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

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

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Key Publications

Cooper EM, Cutcliffe C, Kristiansen TZ, Pandey A, Pickart CM, Cohen RE. (2009). K63-specific deubiquitination by two JAMM/MPN+ complexes: BRISC-associated BRCC36 and proteasomal POH1. EMBO Journal. 28, 621-631.  PubMed Link

Chaerkady R, Thuluvath PJ, Nalli A, Vivekanandan P, Simmers J, Torbenson M, Pandey A. (2009). 18-O labeling for a quantitative proteomic analysis of glycoproteins in hepatocellular carcinoma. Clin Proteomics. 4, 137-155PubMed Link

Kandasamy K, Keerthikumar S, Goel R, Mathivanan S, Patankar N, Shafreen B, Renuse S, Pawar H, Ramachandra YL, Acharya PK, Ranganathan P, Chaerkady R, Prasad TS, Pandey A. (2008). Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Res. 37(Database issue), D773-781.  PubMed Link

HOT PAPER!  Molina H, Yang Y, Ruch T, Kim JW, Mortensen P, Otto T, Nalli A, Tang QQ, Lane MD, Chaerkady R, Pandey A. (2009). Temporal Profiling of the Adipocyte Proteome during Differentiation Using a Five-Plex SILAC Based Strategy. J Proteome Res. 8, 48-58.  PubMed Link

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

HOT PAPER!  Guha U, Chaerkady R, Kashyap M, Marimuthu A, Patterson S, Gowda H, Dowdle J, Gucek M, Bader JS, Lash A, Pandey A, Varmus H. (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. Proc Natl Acad Sci U S A. 105, 14112-14117.  PubMed Link

Luo W, Slebos RJ, Hill S, Li M, Brábek J, Amanchy R, Chaerkady R, Pandey A, Ham AJ, Hanks SK. (2008). Global Impact of Oncogenic Src on a Phosphotyrosine Proteome. J. Proteome Res. 7, 3447-3460.  PubMed Link

Mathivanan S, Pandey A. (2008). Human Proteinpedia as a resource for clinical proteomics. Mol. Cell. Proteomics. 7(10), 2038-2047.  PubMed Link

Mathivanan S, Ahmed M, Ahn NG, Pandey A, et al. (2008). Human Proteinpedia enables sharing of human proteomic data. Nature Biotechnology. 26, 164-167.  PubMed Link

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

Zhong L, Roybal J, Chaerkady R, Zhang W, Choi K, Tran H, Yan S, Strieter RM, Pandey A, Kurie JM. (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 Link

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

Bhandari R, Saiardi A, Ahmadibeni Y, Snowman AM, Resnick AC, Kristiansen TZ, Molina H, Pandey A, Werner JK Jr, Juluri KR, Xu Y, Prestwich GD, Parang K, Snyder SH. (2007). Protein pyrophosphorylation by inositol pyrophosphates is a posttranslational event. Proc Natl Acad Sci U S A. 104, 15305-15310.  PubMed Link

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

Harsha HC, Molina H, Pandey A. (2007). Quantitative proteomics using stable isotope labeling with amino acids in cell culture (SILAC). Nature Protocols. 3, 505-516.  PubMed Link

Molina H, Horn DM, Tang N, Mathivanan S, Pandey A. (2007). Global Proteomic Profiling of Phosphopeptides using Electron Transfer Dissociation Tandem Mass Spectrometry. Proc Natl Acad Sci U S A. 104, 2199-2204.  PubMed Link

Wang Z, Pandey A, Hart GW. (2007). Dynamic interplay between O-GlcNAcylation and GSK-3-dependent phosphorylation. Mol Cell Proteomics. 6, 1365-1379.  PubMed Link

Zhong J, Molina H, Pandey A. Phosphoproteomics. Current Protocols in Protein Science. John Wiley & Sons, Ltd., Chichester. 2007. 50:24.4.1-24.4.21.  PubMed Link

Cole PA. (2006). Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc Natl Acad Sci U S A. 103, 9773-9778.  PubMed Link

Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 38, 285-293.  PubMed Link

Gronborg M, Kristiansen TZ, Iwahori A, Chang R, Reddy R, Sato N, Molina H, Jensen ON, Hruban RH, Goggins MG, Maitra A, Pandey A. (2006). Biomarker discovery from pancreatic cancer secretome using a differential proteomics approach. Mol Cell Proteomics. 5, 157-171.  PubMed Link

Mathivanan S, Periaswamy B, Gandhi TKB, Kandasamy K, Suresh S, Mohmood R, Ramachandra YL, Pandey A. (2006). An Evaluation of Human Protein-Protein Interaction Data in the Public Domain. BMC Bioinformatics. 7, S19.  PubMed Link

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

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

Wang D, Kalume D, Pickart C, Pandey A, Cotter RJ. (2006). Identification of protein ubiquitylation by electrospray ionization tandem mass spectrometric analysis of sulfonated tryptic peptides. Analytical Chemistry. 78, 3681-3687.  PubMed Link

Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 38, 285-293.  PubMed Link

Amanchy R, Kalume DE, Iwahori A, Zhong J, Pandey, A. (2005). Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). J. Proteome Res. 4, 1661-1671.  PubMed Link

Amanchy R, Kalume DE, 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 Link

Gronborg M, Kristiansen TZ, Iwahori A, Chang R, Reddy R, Sato N, Molina H, Jensen ON, Hruban RH, Goggins MG, Maitra A, Pandey A. (2005). Biomarker discovery from pancreatic cancer secretome using a differential proteomics approach. Mol. Cell. Proteomics. 5, 157-171.  PubMed Link

Hyland EM, Cosgrove MS, Molina H, Wang D, Pandey A, Cotter R, Boeke JD. (2005). Insights into the Role of Histone H3 and Histone H4 Core Modifiable Residues in Saccharomyces cerevisiae. Mol. Cell. Biol. 25, 10060-10070.  PubMed Link

Harsha HC, Suresh S, Amanchy R, Deshpande N, Shanker K, Yatish AJ, Muthusamy B, Vrushabendra BM, Rashmi BP, Chandrika KN, Padma N, Sharma S, Badano JL, Ramya MA, Chandran S, Menezes M, Katsanis N, Deshpande KS, Raghothama C, Prasad CK, Pandey A. (2005). A manually curated functional annotation of the human X chromosome. Nature Genetics. 37, 331-332.  PubMed Link

Molina H, Parmigiani G, 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 Link

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

Ibarrola N, Molina H, Iwahori A, 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 Link

Kristiansen TZ, Bunkenborg J, Gronborg M, Molina H, Thuluvath PJ, Argani P, Goggins MG, Maitra A, Pandey, A. (2004). A comprehensive proteomic analysis of human bile. Molecular and Cellular Proteomics. 3, 715-728.  PubMed Link

Ibarrola N, Kalume DE, Gronborg M, Iwahori A, Pandey A. (2003). A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture. Analytical Chemistry. 75, 6043-6049.  PubMed Link

Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, 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 Link

Gronborg M, Kristiansen TZ, Stensballe A, Andersen JS, Ohara O, Mann M, Jensen ON, 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 Link



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