2013
Hansen, A. M., Chaerkady, R., Sharma, J., Díaz-Mejía, J. J., Tyagi, N., Renuse, S., Jacob, H. K. C., Pinto, S. M., Sahasrabuddhe, N. A., Kim, M. S., Delange, B., Srinivasan, N., Emili, A., Kaper, J. and Pandey, A. (2013). The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathogens. In press
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. [PubMed]
Ambekar, S. A., Nirujogi, R. S.,
Srikanth, S. M., Chavan, S., Kelkar, D. S., Hinduja, I., Zaveri, K.,
Prasad, T. S. K., Harsha, H. C., Pandey, A. and Mukherjee, S. (2013).
Proteomic analysis of human follicular fluid: A new perspective towards
understanding folliculogenesis. Journal of Proteomics. [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. [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. BBA - Proteins and Proteomics. [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.
K., Harsha, H. C., Patole, M. S. and Pandey, A. (2013). Moving from unsequenced
to sequenced genome: reanalysis of the proteome of Leishmania donovani. Journal
of Proteomics. [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. [PubMed]
Sandhya, V. K., Raju, R., Verma, R., Advani, J., Sharma, R., Radhakrishnan, A., Nanjappa, V., Narayana, J., Somani, B. L., Mukherjee, K. K., Pandey, A., Christopher, R. and Prasad, T. S. K. (2013). A network map of BDNF/TRKB and BDNF/p75NTR signaling system. Journal of Cell Communication and Signaling. [PubMed]
Balakrishnan, L., Soman, S., Patil, Y. B., Advani, J., Thomas, J. K., Venkatesh, D. D., Urmila, K. K., Harsha, H. C., Prasad, T. S. K., Raju, R., Pandey, A., Dimitriadis, E., and Chatterjee, A. (2013). IL-11/IL11RA
receptor mediated signaling: a web accessible knowledgebase. Cell
Communication and Adhesion. [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., Kumar, G. S. S., Selvan, L. D. N., Mahadevan,
A., Renuse, S., Kumar, P., Pawar, H., Sahasrabuddhe, N. A., Suja, M. S., Ramachandra,
Y. L., Prasad, T. S. K., Madhusudhana, S. N., Harsha, H. C., Chaerkady, R.,
Satishchandra, P., Pandey, A. and Shankar, S. K. (2013). Quantitative proteomics
for identifying biomarkers for Rabies. Clinical Proteomics. 10:3. [PubMed]
Harsha, H. C., Pinto, S. M. and Pandey, A. (2013). Proteomic
strategies to characterize signaling pathways. Methods in Molecular Biology.
1007, 359-377. [PubMed]
Muthusamy, B., Thomas, J. K., Prasad, T. S. K. and Pandey, A. (2013). Access guide to Human Proteinpedia. Current Protocols in Bioinformatics. 41:1.21.1-1.21.15. [PubMed]
Kashyap, M. K., Pawar, H., Keerthikumar, S., Sharma, J., Goel, R., Mahmood, R., Vijaya Kumar, M., Veerendra Kumar, K. V., Pandey, A., Kumar, R. V., Prasad, T. S. K. and Harsha, H. C. (2013). Evaluation of protein expression pattern of stanniocalcin 2, insulin-like growth factor-binding protein 7, inhibin beta A and four and a half LIM domains 1 in esophageal squamous cell carcinoma. Cancer Biomarkers. 12, 1-9. [PubMed]
Soman, S., Raju, R., Sandhya, V. K., Advani, J., Khan, A. A., Harsha, H. C., Prasad, T. S. K., Sudhakaran, P. R., Pandey, A. and Adishesha, P. K. (2013). A multicellular signal transduction network of AGE/RAGE signaling. Journal of Cell Communication and Signaling. 7, 19-23. [PubMed]
Huang, T. C., Pinto, S. M. and Pandey, A. (2013). Proteomics for understanding microRNA biology.Proteomics. 13, 558-567. [PubMed]
Pawar, H., Maharudraiah, J., Kashyap, M. K., Sharma, J., Srikanth, M. S., Choudhary, R., Chavan, S., Sathe, G., Manju, H .C., Veerendra Kumar, K. V., Vijayakumar, M., Sirdeshmukh, R., Harsha, H. C., Prasad, T. S. K., Pandey, A. and Kumar, R. V. (2013). Downregulation of cornulin in esophageal squamous cell carcinoma. Acta Histochemica. 115, 89-99. [PubMed]
2012
Marimuthu, A., Subbannayya, Y.,
Sahasrabuddhe, N. A., Balakrishnan, L., Syed, N., Sekhar, N. R.,
Katte, T. V., Pinto, S. M., Srikanth, S. M., Kumar, P., Pawar,
H., Kashyap, M. K., Maharudraiah, J., Ashktorab, H., Smoot, D.
T., Ramaswamy,
G., Kumar, R. V., Cheng, Y., Meltzer, S. J., Roa, J. C., Chaerkady,
R., Prasad, T. S. K., Harsha, H. C., Chatterjee, A. and Pandey,
A. (2012). SILAC-based quantitative proteomic analysis of gastric
cancer secretome. Proteomics - Clinical Applications. [PubMed]
Dey, G., Radhakrishnan, A., Syed, N., Thomas, J. K., Nadig, A., Srikumar, K., Mathur, P. P., Pandey, A., Lin, S. K., Raju, R. and Prasad, T. S. K. (2012). Signaling network of Oncostatin M pathway. Journal of Cell Communication and Signaling. 7, 103-108. [PubMed]
Kumar, G. S. S., Venugopal, A. K., Mahadevan, A., Renuse, S., Harsha, H. C., Sahasrabuddhe, N. A., Pawar, H., Sharma, R., Kumar, P., Rajagopalan, S., Waddell, K., Ramachandra, Y. L., Satishchandra, P., Chaerkady, R., Prasad, T. S. K., Shankar, S. K. and Pandey, A. (2012). Quantitative proteomics for identifying biomarkers for tuberculous meningitis. Clinical Proteomics. 9, 12-24 [PubMed]
Luo, W., Chang, R., Zhong, J., Pandey, A. and Semenza, G. L. (2012). The
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 U.S.A. 109, 19889–19890. [PubMed]
Kumar, G. S. S., Venugopal, A. K., Kashyap, M. K., Raju, R., Marimuthu, A., Palapetta, S. M., Subbannayya, Y., Goel, R., Chawla, A., Dikshit, J. B., Tata, P., Harsha, H. C., Maharudraiah, J., Ramachandra, Y. L., Satishchandra, P., Prasad, T. S. K., Pandey, A., Mahadevan, A. and Shankar, S. K. (2012).Gene expression profiling of tuberculous meningitis co-infected with HIV. Journal of Proteomics and Bioinformatics. 5, 235-244. [PubMed]
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, 2853-2863. [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, 5301-5310. [PubMed]
Martinez-Ferrando, I., Chaerkady, R., Zhong, J., Molina, H.,
Kishore, H., Herbst-Robinson, K., Dancy, B. M., Katju, V., Bose, R., Zhang,
J., Pandey, A. and Cole, P. A. (2012). Identification of targets of c-Src tyrosine
kinase by chemical complementation and phosphoproteomics. Molecular and
Cellular Proteomics. 11, 355-369. [PubMed]
Do Vale, L. H., Gómez-Mendoza, D. P., Kim, M. S.,
Pandey, A., Ricart, C. A., Ximenes-Filho, E. and
Sousa, M. V. (2012). Secretome analysis of the
fungus Trichoderma harzianum grown on cellulose. Proteomics. 12, 2716-2728. [PubMed]
Kalra, H., Simpson, R. J., Ji,
H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V. C., Borràs,
F. E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton,
A., Cocucci, E., Falcon-Perez, J. M., Gabrielsson, S., Gho, Y.
S., Gupta, D., Harsha, H. C., Hendrix, A., Hill, A. F., Inaal,
J. M., Jenster, G., Kiang, L. S., Krämer-Albers, E-M., Llorente,
A., Lötvall, J., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland,
R., Nolte-'t Hoen, E. N. M., Pandey, A., Patel, T., Piper, M. G.,
Pluchino, S., Prasad, T. S. K., Rajendran, L., Raposo, G., Record,
M., Reid, G. E., Sánchez-Madrid, F., Schiffelers, R. M.,
Siljander, P., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H.,
van Balkom, B. W. M., Vázquez, J., Vidal, M., Yáñez-Mó,
M., Zoeller, M. and Mathivanan, S. (2012). Vesiclepedia: A compendium
for extracellular vesicles with continuous community annotation. PLoS
Biology. 10, e1001450. [PubMed]
Telikicherla, D., Marimuthu, A., Kashyap, M. K., Ramachandra, Y. L., Mohan,
S., Roa, J. C., Maharudraiah, J., and Pandey, A. (2012). Overexpression of
Ribosome Binding Protein 1 (RRBP1) in breast cancer. Clinical Proteomics. 2012, 9:7. [PubMed]
Bhattacharjee, M., Raju, R., Radhakrishnan, A., Nanjappa, V., Muthusamy, B., Singh, K., Kuppusaami, D., Lingala, B. T., Pan, A., Mathur, P. P., Harsha, H. C., Prasad, T. S. K., Atkins, G. J., Pandey, A. and Chatterjee, A. (2012). A bioinformatics resource for TWEAK-Fn14 signaling pathway. Journal of Signal Transduction. Article ID 376470. [PubMed]
Kim, M. S., Kuppireddy, S. V., Sakamuri, S., Singal, M., Getnet, D., Harsha,
H. C., Goel, R., Balakrishnan, L., Jacob, H. K. C., Kashyap, M. K., Tankala,
S. G., Maitra, A., Iacobuzio-Donahue, C. A., Jaffee, E., Goggins, M. G.,
Velculescu, V. E., Hruban, R. H. and Pandey, A. (2012). Rapid characterization
of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs). Journal
of Proteome Research. 11,5556-5563[PubMed]
Renuse, S., Harsha, H. C., Kumar, P., Acharya, P. K., Sharma,
J., Goel, R., Kumar, G. S. S., Raju, R., Prasad, T. S. K., Slotta, T. and Pandey,
A. (2012). Proteomic analysis of an unsequenced plant - Mangifera indica. Journal
of Proteomics. 75, 5793-5796. [PubMed]
Telikicherla, D., Maharudraiah, J., Pawar, H., Marimuthu,
A., Kashyap, M. K., Ramachandra, Y. L., Roa, J. C. and Pandey, A. (2012).
Overexpression
of Kinesin Associated Protein 3 (KIFAP3) in breast cancer. Journal
of Proteomics and Bioinformatics. 5, 122-126. [PubMed]
Radhakrishnan, A., Raju, R., Tuladhar, N., Subbannayya, T.,
Thomas, J. K., Goel, R., Telikicherla, D., Palapetta, S. M., Rahiman, B. A.,
Venkatesh, D. D., Urmila, K. K., Harsha, H. C., Mathur, P. P., Prasad, T. S.
K., Pandey, A., Shemanko, C. and Chatterjee, A. (2012). A
pathway map of prolactin signaling. Journal of Cell Communication and Signaling. 11, 355-369. [PubMed]
Venugopal, A. K., Kumar, G. S. S., Mahadevan, A.,
Selvan, L. D. N., Marimuthu, A., Dikshit, J. B., Tata, P., Ramachandra,
Y. L., Chaerkady,
R., Sinha, S., Chandramouli, B. A., Arivazhagan, A., Satishchandra,
P., Shankar, S. K. and Pandey, A. (2012). Transcriptomic profiling of medial temporal lobe epilepsy. Journal of Proteomics and Bioinformatics.
5, 31-39. [PubMed]
Zhong, J., Kim, M. S., Chaerkady, R., Wu, X., Huang, T. C., Getnet, D., Mitchell, C. J., Palapetta, S. M., Sharma, J., O'Meally, R. N., Cole, R. N., Yoda, A., Moritz, A., Loriaux, M. M., Rush, J., Weinstock, D. M., Tyner, J. W. and Pandey, A. (2012). TSLP signaling network revealed by SILAC-based phosphoproteomics. Molecular and Cellular Proteomics. 11, M112.017764. [PubMed]
Huang, T. C., Sahasrabuddhe, N. A., Kim, M. S., Getnet, D., Yang, Y., Peterson,
J. M., Ghosh, B., Chaerkady, R., Leach, S. D., Marchionni, L., Wong, G. W.
and Pandey A. (2012).Regulation of lipid metabolism by Dicer revealed through SILAC
Mice. Journal of Proteome Research. 11, 2193-2205. [PubMed]
Agyeman, A. S., Chaerkady, R., Shaw, P. G., Davidson, N. E., Visvanathan,
K., Pandey, A. and Kensler, T. W. (2012). Transcriptomic and proteomic profiling
of KEAP1 disrupted and sulforaphane treated human breast epithelial cells
reveals common expression profiles. Breast Cancer Research and Treatment.
132, 175-187. [PubMed]
Polisetty, R. V., Gautam, P., Sharma, R., Harsha, H. C., Nair,
S. C., Gupta, M. K., Uppin, M. S., Challa, S., Puligopu, A. K.,
Ankathi, P., Purohit, A. K., Chandak, G. R., Pandey, A. and Sirdeshmukh,
R. (2012).
LC-MS/MS analysis
of differentially expressed glioblastoma membrane proteome reveals
altered calcium signalling and other protein groups of regulatory
functions. Molecular and Cellular Proteomics. 11, M111.013565.[PubMed]
Nagaraj, S. H., Harsha, H. C., Reverter, A., Colgrave, M. L., Sharma, R.,
Andronicos, N., Hunt, P., Menzies, M., Lees, M. S., Sekhar, N. R., Pandey,
A. and Ingham, A. (2012). Proteomic analysis of the abomasal mucosal response
following infection by the nematode, Haemonchus contortus, in genetically
resistant and susceptible sheep. Journal of Proteomics. . 75, 2141-2152. [PubMed]
Prasad, T. S. K., Harsha, H. C., Keerthikumar, S., Sekhar,
N. R., Selvan, L. D. N., Kumar, P., Pinto, S. M., Muthusamy,
B., Subbannayya, Y., Renuse, S., Chaerkady, R., Mathur, P. P., Ravikumar,
R. and Pandey,
A. (2012). Proteogenomic analysis of Candida
glabrata using high resolution mass spectrometry. Journal of Proteome
Research. 11, 247-260. [PubMed]
Goel, R., Harsha, H. C., Pandey, A. and Prasad, T. S. K. (2012). Human Protein
Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Molecular
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8, 453-463. [PubMed]
Pawar, H., Sahasrabuddhe, N. A., Renuse, S., Keerthikumar, S., Sharma, J.,
Kumar, G. S. S., Venugopal, A., Sekhar, N. R., Kelkar, D. S., Nemade, H.,
Khobragade, S. N., Muthusamy, B., Kandasamy, K., Harsha, H. C., Chaerkady,
R., Patole,
M. S. and Pandey, A. (2012). A proteogenomic approach
to map the proteome of an unsequenced pathogen - Leishmania donovani. Proteomics.
12, 832-844. [PubMed]
Kim, M. S. and Pandey, A. (2012). Electron transfer dissociation
mass spectrometry in proteomics. Proteomics. 12, 530-542. [PubMed]
2011
Goel, R., Raju, R., Maharudraiah, J., Kumar, G. S. S., Ghosh,
K., Kumar, A., Lashmi, P. T., Sharma, J., Sharma, R., Balakrishnan, L., Pan,
A., Kandasamy,
K., Christopher, R., Krishna, V., Mohan, S. S., Harsha, H. C., Mathur, P.
P., Pandey, A. and Prasad, T. S. K. (2011). A signaling network of thyroid-stimulating
hormone. Journal of Proteomics and Bioinformatics. 4,
238-241. [PubMed]
Kinsinger, C. R., Apffel, J., Baker, M., Bian, X., Borchers, C. H., Bradshaw, R. A., Brusniak, M. Y., Chan D. W., Deutsch, E. W., Domon, B., Gorman, J., Grimm, R., Hancock, W., Hermjakob, H., Horn, D., Hunter, C., Kolar, P., Kraus, H. J., Langen, H., Linding, R., Moritz, R. L., Omenn, G. S., Orlando, R., Pandey, A., Ping, P., Rahbar, A., Rivers, R., Seymour, S. L., Simpson, R. L., Slotta, D., Smith, R. D., Stein, S. E., Tabb, D. L., Tagle, D., Yates, J. R. 3rd. and Rodriguez, H. (2011). Recommendations for mass apectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Molecular and Cellular Proteomics.
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Telikicherla, D., Ambekar, A., Palapetta, S. M., Dwivedi, S. B., Raju, R., Sharma, J., Prasad, T. S. K., Ramachandra, Y. L., Mohan, S. S., Maharudraiah, J., Mukherjee, S. and Pandey, A. (2011). A comprehensive curated resource for Follicle Stimulating Hormone signaling. BMC Research Notes. 4,
408. [PubMed]
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. 2011:bar032. [PubMed]
Nanjappa, V., Raju, R., Muthusamy, B., Sharma, J., Thomas, J. K., Nidhina, P. A. H., Harsha, H. C., Pandey, A., Anilkumar G. and Prasad, T. S. K. (2011). A comprehensive curated reaction map of leptin signaling pathway. Journal of Proteomics and Bioinformatics. 4, 184-189. [PubMed]
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]
Raju, R., Balakrishnan, L., Nanjappa, V., Bhattacharjee, M., Getnet, D.,
Muthusamy, B., Thomas, J. K., Sharma, J., Rahiman, B. A., Harsha, H. C.,
Shankar, S., Prasad, T. S. K., Mohan, S. S., Bader, G. D., Wani, M. R.
and Pandey, A. (2011). A comprehensive manually curated reaction map of
RANKL/RANK signaling pathway. Database. 2011:bar021. [PubMed]
Pawar, H., Kashyap, M. K., Sahasrabuddhe, N. A., Renuse, S., Harsha, H. C., Kumar, P., Sharma, J., Kandasamy, K., Marimuthu, A., Nair, B., Rajagopalan, S., Maharudraiah, J., Premalatha, C. S., Veerendra Kumar, K. V., Vijayakumar, M., Chaerkady, R., Prasad, T. S. K., Kumar, R. V. and Pandey, A. (2011). Quantitative
tissue proteomics of esophageal squamous cell carcinoma for novel
biomarker discovery. Cancer Biology and Therapy. 12, 510-522. [PubMed]
Shao, H., Chaerkady, R., Chen, S., Pinto, S. M., Sharma,
R., Delanghe, B., Birk, D., Pandey, A. and Chakravarti, S. (2011). Proteome
profiling of wild type and lumican-deficient mouse corneas. Journal of
Proteomics. 74, 1895-1905. [PubMed]
Kim, M. S., Zhong, J., Kandasamy, K., Delanghe, B. and Pandey,
A. (2011). Systematic evaluation of alternating CID and ETD fragmentation
for phosphorylated peptides. Proteomics.
11, 2568-2572. [PubMed]
Marimuthu, A., O'Meally, R., Chaerkady, R., Subbannayya, Y., Nanjappa, V.,
Kumar, P., Kelkar, D., Pinto, S., Sharma, R., Renuse, S., Goel, R., Christopher,
R., Delanghe, B., Cole, R. N., Harsha, H. C. and Pandey, A. (2011). A comprehensive
map of the human urinary proteome. Journal of Proteome Research. 10,
2734-2743. [PubMed].
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]
Kumar, G. S. S., Venugopal, A. K., Selvan, L. D. N., Marimuthu,
A., Keerthikumar, S., Pathare, S., Dikshit, J. B., Tata, P.,
Hariharan, R., Prasad, T. S. K., Harsha, H. C., Ramachandra,
Y. L., Mahadevan, A., Chaerkady, R., Shankar, S. K. and Pandey,
A. (2011). Gene Expression Profiling of Tuberculous Meningitis. Journal
of Proteomics and Bioinformatics. 4,
98-105. [PubMed]
Amanchy, R., Kandasamy, K., Mathivanan, S., Periaswamy, B., Reddy, R.,
Yoon, W. H., Joore, J., Beer, M. A., Cope, L. and Pandey, A. (2011). Identification
of novel phosphorylation motifs through an integrative computational and
experimental analysis of the human phosphoproteome. Journal of Proteomics
and Bioinformatics. 4, 22-35. [PubMed]
Marimuthu, A., Jacob, H. K. C., Jakharia, A., Subbannayya, Y., Keerthikumar,
S., Kashyap, M. K., Goel, R., Balakrishnan, L., Dwivedi, S., Pathare, S., Dikshit,
J. B., Maharudraiah, J., Singh, S., Kumar, G. S. S., Vijayakumar, M., Veerendra
Kumar, K. V., Premalatha, C. S., Tata, P., Hariharan, R., Roa, J. C., Prasad,
T. S. K., Chaerkady, R., Kumar, R. V. and Pandey, A. (2011). Gene expression
profiling of gastric cancer. Journal of Proteomics and Bioinformatics. 4, 74-82. [PubMed]
Wang, Q., Chaerkady, R., Wu, J., Hwang, H., J., Papadopoulos, N., Kopelovich,
L., Maitra, A., Matthei, H., Eshleman, J., Hruban, R., Kinzler, K. W., Pandey,
A. and Vogelstein, B. (2011). Mutant proteins as cancer-specific biomarkers. Proceedings of the National Academy of Sciences U.S.A. 108, 2444-2449.
[PubMed]
Renuse, S., Chaerkady, R. and Pandey, A. (2011). Proteogenomics. Proteomics. 11, 620-630.
[PubMed]
Zhong, J., Chaerkady, R., Kandasamy, K., Gucek, M., Cole, R.N. and Pandey,
A. (2011). The interactome of a PTB domain-containing adapter protein, Odin,
revealed by SILAC. Journal of Proteomics. 74, 294-303.
[PubMed]
2010
Harsha, H. C. and Pandey, A. (2010). Phosphoproteomics in Cancer. Molecular
Oncology.
4, 482-495.
[PubMed]
Chen, H., Pimienta, G., Gu, Y., Sun, X., Hu, J., Kim, M. S., Chaerkady,
R., Gucek, M., Cole, R. N., Sukumar, S. and Pandey, A. (2010). Proteomic characterization
of Her2/neu-overexpressing breast cancer cells. Proteomics. 10, 3800-3810.
[PubMed]
Prasad, T. S. K., Keerthikumar, S., Chaerkady, R., Kandasamy, K., Renuse,
S., Marimuthu, A., Venugopal, A. K., Thomas, J. K., Jacob, H. K.
C., Goel, R., Pawar, H., Sahasrabuddhe, N. A., Krishna, V., Nair, B. G.,
Gucek, M.,
Cole, R. N., Ravikumar, R., Harsha, H. C. and Pandey, A. (2010).
Comparative proteomic analysis of Candida
albicans and Candida glabrata. Clinical Proteomics.
6, 163-173.
[PubMed]
Goel, R., Muthusamy, B., Pandey, A. and Prasad, T. S. K. (2010). Human Protein
Reference Database and Human Proteinpedia as discovery resources for molecular
biotechnology. Molecular Biotechnology. 48, 87-95. [PubMed]
Zhong, J., Krawczyk, S. A., Chaerkady, R., Huang, H., Goel, R., Bader, J.
S., Wong, G. W., Corkey, B. E. and Pandey, A. (2010). Temporal profiling
of the secretome during adipogenesis in humans. Journal of Proteome Research. 9,
5228-5238. [PubMed]
Alvarez, H., Montgomery, E. A., Karikari, C., Canto, M. I., Dunbar, K.
B., Wang, J. S., Feldmann, G., Hong , S. M., Haffner, M. C., Meeker, A.
K., Holland, S. J., Yu , J., Heckrodt , T. J., Zhang, J., Ding, P., Goff,
D., Singh,
R., Roa, J. C., Marimuthu, A., Riggins, G. J., Eshelman, J. R., Nelkin,
B.
D., Pandey, A. and Maitra, A. (2010). The Axl receptor tyrosine kinase
is an adverse prognostic factor and a therapeutic target in esophageal adenocarcinoma. Cancer
Biology and Therapy. 10, 1009-1018. [PubMed]
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I.,
Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores,
I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes,
A. C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S.,
Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed,
M., Anwar,
N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons,
F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E.,
Reubenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K.,
Braun, B., Whirl-Carrillo,
M., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw,
R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J.,
Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L.,
Shah, N.,
Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky,
A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem,
M.,
Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Novere, N. L., Maltsev,
N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C. and
Bader, G. D. (2010). BioPAX - A community standard for pathway data sharing. Nature
Biotechnology. 28,
935-942. [PubMed]
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]
Hijikata, A., Raju, R., Keerthikumar, S., Ramabadran, S., Balakrishnan,
L., Ramadoss, S. K., Pandey, A., Mohan, S. and Ohara, O. (2010). Mutation@A
Glance: An integrative web application for analysing mutations from human
genetic
diseases. DNA Research. 17, 197-208. [PubMed]
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]
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 Genetics: Methods and Protocols. Hisashi
Koga, Editor. (Humana Press, Totowa, New Jersey, USA) Methods in
Molecular Biology . 577, 67-79. [PubMed]
Keerthikumar, S., Bhadra, S., Kandasamy, K., Raju, R., Ramachandra, Y.
L., Bhattacharyya, C., Imai, K., Ohara, O., Mohan, S. and Pandey, A.
(2009). Prediction of candidate primary immunodeficiency disease genes
using a support vector machine learning approach. DNA Research.16, 345-351. [PubMed]
Parikh, K., Diks, S. H., Tuynman, J. H., Verhaar, A., Lowenberg, 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, 7170-7180. [PubMed]
Kandasamy, K., Keerthikumar, S., Raju, R., Prasad, T. S. K., Ramachandra,
Y. L., Mohan, S. and Pandey, A. (2009). PathBuilder - open source software
for annotating and developing pathway resources. Bioinformatics. 25, 2860-2862. [PubMed]
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]
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, 621-631.
[PubMed]
Molina, H., Yang, Y., Ruch, T., Kim, J. W., Mortensen, P., Otto, T.,
Nalli, A., Tang, Q. Q., Lane, M. D., Chaerkady, R. and Pandey, A. (2009).
Temporal profiling of the adipocyte proteome during differentiation using
a 5-plex SILAC based strategy. Journal of Proteome Research. 8, 48-58. [PubMed]
Li, X., Molina, H., Huang, H., Zhang, 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 C/EBPbeta: Role during adipocyte differentiation. Journal of
Biological Chemistry. 284, 19248-19254. [PubMed]
Ghosh, A. K., Devenport, M., Jethwaney, D., Kalume, D. E., Pandey, A.,
Anderson, V. E., Sultan, A. A., Kumar, N. and Jacobs-Lorena, M. (2009).
Malaria parasite invasion of the mosquito salivary gland requires interaction
between the Plasmodium TRAP and the Anopheles Saglin proteins. PLoS Pathogens. 5, e1000265.
[PubMed]
Prasad, T. S. K., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S.,
Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal,
A., Balakrishnan, L., Marimuthu, A., Banerjee, S., Somanathan, D. S.,
Sebastian, A., Rani, S., Ray, S., Kishore, C. J. H., Kanth, S., Ahmed,
M., Kashyap, M., Mohmood, R., Ramachandra, Y. L., Krishna, V., Rahiman,
A. B., Mohan, S., Ranganathan, P., Ramabadran, S., Chaerkady, R. and
Pandey, A. (2009). Human Protein Reference Database - 2009 update. Nucleic Acids Research. 37, D767-D772.
[PubMed]
Kashyap, M., Marimuthu, A., Kishore, C. J. H., Peri, S., Keerthikumar,
S., Prasad, T. S. K., Mahmood, R., Rao, S., Ranganathan, P., Vijayakumar,
M., Veerendra Kumar, K. V., Montgomery, E. A, Kumar, R. V. and Pandey,
A. (2009). Genomewide mRNA profiling of esophageal squamous cell carcinoma
for identification of cancer biomarkers. Cancer Biology and Therapy. 8,
16-26.
[PubMed]
Keerthikumar, S., Raju, R., Kandasamy, K., Hijikata, A., Ramabadran,
S., Balakrishnan, L., Ahmed, M., Rani, S., Selvan, L. N., Somanathan,
D. S., Ray, S., Bhattacharjee, M., Gollapudi, S., Ramachandra, Y. L.,
Bhadra, S., Bhattacharyya, C., Imai, K., Nonoyama, S., Kanegane, H.,
Miyawaki, T., Pandey, A., Ohara, O. and Mohan, S. (2009). RAPID: Resource
of Asian Primary Immunodeficiency Diseases. Nucleic Acids Research. 37,
D863-D867.
[PubMed]
Kandasamy, K., Keerthikumar, S., 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]
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]
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
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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.
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Kim, J. W., Molina, H., Pandey, A. and Lane, M. D. (2007).
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of 3T3-L1 preadipocytes. Biochem. Biophys. Res. Commun. 354, 517-521.
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2006
Mathivanan, S., Periaswamy, B., Gandhi, T. K. B., Kandasamy, K., Suresh, S.,
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Gandhi, T. K. B., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N.,
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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.
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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.
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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.
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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.
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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.
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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.
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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.,
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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.
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Ping, P., Vondriska, T. M., Creighton, C. J., Gandhi, T. K. B., Yang, Z., Menon,
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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.
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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.
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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.
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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]
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.
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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.
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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.
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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.
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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
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2002
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,
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[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.
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Steen, H. and Pandey, A.
(2002).
Proteomics goes quantitative: measuring protein abundance.
Trends in Biotechnology. 20, 361-364. [PubMed]
Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen,
D. B., Steen, H., Pandey, A.
and Mann, M. (2002).
Stable isotope labeling by amino acids
in
cell culture, SILAC, as a simple and accurate approach
to expression proteomics. Molecular and Cellular
Proteomics.
1, 376-386.
[PubMed]
Deshpande, N. and Pandey, A.
(2002).
Mining gene expression data for functional annotation
of genomes. Trends in Biotechnology. 20, 282. [PubMed]
Shankar, S. H. N. and Pandey,
A. (2002).
A novel mode of activating the JAK-STAT signaling pathway.
Trends in Biochemical Sciences. 27, 336. [PubMed]
Kristiansen, T. Z. and Pandey,
A. (2002).
Resources for full-length cDNAs. Trends in Biochemical
Sciences. 27, 266-267.
[PubMed]
Schiemann, W. P., Blobe, G. C., Kalume, D. E., Pandey,
A. and Lodish, H. F. (2002).
Context-specific effects of
fibulin-5 (DANCE/ EVEC) on cell proliferation, motility,
and invasion: Fibulin-5 is induced by TGF-beta and affects
protein kinase cascades. Journal of Biological Chemistry.
277, 27367-27377.
[PubMed]
Dan, I., Watanabe, N. M., Kajikawa, E., Ishida, T., Pandey,
A. and Kusumi, A. (2002).
Overlapping of MINK and CHRNE
gene loci in the course of mammalian evolution. Nucleic
Acids Research. 30, 2906-2910.
[PubMed]
Pandey, A.,
Dan, I., Kristiansen, T. Z., Watanabe, N. M., Voldby,
J., Kajikawa, E., Khosravi-Far,
R., Blagoev, B. and Mann, M. (2002).
Cloning and characterisation
of PAK5, a novel member of mammalian p21-activated kinase-II
subfamily that is predominantly expressed in brain. Oncogene.
21, 3939-3948.
[PubMed]
Mann, M., Ong, S. E., Grønborg, M., Steen, H.,
Jensen, O. N. and Pandey, A.
(2002).
Analysis of protein phosphorylation using mass spectrometry:
deciphering the phosphoproteome. Trends in Biotechnology.
20, 261-268.
[PubMed]
Kratchmarova, I., Kalume, D. E., Blagoev, B., Scherer,
P. E., Podtelejnikov, A. V., Molina, H., Bickel, P. E.,
Andersen, J. S., Fernandez, M. M., Bunkenborg, J., Roepstorff,
P., Kristiansen, K., Lodish, H. F., Mann, M. and Pandey,
A. (2002).
A proteomic approach for identification of secreted
proteins during the differentiation of 3T3-L1 preadipocytes
to adipocytes. Molecular and Cellular Proteomics. 1, 213-222.
[PubMed]
Pandey, A.,
Ibarrola, N., Kratchmarova, I., Fernandez, M. M., Constantinescu,
S. N,
Ohara, O., Sawasdikosol, S., Lodish, H. F. and Mann,
M. (2002).
A novel Src homology 2 domain-containing molecule, Src-like
adapter protein-2 (SLAP-2), which negatively regulates
T cell receptor signaling. Journal of Biological Chemistry.
277, 19131-19138.
[PubMed]
Dan, I., Ong, S. E., Watanabe, N. M., Blagoev, B., Nielsen,
M. M., Kajikawa, E., Kristiansen, T. Z., Mann, M. and
Pandey, A. (2002).
Cloning of MASK,
a novel member of the mammalian germinal center kinase-III
subfamily, with apoptosis-inducing properties. Journal
of Biological Chemistry. 277, 5929-5939.
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Blagoev, B., Nielsen, M. M., Angrist, M., Chakravarti,
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Cloning
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2001
Peri, S. and Pandey,
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A reassessment of the translation initiation codon in
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Blagoev, B. and Pandey, A.
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Microarrays go live - new prospects for proteomics. Trends
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Peri, S., Steen, H. and Pandey,
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GPMAW - a software tool for analyzing proteins
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Mann, M., Hendrickson, R. C. and Pandey,
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Analysis of proteins and proteomes by mass spectrometry.
Annual Review of Biochemistry. 70, 437-473.
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Peri, S., Ibarrola, N., Blagoev, B., Mann, M. and Pandey,
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Common pitfalls in bioinformatics based analyses:
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Ong, S. E. and Pandey, A.
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An evaluation of the use of two dimensional gel electrophoresis
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Mann, M. and Pandey, A.
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Use of mass spectrometry-derived data to annotate nucleotide
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Kratchmarova, I., Sosinowski, T., Weiss, A., Witter,
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Characterization of promoter region and genomic structure
of the murine and human genes encoding Src like adapter
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Gene. 262, 267-273.
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2000
Pandey, A.,
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M., Mann, M. and
Lodish, H. F.
(2000).
Identification of a novel immunoreceptor
tyrosine-based activation motif (ITAM) - containing
molecule,
STAM2, by mass spectrometry and its involvement in growth
factor and cytokine receptor signaling pathways. Journal
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[PubMed]
Pandey, A.
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Proteomics to study genes and genomes. Nature. 405, 837-846.
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Pandey, A.,
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Use of mass spectrometry to study signaling
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Pandey, A.,
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Cloning of a receptor
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Nature Immunology. 1, 59-64.
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M. and Lodish,
H. F.
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Analysis of receptor signaling pathways by mass
spectrometry: identification of vav-2 as a substrate
of the epidermal
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1999
Pandey, A.
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Nucleotide Sequence Databases: A gold
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Trends in Biochemical Sciences. 24, 276-280.
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