Research highlights
All publications
2023
- Mun, D. G., Budhraja, R., Bhat, A. F., Zenka, R. M., Johnson., K. L., Moghekar, A. and Pandey, A. (2023). Four-dimensional proteomics analysis of human cerebrospinal fluid using on a trapped ion mobility mass spectrometer using PASEF. Proteomics. 8;e2200507. [PubMed]
2022
George, I. A., Sathe, G., Ghose, V., Chougule, A., Chandrani, P., Patil, V., Noronha, V., Venkataramanan, R., Limaye, S., Pandey, A., Prabhash, K., Kumar, P. (2022). Integrated proteomics and phosphoproteomics revealed druggable kinases in neoadjuvant chemotherapy resistant tongue cancer. Frontiers in Cell and Developmental Biology. [PubMed]
Ramarajan, M. G., Saraswat, M., Budhraja, R., Garapati, K., Raymond, K. and Pandey, A. (2022). Mass spectrometric analysis of chondroitin sulfate-linked peptides. Journal of Proteins and Proteomics. 1-17. [PubMed]
Conboy, C. B., Yonkus, J. A., Buckarma, E. H., Mun, D. G., Werneburg, N. W., Watkins, R. D., Alva-Ruiz, R., Tomlinson, J. L., Guo, Y., Wang, J., O’Brien, D., McCabe, C. E., Jessen, E., Graham, R. P., Buijsman, R. C., Vu, D., de Man, J., Ilyas, S. I., Truty, M. J., Borad, M., Pandey, A., Gores, G. J., Smoot, R. L. (2022). LCK inhibition downregulates YAP activity and is therapeutic in patient-derived models of cholangiocarcinoma. Journal of Hepatology. S0168-8278(22)03121-X. [PubMed]
Rai, A., Yelamanchi, S. D., Radotra, B. D., Gupta, S. K., Mukherjee, K. K., Tripathi, M., Chhabra, R., Ahuja, C. K., Kumar, N., Pandey, A., Korbonits, M., Dutta, P. and Gaston-Massuet, C. (2022). Phosphorylation of β-catenin at Serine552 correlates with invasion and recurrence of non-functioning pituitary neuroendocrine tumours. Acta Neuropathologica Communications. 10(1):138. [PubMed]
Budhraja, R., Saraswat, M., De Graef, D., Ranatunga, W., Ramarajan, M. G., Mousa, J., Kozicz, T., Pandey, A., Morava, E. (2022). N-glycoproteomics reveals distinct glycosylation alterations in NGLY1-deficient patient-derived dermal fibroblasts. Journal of inherited metabolic disease. 8(28): eabn3326. [PubMed]
Muylle, E., Jiang, H., Johnsen, C., Byeon, S. K., Ranatunga, W., Garapati, K., Zenka, R. M., Preston, G., Pandey, A., Kozicz, T., Fang, F., Morava, E. (2022). TRIT1 defect leads to a recognizable phenotype of myoclonic epilepsy, speech delay, strabismus, progressive spasticity, and normal lactate levels. Journal of Inherited Metabolic Disease. [PubMed]
Wang, L., Lin, G., Zuo, Z., Li, Y., Byeon, S. K., Pandey, A., Bellen, H. J. (2022). Neuronal activity induces glucosylceramide that is secreted via exosomes for lysosomal degradation in glia. Science Advances. 8(28): eabn3326. [PubMed]
Vanderboom, P. M., Renuse, S., Maus, A. D., Madugundu, A. K., Kemp, J. V., Gurtner, K. M., Singh, R. J., Grebe, S. K., Pandey, A. and Dasari, S. (2022). Machine Learning-Based Fragment Selection Improves the Performance of Qualitative PRM Assays. Journal of Proteome Research. 21(8):2045-2054. [PubMed]
Byeon, S. K., Madugundu, A. K., Garapati, K., Ramarajan, M. G., Saraswat, M., Kumar, M. P., Hughes, T., Shah, R., Patnaik, M. M., Chia, N., Ashrafzadeh-Kian, S., Yao, J. D., Pritt, B. S., Cattaneo, R., Salama, M. E., Zenka, R. M., Kipp, B. R., Grebe, S. K. G., Singh, R. J., Sadighi Akha, A. A., Algeciras-Schimnich, A., Dasari, S., Olson, J. E., Walsh, J. R., Venkatakrishnan, A. J., Jenkinson, G., O’Horo, J. C., Badley, A. D., and Pandey, A. (2022). Development of a multi-omics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study. The Lancet Digital Health. [PubMed]
Saraswat, M., Garapati, K., Kim, J., Budhraja, R. and Pandey, A. (2022). Proteomic alterations in extracellular vesicles induced by oncogenic PIK3CA mutations. Proteomics. 11; e2200077. [PubMed]
Renuse, R., Benson, L., Vanderboom, P. M., Ruchi, F. N. U., Yadav, Y. R., Johnson, K., Brown, B. M., Peterson, J. A., Basu, R., McCormick, D. J., Pandey, A. and Basu, A. (2022). 13C15N – Glucagon-based novel isotope dilution mass spectrometry method for measurement of glucagon metabolism in human. Clinical Proteomics. 19:16. [PubMed]
Mangalaparthi, K. K., Chavan, S., Madugundu, A. K., Renuse, S., Vanderboom, P. M., Maus, A. D., Kemp, J., Kipp, B. R., Grebe, S. K., Singh, R. J., Pandey, A. (2022). Correction: A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples. Clinical Proteomics. [PubMed]
Saraswat, M., Mangalaparthi, K. K., Garapati, K. and Pandey, A. (2022). TMT-Based multiplexed quantitation of N-Glycopeptides reveals glycoproteome remodeling induced by oncogenic mutations. ACS Omega. 7, 11023. [PubMed]
Parthasarathi, K. T. S., Mandal, S., Singh, S., Gundimeda, S., Jolly, M. K., Pandey, A. and Sharma, J. (2022). In silico analysis of ion channels and their correlation with epithelial to mesenchymal transition in breast cancer. Cancers. 14(6), 1444. [PubMed]
Munjal, N. S., Sapra, D., Parthasarathi, K. T. S., Goyal, A., Pandey, A., Banerjee, M. and Sharma, J. (2022). Deciphering the Interactions of SARS-CoV-2 Proteins with Human Ion Channels Using Machine-Learning-Based Methods. Pathogens 11(2), 259. [PubMed]
Jain, A., Sambath, J., Sathe, G., George, I. A., Pandey, A., Thompson, E. W. and Kumar, P. (2022). Pan-cancer quantitation of epithelial-mesenchymal transition dynamics using parallel reaction monitoring-based targeted proteomics approach. Journal of Translational Medicine. 11;20(1):84. [PubMed]
Maus, A., Renuse, S., Kemp, J., Madugundu, A. K., Vanderboom, P. M., Blommel, J., Jerde, C., Dasari, S., Kipp, B. R., Singh, R. J., Grebe, S. K. and Pandey, A. (2022). Targeted detection of SARS-CoV-2 nucleocapsid sequence variants by mass spectrometric analysis of tryptic peptides. Journal of Proteome Research. [PubMed]
Maus, A., Renuse, S., Kemp, J., Moehnke, K., Mangalaparthi, K. K., Chavan, S., Madugundu, A. K., Vanderboom, P. M., Dasari, S., Kipp, B. R., Singh, R. J., Grebe, S. K. and Pandey, A. (2022). Comparison of anti-peptide and anti-protein antibody-based purification techniques for detection of SARS-CoV-2 by targeted LC-MS/MS. Advances in Sample Preparation. 2; 100018. [Article]
2021
Byeon, S. K., Madugundu, A. K., and Pandey, A. (2021). Automated data-driven mass spectrometry for improved analysis of lipids with dual dissociation techniques. Journal of mass spectrometry and advances in the clinical lab. 22, 43–49. [PubMed]
Rowan, D. J., Mangalaparthi, K. K., Singh, S., Moreira, R. K., Mounajjed, T., Lamps, L., Westerhoff, M., Cheng, J., Bellizzi, A. M., Allende, D. S., Pandey, A., and Graham, R. P. (2021). Metallothionein immunohistochemistry has high sensitivity and specificity for detection of Wilson disease. Modern pathology : an official journal of the United States and Canadian Academy of Pathology. [PubMed]
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Singh, S., Bhat, M. Y., Sathe, G., Gopal, C., Sharma, J., Madugundu, A. K., Joshi, N. S., and Pandey, A. (2021). Proteomic signatures of diffuse and intestinal subtypes of Gastric Cancer. Cancers. 13, 5930. [PubMed]
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Nakao, Y., Fukushima, M., Mauer, A. S., Liao, C. Y., Ferris, A., Dasgupta, D., Heppelmann, C. J., Vanderboom, P. M., Saraswat, M., Pandey, A., Nair, K. S., Allen, A. M., Nakao, K., and Malhi, H. (2021). A comparative proteomic analysis of extracellular vesicles associated with lipotoxicity. Frontiers in cell and developmental biology. 9. [PubMed]
Mangalaparthi, K. K., Chavan, S., Madugundu, A. K., Renuse, S., Vanderboom, P. M., Maus, A. D., Kemp, J., Kipp, B. R., Grebe, S. K., Singh, R. J., and Pandey, A. (2021). A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples. Clinical proteomics. 18, 25. [PubMed]
SLigezka, A. N., Radenkovic, S., Saraswat, M., Garapati, K., Ranatunga, W., Krzysciak, W., Yanaihara, H., Preston, G., Brucker, W., McGovern, R. M., Reid, J. M., Cassiman, D., Muthusamy, K., Johnsen, C., Mercimek-Andrews, S., Larson, A., Lam, C., Edmondson, A. C., Ghesquière, B., Witters, P., … Morava, E. (2021). Sorbitol is a severity biomarker for PMM2-CDG with therapeutic implications. Annals of neurology. 90, 887–900. [PubMed]
Byeon, S. K., Khanam, R., Rahman, S., Hasan, T., Rizvi, S., Madugundu, A. K., Ramarajan, M. G., Jung, J. H., Chowdhury, N. H., Ahmed, S., Raqib, R., Kim, K. P., Piazza, A. L., Rinaldo, P., Pandey, A., Baqui, A. H., and Amanhi Bio-Banking Study Group (2021). Maternal serum lipidomics identifies lysophosphatidic acid as a predictor of small for gestational age neonates. Molecular omics. 17, 956–966.[PubMed]
Parthasarathi, K., Munjal, N. S., Dey, G., Kumar, A., Pandey, A., Balakrishnan, L., and Sharma, J. (2021). A pathway map of signaling events triggered upon SARS-CoV infection. Journal of cell communication and signaling. 15, 595–600. [PubMed]
Wu, X., Wang, L., Pearson, N. A., Renuse, S., Cheng, R., Liang, Y., Mun, D. G., Madugundu, A. K., Xu, Y., Gill, P. S. and Pandey, A. (2021). Quantitative tyrosine phosphoproteome profiling of AXL receptor tyrosine kinase signaling network. Cancers. 13, 4234. [PubMed]
Tahir, R., Madugundu, A. K., Udainiya, S., Cutler, J. A., Renuse, S., Wang, L., Pearson, N. A., Mitchell, C. J., Mahajan, N., Pandey, A. and Wu, X. (2021). Proximity-Dependent biotinylation to elucidate the interactome of TNK2 nonreceptor tyrosine kinase. Journal of Proteome Research. 20, 4566-4577. [PubMed]
Alexander, M. P., Mangalaparthi, K. K., Madugundu, A. K., Moyer, A. M., Adam, B. A., Mengel, M., Singh, S., Herrmann, S. M., Rule, A. D., Cheek, E. H., Herrera Hernandez, L. P., Graham, R. P., Aleksandar, D., Aubry, M. C., Roden, A. C., Hagen, C. E., Quinton, R. A., Bois, M. C., Lin, P. T., Maleszewski, J. J., Cornell, L. D., Sethi, S., Pavelko, K. D., Charlesworth, J., Narasimhan, R., Larsen, C. P., Rizza, S. A., Nasr, S. H., Grande, J. P., McKee, T. D., Badley, A. D., Pandey, A. and Taner, T. (2021). Acute kidney injury in severe COVID-19 has similarities to sepsis-associated kidney injury: A multi-omics study. Mayo Clinic Proceedings. 96, 2561–2575. [PubMed]
Vanderboom, P. M., Mun, D. G., Madugundu, A. K., Mangalaparthi, K. K., Saraswat, M., Garapati, K., Chakraborty, R., Ebihara, H., Sun, J. and Pandey, A. (2021). Proteomic signature of host response to sars-cov-2 infection in the nasopharynx. Molecular & Cellular Proteomics : MCP. 20, 100134. [PubMed]
Kolar, E. A., Shi, X., Clay, E. M., Moser, A. B., Lal, B., Nirujogi, R. S., Pandey, A., Bandaru, V. V. R., Laterra, J., Pei, Z. and Watkins, P. A. (2021). Very long-chain acyl-coa synthetase 3 mediates onco-sphingolipid metabolism in malignant glioma. Medical Research Archives. 9, 2433. [PubMed]
Saraswat, M., Garapati, K., Mun, D. G. and Pandey, A. (2021). Extensive heterogeneity of glycopeptides in plasma revealed by deep glycoproteomic analysis using size-exclusion chromatography. Molecular Omics. 17, 939-947. [PubMed]
Renuse, S., Madamsetty, V. S., Mun, D. G., Madugundu, A. K., Singh, S., Udainiya, S., Mangalaparthi, K. K., Kim, M. S., Liu, R., Kumar, S. R., Krasnoperov, V., Truty, M., Graham, R. P., Gill, P. S., Mukhopadhyay, D. and Pandey, A. (2021). Tyrosine phosphoproteomics of patient-derived xenografts reveals ephrin type-b receptor 4 tyrosine kinase as a therapeutic target in pancreatic cancer. Cancers. 13, 3404. [PubMed]
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Mun, D. G., Vanderboom, P. M., Madugundu, A. K., Garapati, K., Chavan, S., Peterson, J. A., Saraswat, M. and Pandey, A. (2021). DIA-Based proteome profiling of nasopharyngeal swabs from COVID-19 patients. Journal of Proteome Research. 20, 4165-4175. [PubMed]
Byeon, S. K., Ramarajan, M. G., Madugundu, A. K., Oglesbee, D., Vernon, H. J. and Pandey, A. (2021). High-resolution mass spectrometric analysis of cardiolipin profiles in barth syndrome. Mitochondrion. 60, 27-32. [PubMed]
Karon, B. S., Donato, L., Bridgeman, A. R., Blommel, J. H., Kipp, B., Maus, A., Renuse, S., Kemp, J., Madugundu, A. K., Vanderboom, P. M., Chavan, S., Dasari, S., Singh, R. J., Grebe, S. K. G. and Pandey, A. (2021). Analytical sensitivity and specificity of four point of care rapid antigen diagnostic tests for sars-cov-2 using real-time quantitative PCR, quantitative droplet digital PCR, and a mass spectrometric antigen assay as comparator methods. Clinical Chemistry. 67, 1545–1553. [PubMed]
Renuse, S., Vanderboom, P. M., Maus, A. D., Kemp, J. V., Gurtner, K. M., Madugundu, A. K., Chavan, S., Peterson, J. A., Madden, B. J., Mangalaparthi, K. K., Mun, D. G., Singh, S., Kipp, B. R., Dasari, S., Singh, R. J., Grebe, S. K. and Pandey, A. (2021). A mass spectrometry-based targeted assay for detection of sars-cov-2 antigen from clinical specimens. Ebiomedicine. 69, 103465. [PubMed]
Byeon, S. K., Madugundu, A. K., Jain, A. P., Bhat, F. A., Jung, J. H., Renuse, S., Darrow, J., Bakker, A., Albert, M., Moghekar, A. and Pandey, A. (2021). Cerebrospinal fluid lipidomics for biomarkers of alzheimer’s disease. Molecular Omics. 17, 454-463. [PubMed]
Chavan, S., Mangalaparthi, K. K., Singh, S., Renuse, S., Vanderboom, P. M., Madugundu, A. K., Budhraja, R., McAulay, K., Grys, T. E., Rule, A. D., Alexander, M. P., O’Horo, J. C., Badley, A. D. and Pandey, A. (2021). Mass spectrometric analysis of urine from COVID-19 patients for detection of sars-cov-2 viral antigen and to study host response. Journal of Proteome Research. 20, 3404-3413. [PubMed]
Ma, S. X., Seo, B. A., Kim, D., Xiong, Y., Kwon, S. H., Brahmachari, S., Kim, S., Kam, T. I., Nirujogi, R. S., Kwon, S. H., Dawson, V. L., Dawson, T. M., Pandey, A., Na, C. H. and Ko, H. S. (2021). Complement and coagulation cascades are potentially involved in dopaminergic neurodegeneration in α-synuclein-based mouse models of parkinson’s disease. Journal of Proteome Research. 20, 3428-3443. [PubMed]
Liang, R., Menon, V., Qiu, J., Arif, T., Renuse, S., Lin, M., Nowak, R., Hartmann, B., Tzavaras, N., Benson, D. L., Chipuk, J. E., Fribourg, M., Pandey, A., Fowler, V. and Ghaffari, S. (2021). Mitochondrial localization and moderated activity are key to murine erythroid enucleation. Blood Advances. 5, 2490-2504. [PubMed]
Sadras, T., Martin, M., Kume, K., Robinson, M. E., Saravanakumar, S., Lenz, G., Chen, Z., Song, J. Y., Siddiqi, T., Oksa, L., Knapp, A. M., Cutler, J., Cosgun, K. N., Klemm, L., Ecker, V., Winchester, J., Ghergus, D., Soulas-Sprauel, P., Kiefer, F., Heisterkamp, N., Pandey, A., Ngo, V., Wang, L., Jumaa, H., Buchner, M., Ruland, J., Chan, W. C., Meffre, E., Martin, T. and Müschen, M. (2021). Developmental partitioning of SYK and ZAP70 prevents autoimmunity and cancer. Molecular Cell. 81, 2094-2111.e9. [PubMed]
Muthusamy, B., Bellad, A., Girimaji, S. C. and Pandey, A. (2021). Shukla-Vernon syndrome: A second family with a novel variant in the bcorl1 gene. Genes. 12, 452. [PubMed]
Pillai, S., Kriplani, A., Chawla, A., Somani, B., Pandey, A., Prabhu, R., Choudhury, A., Pandit, S., Taori, R. and Hegde, P. (2021). Acute kidney injury post-percutaneous nephrolithotomy (PNL): prospective outcomes from a university teaching hospital. Journal of Clinical Medicine. 10, 1373. [PubMed]
Wong, X., Cutler, J. A., Hoskins, V. E., Gordon, M., Madugundu, A. K., Pandey, A. and Reddy, K. L. (2021). Mapping the micro-proteome of the nuclear lamina and lamina-associated domains. Life Science Alliance. 4. [PubMed]
Acoba, M. G., Alpergin, E. S. S., Renuse, S., Fernández-Del-Río, L., Lu, Y. W., Khalimonchuk, O., Clarke, C. F., Pandey, A., Wolfgang, M. J. and Claypool, S. M. (2021). The mitochondrial carrier SFXN1 is critical for complex III integrity and cellular metabolism. Cell Reports. 34, 108869. [PubMed]
Martinez, M., Renuse, S., Kreimer, S., O’Meally, R., Natov, P., Madugundu, A. K., Nirujogi, R. S., Tahir, R., Cole, R., Pandey, A. and Zachara, N. E. (2021). Quantitative proteomics reveals that the OGT interactome is remodeled in response to oxidative stress. Molecular & Cellular Proteomics : Mcp. 20, 100069. [PubMed]
Gondkar, K., Sathe, G., Joshi, N., Nair, B., Pandey, A. and Kumar, P. (2021). Integrated proteomic and phosphoproteomics analysis of DKK3 signaling reveals activated kinase in the most aggressive gallbladder cancer. Cells. 10 . [PubMed]
Sathe, G., Deepha, S., Gayathri, N., Nagappa, M., Parayil Sankaran, B., Taly, A. B., Khanna, T., Pandey, A. and Govindaraj, P. (2021). Ethylmalonic encephalopathy ETHE1 p. D165H mutation alters the mitochondrial function in human skeletal muscle proteome. Mitochondrion. 58, 64-71. [PubMed]
Sivagurunathan, S., Selvan, L. D. N., Khan, A. A., Parameswaran, S., Bhattacharjee, H., Gogoi, K., Gowda, H., Keshava Prasad, T. S., Pandey, A., Kumar, S. A., Rishi, P., Rishi, E., Ratra, D., Bhende, M., Janakiraman, N., Biswas, J. and Krishnakumar, S. (2021). Proteomics-based approach for differentiation of age-related macular degeneration sub-types. Indian Journal of Ophthalmology. 69, 647-654. [PubMed]
Lin, R., Learman, L. N., Na, C. H., Renuse, S., Chen, K. T., Chen, P. Y., Lee, G. H., Xiao, B., Resnick, S. M., Troncoso, J. C., Szumlinski, K. K., Linden, D. J., Park, J. M., Savonenko, A., Pandey, A. and Worley, P. F. (2021). Persistently elevated mtor complex 1-S6 kinase 1 disrupts darpp-32-dependent d1 dopamine receptor signaling and behaviors. Biological Psychiatry. 89, 1058-1072. [PubMed]
Radenkovic, S., Fitzpatrick-Schmidt, T., Byeon, S. K., Madugundu, A. K., Saraswat, M., Lichty, A., Wong, S. Y. W., McGee, S., Kubiak, K., Ligezka, A., Ranatunga, W., Zhang, Y., Wood, T., Friez, M. J., Clarkson, K., Pandey, A., Jones, J. R. and Morava, E. (2021). Expanding the clinical and metabolic phenotype of DPM2 deficient congenital disorders of glycosylation. Molecular Genetics and Metabolism. 132, 27-37. [PubMed]
Tahir, R., Renuse, S., Udainiya, S., Madugundu, A. K., Cutler, J. A., Nirujogi, R. S., Na, C. H., Xu, Y., Wu, X. and Pandey, A. (2021). Mutation-Specific and common phosphotyrosine signatures of kras G12D and G13D alleles. Journal of Proteome Research. 20, 670-683. [PubMed]
Sathe, G., Albert, M., Darrow, J., Saito, A., Troncoso, J., Pandey, A. and Moghekar, A. (2021). Quantitative proteomic analysis of the frontal cortex in alzheimer’s disease. Journal of Neurochemistry. 156, 988-1002. [PubMed]
2020
Carvalho, A. S., Moraes, M. C. S., Hyun Na, C., Fierro-Monti, I., Henriques, A., Zahedi, S., Bodo, C., Tranfield, E. M., Sousa, A. L., Farinho, A., Rodrigues, L. V., Pinto, P., Bárbara, C., Mota, L., Abreu, T. T., Semedo, J., Seixas, S., Kumar, P., Costa-Silva, B., Pandey, A. and Matthiesen, R. (2020). Is the proteome of bronchoalveolar lavage extracellular vesicles a marker of advanced lung cancer? Cancers. 12. [PubMed]
Krug, K., Jaehnig, E. J., Satpathy, S., Blumenberg, L., Karpova, A., Anurag, M., Miles, G., Mertins, P., Geffen, Y., Tang, L. C., Heiman, D. I., Cao, S., Maruvka, Y. E., Lei, J. T., Huang, C., Kothadia, R. B., Colaprico, A., Birger, C., Wang, J., Dou, Y., Wen, B., Shi, Z., Liao, Y., Wiznerowicz, M., Wyczalkowski, M. A., Chen, X. S., Kennedy, J. J., Paulovich, A. G., Thiagarajan, M., Kinsinger, C. R., Hiltke, T., Boja, E. S., Mesri, M., Robles, A. I., Rodriguez, H., Westbrook, T. F., Ding, L., Getz, G., Clauser, K. R., Fenyö, D., Ruggles, K. V., Zhang, B., Mani, D. R., Carr, S. A., Ellis, M. J., Gillette, M. A. and Clinical Proteomic Tumor Analysis, Consortium. (2020). Proteogenomic landscape of breast cancer tumorigenesis and targeted therapy. Cell. 183, 1436-1456.e31. [PubMed]
Radenkovic, S., Fitzpatrick-Schmidt, T., Byeon, S. K., Madugundu, A. K., Saraswat, M., Lichty, A., Wong, S. Y. W., McGee, S., Kubiak, K., Ligezka, A., Ranatunga, W., Zhang, Y., Wood, T., Friez, M. J., Clarkson, K., Pandey, A., Jones, J. R. and Morava, E. (2020). Expanding the clinical and metabolic phenotype of DPM2 deficient congenital disorders of glycosylation. Molecular Genetics and Metabolism. [PubMed]
Hu, Y., Pan, J., Shah, P., Ao, M., Thomas, S. N., Liu, Y., Chen, L., Schnaubelt, M., Clark, D. J., Rodriguez, H., Boja, E. S., Hiltke, T., Kinsinger, C. R., Rodland, K. D., Li, Q. K., Qian, J., Zhang, Z., Chan, D. W., Zhang, H. and Clinical Proteomic Tumor Analysis, Consortium. (2020). Integrated proteomic and glycoproteomic characterization of human high-grade serous ovarian carcinoma. Cell Reports. 33, 108276. [PubMed]
Mun, D. G., Renuse, S., Saraswat, M., Madugundu, A., Udainiya, S., Kim, H., Park, S. R., Zhao, H., Nirujogi, R. S., Na, C. H., Kannan, N., Yates JR, 3. r. d., Lee, S. W. and Pandey, A. (2020). PASS-DIA: A data-independent acquisition approach for discovery studies. Analytical Chemistry. 92, 14466-14475. [PubMed]
Korhonen, P. K., Gasser, R. B., Ma, G., Wang, T., Stroehlein, A. J., Young, N. D., Ang, C. S., Fernando, D. D., Lu, H. C., Taylor, S., Reynolds, S. L., Mofiz, E., Najaraj, S. H., Gowda, H., Madugundu, A., Renuse, S., Holt, D., Pandey, A., Papenfuss, A. T. and Fischer, K. (2020). High-quality nuclear genome for sarcoptes scabiei-a critical resource for a neglected parasite. PLOS Neglected Tropical Diseases. 14, e0008720. [PubMed]
Tahir, R., Renuse, S., Udainiya, S., Madugundu, A. K., Cutler, J. A., Nirujogi, R. S., Na, C. H., Xu, Y., Wu, X. and Pandey, A. (2020). Mutation-Specific and common phosphotyrosine signatures of KRAS G12D and G13D alleles. Journal of Proteome Research. [PubMed]
Mangalaparthi, K. K., Patel, K., Khan, A. A., Manoharan, M., Karunakaran, C., Murugan, S., Gupta, R., Gupta, R., Khanna-Gupta, A., Chaudhuri, A., Kumar, P., Nair, B., Kumar, R. V., Prasad, T. S. K., Chatterjee, A., Pandey, A. and Gowda, H. (2020). Mutational landscape of esophageal squamous cell carcinoma in an indian cohort. Frontiers in Oncology. 10, 1457. [PubMed]
Sathe, G., George, I. A., Deb, B., Jain, A. P., Patel, K., Nayak, B., Karmakar, S., Seth, A., Pandey, A. and Kumar, P. (2020). Urinary glycoproteomic profiling of non-muscle invasive and muscle invasive bladder carcinoma patients reveals distinct n-glycosylation pattern of CD44, MGAM, and GINM1. Oncotarget. 11, 3244-3255. [PubMed]
Pandey, A., Stawiski, E. W., Durinck, S., Gowda, H., Goldstein, L. D., Barbhuiya, M. A., Schröder, M. S., Sreenivasamurthy, S. K., Kim, S. W., Phalke, S., Suryamohan, K., Lee, K., Chakraborty, P., Kode, V., Shi, X., Chatterjee, A., Datta, K., Khan, A. A., Subbannayya, T., Wang, J., Chaudhuri, S., Gupta, S., Shrivastav, B. R., Jaiswal, B. S., Poojary, S. S., Bhunia, S., Garcia, P., Bizama, C., Rosa, L., Kwon, W., Kim, H., Han, Y., Yadav, T. D., Ramprasad, V. L., Chaudhuri, A., Modrusan, Z., Roa, J. C., Tiwari, P. K., Jang, J. Y. and Seshagiri, S. (2020). Integrated genomic analysis reveals mutated ELF3 as a potential gallbladder cancer vaccine candidate. Nature Communications. 11, 4225. [PubMed]
Puttamallesh, V. N., Deb, B., Gondkar, K., Jain, A., Nair, B., Pandey, A., Chatterjee, A., Gowda, H. and Kumar, P. (2020). Quantitative proteomics of urinary bladder cancer cell lines identify UAP1 as a potential therapeutic target. Genes. 11. [PubMed]
Sathe, G., Albert, M., Darrow, J., Saito, A., Troncoso, J., Pandey, A. and Moghekar, A. (2020). Quantitative proteomic analysis of the frontal cortex in Alzheimer’s disease. Journal of Neurochemistry. [PubMed]
Sharma, T., Datta, K. K., Kumar, M., Dey, G., Khan, A. A., Mangalaparthi, K. K., Saharan, P., Chinnapparaj, S., Aggarwal, A., Singla, N., Ghosh, S., Rawat, A., Dhandapani, S., Salunke, P., Chhabra, R., Singh, D., Takkar, A., Gupta, S. K., Prasad, T. S. K., Gowda, H., Mukherjee, K. K., Pandey, A. and Bhagat, H. (2020). Intracranial aneurysm biomarker candidates identified by a proteome-wide study. OMICS: A Journal of Integrative Biology. 24, 483-492. [PubMed]
Muthusamy, B., Bellad, A., Prasad, P., Bandari, A. K., Bhuvanalakshmi, G., Kiragasur, R. M., Girimaj, S. C. and Pandey, A. (2020). A novel LINS1 truncating mutation in autosomal recessive nonsyndromic intellectual disability. Frontiers in Psychiatry. 11, 354. [PubMed]
Bellad, A., Bandari, A. K., Pandey, A., Girimaji, S. C. and Muthusamy, B. (2020). A novel missense variant in PHF6 gene causing börjeson-forssman-lehman syndrome. Journal of Molecular Neuroscience : Mn. 70, 1403-1409. [PubMed]
Na, C. H., Sathe, G., Rosenthal, L. S., Moghekar, A. R., Dawson, V. L., Dawson, T. M. and Pandey, A. (2020). Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid. Clinical Proteomics. 17, 13. [PubMed]
Babu, N., Pinto, S. M., Biswas, M., Subbannayya, T., Rajappa, M., Mohan, S. V., Advani, J., Rajagopalan, P., Sathe, G., Syed, N., Radhakrishna, V. D., Muthusamy, O., Navani, S., Kumar, R. V., Gopisetty, G., Rajkumar, T., Radhakrishnan, P., Thiyagarajan, S., Pandey, A., Gowda, H., Majumder, P. and Chatterjee, A. (2020). Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer. Gastric Cancer : Official Journal of The International Gastric Cancer Association and The Japanese Gastric Cancer Association. 23, 796-810. [PubMed]
Sathe, G., Mangalaparthi, K. K., Jain, A., Darrow, J., Troncoso, J., Albert, M., Moghekar, A. and Pandey, A. (2020). Multiplexed phosphoproteomic study of brain in patients with alzheimer’s disease and age-matched cognitively healthy controls. OMICS: A Journal of Integrative Biology. 24, 216-227. [PubMed]
Renuse, S., Madugundu, A. K., Jung, J. H., Byeon, S. K., Goldschmidt, H. L., Tahir, R., Meyers, D., Kim, D. I., Cutler, J., Kim, K. P., Wu, X., Huganir, R. L. and Pandey, A. (2020). Signature fragment ions of biotinylated peptides. Journal of The American Society For Mass Spectrometry. 31, 394-404. [PubMed]
Creed, T. M., Baldeosingh, R., Eberly, C. L., Schlee, C. S., Kim, M., Cutler, J. A., Pandey, A., Civin, C. I., Fossett, N. G. and Kingsbury, T. J. (2020). The PAX-SIX-EYA-DACH network modulates GATA-FOG function in fly hematopoiesis and human erythropoiesis. Development (cambridge, England). 147. [PubMed]
Tornheim, J. A., Madugundu, A. K., Paradkar, M., Fukutani, K. F., Queiroz, A. T. L., Gupte, N., Gupte, A. N., Kinikar, A., Kulkarni, V., Balasubramanian, U., Sreenivasamurthy, S., Raja, R., Pradhan, N., Shivakumar, S. V. B. Y., Valvi, C., Hanna, L. E., Andrade, B. B., Mave, V., Pandey, A., Gupta, A. and CTRIUMPh RePORT India Study, T. e. a. m. .. (2020). Transcriptomic profiles of confirmed pediatric tuberculosis patients and household contacts identifies active tuberculosis, infection, and treatment response among Indian children. The Journal of Infectious Diseases. 221, 1647-1658. [PubMed]
Raja, R., Pandey, A. and Kumar, P. (2020). Epithelial to mesenchymal plasticity: role in cancer progression. Frontiers in Bioscience (landmark Edition). 25, 838-873. [PubMed]
Carvalho, A. S., Baeta, H., Silva, B. C., Moraes, M. C. S., Bodo, C., Beck, H. C., Rodriguez, M. S., Saraswat, M., Pandey, A. and Matthiesen, R. (2020). Extra-cellular vesicles carry proteome of cancer hallmarks. Frontiers in Bioscience (landmark Edition). 25, 398-436. [PubMed]
2019
Gondkar, K., Patel, K., Patil Okaly, G. V., Nair, B., Pandey, A., Gowda, H. and Kumar, P. (2019). Dickkopf homolog 3 (DKK3) acts as a potential tumor suppressor in gallbladder cancer. Frontiers in Oncology. 9, 1121. [PubMed]
Maus, A., Kemp, J., Milosevic, D., Renuse, S., Pandey, A., Singh, R. J. and Grebe, S. K. G. (2019). Center of mass calculation in combination with MS/MS allows robust identification of single amino acid polymorphisms in clinical measurements of insulin-like growth factor 1. Journal of Proteome Research. [PubMed]
Shinde, V., Hu, N., Renuse, S., Mahale, A., Pandey, A., Eberhart, C., Stone, D., Al-Swailem, S. A., Maktabi, A. and Chakravarti, S. (2019). Mapping keratoconus molecular substrates by multiplexed high-resolution proteomics of unpooled corneas. OMICS: A Journal of Integrative Biology. 23, 583-597. [PubMed]
Rajagopalan, P., Jain, A. P., Nanjappa, V., Patel, K., Mangalaparthi, K. K., Babu, N., Cavusoglu, N., Roy, N., Soeur, J., Breton, L., Pandey, A., Gowda, H., Chatterjee, A. and Misra, N. (2019). Proteome-wide changes in primary skin keratinocytes exposed to diesel particulate extract-a role for antioxidants in skin health. Journal of Dermatological Science. In press. [PubMed]
Bandari, A. K., Muthusamy, B., Bhat, S., Govindaraj, P., Rajagopalan, P., Dalvi, A., Shankar, S., Raja, R., Reddy, K. S., Madkaikar, M. and Pandey, A. (2019). A novel splice site mutation in IFNGR2 in patients with primary immunodeficiency exhibiting susceptibility to mycobacterial diseases. Frontiers in Immunology. 10, 1964. [PubMed]
Anzmann, A. F., Pinto, S., Busa, V., Carlson, J., McRitchie, S., Sumner, S., Pandey, A. and Vernon, H. J. (2019). Multi-omics studies in cellular models of methylmalonic acidemia and propionic acidemia reveal dysregulation of serine metabolism. Biochimica Et Biophysica Acta – Molecular Basis of Disease. 1865, 165538. [PubMed]
Cutler, J. A., Udainiya, S., Madugundu, A. K., Renuse, S., Xu, Y., Jung, J., Kim, K. P., Wu, X. and Pandey, A. (2019). Integrative phosphoproteome and interactome analysis of the role of Ubash3b in BCR-ABL signaling. Leukemia. [PubMed]
Dalton, W. B., Helmenstine, E., Walsh, N., Gondek, L. P., Kelkar, D. S., Read, A., Natrajan, R., Christenson, E. S., Roman, B., Das, S., Zhao, L., Leone, R. D., Shinn, D., Groginski, T., Madugundu, A. K., Patil, A., Zabransky, D. J., Medford, A., Lee, J., Cole, A. J., Rosen, M., Thakar, M., Ambinder, A., Donaldson, J., DeZern, A. E., Cravero, K., Chu, D., Madero-Marroquin, R., Pandey, A., Hurley, P. J., Lauring, J. and Park, B. (2019). Hotspot SF3B1 mutations induce metabolic reprogramming and vulnerability to serine deprivation. The Journal of Clinical Investigation. 130, . [PubMed]
Shears, M. J., Nirujogi, R. S., Swearingen, K. E., Renuse, S., Mishra, S., Jaipal Reddy, P., Moritz, R. L., Pandey, A. and Sinnis, P. (2019). Proteomic analysis of plasmodium merosomes: the link between liver and blood stages in malaria. Journal of Proteome Research. 18, 3404-3418. [PubMed]
Mun, D. G., Nam, D., Kim, H., Pandey, A. and Lee, S. W. (2019). Accurate precursor mass assignment improves peptide identification in data-independent acquisition mass spectrometry. Analytical Chemistry. 91, 8453-8460. [PubMed]
Dutta, P., Reddy, K. S., Rai, A., Madugundu, A. K., Solanki, H. S., Bhansali, A., Radotra, B. D., Kumar, N., Collier, D., Iacovazzo, D., Gupta, P., Raja, R., Gowda, H., Pandey, A., Devgun, J. S. and Korbonits, M. (2019). Surgery, octreotide, temozolomide, bevacizumab, radiotherapy, and pegvisomant treatment of an AIP mutation‒positive child. The Journal of Clinical Endocrinology and Metabolism. 104, 3539-3544. [PubMed]
Bandari, A. K., Bhat, S., Archana, M. V., Yadavalli, S., Patel, K., Rajagopalan, P., Madugundu, A. K., Madkaikar, M., Reddy, K., Muthusamy, B. and Pandey, A. (2019). Family-based next-generation sequencing study identifies an IL2RG variant in an infant with primary immunodeficiency. OMICS: A Journal of Integrative Biology. 23, 285-290. [PubMed]
Vasaikar, S., Huang, C., Wang, X., Petyuk, V. A., Savage, S. R., Wen, B., Dou, Y., Zhang, Y., Shi, Z., Arshad, O. A., Gritsenko, M. A., Zimmerman, L. J., McDermott, J. E., Clauss, T. R., Moore, R. J., Zhao, R., Monroe, M. E., Wang, Y. T., Chambers, M. C., Slebos, R. J. C., Lau, K. S., Mo, Q., Ding, L., Ellis, M., Thiagarajan, M., Kinsinger, C. R., Rodriguez, H., Smith, R. D., Rodland, K. D., Liebler, D. C., Liu, T., Zhang, B. and Clinical Proteomic Tumor Analysis Consortium. (2019). Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities. Cell. 177, 1035-1049.e19. [PubMed]
Madugundu, A. K., Na, C. H., Nirujogi, R. S., Renuse, S., Kim, K. P., Burns, K. H., Wilks, C., Langmead, B., Ellis, S. E., Collado-Torres, L., Halushka, M. K., Kim, M. S. and Pandey, A. (2019). Integrated transcriptomic and proteomic analysis of primary human umbilical vein endothelial cells. Proteomics. 19, e1800315. [PubMed]
Na, C. H., Sharma, N., Madugundu, A. K., Chen, R., Aksit, M. A., Rosson, G. D., Cutting, G. R. and Pandey, A. (2019). Integrated transcriptomic and proteomic analysis of human eccrine sweat glands identifies missing and novel proteins. Molecular & Cellular Proteomics. 18, 1382-1395. [PubMed]
Deva Magendhra Rao, A. K., Patel, K., Korivi Jyothiraj, S., Meenakumari, B., Sundersingh, S., Sridevi, V., Rajkumar, T., Pandey, A., Chatterjee, A., Gowda, H. and Mani, S. (2019). Identification of lncRNAs associated with early-stage breast cancer and their prognostic implications. Molecular Oncology. 13, 1342-1355. [PubMed]
Advani, J., Verma, R., Chatterjee, O., Pachouri, P. K., Upadhyay, P., Singh, R., Yadav, J., Naaz, F., Ravikumar, R., Buggi, S., Suar, M., Gupta, U. D., Pandey, A., Chauhan, D. S., Tripathy, S. P., Gowda, H. and Prasad, T. S. K. (2019). Whole genome sequencing of Mycobacterium tuberculosis clinical isolates from India reveals genetic heterogeneity and region-specific variations that might affect drug susceptibility. Frontiers in Microbiology. 10, 309. [PubMed]
Muthusamy, B., Nguyen, T. T., Bandari, A. K., Basheer, S., Selvan, L. D. N., Chandel, D., Manoj, J., Gayen, S., Seshagiri, S., Chandra Girimaji S and Pandey, A. (2019). Exome sequencing reveals a novel splice site variant in HUWE1 gene in patients with suspected say-meyer syndrome. European Journal of Medical Genetics. [PubMed]
Subbannayya, T., Leal-Rojas, P., Zhavoronkov, A., Ozerov, I. V., Korzinkin, M., Babu, N., Radhakrishnan, A., Chavan, S., Raja, R., Pinto, S. M., Patil, A. H., Barbhuiya, M. A., Kumar, P., Guerrero-Preston, R., Navani, S., Tiwari, P. K., Kumar, R. V., Prasad, T. S. K., Roa, J. C., Pandey, A., Sidransky, D., Gowda, H., Izumchenko, E. and Chatterjee, A. (2019). PIM1 kinase promotes gallbladder cancer cell proliferation via inhibition of proline-rich akt substrate of 40 KDa (PRAS40). Journal of Cell Communication and Signaling. 13, 163-177. [PubMed]
Sathe, G., Na, C. H., Renuse, S., Madugundu, A. K., Albert, M., Moghekar, A. and Pandey, A. (2019). Quantitative proteomic profiling of cerebrospinal fluid to identify candidate biomarkers for alzheimer’s disease. PROTEOMICS – Clinical Applications. 13, e1800105. [PubMed]
2018
Yelamanchi, S. D., Tyagi, A., Mohanty, V., Dutta, P., Korbonits, M., Chavan, S., Advani, J., Madugundu, A. K., Dey, G., Datta, K. K., Rajyalakshmi, M., Sahasrabuddhe, N. A., Chaturvedi, A., Kumar, A., Das, A. A., Ghosh, D., Jogdand, G. M., Nair, H. H., Saini, K., Panchal, M., Sarvaiya, M. A., Mohanraj, S. S., Sengupta, N., Saxena, P., Subramani, P. A., Kumar, P., Akkali, R., Reshma, S. V., Santhosh, R. S., Rastogi, S., Kumar, S., Ghosh, S. K., Irlapati, V. K., Srinivasan, A., Radotra, B. D., Mathur, P. P., Wong, G. W., Satishchandra, P., Chatterjee, A., Gowda, H., Bhansali, A., Pandey, A., Shankar, S. K., Mahadevan, A. and Prasad, T. S. K. (2018). Proteomic analysis of the human anterior pituitary gland. OMICS : A Journal of Integrative Biology. 22, 759-769. [PubMed]
Pertea, M., Shumate, A., Pertea, G., Varabyou, A., Breitwieser, F. P., Chang, Y. C., Madugundu, A. K., Pandey, A. and Salzberg, S. L. (2018). CHESS: A new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. Genome Biology. 19, 208. [PubMed]
Alexander, E. J., Ghanbari Niaki, A., Zhang, T., Sarkar, J., Liu, Y., Nirujogi, R. S., Pandey, A., Myong, S. and Wang, J. (2018). Ubiquilin 2 modulates ALS/FTD-linked FUS-RNA complex dynamics and stress granule formation. Proceedings of The National Academy of Sciences of The United States of America. 115, E11485-E11494. [PubMed]
Sathe, G., Na, C. H., Renuse, S., Madugundu, A., Albert, M., Moghekar, A. and Pandey, A. (2018). Phosphotyrosine profiling of human cerebrospinal fluid. Clinical Proteomics. 15, 29. [PubMed]
Advani, J., Sharma, K., Verma, R., Chatterjee, O., Solanki, H. S., Sharma, A., Varma, S., Modi, M., Ray, P., Sharma, M., Dhillion, M. S., Pandey, A., Gowda, H. and Prasad, T. S. K. (2018). Data on whole genome sequencing of extrapulmonary tuberculosis clinical isolates from India. Data in Brief. 20, 617-622. [PubMed]
Patil, A. H., Datta, K. K., Behera, S. K., Kasaragod, S., Pinto, S. M., Koyangana, S. G., Mathur, P. P., Gowda, H., Pandey, A. and Prasad, T. S. K. (2018). Dissecting candida pathobiology: post-translational modifications on the Candida tropicalis proteome. OMICS: A Journal of Integrative Biology. 22, 544-552. [PubMed]
Madugundu, A. K., Muthusamy, B., Sreenivasamurthy, S. K., Bhavani, C., Sharma, J., Kumar, B., Murthy, K. R., Ravikumar, R. and Pandey, A. (2018). A next-generation sequencing-based molecular approach to characterize a tick vector in lyme disease. OMICS: A Journal of Integrative Biology. 22, 565-574. [PubMed]
Foster, J. W., Shinde, V., Soiberman, U. S., Sathe, G., Liu, S., Wan, J., Qian, J., Dauoud, Y., Pandey, A., Jun, A. S. and Chakravarti, S. (2018). Integrated stress response and decreased ECM in cultured stromal cells from keratoconus corneas. Investigative Ophthalmology & Visual Science. 59, 2977-2986. [PubMed]
Wu, X., Zahari, M. S., Renuse, S., Sahasrabuddhe, N. A., Chaerkady, R., Kim, M. S., Fackler, M. J., Stampfer, M., Gabrielson, E., Sukumar, S. and Pandey, A. (2018). Quantitative phosphoproteomic analysis reveals reciprocal activation of receptor tyrosine kinases between cancer epithelial cells and stromal fibroblasts. Clinical Proteomics. 15, 21. [PubMed]
Selvan, L. D. N., Danda, R., Madugundu, A. K., Puttamallesh, V. N., Sathe, G. J., Krishnan, U. M., Khetan, V., Rishi, P., Prasad, T. S. K., Pandey, A., Krishnakumar, S., Gowda, H. and Elchuri, S. V. (2018). Phosphoproteomics of retinoblastoma: A pilot study identifies aberrant kinases. Molecules (basel, Switzerland). 23, E1454. [PubMed]
Rajagopalan, P., Jain, A. P., Nanjappa, V., Patel, K., Mangalaparthi, K. K., Babu, N., Cavusoglu, N., Roy, N., Soeur, J., Breton, L., Pandey, A., Gowda, H., Chatterjee, A. and Misra, N. (2018). Proteome-wide changes in primary skin keratinocytes exposed to diesel particulate extract-a role for antioxidants in skin health. Journal of Dermatological Science. 91, 239-249. [PubMed]
Danda, R., Ganapathy, K., Sathe, G., Madugundu, A. K., Krishnan, U. M., Khetan, V., Rishi, P., Gowda, H., Pandey, A., Subramanian, K., Prasad, T. S. K. and Elchuri, S. V. (2018). Membrane proteome of invasive retinoblastoma: Differential proteins and biomarkers. Proteomics. Clinical Applications. 12, e1700101. [PubMed]
Barbhuiya, M. A., Kashyap, M. K., Puttamallesh, V. N., Kumar, R. V., Wu, X., Pandey, A. and Gowda, H. (2018). Identification of spleen tyrosine kinase as a potential therapeutic target for esophageal squamous cell carcinoma using reverse phase protein arrays. Oncotarget. 9, 18422-18434. [PubMed]
Pinto, S. M., Subbannayya, Y., Rex, D. A. B., Raju, R., Chatterjee, O., Advani, J., Radhakrishnan, A., Prasad, T. S. K., Wani, M. R. and Pandey, A. (2018). A network map of IL-33 signaling pathway. Journal of Cell Communication and Signaling. 12, 615-624. [PubMed]
Heo, S., Diering, G. H., Na, C. H., Nirujogi, R. S., Bachman, J. L., Pandey, A. and Huganir, R. L. (2018). Identification of long-lived synaptic proteins by proteomic analysis of synaptosome protein turnover. Proceedings of The National Academy of Sciences of The United States of America. 115, E3827-E3836. [PubMed]
Solanki, H. S., Raja, R., Zhavoronkov, A., Ozerov, I. V., Artemov, A. V., Advani, J., Radhakrishnan, A., Babu, N., Puttamallesh, V. N., Syed, N., Nanjappa, V., Subbannayya, T., Sahasrabuddhe, N. A., Patil, A. H., Prasad, T. S. K., Gaykalova, D., Chang, X., Sathyendran, R., Mathur, P. P., Rangarajan, A., Sidransky, D., Pandey, A., Izumchenko, E., Gowda, H. and Chatterjee, A. (2018). Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor. Oncoscience. 5, 21-38. [PubMed]
Lee, S. E., Song, J., Bösl, K., Müller, A. C., Vitko, D., Bennett, K. L., Superti-Furga, G., Pandey, A., Kandasamy, R. K. and Kim, M. S. (2018). Proteogenomic analysis to identify missing proteins from haploid cell lines. Proteomics. 18, e1700386. [PubMed]
Wang, Z., Kim, M. S., Martinez-Ferrando, I., Koleske, A. J., Pandey, A. and Cole, P. A. (2018). Analysis of cellular tyrosine phosphorylation via chemical rescue of conditionally active abl kinase. Biochemistry. 57, 1390-1398. [PubMed]
Kim, S., Yun, S. P., Lee, S., Umanah, G. E., Bandaru, V. V. R., Yin, X., Rhee, P., Karuppagounder, S. S., Kwon, S. H., Lee, H., Mao, X., Kim, D., Pandey, A., Lee, G., Dawson, V. L., Dawson, T. M. and Ko, H. S. (2018). GBA1 deficiency negatively affects physiological α-synuclein tetramers and related multimers. Proceedings of The National Academy of Sciences of The United States of America. 115, 798-803. [PubMed]
Kim, D. I., Cutler, J. A., Na, C. H., Reckel, S., Renuse, S., Madugundu, A. K., Tahir, R., Goldschmidt, H. L., Reddy, K. L., Huganir, R. L., Wu, X., Zachara, N. E., Hantschel, O. and Pandey, A. (2018). BioSITe: a method for direct detection and quantitation of site-specific biotinylation. Journal of Proteome Research. 17, 759-769. [PubMed]
Li, Z., Cheng, Z., Raghothama, C., Cui, Z., Liu, K., Li, X., Jiang, C., Jiang, W., Tan, M., Ni, X., Pandey, A., Liu, J. O. and Dang, Y. (2018). USP9X controls translation efficiency via deubiquitination of eukaryotic translation initiation factor 4A1. Nucleic Acids Research. 46, 823-839. [PubMed]
Na, C. H., Barbhuiya, M. A., Kim, M. S., Verbruggen, S., Eacker, S. M., Pletnikova, O., Troncoso, J. C., Halushka, M. K., Menschaert, G., Overall, C. M. and Pandey, A. (2018). Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini. Genome Research. 28, 25-36. [PubMed]
2017
McCall, M. N., Kim, M. S., Adil, M., Patil, A. H., Lu, Y., Mitchell, C. J., Leal-Rojas, P., Xu, J., Kumar, M., Dawson, V. L., Dawson, T. M., Baras, A. S., Rosenberg, A. Z., Arking, D. E., Burns, K. H., Pandey, A. and Halushka, M. K. (2017). Toward the human cellular micrornaome. Genome Research. 27, 1769-1781. [PubMed]
Sreenivasamurthy, S. K., Madugundu, A. K., Patil, A. H., Dey, G., Mohanty, A. K., Kumar, M., Patel, K., Wang, C., Kumar, A., Pandey, A. and Prasad, T. S. K. (2017). Mosquito-borne diseases and omics: tissue-restricted expression and alternative splicing revealed by transcriptome profiling of anopheles stephensi. OMICS: A Journal of Integrative Biology. 21, 488-497. [PubMed]
Sharma, K., Verma, R., Advani, J., Chatterjee, O., Solanki, H. S., Sharma, A., Varma, S., Modi, M., Ray, P., Mukherjee, K. K., Sharma, M., Dhillion, M. S., Suar, M., Chatterjee, A., Pandey, A., Prasad, T. S. K. and Gowda, H. (2017). Whole genome sequencing of mycobacterium tuberculosis isolates from extrapulmonary sites. OMICS: A Journal of Integrative Biology. 21, 413-425. [PubMed]
Sadtler, K., Sommerfeld, S. D., Wolf, M. T., Wang, X., Majumdar, S., Chung, L., Kelkar, D. S., Pandey, A. and Elisseeff, J. H. (2017). Proteomic composition and immunomodulatory properties of urinary bladder matrix scaffolds in homeostasis and injury. Seminars in Immunology. 29, 14-23. [PubMed]
Muthusamy, B., Selvan, L. D. N., Nguyen, T. T., Manoj, J., Stawiski, E. W., Jaiswal, B. S., Wang, W., Raja, R., Ramprasad, V. L., Gupta, R., Murugan, S., Kadandale, J. S., Prasad, T. S. K., Reddy, K., Peterson, A., Pandey, A., Seshagiri, S., Girimaji, S. C. and Gowda, H. (2017). Next-generation sequencing reveals novel mutations in X-linked intellectual disability. OMICS: A Journal of Integrative Biology. 21, 295-303. [PubMed]
Weber, H., Valbuena, J. R., Barbhuiya, M. A., Stein, S., Kunkel, H., García, P., Bizama, C., Riquelme, I., Espinoza, J. A., Kurtz, S. E., Tyner, J. W., Calderon, J. F., Corvalán, A. H., Grez, M., Pandey, A., Leal-Rojas, P. and Roa, J. C. (2017). Small molecule inhibitor screening identifified hsp90 inhibitor 17-aag as potential therapeutic agent for gallbladder cancer. Oncotarget. 8, 26169-26184. [PubMed]
Na, C. H. and Pandey, A. (2017). Mass spectrometry reveals respiratory viral infection biomarkers. EBioMedicine. 18, 21-22. [PubMed]
Lu, Y. W., Acoba, M. G., Selvaraju, K., Huang, T. C., Nirujogi, R. S., Sathe, G., Pandey, A. and Claypool, S. M. (2017). Human adenine nucleotide translocases physically and functionally interact with respirasomes. Molecular Biology of The Cell. 28, 1489-1506. [PubMed]
Pandey, A. (2017). Moving to translational proteomics. Proteomics. 17. [PubMed]
Zhang, X., Maity, T., Kashyap, M. K., Bansal, M., Venugopalan, A., Singh, S., Awasthi, S., Marimuthu, A., Charles Jacob, H. K., Belkina, N., Pitts, S., Cultraro, C. M., Gao, S., Kirkali, G., Biswas, R., Chaerkady, R., Califano, A., Pandey, A. and Guha, U. (2017). Quantitative tyrosine phosphoproteomics of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor-treated lung adenocarcinoma cells reveals potential novel biomarkers of therapeutic response. Molecular & Cellular Proteomics : MCP. 16, 891-910. [PubMed]
Lv, D. W., Zhong, J., Zhang, K., Pandey, A. and Li, R. (2017). Understanding epstein-barr virus life cycle with proteomics: a temporal analysis of ubiquitination during virus reactivation. OMICS: A Journal of Integrative Biology. 21, 27-37. [PubMed]
Verma, R., Pinto, S. M., Patil, A. H., Advani, J., Subba, P., Kumar, M., Sharma, J., Dey, G., Ravikumar, R., Buggi, S., Satishchandra, P., Sharma, K., Suar, M., Tripathy, S. P., Chauhan, D. S., Gowda, H., Pandey, A., Gandotra, S. and Prasad, T. S. (2017). Quantitative proteomic and phosphoproteomic analysis of h37ra and h37rv strains of Mycobacterium tuberculosis. Journal of Proteome Research. 16, 1632-1645. [PubMed]
Schnöder, T. M., Eberhardt, J., Koehler, M., Bierhoff, H. B., Weinert, S., Pandey, A. D., Nimmagadda, S. C., Wolleschak, D., Jöhrens, K., Fischer, T. and Heidel, F. H. (2017). Cell autonomous expression of CXCL-10 in JAK2V617F-mutated MPN. Journal of Cancer Research and Clinical Oncology. 143, 807-820. [PubMed]
Bettridge, J., Na, C. H., Pandey, A. and Desiderio, S. (2017). H3H4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase. Proceedings of The National Academy of Sciences of The United States of America. 114, 1904-1909. [PubMed]
Diering, G. H., Nirujogi, R. S., Roth, R. H., Worley, P. F., Pandey, A. and Huganir, R. L. (2017). Homer1a drives homeostatic scaling-down of excitatory synapses during sleep. Science (new York, N.y.). 355, 511-515. [PubMed]
Prasad, T. S., Mohanty, A. K., Kumar, M., Sreenivasamurthy, S. K., Dey, G., Nirujogi, R. S., Pinto, S. M., Madugundu, A. K., Patil, A. H., Advani, J., Manda, S. S., Gupta, M. K., Dwivedi, S. B., Kelkar, D. S., Hall, B., Jiang, X., Peery, A., Rajagopalan, P., Yelamanchi, S. D., Solanki, H. S., Raja, R., Sathe, G. J., Chavan, S., Verma, R., Patel, K. M., Jain, A. P., Syed, N., Datta, K. K., Khan, A. A., Dammalli, M., Jayaram, S., Radhakrishnan, A., Mitchell, C. J., Na, C. H., Kumar, N., Sinnis, P., Sharakhov, I. V., Wang, C., Gowda, H., Tu, Z., Kumar, A. and Pandey, A. (2017). Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. Genome Research. 27, 133-144. [PubMed]
Wu, X., Zahari, M. S., Renuse, S., Kelkar, D. S., Barbhuiya, M. A., Rojas, P. L., Stearns, V., Gabrielson, E., Malla, P., Sukumar, S., Mahajan, N. P. and Pandey, A. (2017). The non-receptor tyrosine kinase TNK2/ACK1 is a novel therapeutic target in triple negative breast cancer. Oncotarget. 8, 2971-2983. [PubMed]
2016
Ugolino, J., Ji, Y. J., Conchina, K., Chu, J., Nirujogi, R. S., Pandey, A., Brady, N. R., Hamacher-Brady, A. and Wang, J. (2016). Loss of C9orf72 enhances autophagic activity via deregulated mTOR and TFEB signaling. Plos Genetics. 12, e1006443. [PubMed]
Rajagopalan, P., Nanjappa, V., Raja, R., Jain, A. P., Mangalaparthi, K. K., Sathe, G. J., Babu, N., Patel, K., Cavusoglu, N., Soeur, J., Pandey, A., Roy, N., Breton, L., Chatterjee, A., Misra, N. and Gowda, H. (2016). How does chronic cigarette smoke exposure affect human skin? a global proteomics study in primary human keratinocytes. OMICS: A Journal of Integrative Biology. 20, 615-626. [PubMed]
Danda, R., Ganapathy, K., Sathe, G., Madugundu, A. K., Ramachandran, S., Krishnan, U. M., Khetan, V., Rishi, P., Keshava Prasad, T. S., Pandey, A., Krishnakumar, S., Gowda, H. and Elchuri, S. V. (2016). Proteomic profiling of retinoblastoma by high resolution mass spectrometry. Clinical Proteomics. 13, 29. [PubMed]
Radhakrishnan, A., Nanjappa, V., Raja, R., Sathe, G., Puttamallesh, V. N., Jain, A. P., Pinto, S. M., Balaji, S. A., Chavan, S., Sahasrabuddhe, N. A., Mathur, P. P., Kumar, M. M., Prasad, T. S., Santosh, V., Sukumar, G., Califano, J. A., Rangarajan, A., Sidransky, D., Pandey, A., Gowda, H. and Chatterjee, A. (2016). A dual specificity kinase, DYRK1A, as a potential therapeutic target for head and neck squamous cell carcinoma. Scientific Reports. 6, 36132. [PubMed]
Sharma, N., LaRusch, J., Sosnay, P. R., Gottschalk, L. B., Lopez, A. P., Pellicore, M. J., Evans, T., Davis, E., Atalar, M., Na, C. H., Rosson, G. D., Belchis, D., Milewski, M., Pandey, A. and Cutting, G. R. (2016). A sequence upstream of canonical PDZ-binding motif within CFTR COOH-terminus enhances NHERF1 interaction. American Journal of Physiology. Lung Cellular and Molecular Physiology. 311, L1170-L1182. [PubMed]
Cha, S. J., Kim, M. S., Pandey, A. and Jacobs-Lorena, M. (2016). Identification of GAPDH on the surface of plasmodium sporozoites as a new candidate for targeting malaria liver invasion. The Journal of Experimental Medicine. 213, 2099-112. [PubMed]
Raja, R., Sahasrabuddhe, N. A., Radhakrishnan, A., Syed, N., Solanki, H. S., Puttamallesh, V. N., Balaji, S. A., Nanjappa, V., Datta, K. K., Babu, N., Renuse, S., Patil, A. H., Izumchenko, E., Prasad, T. S., Chang, X., Rangarajan, A., Sidransky, D., Pandey, A., Gowda, H. and Chatterjee, A. (2016). Chronic exposure to cigarette smoke leads to activation of p21 (RAC1)-activated kinase 6 (PAK6) in non-small cell lung cancer cells. Oncotarget. 7, 61229-61245. [PubMed]
Zhang, H., Liu, T., Zhang, Z., Payne, S. H., Zhang, B., McDermott, J. E., Zhou, J. Y., Petyuk, V. A., Chen, L., Ray, D., Sun, S., Yang, F., Chen, L., Wang, J., Shah, P., Cha, S. W., Aiyetan, P., Woo, S., Tian, Y., Gritsenko, M. A., Clauss, T. R., Choi, C., Monroe, M. E., Thomas, S., Nie, S., Wu, C., Moore, R. J., Yu, K. H., Tabb, D. L., Fenyö, D., Bafna, V., Wang, Y., Rodriguez, H., Boja, E. S., Hiltke, T., Rivers, R. C., Sokoll, L., Zhu, H., Shih, I. M., Cope, L., Pandey, A., Zhang, B., Snyder, M. P., Levine, D. A., Smith, R. D., Chan, D. W., Rodland, K. D. and CPTAC Investigators. (2016). Integrated proteogenomic characterization of human high-grade serous ovarian cancer. Cell. 166, 755-765. [PubMed]
Bhattacharjee, M., Balakrishnan, L., Renuse, S., Advani, J., Goel, R., Sathe, G., Keshava Prasad, T. S., Nair, B., Jois, R., Shankar, S. and Pandey, A. (2016). Synovial fluid proteome in rheumatoid arthritis. Clinical Proteomics. 13, 12. [PubMed]
Mertins, P., Mani, D. R., Ruggles, K. V., Gillette, M. A., Clauser, K. R., Wang, P., Wang, X., Qiao, J. W., Cao, S., Petralia, F., Kawaler, E., Mundt, F., Krug, K., Tu, Z., Lei, J. T., Gatza, M. L., Wilkerson, M., Perou, C. M., Yellapantula, V., Huang, K. L., Lin, C., McLellan, M. D., Yan, P., Davies, S. R., Townsend, R. R., Skates, S. J., Wang, J., Zhang, B., Kinsinger, C. R., Mesri, M., Rodriguez, H., Ding, L., Paulovich, A. G., Fenyö, D., Ellis, M. J., Carr, S. A. and NCI CPTAC. (2016). Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 534, 55-62. [PubMed]
Mitchell, C. J., Kim, M. S., Na, C. H. and Pandey, A. (2016). PyQuant: A versatile framework for analysis of quantitative mass spectrometry data. Molecular & Cellular Proteomics : MCP. 15, 2829-38. [PubMed]
Mitchell, C. J., Kim, M. S., Zhong, J., Nirujogi, R. S., Bose, A. K. and Pandey, A. (2016). Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans. Molecular Oncology. 10, 910-20. [PubMed]
Radhakrishnan, A., Nanjappa, V., Raja, R., Sathe, G., Chavan, S., Nirujogi, R. S., Patil, A. H., Solanki, H., Renuse, S., Sahasrabuddhe, N. A., Mathur, P. P., Prasad, T. S., Kumar, P., Califano, J. A., Sidransky, D., Pandey, A., Gowda, H. and Chatterjee, A. (2016). Dysregulation of splicing proteins in head and neck squamous cell carcinoma. Cancer Biology & Therapy. 17, 219-29. [PubMed]
Jhaveri, D. T., Kim, M. S., Thompson, E. D., Huang, L., Sharma, R., Klein, A. P., Zheng, L., Le, D. T., Laheru, D. A., Pandey, A., Jaffee, E. M. and Anders, R. A. (2016). Using quantitative seroproteomics to identify antibody biomarkers in pancreatic cancer. Cancer Immunology Research. 4, 225-33. [PubMed]
Mirsafian, H., Manda, S. S., Mitchell, C. J., Sreenivasamurthy, S., Ripen, A. M., Mohamad, S. B., Merican, A. F. and Pandey, A. (2016). Long non-coding RNA expression in primary human monocytes. Genomics. 108, 37-45. [PubMed]
Kim, M. S., Zhong, J. and Pandey, A. (2016). Common errors in mass spectrometry-based analysis of post-translational modifications. Proteomics. 16, 700-14. [PubMed]
Yelamanchi, S. D., Jayaram, S., Thomas, J. K., Gundimeda, S., Khan, A. A., Singhal, A., Keshava Prasad, T. S., Pandey, A., Somani, B. L. and Gowda, H. (2016). A pathway map of glutamate metabolism. Journal of Cell Communication and Signaling. 10, 69-75. [PubMed]
Verma, R., Balakrishnan, L., Sharma, K., Khan, A. A., Advani, J., Gowda, H., Tripathy, S. P., Suar, M., Pandey, A., Gandotra, S., Prasad, T. S. and Shankar, S. (2016). A network map of interleukin-10 signaling pathway. Journal of Cell Communication and Signaling. 10, 61-7. [PubMed]
2015
Pawar, H., Srikanth, S. M., Kashyap, M. K., Sathe, G., Chavan, S., Singal, M., Manju, H. C., Kumar, K. V., Vijayakumar, M., Sirdeshmukh, R., Pandey, A., Prasad, T. S., Gowda, H. and Kumar, R. V. (2015). Downregulation of S100 calcium binding protein A9 in esophageal squamous cell carcinoma. The Scientific World Journal. 2015, 325721. [PubMed]
Li, R., Liao, G., Nirujogi, R. S., Pinto, S. M., Shaw, P. G., Huang, T. C., Wan, J., Qian, J., Gowda, H., Wu, X., Lv, D. W., Zhang, K., Manda, S. S., Pandey, A. and Hayward, S. D. (2015). Phosphoproteomic profiling reveals epstein-barr virus protein kinase integration of DNA damage response and mitotic signaling. Plos Pathogens. 11, e1005346. [PubMed]
Baras, A. S., Mitchell, C. J., Myers, J. R., Gupta, S., Weng, L. C., Ashton, J. M., Cornish, T. C., Pandey, A. and Halushka, M. K. (2015). MiRge – a multiplexed method of processing small RNA-seq data to determine microRNA entropy. PLoS One. 10, e0143066. [PubMed]
Mitchell, C. J., Getnet, D., Kim, M. S., Manda, S. S., Kumar, P., Huang, T. C., Pinto, S. M., Nirujogi, R. S., Iwasaki, M., Shaw, P. G., Wu, X., Zhong, J., Chaerkady, R., Marimuthu, A., Muthusamy, B., Sahasrabuddhe, N. A., Raju, R., Bowman, C., Danilova, L., Cutler, J., Kelkar, D. S., Drake, C. G., Prasad, T. S., Marchionni, L., Murakami, P. N., Scott, A. F., Shi, L., Thierry-Mieg, J., Thierry-Mieg, D., Irizarry, R., Cope, L., Ishihama, Y., Wang, C., Gowda, H. and Pandey, A. (2015). A multi-omic analysis of human naïve CD4+ T cells. Bmc Systems Biology. 9, 75. [PubMed]
Subbannayya, T., Leal-Rojas, P., Barbhuiya, M. A., Raja, R., Renuse, S., Sathe, G., Pinto, S. M., Syed, N., Nanjappa, V., Patil, A. H., Garcia, P., Sahasrabuddhe, N. A., Nair, B., Guerrero-Preston, R., Navani, S., Tiwari, P. K., Santosh, V., Sidransky, D., Prasad, T. S., Gowda, H., Roa, J. C., Pandey, A. and Chatterjee, A. (2015). Macrophage migration inhibitory factor – a therapeutic target in gallbladder cancer. BMC Cancer. 15, 843. [PubMed]
Beachley, V. Z., Wolf, M. T., Sadtler, K., Manda, S. S., Jacobs, H., Blatchley, M. R., Bader, J. S., Pandey, A., Pardoll, D. and Elisseeff, J. H. (2015). Tissue matrix arrays for high-throughput screening and systems analysis of cell function. Nature Methods. 12, 1197-204. [PubMed]
Reddy, P. H., Blackmon, J., Molinar-Lopez, V., Ament, C., Manczak, M., Kandimalla, R., Yin, X., Pandey, A., Kuruva, C. S., Wang, R., Fry, D., Osborn, C., Stonum, K., Quesada, K., Gonzales, R. and Boles, A. (2015). Garrison institute on aging: a new hope for elderly individuals and patients with alzheimer’s disease. Journal of Alzheimer’s Disease : JAD. 48, 547-55. [PubMed]
Nanjappa, V., Renuse, S., Sathe, G. J., Raja, R., Syed, N., Radhakrishnan, A., Subbannayya, T., Patil, A., Marimuthu, A., Sahasrabuddhe, N. A., Guerrero-Preston, R., Somani, B. L., Nair, B., Kundu, G. C., Prasad, T. K., Califano, J. A., Gowda, H., Sidransky, D., Pandey, A. and Chatterjee, A. (2015). Chronic exposure to chewing tobacco selects for overexpression of stearoyl-Coa desaturase in normal oral keratinocytes. Cancer Biology & Therapy. 16, 1593-603. [PubMed]
Wu, X., Zahari, M. S., Ma, B., Liu, R., Renuse, S., Sahasrabuddhe, N. A., Chen, L., Chaerkady, R., Kim, M. S., Zhong, J., Jelinek, C., Barbhuiya, M. A., Leal-Rojas, P., Yang, Y., Kashyap, M. K., Marimuthu, A., Ling, M., Fackler, M. J., Merino, V., Zhang, Z., Zahnow, C. A., Gabrielson, E., Stearns, V., Roa, J. C., Sukumar, S., Gill, P. S. and Pandey, A. (2015). Global phosphotyrosine survey in triple-negative breast cancer reveals activation of multiple tyrosine kinase signaling pathways. Oncotarget. 6, 29143-60. [PubMed]
Wu, X., Zahari, M. S., Renuse, S., Nirujogi, R. S., Kim, M. S., Manda, S. S., Stearns, V., Gabrielson, E., Sukumar, S. and Pandey, A. (2015). Phosphoproteomic analysis identifies focal adhesion kinase 2 (FAK2) as a potential therapeutic target for tamoxifen resistance in breast cancer. Molecular & Cellular Proteomics : MCP. 14, 2887-900. [PubMed]
Zahari, M. S., Wu, X., Pinto, S. M., Nirujogi, R. S., Kim, M. S., Fetics, B., Philip, M., Barnes, S. R., Godfrey, B., Gabrielson, E., Nevo, E. and Pandey, A. (2015). Phosphoproteomic profiling of tumor tissues identifies HSP27 ser82 phosphorylation as a robust marker of early ischemia. Scientific Reports. 5, 13660. [PubMed]
Zahari, M. S., Wu, X., Blair, B. G., Pinto, S. M., Nirujogi, R. S., Jelinek, C. A., Malhotra, R., Kim, M. S., Park, B. H. and Pandey, A. (2015). Activating mutations in PIK3CA lead to widespread modulation of the tyrosine phosphoproteome. Journal of Proteome Research. 14, 3882-3891. [PubMed]
Ewing, A. D., Gacita, A., Wood, L. D., Ma, F., Xing, D., Kim, M. S., Manda, S. S., Abril, G., Pereira, G., Makohon-Moore, A., Looijenga, L. H., Gillis, A. J., Hruban, R. H., Anders, R. A., Romans, K. E., Pandey, A., Iacobuzio-Donahue, C. A., Vogelstein, B., Kinzler, K. W., Kazazian HH, J. r. and Solyom, S. (2015). Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution. Genome Research. 25, 1536-45. [PubMed]
Yu, Y., Gaillard, S., Phillip, J. M., Huang, T. C., Pinto, S. M., Tessarollo, N. G., Zhang, Z., Pandey, A., Wirtz, D., Ayhan, A., Davidson, B., Wang, T. L. and Shih, I. e. M. (2015). Inhibition of spleen tyrosine kinase potentiates paclitaxel-induced cytotoxicity in ovarian cancer cells by stabilizing microtubules. Cancer Cell. 28, 82-96. [PubMed]
Sharma, J., Balakrishnan, L., Datta, K. K., Sahasrabuddhe, N. A., Khan, A. A., Sahu, A., Singhal, A., Getnet, D., Raju, R., Chatterjee, A., Gowda, H., Keshava Prasad, T. S., Shankar, S. and Pandey, A. (2015). A knowledgebase resource for interleukin-17 family mediated signaling. Journal of Cell Communication and Signaling. 9, 291-6. [PubMed]
Sharma, R., Gowda, H., Chavan, S., Advani, J., Kelkar, D., Kumar, G. S., Bhattacharjee, M., Chaerkady, R., Prasad, T. S., Pandey, A., Nagaraja, D. and Christopher, R. (2015). Proteomic signature of endothelial dysfunction identified in the serum of acute ischemic stroke patients by the itraq-based lc-ms approach. Journal of Proteome Research. 14, 2466-79. [PubMed]
Subbannayya, Y., Syed, N., Barbhuiya, M. A., Raja, R., Marimuthu, A., Sahasrabuddhe, N., Pinto, S. M., Manda, S. S., Renuse, S., Manju, H. C., Zameer, M. A., Sharma, J., Brait, M., Srikumar, K., Roa, J. C., Vijaya Kumar, M., Kumar, K. V., Prasad, T. S., Ramaswamy, G., Kumar, R. V., Pandey, A., Gowda, H. and Chatterjee, A. (2015). Calcium calmodulin dependent kinase kinase 2 – a novel therapeutic target for gastric adenocarcinoma. Cancer Biology & Therapy. 16, 336-45. [PubMed]
Jamdhade, M. D., Pawar, H., Chavan, S., Sathe, G., Umasankar, P. K., Mahale, K. N., Dixit, T., Madugundu, A. K., Prasad, T. S., Gowda, H., Pandey, A. and Patole, M. S. (2015). Comprehensive proteomics analysis of glycosomes from leishmania donovani. OMICS: A Journal of Integrative Biology. 19, 157-70. [PubMed]
Pandey, A. and Moran, M. F. (2015). Signal transduction. Proteomics. 15, 179-82. [PubMed]
Maras, J. S., Maiwall, R., Harsha, H. C., Das, S., Hussain, M. S., Kumar, C., Bihari, C., Rastogi, A., Kumar, M., Trehanpati, N., Sharma, S., Pandey, A. and Sarin, S. K. (2015). Dysregulated iron homeostasis is strongly associated with multiorgan failure and early mortality in acute-on-chronic liver failure. Hepatology (baltimore, Md.). 61, 1306-20. [PubMed]
Zhang, X., Belkina, N., Jacob, H. K., Maity, T., Biswas, R., Venugopalan, A., Shaw, P. G., Kim, M. S., Chaerkady, R., Pandey, A. and Guha, U. (2015). Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics. Proteomics. 15, 340-55. [PubMed]
Nirujogi, R. S., Wright JD, J. r., Manda, S. S., Zhong, J., Na, C. H., Meyerhoff, J., Benton, B., Jabbour, R., Willis, K., Kim, M. S., Pandey, A. and Sekowski, J. W. (2015). Phosphoproteomic analysis reveals compensatory effects in the piriform cortex of VX nerve agent exposed rats. Proteomics. 15, 487-99. [PubMed]
Ambekar, A. S., Kelkar, D. S., Pinto, S. M., Sharma, R., Hinduja, I., Zaveri, K., Pandey, A., Prasad, T. S., Gowda, H. and Mukherjee, S. (2015). Proteomics of follicular fluid from women with polycystic ovary syndrome suggests molecular defects in follicular development. The Journal of Clinical Endocrinology and Metabolism. 100, 744-53. [PubMed]
Blair, B. G., Wu, X., Zahari, M. S., Mohseni, M., Cidado, J., Wong, H. Y., Beaver, J. A., Cochran, R. L., Zabransky, D. J., Croessmann, S., Chu, D., Toro, P. V., Cravero, K., Pandey, A. and Park, B. H. (2015). A phosphoproteomic screen demonstrates differential dependence on HER3 for MAP kinase pathway activation by distinct PIK3CA mutations. Proteomics. 15, 318-26. [PubMed]
Pinto, S. M., Nirujogi, R. S., Rojas, P. L., Patil, A. H., Manda, S. S., Subbannayya, Y., Roa, J. C., Chatterjee, A., Prasad, T. S. and Pandey, A. (2015). Quantitative phosphoproteomic analysis of il-33-mediated signaling. Proteomics. 15, 532-44. [PubMed]
Syed, N., Barbhuiya, M. A., Pinto, S. M., Nirujogi, R. S., Renuse, S., Datta, K. K., Khan, A. A., Srikumar, K., Prasad, T. S., Kumar, M. V., Kumar, R. V., Chatterjee, A., Pandey, A. and Gowda, H. (2015). Phosphotyrosine profiling identifies ephrin receptor A2 as a potential therapeutic target in esophageal squamous-cell carcinoma. Proteomics. 15, 374-82. [PubMed]
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. (2015). Identification of mir-145 targets through an integrated omics analysis. Molecular Biosystems. 11, 197-207. [PubMed]
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., Srikumar, K., Gowda, H., Santosh, V., Sidransky, D., Califano, J. A., Pandey, A. and Chatterjee, A. (2015). Silencing of high-mobility group box 2 (HMGB2) modulates cisplatin and 5-fluorouracil sensitivity in head and neck squamous cell carcinoma. Proteomics. 15, 383-93. [PubMed]
Zhong, J., Martinez, M., Sengupta, S., Lee, A., Wu, X., Chaerkady, R., Chatterjee, A., O’Meally, R. N., Cole, R. N., Pandey, A. and Zachara, N. E. (2015). Quantitative phosphoproteomics reveals crosstalk between phosphorylation and o-glcnac in the DNA damage response pathway. Proteomics. 15, 591-607. [PubMed]
Huang, T. C., Cutler, J., Bharne, S., Zhong, J., Weinstock, D., Tyner, J., Gojo, I., Civin, C. and Pandey, A. (2015). Integrated analysis of CRLF2 signaling in acute lymphoblastic leukemia identifies polo-like kinase 1 as a potential therapeutic target. Leukemia & Lymphoma. 56, 1524-7. [PubMed]
Kagohara, L. T., Schussel, J. L., Subbannayya, T., Sahasrabuddhe, N., Lebron, C., Brait, M., Maldonado, L., Valle, B. L., Pirini, F., Jahuira, M., Lopez, J., Letelier, P., Brebi-Mieville, P., Ili, C., Pandey, A., Chatterjee, A., Sidransky, D. and Guerrero-Preston, R. (2015). Global and gene-specific DNA methylation pattern discriminates cholecystitis from gallbladder cancer patients in chile. Future Oncology (london, England). 11, 233-49. [PubMed]
2014
Heydarian, M., Luperchio, T. R., Cutler, J., Mitchell, C. J., Kim, M. S., Pandey, A., Sollner-Webb, B. and Reddy, K. (2014). Prediction of gene activity in early B cell development based on an integrative multi-omics analysis. Journal of Proteomics & Bioinformatics. 7, . [PubMed]
Wu, X., Zahari, M. S., Renuse, S., Jacob, H. K., 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 & Therapy. 15, 1593-9. [PubMed]
Pandey, A. and Pevzner, P. A. (2014). Proteogenomics. Proteomics. 14, 2631-2. [PubMed]
Sahu, A., Kumar, S., Sreenivasamurthy, S. K., Selvan, L. D., 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. and Shankar, S. K. (2014). Host response profile of human brain proteome in toxoplasma encephalitis co-infected with HIV. Clinical Proteomics. 11, 39. [PubMed]
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., Mac Gabhann, F., Pandey, A., Raju, R. and Gowda, H. (2014). Signaling network map of endothelial TEK tyrosine kinase. Journal of Signal Transduction. 2014, 173026. [PubMed]
Renuse, S., Madugundu, A. K., Kumar, P., Nair, B. G., Gowda, H., Prasad, T. S. and Pandey, A. (2014). Proteomic analysis and genome annotation of pichia pastoris, a recombinant protein expression host. Proteomics. 14, 2769-79. [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 signalling pathways by oncogenic PIK3CA mutations. Nature Communications. 5, 4961. [PubMed]
SEQC/MAQC-III Consortium. (2014). A comprehensive assessment of rna-seq accuracy, reproducibility and information content by the sequencing quality control consortium. Nature Biotechnology. 32, 903-14. [PubMed]
Murthy, K. R., Goel, R., Subbannayya, Y., Jacob, H. K., Murthy, P. R., Manda, S. S., Patil, A. H., Sharma, R., Sahasrabuddhe, N. A., Parashar, A., Nair, B. G., Krishna, V., Prasad, T. K., Gowda, H. and Pandey, A. (2014). Proteomic analysis of human vitreous humor. Clinical Proteomics. 11, 29. [PubMed]
Luo, W., Lin, B., Wang, Y., Zhong, J., O’Meally, R., Cole, R. N., Pandey, A., Levchenko, A. and Semenza, G. L. (2014). PHD3-mediated prolyl hydroxylation of nonmuscle actin impairs polymerization and cell motility. Molecular Biology of The Cell. 25, 2788-96. [PubMed]
Tong, Z., Kim, M. S., Pandey, A. and Espenshade, P. J. (2014). Identification of candidate substrates for the golgi tul1 E3 ligase using quantitative digly proteomics in yeast. Molecular & Cellular Proteomics : MCP. 13, 2871-82. [PubMed]
Kelkar, D. S., Provost, E., Chaerkady, R., Muthusamy, B., Manda, S. S., Subbannayya, T., Selvan, L. D., 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., 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 & Cellular Proteomics : MCP. 13, 3184-98. [PubMed]
Zhang, B., Wang, J., Wang, X., Zhu, J., Liu, Q., Shi, Z., Chambers, M. C., Zimmerman, L. J., Shaddox, K. F., Kim, S., Davies, S. R., Wang, S., Wang, P., Kinsinger, C. R., Rivers, R. C., Rodriguez, H., Townsend, R. R., Ellis, M. J., Carr, S. A., Tabb, D. L., Coffey, R. J., Slebos, R. J., Liebler, D. C. and NCI, C. P. T. A. C. .. (2014). Proteogenomic characterization of human colon and rectal cancer. Nature. 513, 382-7. [PubMed]
Manda, S. S., Nirujogi, R. S., Pinto, S. M., Kim, M. S., Datta, K. K., Sirdeshmukh, R., Prasad, T. S., 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, 3166-77. [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., 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]
Dwivedi, S. B., Muthusamy, B., Kumar, P., Kim, M. S., Nirujogi, R. S., Getnet, D., Ahiakonu, P., De, G., Nair, B., Gowda, H., Prasad, T. S., Kumar, N., Pandey, A. and Okulate, M. (2014). Brain proteomics of anopheles gambiae. OMICS: A Journal of Integrative Biology. 18, 421-37. [PubMed]
Kim, M. S., Zhong, Y., Yachida, S., Rajeshkumar, N. V., Abel, M. L., Marimuthu, A., Mudgal, K., Hruban, R. H., Poling, J. S., 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 & Cellular Proteomics : MCP. 13, 2803-11. [PubMed]
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., 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., 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, 575-81. [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., Maitra, A., Gowda, H., Hruban, R. H. and Pandey, A. (2014). Pancreatic cancer database: an integrative resource for pancreatic cancer. Cancer Biology & Therapy. 15, 963-7. [PubMed]
Chaiyarit, S., Singhto, N., Chen, Y. J., Cheng, C. Y., Chiangjong, W., Kanlaya, R., Lam, H. H., Peerapen, P., Sung, T. Y., Tipthara, P., Pandey, A., Poon, T. C., Chen, Y. J., Sirdeshmukh, R., Chung, M. C. and Thongboonkerd, V. (2014). Chromosome-centric human proteome project (C-HPP): chromosome 12. Journal of Proteome Research. 13, 3160-5. [PubMed]
Raju, R., Palapetta, S. M., Sandhya, V. K., Sahu, A., Alipoor, A., Balakrishnan, L., Advani, J., George, B., Kini, K. R., Geetha, N. P., Prakash, H. S., Prasad, T. S., Chang, Y. J., Chen, L., Pandey, A. and Gowda, H. (2014). A network map of FGF-1/FGFR signaling system. Journal of Signal Transduction. 2014, 962962. [PubMed]
Gupta, M. K., Jayaram, S., Madugundu, A. K., Chavan, S., Advani, J., Pandey, A., Thongboonkerd, V. and Sirdeshmukh, R. (2014). Chromosome-centric human proteome project: deciphering proteins associated with glioma and neurodegenerative disorders on chromosome 12. Journal of Proteome Research. 13, 3178-90. [PubMed]
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, 306-15. [PubMed]
Chi, Z., Byrne, S. T., Dolinko, A., Harraz, M. M., Kim, M. S., Umanah, G., Zhong, J., Chen, R., Zhang, J., Xu, J., Chen, L., Pandey, A., Dawson, T. M. and Dawson, V. L. (2014). Botch is a ?-glutamyl cyclotransferase that deglycinates and antagonizes notch. Cell Reports. 7, 681-8. [PubMed]
Martin, I., Kim, J. W., Lee, B. D., Kang, H. C., Xu, J. C., Jia, H., Stankowski, J., Kim, M. S., Zhong, J., Kumar, M., Andrabi, S. A., Xiong, Y., Dickson, D. W., Wszolek, Z. K., Pandey, A., Dawson, T. M. and Dawson, V. L. (2014). Ribosomal protein s15 phosphorylation mediates LRRK2 neurodegeneration in parkinson’s disease. Cell. 157, 472-485. [PubMed]
Pinto, S. M., Manda, S. S., Kim, M. S., Taylor, K., Selvan, L. D., Balakrishnan, L., Subbannayya, T., Yan, F., Prasad, T. S., 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, 2749-60. [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, 863-9. [PubMed]
Haeusler, A. R., Donnelly, C. J., Periz, G., Simko, E. A., Shaw, P. G., Kim, M. S., Maragakis, N. J., Troncoso, J. C., Pandey, A., Sattler, R., Rothstein, J. D. and Wang, J. (2014). C9orf72 nucleotide repeat structures initiate molecular cascades of disease. Nature. 507, 195-200. [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, 165-70. [PubMed]
Zhong, J., Sharma, J., Raju, R., Palapetta, S. M., Prasad, T. S., 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 : The Journal of Biological Databases and Curation. 2014, bau007. [PubMed]
Balakrishnan, L., Nirujogi, R. S., Ahmad, S., Bhattacharjee, M., Manda, S. S., Renuse, S., Kelkar, D. S., Subbannayya, Y., Raju, R., Goel, R., Thomas, J. K., Kaur, N., Dhillon, M., Tankala, S. G., Jois, R., Vasdev, V., Ramachandra, Y., 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]
Nagarajha Selvan, L. D., 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. (2014). Proteogenomic analysis of pathogenic yeast cryptococcus neoformans using high resolution mass spectrometry. Clinical Proteomics. 11, 5. [PubMed]
Vega-Rodríguez, J., Ghosh, A. K., Kanzok, S. M., Dinglasan, R. R., Wang, S., Bongio, N. J., Kalume, D. E., Miura, K., Long, C. A., Pandey, A. and Jacobs-Lorena, M. (2014). Multiple pathways for plasmodium ookinete invasion of the mosquito midgut. Proceedings of The National Academy of Sciences of The United States of America. 111, E492-500. [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., 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]
Nanjappa, V., Thomas, J. K., Marimuthu, A., Muthusamy, B., Radhakrishnan, A., Sharma, R., Ahmad Khan, A., Balakrishnan, L., Sahasrabuddhe, N. A., Kumar, S., Jhaveri, B. N., Sheth, K. V., Kumar Khatana, R., 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. (2014). Plasma proteome database as a resource for proteomics research: 2014 update. Nucleic Acids Research. 42, D959-65. [PubMed]
Ahn, J. M., Kim, M. S., Kim, Y. I., Jeong, S. K., Lee, H. J., Lee, S. H., Paik, Y. K., Pandey, A. and Cho, J. Y. (2014). Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues. Journal of Proteome Research. 13, 137-46. [PubMed]
Kleensang, A., Maertens, A., Rosenberg, M., Fitzpatrick, S., Lamb, J., Auerbach, S., Brennan, R., Crofton, K. M., Gordon, B., Fornace AJ, J. r., Gaido, K., Gerhold, D., Haw, R., Henney, A., Ma’ayan, A., McBride, M., Monti, S., Ochs, M. F., Pandey, A., Sharan, R., Stierum, R., Tugendreich, S., Willett, C., Wittwehr, C., Xia, J., Patton, G. W., Arvidson, K., Bouhifd, M., Hogberg, H. T., Luechtefeld, T., Smirnova, L., Zhao, L., Adeleye, Y., Kanehisa, M., Carmichael, P., Andersen, M. E. and Hartung, T. (2014). Pathways of toxicity. Altex. 31, 53-61. [PubMed]
Selvan, L. D., Renuse, S., Kaviyil, J. E., Sharma, J., Pinto, S. M., Yelamanchi, S. D., Puttamallesh, V. N., Ravikumar, R., Pandey, A., Prasad, T. S. and Harsha, H. C. (2014). Phosphoproteome of cryptococcus neoformans. Journal of Proteomics. 97, 287-95. [PubMed]
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. (2014). Moving from unsequenced to sequenced genome: reanalysis of the proteome of leishmania donovani. Journal of Proteomics. 97, 48-61. [PubMed]
2013
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]
Shaw, P. G., Chaerkady, R., Wang, T., Vasilatos, S., Huang, Y., Van Houten, B., Pandey, A. and Davidson, N. E. (2013). Integrated proteomic and metabolic analysis of breast cancer progression. Plos One. 8, e76220. [PubMed]
Taylor, M. S., Ruch, T. R., Hsiao, P. Y., Hwang, Y., Zhang, P., Dai, L., Huang, C. R., Berndsen, C. E., Kim, M. S., Pandey, A., Wolberger, C., Marmorstein, R., Machamer, C., Boeke, J. D. and Cole, P. A. (2013). Architectural organization of the metabolic regulatory enzyme ghrelin o-acyltransferase. The Journal of Biological Chemistry. 288, 32211-28. [PubMed]
Bhattacharjee, M., Sharma, R., Goel, R., Balakrishnan, L., Renuse, S., Advani, J., Gupta, S. T., Verma, R., Pinto, S. M., Sekhar, N. R., 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. R., Srikanth, S. M., Pinto, S. M., Bhattacharjee, M., Kelkar, D. S., Madugundu, A. K., Dey, G., Mohan, S. S., Krishna, V., Prasad, T. 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., 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. 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. (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., Pinto, S. M., Sahasrabuddhe, N. A., Kim, M. S., Delanghe, B., Srinivasan, N., Emili, A., Kaper, J. B. and Pandey, A. (2013). The escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathogens. 9, e1003403. [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, 3128-38. [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, 122-31. [PubMed]
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. (2013). Proteomic analysis of human follicular fluid: a new perspective towards understanding folliculogenesis. Journal of Proteomics. 87, 68-77. [PubMed]
Harsha, H. C., Pinto, S. M. and Pandey, A. (2013). Proteomic strategies to characterize signaling pathways. Methods in Molecular Biology (clifton, N.j.). 1007, 359-77. [PubMed]
Marimuthu, A., Chavan, S., Sathe, G., Sahasrabuddhe, N. A., Srikanth, S. M., Renuse, S., Ahmad, S., Radhakrishnan, A., Barbhuiya, M. A., Kumar, R. V., Harsha, H. C., Sidransky, D., Califano, J., Pandey, A. and Chatterjee, A. (2013). Identification of head and neck squamous cell carcinoma biomarker candidates through proteomic analysis of cancer cell secretome. Biochimica Et Biophysica Acta. 1834, 2308-16. [PubMed]
Patel, K., Scrimieri, F., Ghosh, S., Zhong, J., Kim, M. S., Ren, Y. R., Morgan, R. A., Iacobuzio-Donahue, C. A., Pandey, A. and Kern, S. E. (2013). FAM190A deficiency creates a cell division defect. The American Journal of Pathology. 183, 296-303. [PubMed]
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. (2013). IL-11/IL11RA receptor mediated signaling: a web accessible knowledgebase. Cell Communication & Adhesion. 20, 81-6. [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. (2013). A network map of BDNF/TRKB and bdnf/p75ntr signaling system. Journal of Cell Communication and Signaling. 7, 301-7. [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]
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. (2013). Quantitative proteomics for identifying biomarkers for rabies. Clinical Proteomics. 10, 3. [PubMed]
Muthusamy, B., Thomas, J. K., Prasad, T. S. and Pandey, A. (2013). Access guide to human proteinpedia. Current Protocols in Bioinformatics. Chapter 1, Unit 1.21. [PubMed]
Dua, V. K., Kumar, A., Pandey, A. C. and Kumar, S. (2013). Insecticidal and genotoxic activity of psoralea corylifolia linn. (fabaceae) against culex quinquefasciatus say, 1823. Parasites & Vectors. 6, 30. [PubMed]
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. (2012-2013). 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 : Section A of Disease Markers. 12, 1-9. [PubMed]
Bhattacharya, S. K., Lee, R. K., Grus, F. H. and Seventh ARVO/Pfizer Ophthalmics Research Institute Conference Working, G. r. o. u. p. .. (2013). Molecular biomarkers in glaucoma. Investigative Ophthalmology & Visual Science. 54, 121-31. [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. (2013). Signaling network of oncostatin M pathway. Journal of Cell Communication and Signaling. 7, 103-8. [PubMed]
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. (2013). SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics. Clinical Applications. 7, 355-66. [PubMed]
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. (2013). A multicellular signal transduction network of AGE/RAGE signaling. Journal of Cell Communication and Signaling. 7, 19-23. [PubMed]
Nanda, N., Singh, O. P., Dua, V. K., Pandey, A. C., Nagpal, B. N., Adak, T., Dash, A. P. and Subbarao, S. K. (2013). Population cytogenetic and molecular evidence for existence of a new species in anopheles fluviatilis complex (diptera: culicidae). Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 13, 218-23. [PubMed]
Huang, T. C., Pinto, S. M. and Pandey, A. (2013). Proteomics for understanding mirna biology. Proteomics. 13, 558-67. [PubMed]
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. (2013). Downregulation of cornulin in esophageal squamous cell carcinoma. Acta Histochemica. 115, 89-99. [PubMed]
2012
Kumar, G. S., Venugopal, A. K., Kashyap, M. K., Raju, R., Marimuthu, A., Palapetta, S. M., Subbanayya, Y., Goel, R., Chawla, A., Dikshit, J. B., Tata, P., Harsha, H. C., Maharudraiah, J., Ramachandra, Y. L., Satishchandra, P., Prasad, T. S., Pandey, A., Mahadevan, A. and Shankar, S. K. (2012). Gene expression profiling of tuberculous meningitis co-infected with HIV. Journal of Proteomics & Bioinformatics. 5, 235-244. [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 & Bioinformatics. 5, 122-126. [PubMed]
Venugopal, A. K., Sameer Kumar, G. S., Mahadevan, A., Selvan, L. D., Marimuthu, A., Dikshit, J. B., Tata, P., Ramachandra, Y., Chaerkady, R., Sinha, S., Chandramouli, B., Arivazhagan, A., Satishchandra, P., Shankar, S. and Pandey, A. (2012). Transcriptomic profiling of medial temporal lobe epilepsy. Journal of Proteomics & Bioinformatics. 5, . [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., Inal, J. M., Jenster, G., Krämer-Albers, E. M., Lim, S. K., Llorente, A., Lötvall, J., Marcilla, A., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-‘t Hoen, E. N., Pandey, A., Patel, T., Piper, M. G., Pluchino, S., Prasad, T. S., Rajendran, L., Raposo, G., Record, M., Reid, G. E., Sánchez-Madrid, F., Schiffelers, R. M., Siljander, P., Stensballe, A., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B. W., Vázquez, J., Vidal, M., Wauben, M. H., Yáñez-Mó, M., Zoeller, M. and Mathivanan, S. (2012). Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PLoS Biology. 10, e1001450. [PubMed]
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. (2012). Quantitative proteomics for identifying biomarkers for tuberculous meningitis. Clinical Proteomics. 9, 12. [PubMed]
Luo, W., Chang, R., Zhong, J., Pandey, A. and Semenza, G. L. (2012). 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. 109, E3367-76. [PubMed]
Ren, Y. R., Chaerkady, R., Hu, S., Wan, J., Qian, J., Zhu, H., Pandey, A. and Kern, S. E. (2012). Unbiased discovery of interactions at a control locus driving expression of the cancer-specific therapeutic and diagnostic target, mesothelin. Journal of Proteome Research. 11, 5301-10. [PubMed]
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. (2012). Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (cmas). Journal of Proteome Research. 11, 5556-63. [PubMed]
van Bodegom, D., Zhong, J., Kopp, N., Dutta, C., Kim, M. S., Bird, L., Weigert, O., Tyner, J., Pandey, A., Yoda, A. and Weinstock, D. M. (2012). Differences in signaling through the b-cell leukemia oncoprotein CRLF2 in response to TSLP and through mutant JAK2. Blood. 120, 2853-63. [PubMed]
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. (2012). Proteomic analysis of an unsequenced plant–mangifera indica. Journal of Proteomics. 75, 5793-6. [PubMed]
Do Vale, L. H., Gómez-Mendoza, D. P., Kim, M. S., Pandey, A., Ricart, C. A., Ximenes F Filho, E. and Sousa, M. V. (2012). Secretome analysis of the fungus trichoderma harzianum grown on cellulose. Proteomics. 12, 2716-28. [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. 9, 7. [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., Pandey, A., Shemanko, C. and Chatterjee, A. (2012). A pathway map of prolactin signaling. Journal of Cell Communication and Signaling. 6, 169-73. [PubMed]
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. (2012). A bioinformatics resource for tweak-fn14 signaling pathway. Journal of Signal Transduction. 2012, 376470. [PubMed]
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. (2012). A proteogenomic approach to map the proteome of an unsequenced pathogen – leishmania donovani. Proteomics. 12, 832-44. [PubMed]
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. (2012). Identification of targets of c-src tyrosine kinase by chemical complementation and phosphoproteomics. Molecular & Cellular Proteomics : MCP. 11, 355-69. [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 & Cellular Proteomics : MCP. 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, 2193-205. [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, 2141-52. [PubMed]
Kim, M. S. and Pandey, A. (2012). Electron transfer dissociation mass spectrometry in proteomics. Proteomics. 12, 530-42. [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 signaling and other protein groups of regulatory functions. Molecular & Cellular Proteomics : MCP. 11, M111.013565. [PubMed]
Goel, R., Harsha, H. C., Pandey, A. and Prasad, T. S. (2012). Human protein reference database and human proteinpedia as resources for phosphoproteome analysis. Molecular Biosystems. 8, 453-63. [PubMed]
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. (2012). Proteogenomic analysis of candida glabrata using high resolution mass spectrometry. Journal of Proteome Research. 11, 247-60. [PubMed]
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. (2012). Recommendations for mass spectrometry data quality metrics for open access data (corollary to the amsterdam principles). Proteomics. 12, 11-20. [PubMed]
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. (2012). Recommendations for mass spectrometry data quality metrics for open access data (corollary to the amsterdam principles). Journal of Proteome Research. 11, 1412-9. [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, 175-87. [PubMed]
2011
Marimuthu, A., Jacob, H. K., Jakharia, A., Subbannayya, Y., Keerthikumar, S., Kashyap, M. K., Goel, R., Balakrishnan, L., Dwivedi, S., Pathare, S., Dikshit, J. B., Maharudraiah, J., Singh, S., Sameer Kumar, G. S., Vijayakumar, M., Veerendra Kumar, K. V., Premalatha, C. S., Tata, P., Hariharan, R., Roa, J. C., Prasad, T. S., Chaerkady, R., Kumar, R. V. and Pandey, A. (2011). Gene expression profiling of gastric cancer. Journal of Proteomics & Bioinformatics. 4, 74-82. [PubMed]
Goel, R., Raju, R., Maharudraiah, J., Sameer Kumar, G. S., Ghosh, K., Kumar, A., Lakshmi, T. P., 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 Keshava Prasad, T. S. (2011). A signaling network of thyroid-stimulating hormone. Journal of Proteomics & Bioinformatics. 4, . [PubMed]
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 JR, 3. r. d. and Rodriguez, H. (2011). Recommendations for mass spectrometry data quality metrics for open access data (corollary to the amsterdam principles). Proteomics. Clinical Applications. 5, 580-9. [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, 4443-53. [PubMed]
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 JR, 3. r. d. and Rodriguez, H. (2011). Recommendations for mass spectrometry data quality metrics for open access data (corollary to the amsterdam principles). Molecular & Cellular Proteomics : MCP. 10, O111.015446. [PubMed]
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. (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., 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 & Cellular Proteomics : MCP. 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. 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 Mohan, S., Schiemann, W. P. and Pandey, A. (2011). NetSlim: high-confidence curated signaling maps. Database : The Journal of Biological Databases and Curation. 2011, bar032. [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., Keshava Prasad, T. S., Okulate, M., Kumar, N. and Pandey, A. (2011). A proteogenomic analysis of anopheles gambiae using high-resolution fourier transform mass spectrometry. Genome Research. 21, 1872-81. [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, 4007-20. [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., Kumar, K. V., Vijayakumar, M., Chaerkady, R., Prasad, T. S., Kumar, R. V., Kumar, R. V. and Pandey, A. (2011). Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biology & Therapy. 12, 510-22. [PubMed]
Raju, R., Balakrishnan, L., Nanjappa, V., Bhattacharjee, M., Getnet, D., Muthusamy, B., Kurian Thomas, J., 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. (2011). A comprehensive manually curated reaction map of rankl/rank-signaling pathway. Database : The Journal of Biological Databases and Curation. 2011, bar021. [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 & Bioinformatics. 4, 22-35. [PubMed]
Hyland, E. M., Molina, H., Poorey, K., Jie, C., Xie, Z., Dai, J., Qian, J., Bekiranov, S., Auble, D. T., Pandey, A. and Boeke, J. D. (2011). An evolutionarily ‘young’ lysine residue in histone H3 attenuates transcriptional output in saccharomyces cerevisiae. Genes & Development. 25, 1306-19. [PubMed]
Luo, W., Hu, H., Chang, R., Zhong, J., Knabel, M., O’Meally, R., Cole, R. N., Pandey, A. and Semenza, G. L. (2011). Pyruvate kinase M2 is a phd3-stimulated coactivator for hypoxia-inducible factor 1. Cell. 145, 732-44. [PubMed]
Shao, H., Chaerkady, R., Chen, S., Pinto, S. M., Sharma, R., Delanghe, B., Birk, D. E., Pandey, A. and Chakravarti, S. (2011). Proteome profiling of wild type and lumican-deficient mouse corneas. Journal of Proteomics. 74, 1895-905. [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, 2568-72. [PubMed]
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. (2011). A comprehensive map of the human urinary proteome. Journal of Proteome Research. 10, 2734-43. [PubMed]
Shaw, P. G., Chaerkady, R., Zhang, Z., Davidson, N. E. and Pandey, A. (2011). Monoclonal antibody cocktail as an enrichment tool for acetylome analysis. Analytical Chemistry. 83, 3623-6. [PubMed]
Nair, S., Pandey, A. D. and Mukhopadhyay, S. (2011). The PPE18 protein of mycobacterium tuberculosis inhibits nf-?b/rel-mediated proinflammatory cytokine production by upregulating and phosphorylating suppressor of cytokine signaling 3 protein. Journal of Immunology (baltimore, Md. : 1950). 186, 5413-24. [PubMed]
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. (2011). Mutant proteins as cancer-specific biomarkers. Proceedings of The National Academy of Sciences of The United States of America. 108, 2444-9. [PubMed]
Renuse, S., Chaerkady, R. and Pandey, A. (2011). Proteogenomics. Proteomics. 11, 620-30. [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]
Goel, R., Muthusamy, B., Pandey, A. and Prasad, T. S. (2011). Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. Molecular Biotechnology. 48, 87-95. [PubMed]
Zachara, N. E., Molina, H., Wong, K. Y., Pandey, A. and Hart, G. W. (2011). The dynamic stress-induced “o-glcnac-ome” highlights functions for o-glcnac in regulating DNA damage/repair and other cellular pathways. Amino Acids. 40, 793-808. [PubMed]
2010
Kashyap, M. K., Marimuthu, A., Peri, S., Kumar, G. S., Jacob, H. K., Prasad, T. S., Mahmood, R., Kumar, K. V., Kumar, M. V., 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, 133-42. [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, 3800-10. [PubMed]
Harsha, H. C. and Pandey, A. (2010). Phosphoproteomics in cancer. Molecular Oncology. 4, 482-95. [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., Ruebenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K. H., 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., Le Novère, N., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C. and Bader, G. D. (2010). The biopax community standard for pathway data sharing. Nature Biotechnology. 28, 935-42. [PubMed]
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. (2010). The axl receptor tyrosine kinase is an adverse prognostic factor and a therapeutic target in esophageal adenocarcinoma. Cancer Biology & Therapy. 10, 1009-18. [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, 5228-38. [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., 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 & Therapy. 10, 796-810. [PubMed]
Yang, Y., Chaerkady, R., Kandasamy, K., Huang, T. C., Selvan, L. D., 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, 1873-82. [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, 1606-11. [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 : An International Journal For Rapid Publication of Reports On Genes and Genomes. 17, 197-208. [PubMed]
Zhong, J. and Pandey, A. (2010). Site-directed mutagenesis reveals a unique requirement for tyrosine residues in il-7ralpha and TSLPR cytoplasmic domains in tslp-dependent cell proliferation. Bmc Immunology. 11, 5. [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, 1359-73. [PubMed]
Zhong, J., Liu, X. and Pandey, A. (2010). Effects of transmembrane and juxtamembrane domains on proliferative ability of TSLP receptor. Molecular Immunology. 47, 1207-15. [PubMed]
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. (2010). NetPath: a public resource of curated signal transduction pathways. Genome Biology. 11, R3. [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, 1029-39. [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)-1alpha but not hif-2alpha. The Journal of Biological Chemistry. 285, 3651-63. [PubMed]
2009
Venugopal, A., Chaerkady, R. and Pandey, A. (2009). Application of mass spectrometry-based proteomics for biomarker discovery in neurological disorders. Annals of Indian Academy of Neurology. 12, 3-11. [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 : An International Journal For Rapid Publication of Reports On Genes and Genomes. 16, 345-51. [PubMed]
Prasad, T. S., Kandasamy, K. and Pandey, A. (2009). Human protein reference database and human proteinpedia as discovery tools for systems biology. Methods in Molecular Biology (clifton, N.j.). 577, 67-79. [PubMed]
Parikh, K., Diks, S. H., Tuynman, J. H., Verhaar, A., Löwenberg, M., Hommes, D. W., Joore, J., Pandey, A. and Peppelenbosch, M. P. (2009). Comparison of peptide array substrate phosphorylation of c-raf and mitogen activated protein kinase kinase kinase 8. PLoS One. 4, e6440. [PubMed]
Kandasamy, K., Pandey, A. and Molina, H. (2009). Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Analytical Chemistry. 81, 7170-80. [PubMed]
Amanchy, R., Zhong, J., Hong, R., Kim, J. H., Gucek, M., Cole, R. N., Molina, H. and Pandey, A. (2009). Identification of c-src tyrosine kinase substrates in platelet-derived growth factor receptor signaling. Molecular Oncology. 3, 439-50. [PubMed]
Kandasamy, K., Keerthikumar, S., Raju, R., Keshava Prasad, T. S., Ramachandra, Y. L., Mohan, S. and Pandey, A. (2009). PathBuilder–open source software for annotating and developing pathway resources. Bioinformatics (oxford, England). 25, 2860-2. [PubMed]
Dua, V. K., Pandey, A. C., Raghavendra, K., Gupta, A., Sharma, T. and Dash, A. P. (2009). Larvicidal activity of neem oil (azadirachta indica) formulation against mosquitoes. Malaria Journal. 8, 124. [PubMed]
Li, X., Molina, H., Huang, H., Zhang, Y. Y., Liu, M., Qian, S. W., Slawson, C., Dias, W. B., Pandey, A., Hart, G. W., Lane, M. D. and Tang, Q. Q. (2009). O-linked n-acetylglucosamine modification on CCAAT enhancer-binding protein beta: role during adipocyte differentiation. The Journal of Biological Chemistry. 284, 19248-54. [PubMed]
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. (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, 405-12. [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, 1374-84. [PubMed]
Pimienta, G., Chaerkady, R. and Pandey, A. (2009). SILAC for global phosphoproteomic analysis. Methods in Molecular Biology (clifton, N.j.). 527, 107-16, x. [PubMed]
Cooper, E. M., Cutcliffe, C., Kristiansen, T. Z., Pandey, A., Pickart, C. M. and Cohen, R. E. (2009). K63-specific deubiquitination by two JAMM/MPN+ complexes: brisc-associated brcc36 and proteasomal poh1. The Embo Journal. 28, 621-31. [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, 1315-26. [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]
Keshava Prasad, T. S., 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 Kishore, C. J., 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. (2009). Human protein reference database–2009 update. Nucleic Acids Research. 37, D767-72. [PubMed]
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. (2009). Genomewide mrna profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biology & Therapy. 8, 36-46. [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., Keshava Prasad, T. S. and Pandey, A. (2009). Human proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Research. 37, D773-81. [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 five-plex SILAC based strategy. Journal of Proteome Research. 8, 48-58. [PubMed]
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. (2009). RAPID: resource of asian primary immunodeficiency diseases. Nucleic Acids Research. 37, D863-7. [PubMed]
2008
Chaerkady, R., Thuluvath, P. J., Kim, M. S., Nalli, A., Vivekanandan, P., Simmers, J., Torbenson, M. and Pandey, A. (2008). O labeling for a quantitative proteomic analysis of glycoproteins in hepatocellular carcinoma. Clinical Proteomics. 4, 137-155. [PubMed]
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. (2008). 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. 105, 16653-8. [PubMed]
Song, D., Chaerkady, R., Tan, A. C., García-García, E., Nalli, A., Suárez-Gauthier, A., López-Ríos, F., Zhang, X. F., Solomon, A., Tong, J., Read, M., Fritz, C., Jimeno, A., Pandey, A. and Hidalgo, M. (2008). Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer. Molecular Cancer Therapeutics. 7, 3275-84. [PubMed]
Kristiansen, T. Z., Harsha, H. C., Grønborg, M., Maitra, A. and Pandey, A. (2008). Differential membrane proteomics using 18o-labeling to identify biomarkers for cholangiocarcinoma. Journal of Proteome Research. 7, 4670-7. [PubMed]
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. (2008). Activated epidermal growth factor receptor as a novel target in pancreatic cancer therapy. Journal of Proteome Research. 7, 4651-8. [PubMed]
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. (2008). 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. 105, 14112-7. [PubMed]
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. (2008). Identification of secreted proteins that mediate cell-cell interactions in an in vitro model of the lung cancer microenvironment. Cancer Research. 68, 7237-45. [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, 4289-98. [PubMed]
Sarker, R., Grønborg, M., Cha, B., Mohan, S., Chen, Y., Pandey, A., Litchfield, D., Donowitz, M. and Li, X. (2008). 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. 19, 3859-70. [PubMed]
Mathivanan, S. and Pandey, A. (2008). Human proteinpedia as a resource for clinical proteomics. Molecular & Cellular Proteomics : MCP. 7, 2038-47. [PubMed]
Luo, W., Slebos, R. J., Hill, S., Li, M., Brábek, J., Amanchy, R., Chaerkady, R., Pandey, A., Ham, A. J. and Hanks, S. K. (2008). Global impact of oncogenic src on a phosphotyrosine proteome. Journal of Proteome Research. 7, 3447-60. [PubMed]
Molina, H., Matthiesen, R., Kandasamy, K. and Pandey, A. (2008). Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Analytical Chemistry. 80, 4825-35. [PubMed]
Harsha, H. C., Molina, H. and Pandey, A. (2008). Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nature Protocols. 3, 505-16. [PubMed]
Mathivanan, S., Ahmed, M., Ahn, N. G., Alexandre, H., Amanchy, R., Andrews, P. C., Bader, J. S., Balgley, B. M., Bantscheff, M., Bennett, K. L., Björling, E., Blagoev, B., Bose, R., Brahmachari, S. K., Burlingame, A. S., Bustelo, X. R., Cagney, G., Cantin, G. T., Cardasis, H. L., Celis, J. E., Chaerkady, R., Chu, F., Cole, P. A., Costello, C. E., Cotter, R. J., Crockett, D., DeLany, J. P., De Marzo, A. M., DeSouza, L. V., Deutsch, E. W., Dransfield, E., Drewes, G., Droit, A., Dunn, M. J., Elenitoba-Johnson, K., Ewing, R. M., Van Eyk, J., Faca, V., Falkner, J., Fang, X., Fenselau, C., Figeys, D., Gagné, P., Gelfi, C., Gevaert, K., Gimble, J. M., Gnad, F., Goel, R., Gromov, P., Hanash, S. M., Hancock, W. S., Harsha, H. C., Hart, G., Hays, F., He, F., Hebbar, P., Helsens, K., Hermeking, H., Hide, W., Hjernø, K., Hochstrasser, D. F., Hofmann, O., Horn, D. M., Hruban, R. H., Ibarrola, N., James, P., Jensen, O. N., Jensen, P. H., Jung, P., Kandasamy, K., Kheterpal, I., Kikuno, R. F., Korf, U., Körner, R., Kuster, B., Kwon, M. S., Lee, H. J., Lee, Y. J., Lefevre, M., Lehvaslaiho, M., Lescuyer, P., Levander, F., Lim, M. S., Löbke, C., Loo, J. A., Mann, M., Martens, L., 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. (2008). Human proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-7. [PubMed]
Karanjawala, Z. E., Illei, P. B., Ashfaq, R., Infante, J. R., Murphy, K., Pandey, A., Schulick, R., Winter, J., Sharma, R., Maitra, A., Goggins, M. and Hruban, R. H. (2008). New markers of pancreatic cancer identified through differential gene expression analyses: claudin 18 and annexin A8. The American Journal of Surgical Pathology. 32, 188-96. [PubMed]
Chaerkady, R. and Pandey, A. (2008). Applications of proteomics to lab diagnosis. Annual Review of Pathology. 3, 485-98. [PubMed]
2007
Chaerkady, R. and Pandey, A. (2007). Quantitative proteomics for identification of cancer biomarkers. Proteomics. Clinical Applications. 1, 1080-9. [PubMed]
Zhong, J., Molina, H. and Pandey, A. (2007). Phosphoproteomics. Current Protocols in Protein Science. Chapter 24, Unit 24.4. [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, 1592-9. [PubMed]
Bhandari, R., Saiardi, A., Ahmadibeni, Y., Snowman, A. M., Resnick, A. C., Kristiansen, T. Z., Molina, H., Pandey, A., Werner JK, J. r., Juluri, K. R., Xu, Y., Prestwich, G. D., Parang, K. and Snyder, S. H. (2007). Protein pyrophosphorylation by inositol pyrophosphates is a posttranslational event. Proceedings of The National Academy of Sciences of The United States of America. 104, 15305-10. [PubMed]
Dinglasan, R. R., Kalume, D. E., Kanzok, S. M., Ghosh, A. K., Muratova, O., Pandey, A. and Jacobs-Lorena, M. (2007). Disruption of plasmodium falciparum development by antibodies against a conserved mosquito midgut antigen. Proceedings of The National Academy of Sciences of The United States of America. 104, 13461-6. [PubMed]
Wang, Z., Pandey, A. and Hart, G. W. (2007). Dynamic interplay between o-linked n-acetylglucosaminylation and glycogen synthase kinase-3-dependent phosphorylation. Molecular & Cellular Proteomics : MCP. 6, 1365-79. [PubMed]
Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R., Tattikota, S. G. and Pandey, A. (2007). A curated compendium of phosphorylation motifs. Nature Biotechnology. 25, 285-6. [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 of The United States of America. 104, 2199-204. [PubMed]
Kim, J. W., Monila, H., Pandey, A. and Lane, M. D. (2007). Upstream stimulatory factors regulate the C/EBP alpha gene during differentiation of 3T3-L1 preadipocytes. Biochemical and Biophysical Research Communications. 354, 517-21. [PubMed]
2006
Mathivanan, S., Periaswamy, B., Gandhi, T. K., 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 Suppl 5, S19. [PubMed]
Liu, B., Molina, H., Kalume, D., Pandey, A., Griffith, J. D. and Englund, P. T. (2006). Role of p38 in replication of trypanosoma brucei kinetoplast DNA. Molecular and Cellular Biology. 26, 5382-93. [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 of The United States of America. 103, 9773-8. [PubMed]
Lerin, C., Rodgers, J. T., Kalume, D. E., Kim, S. H., Pandey, A. and Puigserver, P. (2006). GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of pgc-1alpha. Cell Metabolism. 3, 429-38. [PubMed]
Wang, D., Kalume, D., Pickart, C., Pandey, A. and Cotter, R. J. (2006). Identification of protein ubiquitylation by electrospray ionization tandem mass spectrometric analysis of sulfonated tryptic peptides. Analytical Chemistry. 78, 3681-7. [PubMed]
Moff, S. L., Clark, D. P., Maitra, A., Pandey, A. and Thuluvath, P. J. (2006). Utility of bile duct brushings for the early detection of cholangiocarcinoma in patients with primary sclerosing cholangitis. Journal of Clinical Gastroenterology. 40, 336-41. [PubMed]
Qiao, Y., Molina, H., Pandey, A., Zhang, J. and Cole, P. A. (2006). Chemical rescue of a mutant enzyme in living cells. Science (new York, N.y.). 311, 1293-7. [PubMed]
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. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 38, 285-93. [PubMed]
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. (2006). Human protein reference database–2006 update. Nucleic Acids Research. 34, D411-4. [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. (2006). Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Molecular & Cellular Proteomics : MCP. 5, 157-71. [PubMed]
2005
Raghothama, C., Harsha, H. C., Prasad, C. K. and Pandey, A. (2005). Bioinformatics and proteomics approaches for aging research. Biogerontology. 6, 227-32. [PubMed]
Gandhi, T. K., Chandran, S., Peri, S., Saravana, R., Amanchy, R., Prasad, T. S. and Pandey, A. (2005). A bioinformatics analysis of protein tyrosine phosphatases in humans. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 12, 79-89. [PubMed]
Hyland, E. M., Cosgrove, M. S., Molina, H., Wang, D., Pandey, A., Cottee, R. J. and Boeke, J. D. (2005). Insights into the role of histone H3 and histone H4 core modifiable residues in saccharomyces cerevisiae. Molecular and Cellular Biology. 25, 10060-70. [PubMed]
Suresh, S., Sujatha Mohan, S., Mishra, G., Hanumanthu, G. R., Suresh, M., Reddy, R. and Pandey, A. (2005). Proteomic resources: integrating biomedical information in humans. Gene. 364, 13-8. [PubMed]
Kalume, D. E., Peri, S., Reddy, R., Zhong, J., Okulate, M., Kumar, N. and Pandey, A. (2005). Genome annotation of anopheles gambiae using mass spectrometry-derived data. Bmc Genomics. 6, 128. [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, 3765-77. [PubMed]
Bala, P., Georgantas RW, 3. r. d., Sudhir, D., Suresh, M., Shanker, K., Vrushabendra, B. M., Civin, C. I. and Pandey, A. (2005). TAGmapper: a web-based tool for mapping SAGE tags. Gene. 364, 123-9. [PubMed]
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. (2005). A functional annotation of subproteomes in human plasma. Proteomics. 5, 3506-19. [PubMed]
Omenn, G. S., States, D. J., Adamski, M., Blackwell, T. W., Menon, R., Hermjakob, H., Apweiler, R., Haab, B. B., Simpson, R. J., Eddes, J. S., Kapp, E. A., Moritz, R. L., Chan, D. W., Rai, A. J., Admon, A., Aebersold, R., Eng, J., Hancock, W. S., Hefta, S. A., Meyer, H., Paik, Y. K., Yoo, J. S., Ping, P., Pounds, J., Adkins, J., Qian, X., Wang, R., Wasinger, V., Wu, C. Y., Zhao, X., Zeng, R., Archakov, A., Tsugita, A., Beer, I., Pandey, A., Pisano, M., Andrews, P., Tammen, H., Speicher, D. W. and Hanash, S. M. (2005). Overview of the HUPO plasma proteome project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 5, 3226-45. [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, 951-9. [PubMed]
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. (2005). Plasma proteome database as a resource for proteomics research. Proteomics. 5, 3531-6. [PubMed]
Tang, Q. Q., Grønborg, M., Huang, H., Kim, J. W., Otto, T. C., Pandey, A. and Lane, M. D. (2005). Sequential phosphorylation of CCAAT enhancer-binding protein beta by MAPK and glycogen synthase kinase 3beta is required for adipogenesis. Proceedings of The National Academy of Sciences of The United States of America. 102, 9766-71. [PubMed]
Chowdhury, U. K., Airan, B., Kothari, S. S., Pandey, A., Subramaniam, K. G. and Venugopal, P. (2005). Right pulmonary artery-to-left atrium communication: report of 5 cases. The Annals of Thoracic Surgery. 80, 336-8. [PubMed]
Molina, H., Parmigiani, G. and Pandey, A. (2005). Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. Analytical Chemistry. 77, 2739-44. [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., Ghosh, N., Chandran, S., Menezes, M., Joy, M., Mohan, S. S., Katsanis, N., Deshpande, K. S., Raghothama, C., Prasad, C. K. and Pandey, A. (2005). A manually curated functional annotation of the human X chromosome. Nature Genetics. 37, 331-2. [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 & Cellular Proteomics : MCP. 4, 637-50. [PubMed]
Amanchy, R., Kalume, D. E. and Pandey, A. (2005). Stable isotope labeling with amino acids in cell culture (SILAC) for studying dynamics of protein abundance and posttranslational modifications. Science’s Stke : Signal Transduction Knowledge Environment. 2005, pl2. [PubMed]
2004
Kristiansen, T. Z., Nielsen, M. M., Blagoev, B., Pandey, A. and Mann, M. (2004). Mouse embryonic fibroblasts derived from odin deficient mice display a hyperproliiferative phenotype. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 11, 285-92. [PubMed]
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. (2004). Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression. Cancer Biology & Therapy. 3, 1254-61. [PubMed]
Grønborg, M., Bunkenborg, J., Kristiansen, T. Z., Jensen, O. N., Yeo, C. J., Hruban, R. H., Maitra, A., Goggins, M. G. and Pandey, A. (2004). Comprehensive proteomic analysis of human pancreatic juice. Journal of Proteome Research. 3, 1042-55. [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 & Therapy. 3, 1081-9; discussion 1090-1. [PubMed]
Koopmann, J., Thuluvath, P. J., Zahurak, M. L., Kristiansen, T. Z., Pandey, A., Schulick, R., Argani, P., Hidalgo, M., Iacobelli, S., Goggins, M. and Maitra, A. (2004). Mac-2-binding protein is a diagnostic marker for biliary tract carcinoma. Cancer. 101, 1609-15. [PubMed]
Al-Shami, A., Spolski, R., Kelly, J., Fry, T., Schwartzberg, P. L., Pandey, A., Mackall, C. L. and Leonard, W. J. (2004). A role for thymic stromal lymphopoietin in CD4(+) T cell development. The Journal of Experimental Medicine. 200, 159-68. [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 of The United States of America. 101, 9309-14. [PubMed]
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. (2004). BioBuilder as a database development and functional annotation platform for proteins. Bmc Bioinformatics. 5, 43. [PubMed]
Kristiansen, T. Z., Bunkenborg, J., Gronborg, M., Molina, H., Thuluvath, P. J., Argani, P., Goggins, M. G., Maitra, A. and Pandey, A. (2004). A proteomic analysis of human bile. Molecular & Cellular Proteomics : MCP. 3, 715-28. [PubMed]
Tewari, M., Hu, P. J., Ahn, J. S., Ayivi-Guedehoussou, N., Vidalain, P. O., Li, S., Milstein, S., Armstrong, C. M., Boxem, M., Butler, M. D., Busiguina, S., Rual, J. F., Ibarrola, N., Chaklos, S. T., Bertin, N., Vaglio, P., Edgley, M. L., King, K. V., Albert, P. S., Vandenhaute, J., Pandey, A., Riddle, D. L., Ruvkun, G. and Vidal, M. (2004). Systematic interactome mapping and genetic perturbation analysis of a C. elegans tgf-beta signaling network. Molecular Cell. 13, 469-82. [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., 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’s molecular interaction format–a community standard for the representation of protein interaction data. Nature Biotechnology. 22, 177-83. [PubMed]
Ibarrola, N., Molina, H., Iwahori, A. and Pandey, A. (2004). A novel proteomic approach for specific identification of tyrosine kinase substrates using [13c]tyrosine. The Journal of Biological Chemistry. 279, 15805-13. [PubMed]
Ibarrola, N., Kratchmarova, I., Nakajima, D., Schiemann, W. P., Moustakas, A., Pandey, A. and Mann, M. (2004). Cloning of a novel signaling molecule, AMSH-2, that potentiates transforming growth factor beta signaling. Bmc Cell Biology. 5, 2. [PubMed]
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. (2004). Human protein reference database as a discovery resource for proteomics. Nucleic Acids Research. 32, D497-501. [PubMed]
2003
Ibarrola, N., Kalume, D. E., Gronborg, M., Iwahori, A. and Pandey, A. (2003). A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture. Analytical Chemistry. 75, 6043-9. [PubMed]
Raghothama, C. and Pandey, A. (2003). Absolute systems biology–measuring dynamics of protein modifications. Trends in Biotechnology. 21, 467-70. [PubMed]
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. (2003). Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Research. 13, 2363-71. [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, 263-8. [PubMed]
Steen, H., Fernandez, M., Ghaffari, S., Pandey, A. and Mann, M. (2003). Phosphotyrosine mapping in bcr/abl oncoprotein using phosphotyrosine-specific immonium ion scanning. Molecular & Cellular Proteomics : MCP. 2, 138-45. [PubMed]
Kalume, D. E., Molina, H. and Pandey, A. (2003). Tackling the phosphoproteome: tools and strategies. Current Opinion in Chemical Biology. 7, 64-9. [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 (oxford, England). 19, 169-72. [PubMed]
2002
Andersen, J. S., Rappsilber, J., Steen, H., Pandey, A., Molina, H., Lund, M., Podtelejnikov, A., Lamond, A. I. and Mann, M. (2002). Multi-Protein complexes studied by mass spectrometry. Thescientificworldjournal. 2, 91-92. [PubMed]
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. (2002). Cloning of a novel phosphotyrosine binding domain containing molecule, odin, involved in signaling by receptor tyrosine kinases. Oncogene. 21, 8029-36. [PubMed]
Muthusamy, B. and Pandey, A. (2002). A roadmap of the mouse genome. Trends in Genetics : Tig. 18, 553. [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’s Stke : Signal Transduction Knowledge Environment. 2002, pl16. [PubMed]
Grønborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. S., Ohara, O., Mann, M., Jensen, O. N. and Pandey, A. (2002). A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, frigg, as a protein kinase A substrate. Molecular & Cellular Proteomics : MCP. 1, 517-27. [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, 388-91. [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. The Journal of Biological Chemistry. 277, 42011-6. [PubMed]
Steen, H. and Pandey, A. (2002). Proteomics goes quantitative: measuring protein abundance. Trends in Biotechnology. 20, 361-4. [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 & Cellular Proteomics : MCP. 1, 376-86. [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 & Cellular Proteomics : MCP. 1, 213-22. [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, 2906-10. [PubMed]
Kristiansen, T. Z. and Pandey, A. (2002). Resources for full-length cdnas. Trends in Biochemical Sciences. 27, 266-7. [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 characterization of PAK5, a novel member of mammalian p21-activated kinase-ii subfamily that is predominantly expressed in brain. Oncogene. 21, 3939-48. [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 transforming growth factor-beta and affects protein kinase cascades. The Journal of Biological Chemistry. 277, 27367-77. [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, 261-8. [PubMed]
Kristiansen, T. Z. and Pandey, A. (2002). A database of transcriptional start sites. Trends in Biochemical Sciences. 27, 174. [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. The Journal of Biological Chemistry. 277, 19131-8. [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, 161-8. [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. The Journal of Biological Chemistry. 277, 5929-39. [PubMed]
Steen, H., Kuster, B., Fernandez, M., Pandey, A. and Mann, M. (2002). Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. The Journal of Biological Chemistry. 277, 1031-9. [PubMed]