioinformatics. 19, 169-172. [PubMed]

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

 
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2002 (Number of publications - 21)

 
 
Pandey, A., Blagoev, B., Kratchmarova, I., Fernandez, M., Nielsen, M., Kristiansen, T., Ohara, O., Podtelejnikov, A., Roche, S., Lodish, H. and Mann, M. (2002). Cloning of a novel phosphotyrosine binding domain containing molecule, Odin, involved in signaling by receptor tyrosine kinases. Oncogene. 21, 8029-8036. [PubMed]

 
 
Anand, S. K. and Pandey, A. (2002). Screening large proteins for interaction partners. Trends in Biochemical Sciences. 27, 603. [PubMed]

 
 
Muthusamy, B. and Pandey, A. (2002). A roadmap of the mouse genome. Trends in Genetics. 18, 553. [PubMed]

 
 
Gandhi, T. K. B. and Pandey, A. (2002). Using bioinformatics to identify cis-regulatory sequences. Trends in Biotechnology. 20, 448. [PubMed]

 
 
Blagoev, B., Kratchmarova, I., Nielsen, M. M., Fernandez, M. M., Voldby, J., Andersen, J. S., Kristiansen, K., Pandey, A. and Mann, M. (2002). Inhibition of adipocyte differentiation by Resistin-like molecule alpha. Biochemical characterization of its oligomeric nature. Journal of Biological Chemistry. 277, 42011-42016. [PubMed]

 
 
Steen, H., Pandey, A., Andersen, J. S. and Mann, M. (2002). Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning method. Science STKE 2002(154):PL16. [PubMed]

 
 
Grønborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. A., Ohara, O., Mann, M., Jensen, O. N. and Pandey, A. (2002). A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: Identification of a novel protein, Frigg, as a protein kinase A substrate. Molecular and Cellular Proteomics. 1, 517-527. [PubMed]

 
 
Jebanathirajah, J. A., Peri, S. and Pandey, A. (2002). Toll and Interleukin-1 Receptor (TIR) domain-containing proteins in plants: a genomic perspective. Trends in Plant Science. 7, 388-391. [PubMed]

 
 
Steen, H. and Pandey, A. (2002). 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. (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Molecular and Cellular Proteomics. 1, 376-386. [PubMed]

 
 
Deshpande, N. and Pandey, A. (2002). Mining gene expression data for functional annotation of genomes. Trends in Biotechnology. 20, 282. [PubMed]

 
 
Shankar, S. H. N. and Pandey, A. (2002). A novel mode of activating the JAK-STAT signaling pathway. Trends in Biochemical Sciences. 27, 336. [PubMed]

 
 
Kristiansen, T. Z. and Pandey, A. (2002). 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. (2002). Context-specific effects of fibulin-5 (DANCE/ EVEC) on cell proliferation, motility, and invasion: Fibulin-5 is induced by TGF-beta and affects protein kinase cascades. Journal of Biological Chemistry. 277, 27367-27377. [PubMed]

 
 
Dan, I., Watanabe, N. M., Kajikawa, E., Ishida, T., Pandey, A. and Kusumi, A. (2002). Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution. Nucleic Acids Research. 30, 2906-2910. [PubMed]

 
 
Pandey, A., Dan, I., Kristiansen, T. Z., Watanabe, N. M., Voldby, J., Kajikawa, E., Khosravi-Far, R., Blagoev, B. and Mann, M. (2002). Cloning and characterisation of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain. Oncogene. 21, 3939-3948. [PubMed]

 
 
Mann, M., Ong, S. E., Grønborg, M., Steen, H., Jensen, O. N. and Pandey, A. (2002). Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends in Biotechnology. 20, 261-268. [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. (2002). A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes. Molecular and Cellular Proteomics. 1, 213-222. [PubMed]

 
 
Pandey, A., Ibarrola, N., Kratchmarova, I., Fernandez, M. M., Constantinescu, S. N, Ohara, O., Sawasdikosol, S., Lodish, H. F. and Mann, M. (2002). A novel Src homology 2 domain-containing molecule, Src-like adapter protein-2 (SLAP-2), which negatively regulates T cell receptor signaling. Journal of Biological Chemistry. 277, 19131-19138. [PubMed]

 
 
Dan, I., Ong, S. E., Watanabe, N. M., Blagoev, B., Nielsen, M. M., Kajikawa, E., Kristiansen, T. Z., Mann, M. and Pandey, A. (2002). Cloning of MASK, a novel member of the mammalian germinal center kinase-III subfamily, with apoptosis-inducing properties. Journal of Biological Chemistry. 277, 5929-5939. [PubMed]

 
 
Blagoev, B., Nielsen, M. M., Angrist, M., Chakravarti, A. and Pandey, A. (2002). Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene. Gene. 284, 161-168. [PubMed]

 
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