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

Total number of publications - 69

Chaerkady, R., Harsha, H. C., Nalli, A., Gucek, M., Vivekanandan, P., Akhtar, J., Cole, R. N., Simmers, J., Schulick, R. D., Singh, S., Torbenson, M., Pandey, A. and Thuluvath, P. J. A Quantitative Proteomic Approach for Identification of Potential Biomarkers in Hepatocellular Carcinoma. Journal of Proteome Research. In press.

Sarker, R., Grønborg, M., Cha, B., Mohan, S., Chen, Y., Pandey, A., Litchfield, D., Donowitz, M and Li, X. 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. In press.

Zhong, L., Roybal, J., Chaerkady, R., Zhang, W., Choi, K., Tran, H., Yan, S., Strieter, R. M., Pandey, A. and Kurie, J. M. Identification of secreted proteins that Mediate Cell-Cell Interactions in an In Vitro Model of the Lung Cancer Microenvironment. Cancer Research. In press.

Amanchy, R., Zhong, J., Molina, H., Chaerkady, R, Iwahori, A, Kalume, D. E., Grønborg, M., Joore, J., Cope, L. and Pandey, A. Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. Journal of Proteome Research. In press.

Luo, W., Slebos, R. J., Hill, S., Li, M., Brabek, J., Amanchy, R., Chaerkady, R, Pandey, A., Ham, A-J. L. and Hanks, S. Global impact of oncogenic Src on a phosphotyrosine proteome. Journal of Proteome Research. In press.

Chaerkady, R., Thuluvath, P. J., Nalli, A., Vivekanandan, P., Simmers, J., Torbenson, M. and Pandey, A. ¹⁸O labeling for a quantitative proteomic analysis of glycoproteins in hepatocellular carcinoma. Clinical Proteomics. In press.

Molina, H., Matthiesen, R., Kandasamy, K. and Pandey, A. A Comprehensive Comparison of Collision Induced Dissociation and Electron Transfer Dissociation. Analytical Chemistry. 80, 4825-4835. [PubMed]

Chaerkady, R. and Pandey, A. Applications of proteomics to lab diagnosis. Annual Review of Pathology: Mechanisms of Disease. 3, 485-98. [PubMed]

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

Harsha, H. C., Molina, H. and Pandey, A. 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. Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-7. [PubMed]

  Chaerkady, R. and Pandey, A. Quantitative proteomics for identification of cancer biomarkers. Proteomics Clinical Applications. 1, 1080-1089.

Okulate, M., Kalume, D. E., Chaerkady, R., Reddy, R., Kristiansen, K., Bhattacharyya, M., Pandey, A. and Kumar, N. 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.

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

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

Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R., Tattikota, S. G. and Pandey, A. A compendium of curated phosphorylation-based substrate and binding motifs. Nature Biotechnology. 25, 285-286. [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. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 3, 285-293. [PubMed]

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

Mathivanan, S., Periaswamy, B., Gandhi, T. K. B., Kandasamy, K., Suresh, S., Mohmood, R., Ramachandra, Y. L. and Pandey, A. An Evaluation of Human Protein-Protein Interaction Data in the Public Domain. BMC Bioinformatics. 7, S19. [PubMed]

Sarker, M., Hanumanthu, G. and Pandey, A. 'Plasma Proteome Database' in, Proteomics of human body fluids, Thongboonkerd, V. Editor (Humana Press, Totowa, New Jersey, USA). In Press.

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

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

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

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

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

Kalume, D. E., Peri, S., Zhong, J., Okulate, M., Reddy, R., Humar, N. and Pandey, A. Genome Annotation of Anopheles gambiae using Mass Spectrometry-derived Data. BMC Genomics. 6, 128. [PubMed]

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

Muthusamy, B., Hanumanthu, G., Reshmi, R., Sriranjini, S., Suresh, S., Rekha, B., Srinivas, D., Karthick, L., Vrushabendra, B. M., Sharma, S., Mishra, G., Rashmi, B. P., Kadekar, S., Chatterjee, P., Mangala, K. S., Shivashankar, H. N., Chandrika, K. N., Deshpande, N., Suresh, M., Kannabiran, N., Niranjan, V., Nalli, A., Prasad, T. S. K., Arun, K. S., Reddy, R., Chandran, S., Jadhav, T., Julie, D., Mahesh, M., John, S. L., Palvankar, K., Sudhir, D., P. Bala., 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. Plasma Proteome Database as a resource for proteomics research. Proteomics. 5, 3531-3536. [PubMed]

Ping, P., Vondriska, T. M., Creighton, C. J., Gandhi, T. K. B., Yang, Z., Menon, R., Kwon, M. S., Cho, S. Y., Drwal, G., Kellmann, M., Peri, S., Suresh, S., 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. 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. A manually curated functional annotation of the human X chromosome. Nature Genetics. 37, 331-332. [PubMed]

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

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

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

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

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

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

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

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

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

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

Anand, S.K. and Pandey, A. Screening large proteins for interaction partners. Trends in Biochemical Sciences. 27, 603.

Muthusamy, B. and Pandey, A. A roadmap of the mouse genome. Trends in Genetics. 18, 553.

Gandhi, T.K.B. and Pandey, A. Using bioinformatics to identify cis-regulatory sequences. Trends in Biotechnology. 20, 448.

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

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

Grønborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. A., Ohara,O., Mann, M., Jensen, O. N. and Pandey, A. 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. Toll and Interleukin-1 Receptor (TIR) domain-containing proteins in plants: a genomic perspective. Trends in Plant Science. 7, 388-391. [PubMed]

Steen, H. and Pandey, A. 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. 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. Mining gene expression data for functional annotation of genomes. Trends in Biotechnology. 20, 282. [PubMed]

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

Kristiansen, T. Z. and Pandey, A. 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. 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. 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. 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. 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. 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. 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. Cloning of MASK, a novel member of the mammalian germinal center kinase-III subfamily, with apoptosis-inducing properties. Journal of Biological Chemistry. 277, 5929-5939. [PubMed]

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