Akhilesh Pandey, M.D., Ph.D.Image

Professor of Biological Chemistry, Pathology, Oncology, and Institute of Genetic Medicine

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Contact Information

527 Broadway Research Building
733 N. Broadway
Baltimore, MD 21205
Phone: (410)-502-6662
Fax: (410)-502-7544
This e-mail address is being protected from spambots. You need JavaScript enabled to view it

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Link to Dr. Pandey's Lab Page

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Research Interests

A thorough functional analysis of the genome demands a good understanding of its proteome. Combining molecular biology, genetics and proteomics, our laboratory is investigating cell surface receptors, their signal transductions, potential biomarkers of cancers, stem cells and targets of microRNAs. Cell surface receptors transmit signals to the interior of the cell upon binding to a ligand. These signals are generally transmitted through proteins with catalytic activity (such as kinases) as well as those without any catalytic activity (such as adapters). Protein phosphorylation is a major mechanism of regulating the activity of these proteins and the formation of multi-protein complexes. By using state-of-the-art mass spectrometry, we have identified novel proteins that are involved in signal transduction through receptor tyrosine kinases (EGF and PDGF receptors), cytokine receptors (IL-3 and TSLP receptor), antigen receptors (T and B cell receptors), oncogenic kinases (Bcr-Abl) as well as receptor serine-threonine kinases (TGF-beta and BMP receptors). Quantitative proteomic approaches including iTRAQ and SILAC have helped us find potential biomarkers in cancers of pancreas, liver, stomach, esophagus, bile duct and breast. These methods also enabled us to develop methods to identify potential targets of microRNAs such as miR-21 and miR-143. To catalog all human proteins, their modular domain structures and interaction partner, we established two unique databases, Human Protein Reference Database, which serves as a curated online reference of human proteins. We also created NetPath, a curating resource of signal transduction pathways in humans. Recently, we initiated a community resource, Human Proteinpedia for sharing and integrating human protein data from various experimental platforms.

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Selected Publications

2012

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

Polisetty, R. V., Gautam, P., Sharma, R., Harsha, H. C., Nair, S. C., Gupta, M. K., Uppin, M. S., Challa, S., Puligopu, A. K., Ankathi, P., Purohit, A. K., Chandak, G. R., Pandey, A. and Sirdeshmukh, R. (2012). LC-MS/MS Analysis of Differentially Expressed Glioblastoma Membrane Proteome Reveals Altered Calcium Signalling and other Protein Groups of Regulatory Functions. Molecular and Cellular Proteomics[PubMed]

Prasad, T. S. K., Harsha, H. C., Keerthikumar, S., Sekhar, N. R., Selvan, L. D. N., Kumar, P., Pinto, S. M., Muthusamy, B., Subbannayya, Y., Renuse, S., Chaerkady, R., Mathur, P. P., Ravikumar, R. and Pandey, A. (2011). Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry. Journal of Proteome Research. 11, 247-260. [PubMed]

Goel, R., Harsha, H. C., Pandey, A. and Prasad, T. S. K. (2011). Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Molecular Biosystems. 8, 453-63. [PubMed]

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2011

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Kim, M. S. and Pandey, A. (2011). Electron transfer dissociation mass spectrometry in proteomics. Proteomics. [PubMed]

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

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

Raju, R., Nanjappa, V., Balakrishnan, L., Radhakrishnan, A., Thomas, J. K., Sharma, J., Tian, M., Palapetta, S. M., Subbannayya, T., Sekhar, N. R., Muthusamy, B., Goel, R., Subbannayya, Y., Telikicherla, D., Bhattacharjee, M., Pinto, S., Syed, N., Srikanth, M. S., Sathe, G. J., Ahmad, S., Chavan, S. N., Kumar, G. S. S., Marimuthu, A., Prasad, T. S. K., Harsha, H. C., Rahiman, B. A., Ohara, O., Bader, G. D., Mohan, S. S., Schiemann, W. P. and Pandey, A. (2011). Netslim: High-confidence curated signaling maps. Database[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, 1306-1319. [PubMed]

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

Chaerkady, R., Letzen, B., Renuse, S., Sahasrabuddhe, N. A., Kumar, P., All, A. H., Thakor, N. V., Delanghe, B., Gearhart, J. D., Pandey, A. and Kerr, C. L. (2011). Quantitative temporal proteomic analysis of human embryonic stem cell differentiation into oligodendrocyte progenitor cells. Proteomics. 11, 4007-4020. [PubMed]

Pawar, H., Kashyap, M. K., Sahasrabuddhe, N. A., Renuse, S., Harsha, H. C., Kumar, P., Sharma, J., Kandasamy, K., Marimuthu, A., Nair, B., Rajagopalan, S., Maharudraiah, J., Premalatha, C. S., Veerendra Kumar, K. V., Vijayakumar, M., Chaerkady, R., Prasad, T. S. K., Kumar, R. V. and Pandey, A. (2011). Quantitative Tissue Proteomics of Esophageal Squamous Cell Carcinoma for Novel Biomarker Discovery. Cancer Biology and Therapy. 12, 510-522. [PubMed]

Agyeman, A. S., Chaerkady, R., Shaw, P. G., Davidson, N. E., Visvanathan, K., Pandey, A. and Kensler, T. W. (2011). Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane treated human breast epithelial cells reveals common expression profiles. Breast Cancer Research and Treatment. 132, 175-187. [PubMed]

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

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

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, 732-744. [PubMed]

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

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

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

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

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2010

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

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

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

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

Zachara, N. E., Molina, H., Wong, K. Y., Pandey, A. and Hart, G. W. (2010). 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]

Kashyap, M. K., Harsha, H. C., Renuse, S., Pawar, H., Sahasrabuddhe, N. A., Kim, M. S., Marimuthu, A., Keerthikumar, S., Muthusamy, B., Kandasamy, K., Subbannayya, Y., Prasad, T. S. K., Mahmood, R., Chaerkady, R., Meltzer, S. J., Kumar, R. V., Rustgi, A. K. and Pandey, A. (2010). SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biology and Therapy. 10, 796-810. [PubMed]

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

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

Zhong, J. and Pandey, A. (2010). Site-directed mutagenesis reveals a unique requirement for tyrosine residues in IL-7R alpha and TSLPR cytoplasmic domains in TSLP-dependent cell proliferation. BMC Immunology. 11:5. [PubMed]

Zhong, J., Liu, X. and Pandey, A. (2010). Effects of transmembrane and juxtamembrane domains on proliferative ability of TSLP receptor. Molecular Immunology. 47, 1207-1215.[PubMed]

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

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

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

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

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

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2009


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

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

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

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

Harsha, H. C., Kandasamy, K., Ranganathan, P., Rani, S., Ramabadran, S., Gollapudi, S., Balakrishnan, L., Dwivedi, S. B., Telikicherla, D., Selvan, L. D. N., Goel, R., Mathivanan, S., Marimuthu, A., Kashyap, M. K., Vizza, R. F., Mayer, R. J., DeCaprio, J. A., Srivastava, S., Hanash, S. M., Hruban, R. H. and Pandey, A. (2009). A compendium of potential biomarkers of pancreatic cancer. PLoS Medicine. 6, e1000046. [PubMed]

Ranganathan, P., Harsha, H. C. and Pandey, A. (2009). Molecular alterations in exocrine neoplasms of the pancreas. Archives of Pathology & Laboratory Medicine. 133, 405-412.[PubMed]

Chaerkady, R., Kerr, C. L., Marimuthu, A., Kelkar, D. S., Kashyap, M. K., Gucek, M., Gearhart, J. D. and Pandey, A. (2009). Temporal analysis of neural differentiation using quantitative proteomics. Journal of Proteome Research. 8, 1315-1326. [PubMed]

Molina, H., Yang, Y., Ruch, T., Kim, J. W., Mortensen, P., Otto, T., Nalli, A., Tang, Q. Q., Lane, M. D., Chaerkady, R. and Pandey, A. (2009). Temporal profiling of the adipocyte proteome during differentiation using a 5-plex SILAC based strategy. Journal of Proteome Research. 8, 48-58. [PubMed]

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

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2008


Kristiansen, T. Z., Harsha, H. C., Grønborg, M., Maitra, A. and Pandey, A. (2008). Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma.Journal of Proteome Research. 8, 4670-4677. [PubMed]

Harsha, H. C., Jimeno, A., Molina, H., Mihalas, A., Goggins, M., Hruban, R., Schulick, R., Kamath, U., Maitra, A., Hidalgo, M. and Pandey, A. (2008). Activated epidermal growth factor receptor as a novel target in pancreatic cancer therapy. Journal of Proteome Research. 7, 4651-4658. [PubMed]

Chaerkady, R., Harsha, H. C., Nalli, A., Gucek, M., Vivekanandan, P., Akhtar, J., Cole, R. N., Simmers, J., Schulick, R. D., Singh, S., Torbenson, M., Pandey, A. and Thuluvath, P. J. (2008). A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma. Journal of Proteome Research. 7, 4289-4298. [PubMed]

Dixon, S., Fedyshyn, Y., Koh, J., Prasad, T. S. K., Chahwan, C., Chua, G., Toufighi, K., Baryshnikova, A., Hayles, J., Hoe, K., Kim, D., Park, H., Myers, C., Pandey, A., Durocher, D., Andrews, B. and Boone, C. (2008). Significant conservation of synthetic lethal genetic interaction networks between distantly-related eukaryotes. Proceedings of the National Academy of Sciences U.S.A. 105, 16653-16658. [PubMed]

Guha, U., Chaerkady, R., Marimuthu, A., Patterson, S., Kashyap, M., Harsha, H. C., Bader, J., Lash, A., Pandey, A. and Varmus, H. E. (2008). Comparisons of tyrosine-phosphorylated proteins in immortalized human bronchial epithelial cells and lung adenocarcinoma cell lines expressing lung cancer-specific alleles of EGFR and KRAS. Proceedings of the National Academy of Sciences U.S.A. 105, 14112-14117. [PubMed]

Song, D., Chaerkady, R., Tan, A., Garcia-Garcia, E., Nalli, A., Gauthier, A., Rios, F., Zhang, X., Solomon, A., Tong, J., Read, M., Fritz, C., Jimeno, A., Pandey, A. and Hidalgo, M. (2008). Antitumor activity and molecular effects of the novel Hsp 90 inhibitor, IPI-504, in pancreatic cancer. Molecular Cancer Therapeutics. 7, 3275-3284. [PubMed]

Mathivanan, S. and Pandey, A. (2008). Human Proteinpedia as a resource for clinical proteomics. Molecular and Cellular Proteomics. 7, 2038-2047. [PubMed]

Sarker, R., Grønborg, M., Cha, B., Mohan, S., Chen, Y., Pandey, A., Litchfield, D., Donowitz, M. and Li, X. (2008). CK2 binds to the C-Terminus of NHE3 and stimulates NHE3 basal activity by phosphorylating a separate site in NHE3. Molecular Biology of the Cell. 19, 3859-3870. [PubMed]

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

Amanchy, R., Zhong, J., Molina, H., Chaerkady, R., Iwahori, A., Kalume, D. E., Grønborg, M., Joore, J., Cope, L. and Pandey, A. (2008). Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. Journal of Proteome Research. 7, 3900-3910. [PubMed]

Luo, W., Slebos, R. J., Hill, S., Li, M., Brabek, J., Amanchy, R., Chaerkady, R, Pandey, A., Ham, A. J. L. and Hanks, S. (2008). Global impact of oncogenic Src on a phosphotyrosine proteome. Journal of Proteome Research. 7, 3447-3460. [PubMed]

Chaerkady, R., Thuluvath, P. J., Kim, M. S., Nalli, A., Vivekanandan, P., Simmers, J., Torbenson, M. and Pandey, A. (2008). 18O labeling for a quantitative proteomic analysis of glycoproteins in hepatocellular carcinoma. Clinical Proteomics. 4, 137-155. [PubMed]

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

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

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. Am J Surg Pathol. 32, 188-196. [PubMed]

Harsha, H. C., Molina, H. and Pandey, A. (2008). Quantitative proteomics using stable isotope labeling with amino acids in cell culture (SILAC). Nature Protocols. 3, 505-516. [PubMed]

Mathivanan, S., Ahmed, M., 157 coauthors and Pandey, A. (2008). Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-167. [PubMed]

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2007


Zhong, J., Molina, H. and Pandey, A. (2007). Phosphoproteomics. Current Protocols in Protein Science. 24, 24.4 [PubMed]

Bhandari, R., Saiardi, A., Ahmadibeni, Y., Snowman, A. M., Resnick, A. C., Kristiansen, T. Z., Molina, H., Pandey, A., Werner, J. K. Jr., Juluri, K. R., Xu, Y., Prestwich, G. D., Parang, K. and Snyder, S. H. (2007). Protein pyrophosphorylation by inositol pyrophosphates is a posttranslational event. Proceedings of the National Academy of Sciences, USA. 104, 15305-15310.[PubMed]

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

Okulate, M., Kalume, D. E., Chaerkady, R., Reddy, R., Kristiansen, K., Bhattacharyya, M., Pandey, A. and Kumar, N. (2007). Identification and molecular characterization of a novel protein Saglin as a target of monoclonal antibodies affecting salivary gland infectivity of Plasmodium sporozoites. Insect Molecular Biology. 16, 711-722. [PubMed]

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

Grønborg, M., Maitra, A. and Pandey, A. (2007). 'Proteomics of human pancreatic juice' in, Proteomics of human body fluids, pages 377-397 Thongboonkerd, V. Editor (Humana Press, Totowa, New Jersey, USA). [PubMed]

Kristiansen, T. Z., Maitra, A. and Pandey, A. (2007). 'Proteomics of human bile' in, Proteomics of human body fluids, pages 399-414 Thongboonkerd, V. Editor (Humana Press, Totowa, New Jersey, USA). [PubMed]

Lucito, R., Suresh, S., Walter, K., Pandey, A., Lakshmi, B., Krasnitz, A., Sebat, J., Wigler, M., Klein, A. P., Brune, K., Palmisano, E., Maitra, A., Goggins, M. and Hruban, R. H. (2007). Copy-number variants in patients with a strong family history of pancreatic cancer. Cancer Biology & Therapy. 6, 1-8. [PubMed]

Dinglasan, R. R., Kalume, D. E., Kanzok, S. M., Ghosh, A. K., Muratova, O., Pandey, A. and Jacobs-Lorena, M. (2007). Disruption of Plasmodium falciparum development by antibodies against a conserved mosquito midgut antigen. Proceedings of the National Academy of Sciences, USA. 104, 13461-13466. [PubMed]

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

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

Wang, Z., Pandey, A. and Hart, G. W. (2007). Dynamic interplay between O-GlcNAcylation and GSK-3-dependent phosphorylation. Molecular and Cellular Proteomics. 6, 1365-1379.[PubMed]

Kim, J. W., Molina, H., Pandey, A. and Lane, M. D. (2007). Upstream stimulatory factors regulate the C/EBPalpha gene during differentiation of 3T3-L1 preadipocytes. Biochem. Biophys. Res. Commun. 354, 517-521. [PubMed]

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2006


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

Gandhi, T. K. B., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periyaswamy, B., Mishra, G., Nandakumar, K., Shen, B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J. S. and Pandey, A. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 3, 285-293. [PubMed]

Qiao, Y., Molina, H., Pandey, A., Zhang, J. and Cole, P. A. (2006). Chemical rescue of a mutant enzyme in living cells. Science. 311, 1293-1297. [PubMed]

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

Lerin, C., Rodgers, J. T., Kalume, D. E., Kim, S. H., Pandey, A. and Puigserver, P. (2006). GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of PGC-1alpha. Cell Metabolism. 3, 429-438. [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, 3681-3687. [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, 336-341. [PubMed]

Hyland, E. M., Cosgrove, M. S., Molina, H., Wang, D., Pandey, A., Cotter, R. J. and Boeke, J. D. (2006). Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Molecular and Cellular Biology. 25, 10060-10070. [PubMed]

Liu, B., Molina, H., Kalume, D., Pandey, A., Griffith, J. D. and Englund, P. (2006). Role of p38 in replication of Trypanosoma brucei kinetoplast DNA. Molecular and Cellular Biology. 26, 5382-5393. [PubMed]

Grønborg, M., Kristiansen, T. Z., Iwahori, A., Chang, R., Reddy, R., Sato, N., Molina, H., Jensen, O. N., Hruban, R. H., Goggins, M. G., Maitra, A. and Pandey, A. (2006). Biomarker discovery from pancreatic cancer secretome using a differential proteomics approach. Molecular and Cellular Proteomics. 5, 157-171. [PubMed]

Mishra, G., Suresh, M., Kumaran, K., Kannabiran, N., Suresh, S., Bala, P., Shivkumar, K., Anuradha, N., Reddy, R., Raghavan, T. M., Menon, S., Hanumanthu, G., Gupta, M., Upendran, S., Gupta, S., Mahesh, M., Jacob, B., Matthew, P., Chatterjee, P., Arun, K. S., Sharma, S., Chandrika, K. N., Deshpande, N., Palvankar, K., Raghavnath, R., Krishnakanth, K., Karathia, H., Rekha, B., Rashmi, N. S., Vishnupriya, G., Kumar, H. G. M., Nagini, M., Kumar, G. S. S., Jose, R., Deepthi, P., Mohan, S. S., Gandhi, T. K. B., Harsha, H. C., Deshpande, K. S., Sarker, M., Prasad, T. S. K. and Pandey, A. (2006). Human Protein Reference Database - 2006 Update. Nucleic Acids Research. 34, D411-D414. [PubMed]

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2005


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

Amanchy, R., Kalume, D. E., Iwahori, A., Zhong, J. and Pandey, A. (2005). Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC).Journal of Proteome Research. 4, 1661-1671. [PubMed]

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

Muthusamy, B., Hanumanthu, G., Reshmi, R., Sriranjini, S., Suresh, S., Rekha, B., Srinivas, D., Karthick, L., Vrushabendra, B. M., Sharma, S., Mishra, G., Rashmi, B. P., Kadekar, S., Chatterjee, P., Mangala, K. S., Shivashankar, H. N., Chandrika, K. N., Deshpande, N., Suresh, M., Kannabiran, N., Niranjan, V., Nalli, A., Prasad, T. S. K., Arun, K. S., Reddy, R., Chandran, S., Jadhav, T., Julie, D., Mahesh, M., John, S. L., Palvankar, K., Sudhir, D., Bala, P., Jithesh, M. K., Rashmi, N. S., Vishnupriya, G., Dhar, K., Reshma, S., Chaerkady, R., Prasad, C. K. Gandhi, T. K. B., Harsha, H. C., Mohan, S. S., Deshpande, K. S., Sarker, M. and Pandey, A. (2005). Plasma proteome database as a resource for proteomics research.Proteomics. 5, 3531-3536. [PubMed]

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

Ping, P., Vondriska, T. M., Creighton, C. J., Gandhi, T. K. B., Yang, Z., Menon, R., Kwon, M. S., Cho, S. Y., Drwal, G., Kellmann, M., Peri, S., Suresh, S., Gronborg, M., Molina, H., Chaerkady, R., Rekha, B., Muthusamy, B., Shet, A. S., Gerszten, R. E., Wu, H., Raftery, M., Wasinger, V., Schulz-Knappe, P., Hanash, S. M., Paik, Y. K., Hancock, W. S., States, D. J., Omenn, G. S. and Pandey, A. (2005). A functional annotation of subproteomes in human plasma. Proteomics. 5, 3506-3519. [PubMed]

Harsha, H. C., Suresh, S., Amanchy, R., Deshpande, N., Shanker, K., Yatish, A. J., Muthusamy, B., Vrushabendra, B. M., Rashmi, B. P., Chandrika, K. N., Padma, N., Sharma, S., Badano, J. L, Ramya, M. A., Shivashankar, H. N., Peri, S., Choudhury, D. R., Kavitha, M. P., Saravana, R., Niranjan, V., Gandhi, T. K. B., Ghosh, N., Chandran, S., Menezes, M., Joy, M., Mohan, S. S., Katsanis, N., Deshpande, K. S., Chaerkady, R., Prasad, C. K., and Pandey, A. (2005). A manually curated functional annotation of the human X chromosome. Nature Genetics. 37, 322-323. [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 3 beta is required for adipogenesis. Proceedings of the National Academy of Sciences. U.S.A. 102, 9766-9771. [PubMed]

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

Chaerkady, R., Harsha, H. C., Prasad, C. K. and Pandey, A. (2005). Bioinformatics and proteomics approaches for aging research. Biogerontology. 6, 227-232. [PubMed]

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

Suresh, S., Mohan, S., Mishra, G., Hanumanthu, G., Suresh, M., Reddy, R. and Pandey, A. (2005). Proteomic resources: integrating biomedical information in humans. Gene. 364, 13-18.[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, 2739-2744. [PubMed]

Gandhi, T. K. B., Chandran, S., Peri, S., Saravana, R., Amanchy, R., Prasad, T. S. K and Pandey, A. (2005). A bioinformatics analysis of protein tyrosine phosphatases in humans. DNA Research. 12, 79-89. [PubMed]

Kalume, D. E., Okulate, M., Zhong, J., Reddy, R., Suresh, S., Deshpande, N., Kumar, N. and Pandey, A. (2005). A proteomic analysis of salivary glands of female Anopheles gambiae mosquito. Proteomics. 5, 3765-3777. [PubMed]

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

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2004


Grønborg , M., Bunkenborg, J., Kristiansen, T. Z., Jensen, O. N., Yeo, C. J., Hruban, R. H., Maitra, A., Goggins, M. G. and Pandey A. (2004). Comprehensive proteomic analysis of human pancreatic juice. Journal of Proteome Research. 3, 1042-1055. [PubMed]

Cao, D., Hustinx, S. R., Sui, G., Bala, P., Sato, N., Martin, S., Maitra, A., Murphy, K. M., Cameron, J. L., Yeo, C. J., Kern, S. E., Goggins, M., Pandey, A. and Hruban, R. H. (2004). Identification of novel highly expressed genes in pancreatic ductal adenocarcinomas through a bioinformatics analysis of expressed sequence tags. Cancer Biology and Therapy. 3, 1081-1089. [PubMed]

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, 1609-1615. [PubMed]

Kristiansen, T. Z., Nielsen, M. M., Blagoev, B., Pandey, A. and Mann, M. (2004). Mouse embryonic fibroblasts derived from Odin deficient mice display a hyperproliferative phenotype.DNA Research. 11, 285-292. [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 and Cellular Proteomics. 3, 715-728. [PubMed]

Rhodes, D. R., Yu, J., Shanker, K., Deshpande, N., Varambally, R, Ghosh, D., Barrette, T., Pandey, A. and Chinnaiyan, A. M. (2004). Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proceedings of the National Academy of Sciences, USA. 101, 9309-9314. [PubMed]

Navarro, J. D., Talreja, N., Peri, S., Vrushabendra, B. M., Rashmi, B. P., Padma, N., Surendranath, S., Jonnalagadda, C. K., Kousthub, P. S., Deshpande, N., Shanker, K. and Pandey, A. (2004). BioBuilder as a database development and functional annotation platform for proteins. BMC Bioinformatics. 5, 43. [PubMed]

Ibarrola, N., Chaerkady, R. and Pandey, A. Proteomic analysis of the adipocyte secretome, in, Genomics and Proteomics in Nutrition, Berdanier C. D. and Moustaid-Moussa, N. Eds., Marcel Dekker, Inc. New York. pp 393-411.

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

Ibarrola, N., Molina, H., Iwahori, A. and Pandey, A. (2004). A novel proteomic approach for specific identification of tyrosine kinase substrates using 13C-labeled tyrosine. Journal of Biological Chemistry. 279, 15805-15813. [PubMed]

Ibarrola, N., Kratchmarova, I., Nakajima, D., Schiemann, W. P., Moustakas, A., Pandey, A. and Mann, M. (2004). Cloning of a novel signaling molecule, AMSH-2, that potentiates transforming growth factor beta signaling. BMC Cell Biology. 5, 2 . [PubMed]

Rhodes, D. R., Yu, J., Shanker, K., Deshpande, N., Varambally, R., Ghosh, D., Barrette, T., Pandey, A. and Chinnaiyan, A. M. (2004). Oncomine: A cancer microarray database and integrated data-mining platform. Neoplasia. 6, 1-6. [PubMed]

Tewari, M., Hu, P. J., Ahn, J. S., Ayivi-Guedehoussou, N., Vidalain, P. O., Li, S., Milstein, S., Armstrong, C. M., Boxem, M., Butler, M. D., Busiguina, S, Rual, J. F., Ibarrola, N, Chaklos, S. T., Bertin, N., Vaglio, P., Edgley, M. L., King, K. V., Albert, P. S., Vandenhaute, J., Pandey, A., Riddle, D. L., Ruvkun, G. and Vidal, M. (2004). Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Molecular Cell. 13, 469-482. [PubMed]

Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y., Zeng, R., Rana, D., Nikolski, M., Husi, H., Brun, C., Shanker, K., Grant, S. G. N., Sander, C., Bork, P., Zhu, W., Pandey, A., Brazma, A., Jacq, B., Vidal, M., Sherman, D., Legrain, P., Cesareni, G., Xenarios, I., Eisenberg, D., Steipe, B., Hogue, C. and Apweiler, R. (2004). The HUPO PSI Molecular Interaction Format - A community standard for the representation of protein interaction data. Nature Biotechnology. 22, 177-183. [PubMed]

Peri, S., Navarro, J. D., Kristiansen, T. Z., Amanchy, R., Surendranath, V., Muthusamy, B., Gandhi, T. K. B., Chandrika, K. N., Deshpande, N., Suresh, S., Rashmi, B. P., Shanker, K., Padma, N., Niranjan, V., Harsha, H. C., Talreja, N., Vrushabendra, B. M., Ramya, M. A., Yatish, A. J., Joy, M., Shivashankar, H. N., Kavitha, M. P., Menezes, M., Choudhury, D. R., Ghosh, N., Saravana, R., Chandran, S., Mohan, S., Jonnalagadda, C. K., Prasad, C. K., Kumar-Sinha, C., Deshpande, K. S. and Pandey, A. (2004). Human Protein Reference Database as a discovery resource for proteomics. Nucleic Acids Research. 32, D497-D501. [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, 6043-6049. [PubMed]

Chaerkady, R. and Pandey, A. (2003). Absolute systems biology - measuring dynamics of protein modifications. Trends in Biotechnology. 21, 467-470. 
[PubMed]

Peri, S., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T. K. B., Gronborg, M., Ibarrola, N., Deshpande, N., Shanker, K., Shivashankar, H. N., Rashmi, B. P., Ramya, M. A., Zhao, Z., Chandrika, K. N., Padma, N., Harsha, H. C., Yatish, A. J., Kavitha, M. P., Menezes, M., Choudhury, D. R., Suresh, S., Ghosh, N., Saravana, R., Chandran, S., Krishna, S., Joy, M., Anand, S. K., Madavan, V., Joseph, A., Wong, G. W., Schiemann, W. P., Constantinescu, S. N., Huang, L., Khosravi-Far, R., Steen, H., Tewari, M., Ghaffari, S., Blobe, G. C., Dang, C. V., Garcia, J. G. N., Pevsner, J., Jensen, O. N., Roepstorff, P., Deshpande, K. S., Chinnaiyan, A. M., Hamosh, A., Chakravarti, A. and Pandey, A. (2003). Development of Human Protein Reference Database as an initial platform for approaching systems biology in humans. Genome Research. 13, 2363-2371. [PubMed]

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

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 and Cellular Proteomics. 2, 138-145. [PubMed]

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

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

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


2002

 

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

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

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

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 (RELM alpha): Biochemical characterization of its oligomeric nature. Journal of Biological Chemistry. 277, 42011-42016. [PubMed]

Steen, H. and Pandey, A. (2002). Proteomics goes quantitative: measuring protein abundance. Trends in Biotechnology. 20, 361-364. [PubMed]

Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A. and Mann, M. (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Molecular and Cellular Proteomics. 1, 376-386. [PubMed]

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

 

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

 

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

 

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Schiemann, W. P., Blobe, G. C., Kalume, D. E., Pandey, A. and Lodish, H. F. (2002). Context-specific effects of fibulin-5 (DANCE/ EVEC) on cell proliferation, motility, and invasion: Fibulin-5 is induced by TGF-beta and affects protein kinase cascades. Journal of Biological Chemistry. 277, 27367-27377. [PubMed]

 

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

 

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

 

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Mann, M., Ong, S. E., Grønborg, M., Steen, H., Jensen, O. N. and Pandey, A. (2002). Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome.Trends in Biotechnology. 20, 261-268. [PubMed]

 

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Kratchmarova, I., Kalume, D. E., Blagoev, B., Scherer, P. E., Podtelejnikov, A. V., Molina, H., Bickel, P. E., Andersen, J. S., Fernandez, M. M., Bunkenborg, J., Roepstorff, P., Kristiansen, K., Lodish, H. F., Mann, M. and Pandey, A. (2002). A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes. Molecular and Cellular Proteomics. 1, 213-222. [PubMed]

 

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

 

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

 

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

 

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