Publications

1. Byeon SK, Kim J, Wegwerth PJ, Zenka R, George JP, Pinto E Vairo F, Oglesbee D, Schultz MJ, Matern D, Pandey A. Development of a Multiplexed Sphingolipids Method for Diagnosis of Inborn Errors of Ceramide Metabolism. Clin Chem. 2024 Nov 4; 70 (11):1366-1374
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2. Kim J, Byeon SK, Oglesbee D, Schultz MJ, Matern D, Pandey A. A multiplexed targeted method for profiling of serum gangliosides and glycosphingolipids: application to GM2-gangliosidosis. Anal Bioanal Chem. 2024 Nov; 416 (26):5689-5699 Epub 2024 Aug 27
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3. Ramarajan MG, Parthasarathy KTS, Gaikwad KB, Joshi N, Garapati K, Kandasamy RK, Sharma J, Pandey A. Alterations in Hurler-Scheie Syndrome Revealed by Mass Spectrometry-Based Proteomics and Phosphoproteomics Analysis. OMICS. 2024 Oct 29 [Epub ahead of print]
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4. Hazra D, Chawla K, S M F, Sintchenko V, Magazine R, Martinez E, Pandey A. The impact of anti-tuberculosis treatment on respiratory tract microbiome in pulmonary tuberculosis. Microbes Infect. 2024 Oct 19; 105432 [Epub ahead of print]
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5. Gaikwad KB, Babu JS, Parthasarathi KTS, Narayanan J, Padmanabhan P, Pandey A, Gundimeda S, Elchuri SV, Sharma J. Computational approaches for identifications of altered ion channels in keratoconus. Eye (Lond). 2024 Oct 17 [Epub ahead of print]
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6. Tang H, Yan H, Shivaram S, Lehman S, Sharma N, Smadbeck J, Zepeda-Mendoza C, Tian S, Asmann Y, Vachon C, Gaspar Maia A, Keats J, Bergsagel PL, Fonseca R, Stewart AK, Hsu JS, Kandasamy RK, Pandey A, Kaddoura MA, Maura F, Mitra A, Rajkumar SV, Kumar SK, Elhaik E, Braggio E, Baughn LB. Functional variant rs9344 at 11q13.3 regulates CCND1 expression in multiple myeloma with t(11;14). Leukemia. 2024 Oct 14 [Epub ahead of print]
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7. Zhou X, Li M, Ai M, Li Y, Zhu X, Hansen MJ, Zhong J, Johnson KL, Zenka R, Pandey A, Pease LR, Zeng H. PP2A catalytic subunit alpha is critically required for CD8(+) T-cell homeostasis and antibacterial responses. Eur J Immunol. 2024 Oct; 54 (10):e2451080 Epub 2024 July 28
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8. Garapati K, Ranatunga W, Joshi N, Budhraja R, Sabu S, Kantautas KA, Preston G, Perlstein EO, Kozicz T, Morava E, Pandey A. N-glycoproteomic and proteomic alterations in SRD5A3-deficient fibroblasts. Glycobiology. 2024 Sep 30; 34 (11)
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9. Sun ND, Carr AR, Krogman EN, Chawla Y, Zhong J, Guttormson MC, Chan M, Hsu MA, Dong H, Bogunovic D, Pandey A, Rogers LM, Ting AT. TBK1 and IKKepsilon protect target cells from IFNgamma-mediated T cell killing via an inflammatory apoptotic mechanism. bioRxiv. 2024 Aug 8 Epub 2024 Aug 08
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10. Budhraja R, Joshi N, Radenkovic S, Kozicz T, Morava E, Pandey A. Dysregulated proteome and N-glycoproteome in ALG1-deficient fibroblasts. Proteomics. 2024 Aug; 24 (15):e2400012 Epub 2024 Mar 12
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11. Stezin A, Sathe GJ, Gajbhiye A, Bharadwaj S, Ghose V, Bellad A, Malo PK, Holla V, Hegde S, Bharath RD, Saini J, Jain S, Yadav R, Pandey A, Pal PK. Dysregulated Cerebrospinal Fluid Proteome of Spinocerebellar Ataxia Type 2 and its Clinical Implications. Mov Disord. 2024 Aug; 39 (8):1418-1423 Epub 2024 May 20
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12. Mun DG, Bhat FA, Joshi N, Sandoval L, Ding H, Jain A, Peterson JA, Kang T, Pujari GP, Tomlinson JL, Budhraja R, Zenka RM, Kannan N, Kipp BR, Dasari S, Gaspar-Maia A, Smoot RL, Kandasamy RK, Pandey A. Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry. Commun Biol. 2024 Jul 19; 7 (1):884 Epub 2024 July 19
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13. Xie X, Truong T, Huang S, Johnston SM, Hovanski S, Robinson A, Webber KGI, Lin HL, Mun DG, Pandey A, Kelly RT. Multicolumn Nanoflow Liquid Chromatography with Accelerated Offline Gradient Generation for Robust and Sensitive Single-Cell Proteome Profiling. Anal Chem. 2024 Jul 2; 96 (26):10534-10542 Epub 2024 June 25
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14. Bellad A, Rangiah K, Sathe G, Dey G, Appadorai PK, Lokanatha H, Murthy PR, Gowdra A, Pandey A. Identification of a rare [(G)gamma((A)gammadeltabeta)(0)] -thalassemia using tandem mass spectrometry. Proteomics. 2024 Jul; 24 (14):e2300495 Epub 2024 Jan 11
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15. Vasanthaiah S, Verma R, Kumar A, Bandari AK, George J, Rastogi M, Manjunath GK, Sharma J, Kumar A, Subramani J, Chawla K, Pandey A. Culture-Free Whole Genome Sequencing of Mycobacterium tuberculosis Using Ligand-Mediated Bead Enrichment Method. Open Forum Infect Dis. 2024 Jul; 11 (7):ofae320 Epub 2024 June 15
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16. Budhraja R, Radenkovic S, Jain A, Muffels IJJ, Ismaili MHA, Kozicz T, Pandey A, Morava E. Liposome-encapsulated mannose-1-phosphate therapy improves global N-glycosylation in different congenital disorders of glycosylation. Mol Genet Metab. 2024 Jun; 142 (2):108487 Epub 2024 May 07
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17. Starosta RT, Lee AJ, Toolan ER, He M, Wongkittichote P, Daniel EJP, Radenkovic S, Budhraja R, Pandey A, Sharma J, Morava E, Nguyen H, Dickson PI. D-mannose as a new therapy for fucokinase deficiency-related congenital disorder of glycosylation (FCSK-CDG). Mol Genet Metab. 2024 Jun; 142 (2):108488 Epub 2024 May 09
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18. Jackson LE, Tomlinson JL, Alva-Ruiz R, Gregory LA, Byeon SK, Abdelrahman AM, Mun DG, Grant CW, Fogarty ZC, Wang C, Roberts LR, Graham RP, Borad MJ, Ilyas SI, Gores GJ, Pandey A, Athreya AP, Smoot RL. Metabolome-wide association identifies altered metabolites and metabolic pathways in the serum of patients with cholangiocarcinoma. JHEP Rep. 2024 Jun; 6 (6):101068 Epub 2024 Mar 18
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19. Garapati K, Jain A, Madden BJ, Mun DG, Sharma J, Budhraja R, Pandey A. Defining albumin as a glycoprotein with multiple N-linked glycosylation sites. J Transl Med. 2024 May 13; 22 (1):454
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20. Kang T, Budhraja R, Kim J, Joshi N, Garapati K, Pandey A. Global O-glycoproteome enrichment and analysis enabled by a combinatorial enzymatic workflow. Cell Rep Methods. 2024 Apr 22; 4 (4):100744 Epub 2024 Apr 05
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21. Wilson E, Cava JK, Chowell D, Raja R, Mangalaparthi KK, Pandey A, Curtis M, Anderson KS, Singharoy A. The electrostatic landscape of MHC-peptide binding revealed using inception networks. Cell Syst. 2024 Apr 17; 15 (4):362-373.e7 Epub 2024 Mar 29
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22. Garapati K, Budhraja R, Saraswat M, Kim J, Joshi N, Sachdeva GS, Jain A, Ligezka AN, Radenkovic S, Ramarajan MG, Udainiya S, Raymond K, He M, Lam C, Larson A, Edmondson AC, Sarafoglou K, Larson NB, Freeze HH, Schultz MJ, Kozicz T, Morava E, Pandey A. A complement C4-derived glycopeptide is a biomarker for PMM2-CDG. JCI Insight. 2024 Apr 8; 9 (7) Epub 2024 Apr 08
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23. Jia J, Ji W, Saliba AN, Csizmar CM, Ye K, Hu L, Peterson KL, Schneider PA, Meng XW, Venkatachalam A, Patnaik MM, Webster JA, Smith BD, Ghiaur G, Wu X, Zhong J, Pandey A, Flatten KS, Deng Q, Wang H, Kaufmann SH, Dai H. AMPK inhibition sensitizes acute leukemia cells to BH3 mimetic-induced cell death. Cell Death Differ. 2024 Apr; 31 (4):405-416 Epub 2024 Mar 27
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24. Radenkovic S, Budhraja R, Klein-Gunnewiek T, King AT, Bhatia TN, Ligezka AN, Driesen K, Shah R, Ghesquiere B, Pandey A, Kasri NN, Sloan SA, Morava E, Kozicz T. Neural and metabolic dysregulation in PMM2-deficient human in vitro neural models. Cell Rep. 2024 Mar 26; 43 (3):113883 Epub 2024 Mar 01
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25. Khade OS, Sasidharan S, Jain A, Maradani BS, Chatterjee A, Gopal D, Ravi Kumar RK, Krishnakumar S, Pandey A, Janakiraman N, Elchuri SV, Gundimeda S. Identification of dysregulation of sphingolipids in retinoblastoma using liquid chromatography-mass spectrometry. Exp Eye Res. 2024 Mar; 240:109798 Epub 2024 Jan 19
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26. Bhat FA, Mangalaparthi KK, Ding H, Jain A, Hsu JS, Peterson JA, Zenka RM, Mun DG, Kandasamy RK, Pandey A. Exploration of Nitrotyrosine-Containing Proteins and Peptides by Antibody-Based Enrichment Strategies. Mol Cell Proteomics. 2024 Mar; 23 (3):100733 Epub 2024 Feb 10
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27. Joshi N, Garapati K, Ghose V, Kandasamy RK, Pandey A. Recent progress in mass spectrometry-based urinary proteomics. Clin Proteomics. 2024 Feb 22; 21 (1):14
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28. Monroe JM, Quach HQ, Punia S, Enninga EAL, Fedyshyn Y, Girsch JH, Fedyshyn B, Lemens M, Littlefield D, Behl S, Sintim-Aboagye E, Mejia Plazas MC, Yamaoka S, Ebihara H, Pandey A, Correia C, Ung CY, Li H, Vassallo R, Sun J, Johnson EL, Olson JE, Theel ES, Badley AD, Kennedy RB, Theiler RN, Chakraborty R. Vertical Transmission of SARS-CoV-2-Specific Antibodies and Cytokine Profiles in Pregnancy. J Infect Dis. 2024 Feb 14; 229 (2):473-484
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29. Enninga EAL, Quach HQ, Jang JS, de Araujo Correia MCM, Fedyshyn Y, Fedyshyn B, Lemens M, Littlefield D, Behl S, Sintim-Aboagye E, Mejia Plazas MC, Cardenas MC, Chakraborty S, Yamaoka S, Ebihara H, Pandey A, Li H, Badley AD, Johnson EL, Sun J, Norgan AP, Theiler RN, Chakraborty R. Maternal SARS-CoV-2 infection in pregnancy disrupts gene expression in Hofbauer cells with limited impact on cytotrophoblasts. PLoS Pathog. 2024 Feb; 20(2):e1011990. Epub 2024 Feb 07.
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30. Singh S, Parthasarathi KTS, Bhat MY, Gopal C, Sharma J, Pandey A. Profiling Kinase Activities for Precision Oncology in Diffuse Gastric Cancer. OMICS. 2024 Feb; 28 (2):76-89 Epub 2024 Jan 25
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31. Patel K, Rao DM, Sundersingh S, Velusami S, Rajkumar T, Nair B, Pandey A, Chatterjee A, Mani S, Gowda H. MicroRNA Expression Profile in Early-Stage Breast Cancers. Microrna. 2024; 13 (1):71-81
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32. Wilkins JM, Mangalaparthi KK, Netzel BC, Sherman WA, Guo Y, Kalinowska-Lyszczarz A, Pandey A, Lucchinetti CF. Proteomics analysis of periplaque and chronic inactive multiple sclerosis lesions. Front Mol Neurosci. 2024; 17:1448215 Epub 2024 Aug 21
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33. Cruz-Gonzalez G, Meschia JF, Madden BJ, Prudencio M, Polania-Sandoval CA, Hartwell J, Oyefeso E, Benchaaboune R, Brigham T, Sandhu SJS, Charlesworth C, Pujari GP, Petrucelli L, Pandey A, Erben Y. Recent advances in proteomic analysis to study carotid artery plaques. JVS Vasc Sci. 2024; 5:100215 Epub 2024 Aug 24
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34. Jayaraman S, Wu X, Kalari KR, Tang X, Kuffel MJ, Bruinsma ES, Jalali S, Peterson KL, Correia C, Kudgus RA, Kaufmann SH, Renuse S, Ingle JN, Reid JM, Ames MM, Fields AP, Schellenberg MJ, Hawse JR, Pandey A, Goetz MP. Endoxifen downregulates AKT phosphorylation through protein kinase C beta 1 inhibition in ERa+ breast cancer. NPJ Breast Cancer. 2023 Dec 19; 9(1):101.
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35. Garapati K, Ding H, Charlesworth MC, Kim Y, Zenka R, Saraswat M, Mun DG, Chavan S, Shingade A, Lucien F, Zhong J, Kandasamy RK, Pandey A. sBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides. Clin Proteomics. 2023 Dec 5; 20 (1):56 Epub 2023 Dec 05
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36. Bellad A, Holla VV, Kumari R, Kamble N, Yadav R, Pandey A, Pal PK, Muthusamy B. Loss of function variants in L2HGDH gene causing L-2-hydroxyglutaric aciduria. Acta Neurol Belg. 2023 Dec; 123 (6):2315-2323 Epub 2023 June 28
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37. Mun DG, Joshi NS, Budhraja R, Sachdeva GS, Kang T, Bhat FA, Ding H, Madden BJ, Zhong J, Pandey A. Automated Sample Preparation Workflow for Tandem Mass Tag-Based Proteomics. J Am Soc Mass Spectrom. 2023 Oct 4; 34 (10):2087-2092 Epub 2023 Sept 01
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38. Worley G, Byeon SK, Smith PB, Hart SJ, Young SP, Pandey A, Kishnani PS. An exploratory study of plasma ceramides in comorbidities in Down syndrome. Am J Med Genet A. 2023 Sep; 191(9):2300-2311. Epub 2023 Jun 21.
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39. Dhar D, Holla VV, Kumari R, Sriram N, Saini J, Yadav R, Pandey A, Kamble N, Muthusamy B, Pal PK. KMT2B-Related Dystonia in Indian Patients With Literature Review and Emphasis on Asian Cohort. J Mov Disord. 2023 Sep; 16 (3):285-294 Epub 2023 June 13
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40. Fisher CR, Mangalaparthi KK, Greenwood-Quaintance KE, Abdel MP, Pandey A, Patel R. Mass spectrometry-based proteomic profiling of sonicate fluid differentiates Staphylococcus aureus periprosthetic joint infection from non-infectious failure: A pilot study. Proteomics Clin Appl. 2023 Sep; 17 (5):e2200071 Epub 2023 Mar 27
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41. Dutta D, Kanca O, Byeon SK, Marcogliese PC, Zuo Z, Shridharan RV, Park JH, Lin G, Ge M, Heimer G, Kohler JN, Wheeler MT, Kaipparettu BA, Pandey A, Bellen HJ, Undiagnosed Diseases Network. A defect in mitochondrial fatty acid synthesis impairs iron metabolism and causes elevated ceramide levels. Nat Metab. 2023 Sep; 5 (9):1595-1614 Epub 2023 Aug 31
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42. Ligezka AN, Budhraja R, Nishiyama Y, Fiesel FC, Preston G, Edmondson A, Ranatunga W, Van Hove JLK, Watzlawik JO, Springer W, Pandey A, Morava E, Kozicz T. Interplay of Impaired Cellular Bioenergetics and Autophagy in PMM2-CDG. Genes (Basel). 2023 Aug 4; 14 (8) Epub 2023 Aug 04
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43. Joshi N, Bhat F, Bellad A, Sathe G, Jain A, Chavan S, Sirdeshmukh R, Pandey A. Urinary Proteomics for Discovery of Gastric Cancer Biomarkers to Enable Precision Clinical Oncology. OMICS. 2023 Aug; 27 (8):361-371 Epub 2023 Aug 09
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44. Mun DG, Bhat FA, Ding H, Madden BJ, Natesampillai S, Badley AD, Johnson KL, Kelly RT, Pandey A. Optimizing single cell proteomics using trapped ion mobility spectrometry for label-free experiments. Analyst. 2023 Jul 26; 148 (15):3466-3475 Epub 2023 July 26
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45. Pujari GP, Mangalaparthi KK, Madden BJ, Bhat FA, Charlesworth MC, French AJ, Sachdeva G, Daviso E, Thomann U, McCarthy P, Vasantgadkar S, Bhattacharyya D, Pandey A. A High-Throughput Workflow for FFPE Tissue Proteomics. J Am Soc Mass Spectrom. 2023 Jul 5; 34 (7):1225-1229 Epub 2023 June 02
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46. Jung JH, Yang DQ, Song H, Wang X, Wu X, Kim KP, Pandey A, Byeon SK. Characterization of Lipid Alterations by Oncogenic PIK3CA Mutations Using Untargeted Lipidomics in Breast Cancer. OMICS. 2023 Jul; 27 (7):327-335
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47. Balakrishnan B, Altassan R, Budhraja R, Liou W, Lupo A, Bryant S, Mankouski A, Radenkovic S, Preston GJ, Pandey A, Boudina S, Kozicz T, Morava E, Lai K. AAV-based gene therapy prevents and halts the progression of dilated cardiomyopathy in a mouse model of phosphoglucomutase 1 deficiency (PGM1-CDG). Transl Res. 2023 Jul; 257:1-14 Epub 2023 Jan 26
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48. Sawant M, Wilson A, Sridaran D, Mahajan K, O'Conor CJ, Hagemann IS, Luo J, Weimholt C, Li T, Roa JC, Pandey A, Wu X, Mahajan NP. Epigenetic reprogramming of cell cycle genes by ACK1 promotes breast cancer resistance to CDK4/6 inhibitor. Oncogene. 2023 Jul; 42 (29):2263-2277 Epub 2023 June 17
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49. Khurana H, Muthusamy B, Yanamandra U, Garapati K, Premdeep H, Subramanian S, Pandey A. Whole Exome Sequencing Reveals Novel Variants in Unexplained Erythrocytosis. OMICS. 2023 Jul; 27 (7):299-304 Epub 2023 July 11
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50. Mangalaparthi KK, Patel K, Khan AA, Nair B, Kumar RV, Prasad TSK, Sidransky D, Chatterjee A, Pandey A, Gowda H. Molecular Characterization of Esophageal Squamous Cell Carcinoma Using Quantitative Proteomics. Cancers (Basel). 2023 Jun 23; 15 (13) Epub 2023 June 23
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51. Shortreed NA, Panicker AJ, Mangalaparthi KK, Zhong J, Pandey A, Griffiths LG. Optimization of a high-throughput shotgun immunoproteomics pipeline for antigen identification. J Proteomics. 2023 Jun 15; 281:104906 Epub 2023 Apr 13
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52. Sriram N, Holla VV, Kumari R, Kamble N, Saini J, Mahale R, Netravathi M, Padmanabha H, Gowda VK, Battu R, Pandey A, Yadav R, Muthusamy B, Pal PK. Clinical, imaging and genetic profile of twenty-four patients with pantothenate kinase-associated neurodegeneration (PKAN)- A single centre study from India. Parkinsonism Relat Disord. 2023 Jun; 111:105409 Epub 2023 Apr 23
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53. Mun DG, Budhraja R, Bhat FA, Zenka RM, Johnson KL, Moghekar A, Pandey A. Four-dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF. Proteomics. 2023 May; 23 (10):e2200507 Epub 2023 Feb 19
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54. Qiao W, Chen Y, Zhong J, Madden BJ, Charlesworth CM, Martens YA, Liu CC, Knight J, Ikezu TC, Kurti A, Zhu Y, Meneses A, Rosenberg CL, Kuchenbecker LA, Vanmaele LK, Li F, Chen K, Shue F, Dacquel MV, Fryer J, Pandey A, Zhao N, Bu G. Correction: Trem2 H157Y increases soluble TREM2 production and reduces amyloid pathology. Mol Neurodegener. 2023 Apr 28; 18 (1):28
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55. Zhu B, Wei X, Narasimhan H, Qian W, Zhang R, Cheon IS, Wu Y, Li C, Jones RG, Kaplan MH, Vassallo RA, Braciale TJ, Somerville L, Colca JR, Pandey A, Jackson PEH, Mann BJ, Krawczyk CM, Sturek JM, Sun J. Inhibition of the mitochondrial pyruvate carrier simultaneously mitigates hyperinflammation and hyperglycemia in COVID-19. Sci Immunol. 2023 Apr 14; 8 (82):eadf0348
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56. Qiao W, Chen Y, Zhong J, Madden BJ, Charlesworth CM, Martens YA, Liu CC, Knight J, Ikezu TC, Kurti A, Zhu Y, Meneses A, Rosenberg CL, Kuchenbecker LA, Vanmaele LK, Li F, Chen K, Shue F, Dacquel MV, Fryer J, Pandey A, Zhao N, Bu G. Trem2 H157Y increases soluble TREM2 production and reduces amyloid pathology. Mol Neurodegener. 2023 Jan 31; 18 (1):8
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57. Nicolau S, Dasgupta A, Dasari S, Charlesworth MC, Johnson KL, Pandey A, Doles JD, Milone M. Molecular signatures of inherited and acquired sporadic late onset nemaline myopathies. Acta Neuropathol Commun. 2023 Jan 26; 11 (1):20
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58. Papanikolaou NA, Nikolaidis M, Amoutzias GD, Fouza A, Papaioannou M, Pandey A, Papavassiliou AG. The Dynamic and Crucial Role of the Arginine Methylproteome in Myoblast Cell Differentiation. Int J Mol Sci. 2023 Jan 20; 24 (3)
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59. Lin G, Tepe B, McGrane G, Tipon RC, Croft G, Panwala L, Hope A, Liang AJH, Zuo Z, Byeon SK, Wang L, Pandey A, Bellen HJ. Exploring therapeutic strategies for infantile neuronal axonal dystrophy (INAD/PARK14). Elife. 2023 Jan 16; 12
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60. Conboy CB, Yonkus JA, Buckarma EH, Mun DG, Werneburg NW, Watkins RD, Alva-Ruiz R, Tomlinson JL, Guo Y, Wang J, O'Brien D, McCabe CE, Jessen E, Graham RP, Buijsman RC, Vu D, de Man J, Ilyas SI, Truty MJ, Borad M, Pandey A, Gores GJ, Smoot RL. LCK inhibition downregulates YAP activity and is therapeutic in patient-derived models of cholangiocarcinoma. J Hepatol. 2023 Jan; 78 (1):142-152 Epub 2022 Sept 24
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61. Budhraja R, Saraswat M, De Graef D, Ranatunga W, Ramarajan MG, Mousa J, Kozicz T, Pandey A, Morava E. N-glycoproteomics reveals distinct glycosylation alterations in NGLY1-deficient patient-derived dermal fibroblasts. J Inherit Metab Dis. 2023 Jan; 46 (1):76-91 Epub 2022 Oct 04
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62. Muylle E, Jiang H, Johnsen C, Byeon SK, Ranatunga W, Garapati K, Zenka RM, Preston G, Pandey A, Kozicz T, Fang F, Morava E. TRIT1 defect leads to a recognizable phenotype of myoclonic epilepsy, speech delay, strabismus, progressive spasticity, and normal lactate levels. J Inherit Metab Dis. 2022 Nov; 45 (6):1039-1047 Epub 2022 Sept 21
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63. Saraswat M, Garapati K, Kim J, Budhraja R, Pandey A. Proteomic alterations in extracellular vesicles induced by oncogenic PIK3CA mutations. Proteomics. 2022 Oct; 22 (19-20):e2200077 Epub 2022 July 14
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64. Rai A, Yelamanchi SD, Radotra BD, Gupta SK, Mukherjee KK, Tripathi M, Chhabra R, Ahuja CK, Kumar N, Pandey A, Korbonits M, Dutta P, Gaston-Massuet C. Phosphorylation of beta-catenin at Serine552 correlates with invasion and recurrence of non-functioning pituitary neuroendocrine tumours. Acta Neuropathol Commun. 2022 Sep 16; 10 (1):138 Epub 2022 Sept 16
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65. Byeon SK, Madugundu AK, Garapati K, Ramarajan MG, Saraswat M, Kumar-M P, Hughes T, Shah R, Patnaik MM, Chia N, Ashrafzadeh-Kian S, Yao JD, Pritt BS, Cattaneo R, Salama ME, Zenka RM, Kipp BR, Grebe SKG, Singh RJ, Sadighi Akha AA, Algeciras-Schimnich A, Dasari S, Olson JE, Walsh JR, Venkatakrishnan AJ, Jenkinson G, O'Horo JC, Badley AD, Pandey A. Development of a multiomics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study. Lancet Digit Health. 2022 Sep; 4 (9):e632-e645 Epub 2022 July 11
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66. Goyal P, Kim M, Krishnan U, Mccullough SA, Cheung JW, Kim LK, Pandey A, Borlaug BA, Horn EM, Safford MM, Kamel H. Post-operative atrial fibrillation and risk of heart failure hospitalization. Eur Heart J. 2022 Aug 14; 43 (31):2971-2980
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67. Vanderboom PM, Renuse S, Maus AD, Madugundu AK, Kemp JV, Gurtner KM, Singh RJ, Grebe SK, Pandey A, Dasari S. Machine Learning-Based Fragment Selection Improves the Performance of Qualitative PRM Assays. J Proteome Res. 2022 Aug 5; 21 (8):2045-2054 Epub 2022 July 18
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68. Wang L, Lin G, Zuo Z, Li Y, Byeon SK, Pandey A, Bellen HJ. Neuronal activity induces glucosylceramide that is secreted via exosomes for lysosomal degradation in glia. Sci Adv. 2022 Jul 15; 8(28):eabn3326. Epub 2022 Jul 13.
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69. Rowan DJ, Mangalaparthi KK, Singh S, Moreira RK, Mounajjed T, Lamps L, Westerhoff M, Cheng J, Bellizzi AM, Allende DS, Pandey A, Graham RP. Metallothionein immunohistochemistry has high sensitivity and specificity for detection of Wilson disease. Mod Pathol. 2022 Jul; 35 (7):946-955 Epub 2021 Dec 21
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70. Renuse S, Benson LM, Vanderboom PM, Ruchi FNU, Yadav YR, Johnson KL, Brown BC, Peterson JA, Basu R, McCormick DJ, Pandey A, Basu A. (13)C(15)N: glucagon-based novel isotope dilution mass spectrometry method for measurement of glucagon metabolism in humans. Clin Proteomics. 2022 May 19; 19 (1):16
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71. Mangalaparthi KK, Chavan S, Madugundu AK, Renuse S, Vanderboom PM, Maus AD, Kemp J, Kipp BR, Grebe SK, Singh RJ, Pandey A. Correction: A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples. Clin Proteomics. 2022 May 4; 19 (1):11 Epub 2022 May 04
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72. Saraswat M, Mangalaparthi KK, Garapati K, Pandey A. TMT-Based Multiplexed Quantitation of N-Glycopeptides Reveals Glycoproteome Remodeling Induced by Oncogenic Mutations. ACS Omega. 2022 Apr 5; 7 (13):11023-11032 Epub 2022 Mar 25
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73. Parthasarathi KTS, Mandal S, Singh S, Gundimeda S, Jolly MK, Pandey A, Sharma J. In Silico Analysis of Ion Channels and Their Correlation with Epithelial to Mesenchymal Transition in Breast Cancer. Cancers (Basel). 2022 Mar 11; 14 (6)
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74. Munjal NS, Sapra D, Parthasarathi KTS, Goyal A, Pandey A, Banerjee M, Sharma J. Deciphering the Interactions of SARS-CoV-2 Proteins with Human Ion Channels Using Machine-Learning-Based Methods. Pathogens. 2022 Feb 17; 11 (2)
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75. Jain AP, Sambath J, Sathe G, George IA, Pandey A, Thompson EW, Kumar P. Pan-cancer quantitation of epithelial-mesenchymal transition dynamics using parallel reaction monitoring-based targeted proteomics approach. J Transl Med. 2022 Feb 11; 20 (1):84
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76. Maus A, Renuse S, Kemp J, Madugundu AK, Vanderboom PM, Blommel J, Jerde C, Dasari S, Kipp BR, Singh RJ, Grebe SK, Pandey A. Targeted Detection of SARS-CoV-2 Nucleocapsid Sequence Variants by Mass Spectrometric Analysis of Tryptic Peptides. J Proteome Res. 2022 Jan 7; 21 (1):142-150 Epub 2021 Nov 15
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77. Ramarajan MG, Saraswat M, Budhraja R, Garapati K, Raymond K, Pandey A. Mass spectrometric analysis of chondroitin sulfate-linked peptides. J Proteins Proteom. 2022; 13 (4):187-203 Epub 2022 Oct 02
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78. Maus A, Renuse S, Kemp J, Moehnke K, Mangalaparthi KK, Chavan S, Madugundu AK, Vanderboom PM, Dasari S, Kipp BR, Singh RJ, Grebe SK, Pandey A. Comparison of anti-peptide and anti-protein antibody-based purification techniques for detection of SARS-CoV-2 by targeted LC-MS/MS. Advances in Sample Preparation. 2022; 2:100018
    
79. George IA, Sathe G, Ghose V, Chougule A, Chandrani P, Patil V, Noronha V, Venkataramanan R, Limaye S, Pandey A, Prabhash K, Kumar P. Integrated proteomics and phosphoproteomics revealed druggable kinases in neoadjuvant chemotherapy resistant tongue cancer. Front Cell Dev Biol. 2022; 10:957983 Epub 2022 Oct 28
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80. Saraswat M, Garapati K, Mun DG, Pandey A. Extensive heterogeneity of glycopeptides in plasma revealed by deep glycoproteomic analysis using size-exclusion chromatography. Mol Omics. 2021 Dec 6; 17 (6):939-947 Epub 2021 Dec 06
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81. Byeon SK, Khanam R, Rahman S, Hasan T, Rizvi SJR, Madugundu AK, Ramarajan MG, Jung JH, Chowdhury NH, Ahmed S, Raqib R, Kim KP, Piazza AL, Rinaldo P, Pandey A, Baqui AH, Amanhi Bio-Banking Study Group Group. Maternal serum lipidomics identifies lysophosphatidic acid as a predictor of small for gestational age neonates. Mol Omics. 2021 Dec 6; 17 (6):956-966 Epub 2021 Dec 06
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82. Ligezka AN, Radenkovic S, Saraswat M, Garapati K, Ranatunga W, Krzysciak W, Yanaihara H, Preston G, Brucker W, McGovern RM, Reid JM, Cassiman D, Muthusamy K, Johnsen C, Mercimek-Andrews S, Larson A, Lam C, Edmondson AC, Ghesquiere B, Witters P, Raymond K, Oglesbee D, Pandey A, Perlstein EO, Kozicz T, Morava E. Sorbitol Is a Severity Biomarker for PMM2-CDG with Therapeutic Implications. Ann Neurol. 2021 Dec; 90 (6):887-900 Epub 2021 Oct 26
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83. Parthasarathi KTS, Munjal NS, Dey G, Kumar A, Pandey A, Balakrishnan L, Sharma J. A pathway map of signaling events triggered upon SARS-CoV infection. J Cell Commun Signal. 2021 Dec; 15 (4):595-600 Epub 2021 Sept 06
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84. Singh S, Bhat MY, Sathe G, Gopal C, Sharma J, Madugundu AK, Joshi NS, Pandey A. Proteomic Signatures of Diffuse and Intestinal Subtypes of Gastric Cancer. Cancers (Basel). 2021 Nov 25; 13 (23)
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85. Byeon SK, Madugundu AK, Pandey A. Automated data-driven mass spectrometry for improved analysis of lipids with dual dissociation techniques. J Mass Spectrom Adv Clin Lab. 2021 Nov; 22:43-49 Epub 2021 Oct 28
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86. Karon BS, Donato LJ, Bridgeman AR, Blommel JH, Kipp B, Maus A, Renuse S, Kemp J, Madugundu AK, Vanderboom PM, Chavan S, Dasari S, Singh RJ, Grebe SK, Pandey A. Analytical Sensitivity and Specificity of Four Point of Care Rapid Antigen Diagnostic Tests for SARS-CoV-2 Using Real-Time Quantitative PCR, Quantitative Droplet Digital PCR, and a Mass Spectrometric Antigen Assay as Comparator Methods. Clin Chem. 2021 Nov 1; 67 (11):1545-1553
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87. Mangalaparthi KK, Chavan S, Madugundu AK, Renuse S, Vanderboom PM, Maus AD, Kemp J, Kipp BR, Grebe SK, Singh RJ, Pandey A. A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples. Clin Proteomics 2021 Oct 22; 18 (1):25
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88. Prakash A, Taylor L, Varkey M, Hoxie N, Mohammed Y, Goo YA, Peterman S, Moghekar A, Yuan Y, Glaros T, Steele JR, Faridi P, Parihari S, Srivastava S, Otto JJ, Nyalwidhe JO, Semmes OJ, Moran MF, Madugundu A, Mun DG, Pandey A, Mahoney KE, Shabanowitz J, Saxena S, Orsburn BC. Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants. Cancers (Basel). 2021 Oct 9; 13 (20) Epub 2021 Oct 09
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89. Alexander MP, Mangalaparthi KK, Madugundu AK, Moyer AM, Adam BA, Mengel M, Singh S, Herrmann SM, Rule AD, Cheek EH, Herrera Hernandez LP, Graham RP, Aleksandar D, Aubry MC, Roden AC, Hagen CE, Quinton RA, Bois MC, Lin PT, Maleszewski JJ, Cornell LD, Sethi S, Pavelko KD, Charlesworth J, Narasimhan R, Larsen CP, Rizza SA, Nasr SH, Grande JP, McKee TD, Badley AD, Pandey A, Taner T. Acute Kidney Injury in Severe COVID-19 Has Similarities to Sepsis-Associated Kidney Injury: A Multi-Omics Study. Mayo Clin Proc. 2021 Oct; 96 (10):2561-2575 Epub 2021 July 15
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90. Tahir R, Madugundu AK, Udainiya S, Cutler JA, Renuse S, Wang L, Pearson NA, Mitchell CJ, Mahajan N, Pandey A, Wu X. Proximity-Dependent Biotinylation to Elucidate the Interactome of TNK2 Nonreceptor Tyrosine Kinase. J Proteome Res. 2021 Sep 3; 20 (9):4566-4577 Epub 2021 Aug 24
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91. Byeon SK, Ramarajan MG, Madugundu AK, Oglesbee D, Vernon HJ, Pandey A. High-resolution mass spectrometric analysis of cardiolipin profiles in Barth syndrome. Mitochondrion. 2021 Sep; 60:27-32 Epub 2021 July 15
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92. Wu X, Wang L, Pearson NA, Renuse S, Cheng R, Liang Y, Mun DG, Madugundu AK, Xu Y, Gill PS, Pandey A. Quantitative Tyrosine Phosphoproteome Profiling of AXL Receptor Tyrosine Kinase Signaling Network. Cancers (Basel). 2021 Aug 23; 13 (16)
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93. Mun DG, Vanderboom PM, Madugundu AK, Garapati K, Chavan S, Peterson JA, Saraswat M, Pandey A. DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients. J Proteome Res. 2021 Aug 6; 20 (8):4165-4175 Epub 2021 July 22
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94. Renuse S, Madamsetty VS, Mun DG, Madugundu AK, Singh S, Udainiya S, Mangalaparthi KK, Kim MS, Liu R, Kumar SR, Krasnoperov V, Truty M, Graham RP, Gill PS, Mukhopadhyay D, Pandey A. Tyrosine Phosphoproteomics of Patient-Derived Xenografts Reveals Ephrin Type-B Receptor 4 Tyrosine Kinase as a Therapeutic Target in Pancreatic Cancer. Cancers (Basel). 2021 Jul 7; 13 (14) Epub 2021 July 07
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95. Ma SX, Seo BA, Kim D, Xiong Y, Kwon SH, Brahmachari S, Kim S, Kam TI, Nirujogi RS, Kwon SH, Dawson VL, Dawson TM, Pandey A, Na CH, Ko HS. Complement and Coagulation Cascades are Potentially Involved in Dopaminergic Neurodegeneration in alpha-Synuclein-Based Mouse Models of Parkinson's Disease. J Proteome Res. 2021 Jul 2; 20 (7):3428-3443 Epub 2021 June 01
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96. Chavan S, Mangalaparthi KK, Singh S, Renuse S, Vanderboom PM, Madugundu AK, Budhraja R, McAulay K, Grys TE, Rule AD, Alexander MP, O'Horo JC, Badley AD, Pandey A. Mass Spectrometric Analysis of Urine from COVID-19 Patients for Detection of SARS-CoV-2 Viral Antigen and to Study Host Response. J Proteome Res. 2021 Jul 2; 20 (7):3404-3413 Epub 2021 June 02
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97. Renuse S, Vanderboom PM, Maus AD, Kemp JV, Gurtner KM, Madugundu AK, Chavan S, Peterson JA, Madden BJ, Mangalaparthi KK, Mun DG, Singh S, Kipp BR, Dasari S, Singh RJ, Grebe SK, Pandey A. A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens. EBioMedicine. 2021 Jul; 69:103465 Epub 2021 July 03
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98. Byeon SK, Madugundu AK, Jain AP, Bhat FA, Jung JH, Renuse S, Darrow J, Bakker A, Albert M, Moghekar A, Pandey A. Cerebrospinal fluid lipidomics for biomarkers of Alzheimer's disease. Mol Omics. 2021 Jun 14; 17 (3):454-463
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99. Lin R, Learman LN, Na CH, Renuse S, Chen KT, Chen PY, Lee GH, Xiao B, Resnick SM, Troncoso JC, Szumlinski KK, Linden DJ, Park JM, Savonenko A, Pandey A, Worley PF. Persistently Elevated mTOR Complex 1-S6 Kinase 1 Disrupts DARPP-32-Dependent D1 Dopamine Receptor Signaling and Behaviors. Biol Psychiatry. 2021 Jun 1; 89 (11):1058-1072 Epub 2020 Oct 27
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100. Liang R, Menon V, Qiu J, Arif T, Renuse S, Lin M, Nowak R, Hartmann B, Tzavaras N, Benson DL, Chipuk JE, Fribourg M, Pandey A, Fowler V, Ghaffari S. Mitochondrial localization and moderated activity are key to murine erythroid enucleation. Blood Adv. 2021 May 25; 5 (10):2490-2504
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101. Muthusamy B, Bellad A, Girimaji SC, Pandey A. Shukla-Vernon Syndrome: A Second Family with a Novel Variant in the BCORL1 Gene. Genes (Basel). 2021 Mar 22; 12 (3)
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102. Acoba MG, Alpergin ESS, Renuse S, Fernandez-Del-Rio L, Lu YW, Khalimonchuk O, Clarke CF, Pandey A, Wolfgang MJ, Claypool SM. The mitochondrial carrier SFXN1 is critical for complex III integrity and cellular metabolism. Cell Rep. 2021 Mar 16; 34 (11):108869
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103. Gondkar K, Sathe G, Joshi N, Nair B, Pandey A, Kumar P. Integrated Proteomic and Phosphoproteomics Analysis of DKK3 Signaling Reveals Activated Kinase in the Most Aggressive Gallbladder Cancer. Cells. 2021 Feb 28; 10 (3)
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104. Radenkovic S, Fitzpatrick-Schmidt T, Byeon SK, Madugundu AK, Saraswat M, Lichty A, Wong SYW, McGee S, Kubiak K, Ligezka A, Ranatunga W, Zhang Y, Wood T, Friez MJ, Clarkson K, Pandey A, Jones JR, Morava E. Expanding the clinical and metabolic phenotype of DPM2 deficient congenital disorders of glycosylation. Mol Genet Metab. 2021 Jan; 132 (1):27-37 Epub 2020 Oct 17
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105. Nakao Y, Fukushima M, Mauer AS, Liao CY, Ferris A, Dasgupta D, Heppelmann CJ, Vanderboom PM, Saraswat M, Pandey A, Nair KS, Allen AM, Nakao K, Malhi H. A Comparative Proteomic Analysis of Extracellular Vesicles Associated With Lipotoxicity. Front Cell Dev Biol. 2021; 9:735001 Epub 2021 Nov 04
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106. Vanderboom PM, Mun DG, Madugundu AK, Mangalaparthi KK, Saraswat M, Garapati K, Chakraborty R, Ebihara H, Sun J, Pandey A. Proteomic Signature of Host Response to SARS-CoV-2 Infection in the Nasopharynx. Mol Cell Proteomics. 2021; 20:100134 Epub 2021 Aug 14
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107. Martinez M, Renuse S, Kreimer S, O'Meally R, Natov P, Madugundu AK, Nirujogi RS, Tahir R, Cole R, Pandey A, Zachara NE. Quantitative Proteomics Reveals that the OGT Interactome Is Remodeled in Response to Oxidative Stress. Mol Cell Proteomics. 2021; 20:100069 Epub 2021 Mar 12
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108. Tahir R, Renuse S, Udainiya S, Madugundu AK, Cutler JA, Nirujogi RS, Na CH, Xu Y, Wu X, Pandey A. Mutation-Specific and Common Phosphotyrosine Signatures of KRAS G12D and G13D Alleles. J Proteome Res. 2021 Jan 1; 20 (1):670-683 Epub 2020 Oct 27
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109. Mangalaparthi KK, Madugundu AK, Ryan ZC, Garapati K, Peterson JA, Dey G, Prakash A, Pandey A. Digging deeper into the immunopeptidome: characterization of post-translationally modified peptides presented by MHC I. J Proteins Proteom. 2021; 12 (3):151-160 Epub 2021 June 04
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110. Carvalho AS, Moraes MCS, Hyun Na C, Fierro-Monti I, Henriques A, Zahedi S, Bodo C, Tranfield EM, Sousa AL, Farinho A, Rodrigues LV, Pinto P, Barbara C, Mota L, Abreu TT, Semedo J, Seixas S, Kumar P, Costa-Silva B, Pandey A, Matthiesen R. Is the Proteome of Bronchoalveolar Lavage Extracellular Vesicles a Marker of Advanced Lung Cancer? Cancers (Basel). 2020 Nov 20; 12 (11)
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111. Mun DG, Renuse S, Saraswat M, Madugundu A, Udainiya S, Kim H, Park SR, Zhao H, Nirujogi RS, Na CH, Kannan N, Yates JR 3rd, Lee SW, Pandey A. PASS-DIA: A Data-Independent Acquisition Approach for Discovery Studies. Anal Chem. 2020 Nov 3; 92 (21):14466-14475 Epub 2020 Oct 20
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112. Korhonen PK, Gasser RB, Ma G, Wang T, Stroehlein AJ, Young ND, Ang CS, Fernando DD, Lu HC, Taylor S, Reynolds SL, Mofiz E, Najaraj SH, Gowda H, Madugundu A, Renuse S, Holt D, Pandey A, Papenfuss AT, Fischer K. High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite. PLoS Negl Trop Dis. 2020 Oct; 14 (10):e0008720 Epub 2020 Oct 01
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113. Babu N, Pinto SM, Biswas M, Subbannayya T, Rajappa M, Mohan SV, Advani J, Rajagopalan P, Sathe G, Syed N, Radhakrishna VD, Muthusamy O, Navani S, Kumar RV, Gopisetty G, Rajkumar T, Radhakrishnan P, Thiyagarajan S, Pandey A, Gowda H, Majumder P, Chatterjee A. Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer. Gastric Cancer. 2020 Sep; 23 (5):796-810 Epub 2020 Apr 24
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114. Bellad A, Bandari AK, Pandey A, Girimaji SC, Muthusamy B. A Novel Missense Variant in PHF6 Gene Causing Borjeson-Forssman-Lehman Syndrome. J Mol Neurosci. 2020 Sep; 70 (9):1403-1409 Epub 2020 May 12
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115. Sathe G, George IA, Deb B, Jain AP, Patel K, Nayak B, Karmakar S, Seth A, Pandey A, Kumar P. Urinary glycoproteomic profiling of non-muscle invasive and muscle invasive bladder carcinoma patients reveals distinct N-glycosylation pattern of CD44, MGAM, and GINM1. Oncotarget. 2020 Aug 25; 11 (34):3244-3255
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116. Pandey A, Stawiski EW, Durinck S, Gowda H, Goldstein LD, Barbhuiya MA, Schroder MS, Sreenivasamurthy SK, Kim SW, Phalke S, Suryamohan K, Lee K, Chakraborty P, Kode V, Shi X, Chatterjee A, Datta K, Khan AA, Subbannayya T, Wang J, Chaudhuri S, Gupta S, Shrivastav BR, Jaiswal BS, Poojary SS, Bhunia S, Garcia P, Bizama C, Rosa L, Kwon W, Kim H, Han Y, Yadav TD, Ramprasad VL, Chaudhuri A, Modrusan Z, Roa JC, Tiwari PK, Jang JY, Seshagiri S. Integrated genomic analysis reveals mutated ELF3 as a potential gallbladder cancer vaccine candidate. Nat Commun. 2020 Aug 24; 11 (1):4225
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117. Sharma T, Datta KK, Kumar M, Dey G, Khan AA, Mangalaparthi KK, Saharan P, Chinnapparaj S, Aggarwal A, Singla N, Ghosh S, Rawat A, Dhandapani S, Salunke P, Chhabra R, Singh D, Takkar A, Gupta SK, Prasad TSK, Gowda H, Mukherjee KK, Pandey A, Bhagat H. Intracranial Aneurysm Biomarker Candidates Identified by a Proteome-Wide Study. OMICS. 2020 Aug; 24 (8):483-492 Epub 2020 June 11
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118. Puttamallesh VN, Deb B, Gondkar K, Jain A, Nair B, Pandey A, Chatterjee A, Gowda H, Kumar P. Quantitative Proteomics of Urinary Bladder Cancer Cell Lines Identify UAP1 as a Potential Therapeutic Target. Genes (Basel). 2020 Jul 8; 11 (7) Epub 2020 July 08
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119. Sathe G, Albert M, Darrow J, Saito A, Troncoso J, Pandey A, Moghekar A. Quantitative proteomic analysis of the frontal cortex in Alzheimer's disease. J Neurochem. 2020 Jul 2 Epub 2020 July 02
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120. Tornheim JA, Madugundu AK, Paradkar M, Fukutani KF, Queiroz ATL, Gupte N, Gupte AN, Kinikar A, Kulkarni V, Balasubramanian U, Sreenivasamurthy S, Raja R, Pradhan N, Shivakumar SVBY, Valvi C, Hanna LE, Andrade BB, Mave V, Pandey A, Gupta A, CTRIUMPh RePORT India Study Team. Transcriptomic Profiles of Confirmed Pediatric Tuberculosis Patients and Household Contacts Identifies Active Tuberculosis, Infection, and Treatment Response Among Indian Children. J Infect Dis. 2020 Apr 27; 221 (10):1647-1658
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121. Sathe G, Mangalaparthi KK, Jain A, Darrow J, Troncoso J, Albert M, Moghekar A, Pandey A. Multiplexed Phosphoproteomic Study of Brain in Patients with Alzheimer's Disease and Age-Matched Cognitively Healthy Controls. OMICS. 2020 Apr; 24 (4):216-227 Epub 2020 Mar 17
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122. Renuse S, Madugundu AK, Jung JH, Byeon SK, Goldschmidt HL, Tahir R, Meyers D, Kim DI, Cutler J, Kim KP, Wu X, Huganir RL, Pandey A. Signature Fragment Ions of Biotinylated Peptides. J Am Soc Mass Spectrom. 2020 Feb 5; 31 (2):394-404 Epub 2020 Jan 13
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123. Maus A, Kemp J, Milosevic D, Renuse S, Pandey A, Singh RJ, Grebe SKG. Center of Mass Calculation in Combination with MS/MS Allows Robust Identification of Single Amino Acid Polymorphisms in Clinical Measurements of Insulin-Like Growth Factor-1. J Proteome Res. 2020 Jan 3; 19 (1):186-193 Epub 2019 Dec 09
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124. Creed TM, Baldeosingh R, Eberly CL, Schlee CS, Kim M, Cutler JA, Pandey A, Civin CI, Fossett NG, Kingsbury TJ. The PAX-SIX-EYA-DACH network modulates GATA-FOG function in fly hematopoiesis and human erythropoiesis. Development. 2020 Jan 3; 147 (1) Epub 2020 Jan 03
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125. Muthusamy B, Nguyen TT, Bandari AK, Basheer S, Selvan LDN, Chandel D, Manoj J, Gayen S, Seshagiri S, Chandra Girimaji S, Pandey A. Exome sequencing reveals a novel splice site variant in HUWE1 gene in patients with suspected Say-Meyer syndrome. Eur J Med Genet. 2020 Jan; 63 (1):103635 Epub 2019 Feb 21
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126. Na CH, Sathe G, Rosenthal LS, Moghekar AR, Dawson VL, Dawson TM, Pandey A. Development of a novel method for the quantification of tyrosine 39 phosphorylated alpha- and beta-synuclein in human cerebrospinal fluid. Clin Proteomics. 2020; 17:13 Epub 2020 May 04
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127. Raja R, Pandey A, Kumar P. Epithelial to mesenchymal plasticity: role in cancer progression Frontiers in Bioscience - Landmark. 2020 Jan 1; 25 (5):838-73
     
128. Carvalho AS, Baeta H, Silva BC, Moraes MCS, Bodo C, Beck HC, Rodriguez MS, Saraswat M, Pandey A, Matthiesen R. Extra-cellular vesicles carry proteome of cancer hallmarks Frontiers in Bioscience - Landmark. 2020 Jan 1; 25 (3):398-436
     
129. Muthusamy B, Bellad A, Prasad P, Bandari AK, Bhuvanalakshmi G, Kiragasur RM, Girimaj SC, Pandey A. A Novel LINS1 Truncating Mutation in Autosomal Recessive Nonsyndromic Intellectual Disability. Front Psychiatry. 2020; 11:354 Epub 2020 May 18
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130. Cutler JA, Udainiya S, Madugundu AK, Renuse S, Xu Y, Jung J, Kim KP, Wu X, Pandey A. Integrative phosphoproteome and interactome analysis of the role of Ubash3b in BCR-ABL signaling. Leukemia 2020 Jan; 34 (1):301-305 Epub 2019 Aug 09
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131. Mangalaparthi KK, Patel K, Khan AA, Manoharan M, Karunakaran C, Murugan S, Gupta R, Gupta R, Khanna-Gupta A, Chaudhuri A, Kumar P, Nair B, Kumar RV, Prasad TSK, Chatterjee A, Pandey A, Gowda H. Mutational Landscape of Esophageal Squamous Cell Carcinoma in an Indian Cohort. Front Oncol. 2020; 10:1457 Epub 2020 Aug 20
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132. Anzmann AF, Pinto S, Busa V, Carlson J, McRitchie S, Sumner S, Pandey A, Vernon HJ. Multi-omics studies in cellular models of methylmalonic acidemia and propionic acidemia reveal dysregulation of serine metabolism. Biochim Biophys Acta Mol Basis Dis. 2019 Dec 1; 1865 (12):165538 Epub 2019 Aug 23
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133. Shinde V, Hu N, Renuse S, Mahale A, Pandey A, Eberhart C, Stone D, Al-Swailem SA, Maktabi A, Chakravarti S. Mapping Keratoconus Molecular Substrates by Multiplexed High-Resolution Proteomics of Unpooled Corneas. OMICS. 2019 Nov; 23 (11):583-597 Epub 2019 Oct 25
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134. Rajagopalan P, Jain AP, Nanjappa V, Patel K, Mangalaparthi KK, Babu N, Cavusoglu N, Roy N, Soeur J, Breton L, Pandey A, Gowda H, Chatterjee A, Misra N. Proteome-wide changes in primary skin keratinocytes exposed to diesel particulate extract-A role for antioxidants in skin health. J Dermatol Sci. 2019 Nov; 96 (2):114-124 Epub 2019 Oct 16
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135. Shears MJ, Sekhar Nirujogi R, Swearingen KE, Renuse S, Mishra S, Jaipal Reddy P, Moritz RL, Pandey A, Sinnis P. Proteomic Analysis of Plasmodium Merosomes: The Link between Liver and Blood Stages in Malaria. J Proteome Res. 2019 Sep 6; 18 (9):3404-3418 Epub 2019 July 23
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136. Dutta P, Reddy KS, Rai A, Madugundu AK, Solanki HS, Bhansali A, Radotra BD, Kumar N, Collier D, Iacovazzo D, Gupta P, Raja R, Gowda H, Pandey A, Devgun JS, Korbonits M. Surgery, Octreotide, Temozolomide, Bevacizumab, Radiotherapy, and Pegvisomant Treatment of an AIP MutationPositive Child. J Clin Endocrinol Metab. 2019 Aug 1; 104 (8):3539-3544
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137. Na CH, Nirujogi RS, Renuse S, Kim KP, Burns KH, Wilks C, Langmead B, Ellis SE, Collado-Torres L, Halushka MK, Kim MS, Pandey A. Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. Proteomics. 2019 Aug; 19 (15):e1800315 Epub 2019 June 26
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138. Mun DG, Nam D, Kim H, Pandey A, Lee SW. Accurate Precursor Mass Assignment Improves Peptide Identification in Data-Independent Acquisition Mass Spectrometry. Anal Chem. 2019 Jul 2; 91 (13):8453-8460 Epub 2019 June 17
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139. Na CH, Sharma N, Madugundu AK, Chen R, Aksit MA, Rosson GD, Cutting GR, Pandey A. Integrated Transcriptomic and Proteomic Analysis of Human Eccrine Sweat Glands Identifies Missing and Novel Proteins. Mol Cell Proteomics. 2019 Jul; 18 (7):1382-1395 Epub 2019 Apr 12
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140. Sathe G, Na CH, Renuse S, Madugundu AK, Albert M, Moghekar A, Pandey A. Quantitative Proteomic Profiling of Cerebrospinal Fluid to Identify Candidate Biomarkers for Alzheimer's Disease. Proteomics Clin Appl. 2019 Jul; 13(4):e1800105. Epub 2019 Jan 25.
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141. Deva Magendhra Rao AK, Patel K, Korivi Jyothiraj S, Meenakumari B, Sundersingh S, Sridevi V, Rajkumar T, Pandey A, Chatterjee A, Gowda H, Mani S. Identification of lncRNAs associated with early-stage breast cancer and their prognostic implications. Mol Oncol. 2019 Jun; 13 (6):1342-1355 Epub 2019 May 08
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142. Saner FAM, Herschtal A, Nelson BH, deFazio A, Goode EL, Ramus SJ, Pandey A, Beach JA, Fereday S, Berchuck A, Lheureux S, Pearce CL, Pharoah PD, Pike MC, Garsed DW, Bowtell DDL. Going to extremes: determinants of extraordinary response and survival in patients with cancer. Nat Rev Cancer. 2019 Jun; 19 (6):339-348
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143. Subbannayya T, Leal-Rojas P, Zhavoronkov A, Ozerov IV, Korzinkin M, Babu N, Radhakrishnan A, Chavan S, Raja R, Pinto SM, Patil AH, Barbhuiya MA, Kumar P, Guerrero-Preston R, Navani S, Tiwari PK, Kumar RV, Prasad TSK, Roa JC, Pandey A, Sidransky D, Gowda H, Izumchenko E, Chatterjee A. PIM1 kinase promotes gallbladder cancer cell proliferation via inhibition of proline-rich Akt substrate of 40 kDa (PRAS40). J Cell Commun Signal. 2019 Jun; 13 (2):163-177 Epub 2019 Jan 21
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144. Bandari AK, Bhat S, Archana MV, Yadavalli S, Patel K, Rajagopalan P, Madugundu AK, Madkaikar M, Reddy K, Muthusamy B, Pandey A. Family-Based Next-Generation Sequencing Study Identifies an IL2RG Variant in an Infant with Primary Immunodeficiency. OMICS. 2019 May; 23 (5):285-290
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145. Gondkar K, Patel K, Patil Okaly GV, Nair B, Pandey A, Gowda H, Kumar P. Dickkopf Homolog 3 (DKK3) Acts as a Potential Tumor Suppressor in Gallbladder Cancer. Front Oncol. 2019; 9:1121 Epub 2019 Oct 29
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146. Bandari AK, Muthusamy B, Bhat S, Govindaraj P, Rajagopalan P, Dalvi A, Shankar S, Raja R, Reddy KS, Madkaikar M, Pandey A. A Novel Splice Site Mutation in IFNGR2 in Patients With Primary Immunodeficiency Exhibiting Susceptibility to Mycobacterial Diseases. Front Immunol. 2019; 10:1964 Epub 2019 Aug 21
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147. Alexander EJ, Ghanbari Niaki A, Zhang T, Sarkar J, Liu Y, Nirujogi RS, Pandey A, Myong S, Wang J. Ubiquilin 2 modulates ALS/FTD-linked FUS-RNA complex dynamics and stress granule formation. Proc Natl Acad Sci U S A. 2018 Dec 4; 115 (49):E11485-E11494 Epub 2018 Nov 15
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148. Yelamanchi SD, Tyagi A, Mohanty V, Dutta P, Korbonits M, Chavan S, Advani J, Madugundu AK, Dey G, Datta KK, Rajyalakshmi M, Sahasrabuddhe NA, Chaturvedi A, Kumar A, Das AA, Ghosh D, Jogdand GM, Nair HH, Saini K, Panchal M, Sarvaiya MA, Mohanraj SS, Sengupta N, Saxena P, Subramani PA, Kumar P, Akkali R, Reshma SV, Santhosh RS, Rastogi S, Kumar S, Ghosh SK, Irlapati VK, Srinivasan A, Radotra BD, Mathur PP, Wong GW, Satishchandra P, Chatterjee A, Gowda H, Bhansali A, Pandey A, Shankar SK, Mahadevan A, Prasad TSK. Proteomic Analysis of the Human Anterior Pituitary Gland. OMICS. 2018 Dec; 22 (12):759-769
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149. Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL. CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. Genome Biol. 2018 Nov 28; 19 (1):208
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150. Rajagopalan P, Jain AP, Nanjappa V, Patel K, Mangalaparthi KK, Babu N, Cavusoglu N, Roy N, Soeur J, Breton L, Pandey A, Gowda H, Chatterjee A, Misra N. Proteome-wide changes in primary skin keratinocytes exposed to diesel particulate extract-A role for antioxidants in skin health. J Dermatol Sci. 2018 Sep; 91 (3):239-249 Epub 2018 May 21
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151. Pinto SM, Subbannayya Y, Rex DAB, Raju R, Chatterjee O, Advani J, Radhakrishnan A, Keshava Prasad TS, Wani MR, Pandey A. A network map of IL-33 signaling pathway. J Cell Commun Signal. 2018 Sep; 12 (3):615-624 Epub 2018 Apr 28
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152. Heo S, Diering GH, Na CH, Nirujogi RS, Bachman JL, Pandey A, Huganir RL. Identification of long-lived synaptic proteins by proteomic analysis of synaptosome protein turnover. Proc Natl Acad Sci U S A. 2018 Apr 17; 115 (16):E3827-E3836 Epub 2018 Apr 02
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153. Barbhuiya MA, Kashyap MK, Puttamallesh VN, Kumar RV, Wu X, Pandey A, Gowda H. Identification of spleen tyrosine kinase as a potential therapeutic target for esophageal squamous cell carcinoma using reverse phase protein arrays. Oncotarget. 2018 Apr 6; 9 (26):18422-18434 Epub 2018 Jan 01
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154. Lee SE, Song J, Bosl K, Muller AC, Vitko D, Bennett KL, Superti-Furga G, Pandey A, Kandasamy RK, Kim MS. Proteogenomic Analysis to Identify Missing Proteins from Haploid Cell Lines. Proteomics. 2018 Apr; 18 (8):e1700386
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155. Wang Z, Kim MS, Martinez-Ferrando I, Koleske AJ, Pandey A, Cole PA. Analysis of Cellular Tyrosine Phosphorylation via Chemical Rescue of Conditionally Active Abl Kinase. Biochemistry. 2018 Feb 27; 57 (8):1390-1398 Epub 2018 Feb 06
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156. Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A. BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation. J Proteome Res. 2018 Feb 2; 17 (2):759-769 Epub 2017 Dec 28
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157. Li Z, Cheng Z, Raghothama C, Cui Z, Liu K, Li X, Jiang C, Jiang W, Tan M, Ni X, Pandey A, Liu JO, Dang Y. USP9X controls translation efficiency via deubiquitination of eukaryotic translation initiation factor 4A1. Nucleic Acids Res. 2018 Jan 25; 46 (2):823-839
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158. Kim S, Yun SP, Lee S, Umanah GE, Bandaru VVR, Yin X, Rhee P, Karuppagounder SS, Kwon SH, Lee H, Mao X, Kim D, Pandey A, Lee G, Dawson VL, Dawson TM, Ko HS. GBA1 deficiency negatively affects physiological alpha-synuclein tetramers and related multimers. Proc Natl Acad Sci U S A. 2018 Jan 23; 115 (4):798-803 Epub 2018 Jan 08
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159. Na CH, Barbhuiya MA, Kim MS, Verbruggen S, Eacker SM, Pletnikova O, Troncoso JC, Halushka MK, Menschaert G, Overall CM, Pandey A. Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini. Genome Res. 2018 Jan; 28 (1):25-36 Epub 2017 Nov 21
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160. McCall MN, Kim MS, Adil M, Patil AH, Lu Y, Mitchell CJ, Leal-Rojas P, Xu J, Kumar M, Dawson VL, Dawson TM, Baras AS, Rosenberg AZ, Arking DE, Burns KH, Pandey A, Halushka MK. Toward the human cellular microRNAome. Genome Res. 2017 Oct; 27 (10):1769-1781 Epub 2017 Sept 06
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161. Sreenivasamurthy SK, Madugundu AK, Patil AH, Dey G, Mohanty AK, Kumar M, Patel K, Wang C, Kumar A, Pandey A, Prasad TSK. Mosquito-Borne Diseases and Omics: Tissue-Restricted Expression and Alternative Splicing Revealed by Transcriptome Profiling of Anopheles stephensi. OMICS. 2017 Aug; 21 (8):488-497 Epub 2017 July 14
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162. Cutler JA, Tahir R, Sreenivasamurthy SK, Mitchell C, Renuse S, Nirujogi RS, Patil AH, Heydarian M, Wong X, Wu X, Huang TC, Kim MS, Reddy KL, Pandey A. Differential signaling through p190 and p210 BCR-ABL fusion proteins revealed by interactome and phosphoproteome analysis. Leukemia. 2017 Jul; 31 (7):1513-1524 Epub 2017 Feb 17
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163. Radhakrishnan A, Nanjappa V, Raja R, Sathe G, Puttamallesh VN, Jain AP, Pinto SM, Balaji SA, Chavan S, Sahasrabuddhe NA, Mathur PP, Kumar MM, Prasad TSK, Santosh V, Sukumar G, Califano JA, Rangarajan A, Sidransky D, Pandey A, Gowda H, Chatterjee A. Corrigendum: A dual specificity kinase, DYRK1A, as a potential therapeutic target for head and neck squamous cell carcinoma. Sci Rep. 2017 Jun 26; 7:46864 Epub 2017 June 26
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164. Lu YW, Acoba MG, Selvaraju K, Huang TC, Nirujogi RS, Sathe G, Pandey A, Claypool SM. Human adenine nucleotide translocases physically and functionally interact with respirasomes. Mol Biol Cell. 2017 Jun 1; 28 (11):1489-1506 Epub 2017 Apr 12
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165. Zhang X, Maity T, Kashyap MK, Bansal M, Venugopalan A, Singh S, Awasthi S, Marimuthu A, Charles Jacob HK, Belkina N, Pitts S, Cultraro CM, Gao S, Kirkali G, Biswas R, Chaerkady R, Califano A, Pandey A, Guha U. Quantitative Tyrosine Phosphoproteomics of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor-treated Lung Adenocarcinoma Cells Reveals Potential Novel Biomarkers of Therapeutic Response. Mol Cell Proteomics. 2017 May; 16 (5):891-910 Epub 2017 Mar 22
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166. Muthusamy B, Selvan LDN, Nguyen TT, Manoj J, Stawiski EW, Jaiswal BS, Wang W, Raja R, Ramprasad VL, Gupta R, Murugan S, Kadandale JS, Prasad TSK, Reddy K, Peterson A, Pandey A, Seshagiri S, Girimaji SC, Gowda H. Next-Generation Sequencing Reveals Novel Mutations in X-linked Intellectual Disability. OMICS. 2017 May; 21 (5):295-303
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167. Weber H, Valbuena JR, Barbhuiya MA, Stein S, Kunkel H, Garcia P, Bizama C, Riquelme I, Espinoza JA, Kurtz SE, Tyner JW, Calderon JF, Corvalan AH, Grez M, Pandey A, Leal-Rojas P, Roa JC. Small molecule inhibitor screening identifified HSP90 inhibitor 17-AAG as potential therapeutic agent for gallbladder cancer. Oncotarget. 2017 Apr 18; 8 (16):26169-26184
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168. Verma R, Pinto SM, Patil AH, Advani J, Subba P, Kumar M, Sharma J, Dey G, Ravikumar R, Buggi S, Satishchandra P, Sharma K, Suar M, Tripathy SP, Chauhan DS, Gowda H, Pandey A, Gandotra S, Prasad TS. Quantitative Proteomic and Phosphoproteomic Analysis of H37Ra and H37Rv Strains of Mycobacterium tuberculosis. J Proteome Res. 2017 Apr 7; 16 (4):1632-1645 Epub 2017 Mar 20
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169. Bettridge J, Na CH, Pandey A, Desiderio S. H3K4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase. Proc Natl Acad Sci U S A. 2017 Feb 21; 114 (8):1904-1909 Epub 2017 Feb 07
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170. Diering GH, Nirujogi RS, Roth RH, Worley PF, Pandey A, Huganir RL. Homer1a drives homeostatic scaling-down of excitatory synapses during sleep. Science. 2017 Feb 3; 355 (6324):511-515 Epub 2017 Feb 02
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171. Sadtler K, Sommerfeld SD, Wolf MT, Wang X, Majumdar S, Chung L, Kelkar DS, Pandey A, Elisseeff JH. Proteomic composition and immunomodulatory properties of urinary bladder matrix scaffolds in homeostasis and injury. Semin Immunol. 2017 Feb; 29:14-23 Epub 2017 June 02
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172. Wu X, Zahari MS, Renuse S, Kelkar DS, Barbhuiya MA, Rojas PL, Stearns V, Gabrielson E, Malla P, Sukumar S, Mahajan NP, Pandey A. The non-receptor tyrosine kinase TNK2/ACK1 is a novel therapeutic target in triple negative breast cancer. Oncotarget. 2017 Jan 10; 8 (2):2971-2983
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173. Prasad TS, Mohanty AK, Kumar M, Sreenivasamurthy SK, Dey G, Nirujogi RS, Pinto SM, Madugundu AK, Patil AH, Advani J, Manda SS, Gupta MK, Dwivedi SB, Kelkar DS, Hall B, Jiang X, Peery A, Rajagopalan P, Yelamanchi SD, Solanki HS, Raja R, Sathe GJ, Chavan S, Verma R, Patel KM, Jain AP, Syed N, Datta KK, Khan AA, Dammalli M, Jayaram S, Radhakrishnan A, Mitchell CJ, Na CH, Kumar N, Sinnis P, Sharakhov IV, Wang C, Gowda H, Tu Z, Kumar A, Pandey A. Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. Genome Res. 2017 Jan; 27 (1):133-144 Epub 2016 Nov 15
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174. Lv DW, Zhong J, Zhang K, Pandey A, Li R. Understanding Epstein-Barr Virus Life Cycle with Proteomics: A Temporal Analysis of Ubiquitination During Virus Reactivation. OMICS. 2017 Jan; 21 (1):27-37
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175. Sharma N, LaRusch J, Sosnay PR, Gottschalk LB, Lopez AP, Pellicore MJ, Evans T, Davis E, Atalar M, Na CH, Rosson GD, Belchis D, Milewski M, Pandey A, Cutting GR. A sequence upstream of canonical PDZ-binding motif within CFTR COOH-terminus enhances NHERF1 interaction. Am J Physiol Lung Cell Mol Physiol. 2016 Dec 1; 311 (6):L1170-L1182 Epub 2016 Oct 28
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176. Rajagopalan P, Nanjappa V, Raja R, Jain AP, Mangalaparthi KK, Sathe GJ, Babu N, Patel K, Cavusoglu N, Soeur J, Pandey A, Roy N, Breton L, Chatterjee A, Misra N, Gowda H. How Does Chronic Cigarette Smoke Exposure Affect Human Skin? A Global Proteomics Study in Primary Human Keratinocytes. OMICS. 2016 Nov; 20 (11):615-626
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177. Ugolino J, Ji YJ, Conchina K, Chu J, Nirujogi RS, Pandey A, Brady NR, Hamacher-Brady A, Wang J. Loss of C9orf72 Enhances Autophagic Activity via Deregulated mTOR and TFEB Signaling. PLoS Genet. 2016 Nov; 12 (11):e1006443 Epub 2016 Nov 22
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178. Radhakrishnan A, Nanjappa V, Raja R, Sathe G, Puttamallesh VN, Jain AP, Pinto SM, Balaji SA, Chavan S, Sahasrabuddhe NA, Mathur PP, Kumar MM, Prasad TS, Santosh V, Sukumar G, Califano JA, Rangarajan A, Sidransky D, Pandey A, Gowda H, Chatterjee A. A dual specificity kinase, DYRK1A, as a potential therapeutic target for head and neck squamous cell carcinoma. Sci Rep. 2016 Oct 31; 6:36132
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179. Raja R, Sahasrabuddhe NA, Radhakrishnan A, Syed N, Solanki HS, Puttamallesh VN, Balaji SA, Nanjappa V, Datta KK, Babu N, Renuse S, Patil AH, Izumchenko E, Prasad TS, Chang X, Rangarajan A, Sidransky D, Pandey A, Gowda H, Chatterjee A. Chronic exposure to cigarette smoke leads to activation of p21 (RAC1)-activated kinase 6 (PAK6) in non-small cell lung cancer cells. Oncotarget. 2016 Sep 20; 7 (38):61229-61245
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180. Cha SJ, Kim MS, Pandey A, Jacobs-Lorena M. Identification of GAPDH on the surface of Plasmodium sporozoites as a new candidate for targeting malaria liver invasion. J Exp Med. 2016 Sep 19; 213 (10):2099-112 Epub 2016 Aug 22
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181. Mitchell CJ, Kim MS, Na CH, Pandey A. PyQuant: A Versatile Framework for Analysis of Quantitative Mass Spectrometry Data. Mol Cell Proteomics. 2016 Aug; 15 (8):2829-38 Epub 2016 May 26
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182. Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyo D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD, CPTAC Investigators. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell. 2016 Jul 28; 166 (3):755-765 Epub 2016 June 29
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183. Mirsafian H, Manda SS, Mitchell CJ, Sreenivasamurthy S, Ripen AM, Mohamad SB, Merican AF, Pandey A. Long non-coding RNA expression in primary human monocytes. Genomics. 2016 Jul; 108 (1):37-45 Epub 2016 Jan 08
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184. Mitchell CJ, Kim MS, Zhong J, Nirujogi RS, Bose AK, Pandey A. Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans. Mol Oncol. 2016 Jun; 10 (6):910-20 Epub 2016 Mar 25
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185. Verma R, Balakrishnan L, Sharma K, Khan AA, Advani J, Gowda H, Tripathy SP, Suar M, Pandey A, Gandotra S, Prasad TS, Shankar S. A network map of Interleukin-10 signaling pathway. J Cell Commun Signal. 2016 Mar; 10 (1):61-7 Epub 2015 Aug 08
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186. Yelamanchi SD, Jayaram S, Thomas JK, Gundimeda S, Khan AA, Singhal A, Keshava Prasad TS, Pandey A, Somani BL, Gowda H. A pathway map of glutamate metabolism. J Cell Commun Signal. 2016 Mar; 10 (1):69-75 Epub 2015 Dec 03
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187. Jhaveri DT, Kim MS, Thompson ED, Huang L, Sharma R, Klein AP, Zheng L, Le DT, Laheru DA, Pandey A, Jaffee EM, Anders RA. Using Quantitative Seroproteomics to Identify Antibody Biomarkers in Pancreatic Cancer. Cancer Immunol Res. 2016 Mar; 4 (3):225-33 Epub 2016 Feb 03
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188. Kim MS, Zhong J, Pandey A. Common errors in mass spectrometry-based analysis of post-translational modifications. Proteomics. 2016 Mar; 16 (5):700-14
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189. Danda R, Ganapathy K, Sathe G, Madugundu AK, Ramachandran S, Krishnan UM, Khetan V, Rishi P, Keshava Prasad TS, Pandey A, Krishnakumar S, Gowda H, Elchuri SV. Proteomic profiling of retinoblastoma by high resolution mass spectrometry. Clin Proteomics. 2016; 13:29 Epub 2016 Oct 26
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190. Radhakrishnan A, Nanjappa V, Raja R, Sathe G, Chavan S, Nirujogi RS, Patil AH, Solanki H, Renuse S, Sahasrabuddhe NA, Mathur PP, Prasad TS, Kumar P, Califano JA, Sidransky D, Pandey A, Gowda H, Chatterjee A. Dysregulation of splicing proteins in head and neck squamous cell carcinoma. Cancer Biol Ther. 2016; 17 (2):219-29 Epub 2016 Feb 06
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191. Li R, Liao G, Nirujogi RS, Pinto SM, Shaw PG, Huang TC, Wan J, Qian J, Gowda H, Wu X, Lv DW, Zhang K, Manda SS, Pandey A, Hayward SD. Phosphoproteomic Profiling Reveals Epstein-Barr Virus Protein Kinase Integration of DNA Damage Response and Mitotic Signaling. PLoS Pathog. 2015 Dec; 11 (12):e1005346 Epub 2015 Dec 29
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192. Beachley VZ, Wolf MT, Sadtler K, Manda SS, Jacobs H, Blatchley MR, Bader JS, Pandey A, Pardoll D, Elisseeff JH. Tissue matrix arrays for high-throughput screening and systems analysis of cell function. Nat Methods. 2015 Dec; 12 (12):1197-204 Epub 2015 Oct 19
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193. Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, Sahasrabuddhe NA, Raju R, Bowman C, Danilova L, Cutler J, Kelkar DS, Drake CG, Prasad TS, Marchionni L, Murakami PN, Scott AF, Shi L, Thierry-Mieg J, Thierry-Mieg D, Irizarry R, Cope L, Ishihama Y, Wang C, Gowda H, Pandey A. A multi-omic analysis of human naïve CD4+ T cells. BMC Syst Biol. 2015 Nov 06; 9:75.
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194. Subbannayya T, Leal-Rojas P, Barbhuiya MA, Raja R, Renuse S, Sathe G, Pinto SM, Syed N, Nanjappa V, Patil AH, Garcia P, Sahasrabuddhe NA, Nair B, Guerrero-Preston R, Navani S, Tiwari PK, Santosh V, Sidransky D, Prasad TS, Gowda H, Roa JC, Pandey A, Chatterjee A. Macrophage migration inhibitory factor - a therapeutic target in gallbladder cancer. BMC Cancer. 2015 Nov 4; 15:843 Epub 2015 Nov 04
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195. Wu X, Zahari MS, Renuse S, Nirujogi RS, Kim MS, Manda SS, Stearns V, Gabrielson E, Sukumar S, Pandey A. Phosphoproteomic Analysis Identifies Focal Adhesion Kinase 2 (FAK2) as a Potential Therapeutic Target for Tamoxifen Resistance in Breast Cancer. Mol Cell Proteomics. 2015 Nov; 14 (11):2887-900 Epub 2015 Sept 01
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196. Wu X, Zahari MS, Ma B, Liu R, Renuse S, Sahasrabuddhe NA, Chen L, Chaerkady R, Kim MS, Zhong J, Jelinek C, Barbhuiya MA, Leal-Rojas P, Yang Y, Kashyap MK, Marimuthu A, Ling M, Fackler MJ, Merino V, Zhang Z, Zahnow CA, Gabrielson E, Stearns V, Roa JC, Sukumar S, Gill PS, Pandey A. Global phosphotyrosine survey in triple-negative breast cancer reveals activation of multiple tyrosine kinase signaling pathways. Oncotarget. 2015 Oct 06; 6(30):29143-60.
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197. Ewing AD, Gacita A, Wood LD, Ma F, Xing D, Kim MS, Manda SS, Abril G, Pereira G, Makohon-Moore A, Looijenga LH, Gillis AJ, Hruban RH, Anders RA, Romans KE, Pandey A, Iacobuzio-Donahue CA, Vogelstein B, Kinzler KW, Kazazian HH Jr, Solyom S. Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution. Genome Res. 2015 Oct; 25 (10):1536-45 Epub 2015 Aug 10
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198. Subbannayya Y, Mir SA, Renuse S, Manda SS, Pinto SM, Puttamallesh VN, Solanki HS, Manju HC, Syed N, Sharma R, Christopher R, Vijayakumar M, Veerendra Kumar KV, Keshava Prasad TS, Ramaswamy G, Kumar RV, Chatterjee A, Pandey A, Gowda H. Identification of differentially expressed serum proteins in gastric adenocarcinoma. J Proteomics. 2015 Sep 8; 127 (Pt A):80-8 Epub 2015 May 05
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199. Mir SA, Rajagopalan P, Jain AP, Khan AA, Datta KK, Mohan SV, Lateef SS, Sahasrabuddhe N, Somani BL, Keshava Prasad TS, Chatterjee A, Veerendra Kumar KV, VijayaKumar M, Kumar RV, Gundimeda S, Pandey A, Gowda H. LC-MS-based serum metabolomic analysis reveals dysregulation of phosphatidylcholines in esophageal squamous cell carcinoma. J Proteomics. 2015 Sep 8; 127 (Pt A):96-102 Epub 2015 May 14
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200. Zahari MS, Wu X, Blair BG, Pinto SM, Nirujogi RS, Jelinek CA, Malhotra R, Kim MS, Park BH, Pandey A. Activating Mutations in PIK3CA Lead to Widespread Modulation of the Tyrosine Phosphoproteome. J Proteome Res. 2015 Sep 4; 14 (9):3882-3891 Epub 2015 Aug 20
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201. Zahari MS, Wu X, Pinto SM, Nirujogi RS, Kim MS, Fetics B, Philip M, Barnes SR, Godfrey B, Gabrielson E, Nevo E, Pandey A. Phosphoproteomic profiling of tumor tissues identifies HSP27 Ser82 phosphorylation as a robust marker of early ischemia. Sci Rep. 2015 Sep 2; 5:13660 Epub 2015 Sept 02
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202. Sharma J, Balakrishnan L, Datta KK, Sahasrabuddhe NA, Khan AA, Sahu A, Singhal A, Getnet D, Raju R, Chatterjee A, Gowda H, Keshava Prasad TS, Shankar S, Pandey A. A knowledgebase resource for interleukin-17 family mediated signaling. J Cell Commun Signal. 2015 Sep; 9 (3):291-6 Epub 2015 June 16
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203. Sahasrabuddhe NA, Huang TC, Kumar P, Yang Y, Ghosh B, Leach SD, Chaerkady R, Pandey A. Ablation of Dicer leads to widespread perturbation of signaling pathways. Biochem Biophys Res Commun. 2015 Jul 31; 463 (3):389-94 Epub 2015 May 30
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204. Yu Y, Gaillard S, Phillip JM, Huang TC, Pinto SM, Tessarollo NG, Zhang Z, Pandey A, Wirtz D, Ayhan A, Davidson B, Wang TL, Shih IeM. Inhibition of Spleen Tyrosine Kinase Potentiates Paclitaxel-Induced Cytotoxicity in Ovarian Cancer Cells by Stabilizing Microtubules. Cancer Cell. 2015 Jul 13; 28 (1):82-96 Epub 2015 June 18
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205. Sharma R, Gowda H, Chavan S, Advani J, Kelkar D, Kumar GS, Bhattacharjee M, Chaerkady R, Prasad TS, Pandey A, Nagaraja D, Christopher R. Proteomic Signature of Endothelial Dysfunction Identified in the Serum of Acute Ischemic Stroke Patients by the iTRAQ-Based LC-MS Approach. J Proteome Res. 2015 Jun 5; 14 (6):2466-79 Epub 2015 Apr 24
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206. Murthy KR, Rajagopalan P, Pinto SM, Advani J, Murthy PR, Goel R, Subbannayya Y, Balakrishnan L, Dash M, Anil AK, Manda SS, Nirujogi RS, Kelkar DS, Sathe GJ, Dey G, Chatterjee A, Gowda H, Chakravarti S, Shankar S, Sahasrabuddhe NA, Nair B, Somani BL, Prasad TS, Pandey A. Proteomics of human aqueous humor. OMICS. 2015 May; 19 (5):283-93
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207. Maras JS, Maiwall R, Harsha HC, Das S, Hussain MS, Kumar C, Bihari C, Rastogi A, Kumar M, Trehanpati N, Sharma S, Pandey A, Sarin SK. Dysregulated iron homeostasis is strongly associated with multiorgan failure and early mortality in acute-on-chronic liver failure. Hepatology. 2015 Apr; 61 (4):1306-20 Epub 2015 Mar 10
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208. Jamdhade MD, Pawar H, Chavan S, Sathe G, Umasankar PK, Mahale KN, Dixit T, Madugundu AK, Prasad TS, Gowda H, Pandey A, Patole MS. Comprehensive proteomics analysis of glycosomes from Leishmania donovani. OMICS. 2015 Mar; 19 (3):157-70
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209. Ambekar AS, Kelkar DS, Pinto SM, Sharma R, Hinduja I, Zaveri K, Pandey A, Prasad TS, Gowda H, Mukherjee S. Proteomics of follicular fluid from women with polycystic ovary syndrome suggests molecular defects in follicular development. J Clin Endocrinol Metab. 2015 Feb; 100 (2):744-53 Epub 2014 Nov 13
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210. Syed N, Chavan S, Sahasrabuddhe NA, Renuse S, Sathe G, Nanjappa V, Radhakrishnan A, Raja R, Pinto SM, Srinivasan A, Prasad TS, Srikumar K, Gowda H, Santosh V, Sidransky D, Califano JA, Pandey A, Chatterjee A. Silencing of high-mobility group box 2 (HMGB2) modulates cisplatin and 5-fluorouracil sensitivity in head and neck squamous cell carcinoma. Proteomics. 2015 Jan; 15 (2-3):383-93
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211. Kagohara LT, Schussel JL, Subbannayya T, Sahasrabuddhe N, Lebron C, Brait M, Maldonado L, Valle BL, Pirini F, Jahuira M, Lopez J, Letelier P, Brebi-Mieville P, Ili C, Pandey A, Chatterjee A, Sidransky D, Guerrero-Preston R. Global and gene-specific DNA methylation pattern discriminates cholecystitis from gallbladder cancer patients in Chile. Future Oncol. 2015; 11 (2):233-49 Epub 2014 July 28
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212. Syed N, Barbhuiya MA, Pinto SM, Nirujogi RS, Renuse S, Datta KK, Khan AA, Srikumar K, Prasad TS, Kumar MV, Kumar RV, Chatterjee A, Pandey A, Gowda H. Phosphotyrosine profiling identifies ephrin receptor A2 as a potential therapeutic target in esophageal squamous-cell carcinoma. Proteomics. 2015 Jan; 15 (2-3):374-82
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213. Pinto SM, Nirujogi RS, Rojas PL, Patil AH, Manda SS, Subbannayya Y, Roa JC, Chatterjee A, Prasad TS, Pandey A. Quantitative phosphoproteomic analysis of IL-33-mediated signaling. Proteomics. 2015 Jan; 15 (2-3):532-44
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214. Blair BG, Wu X, Zahari MS, Mohseni M, Cidado J, Wong HY, Beaver JA, Cochran RL, Zabransky DJ, Croessmann S, Chu D, Toro PV, Cravero K, Pandey A, Park BH. A phosphoproteomic screen demonstrates differential dependence on HER3 for MAP kinase pathway activation by distinct PIK3CA mutations. Proteomics. 2015 Jan; 15 (2-3):318-26 Epub 2014 Dec 28
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215. Nirujogi RS, Wright JD Jr, Manda SS, Zhong J, Na CH, Meyerhoff J, Benton B, Jabbour R, Willis K, Kim MS, Pandey A, Sekowski JW. Phosphoproteomic analysis reveals compensatory effects in the piriform cortex of VX nerve agent exposed rats. Proteomics. 2015 Jan; 15 (2-3):487-99
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216. Subbannayya Y, Syed N, Barbhuiya MA, Raja R, Marimuthu A, Sahasrabuddhe N, Pinto SM, Manda SS, Renuse S, Manju HC, Zameer MA, Sharma J, Brait M, Srikumar K, Roa JC, Vijaya Kumar M, Kumar KV, Prasad TS, Ramaswamy G, Kumar RV, Pandey A, Gowda H, Chatterjee A. Calcium calmodulin dependent kinase kinase 2 - a novel therapeutic target for gastric adenocarcinoma. Cancer Biol Ther. 2015; 16 (2):336-45
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217. Zhong J, Martinez M, Sengupta S, Lee A, Wu X, Chaerkady R, Chatterjee A, O'Meally RN, Cole RN, Pandey A, Zachara NE. Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O-GlcNAc in the DNA damage response pathway. Proteomics. 2015 Jan; 15(2-3):591-607.
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218. Huang TC, Renuse S, Pinto S, Kumar P, Yang Y, Chaerkady R, Godsey B, Mendell JT, Halushka MK, Civin CI, Marchionni L, Pandey A. Identification of miR-145 targets through an integrated omics analysis. Mol Biosyst. 2015 Jan; 11 (1):197-207 Epub 2014 Oct 30
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219. Zhang X, Belkina N, Jacob HK, Maity T, Biswas R, Venugopalan A, Shaw PG, Kim MS, Chaerkady R, Pandey A, Guha U. Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics. Proteomics. 2015 Jan; 15 (2-3):340-55
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220. Nanjappa V, Renuse S, Sathe GJ, Raja R, Syed N, Radhakrishnan A, Subbannayya T, Patil A, Marimuthu A, Sahasrabuddhe NA, Guerrero-Preston R, Somani BL, Nair B, Kundu GC, Prasad TK, Califano JA, Gowda H, Sidransky D, Pandey A, Chatterjee A. Chronic exposure to chewing tobacco selects for overexpression of stearoyl-CoA desaturase in normal oral keratinocytes. Cancer Biol Ther. 2015; 16 (11):1593-603 Epub 2015 Sept 21
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221. Baras AS, Mitchell CJ, Myers JR, Gupta S, Weng LC, Ashton JM, Cornish TC, Pandey A, Halushka MK. miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy. PLoS One. 2015; 10 (11):e0143066 Epub 2015 Nov 16
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222. Pawar H, Srikanth SM, Kashyap MK, Sathe G, Chavan S, Singal M, Manju HC, Kumar KV, Vijayakumar M, Sirdeshmukh R, Pandey A, Prasad TS, Gowda H, Kumar RV. Downregulation of S100 Calcium Binding Protein A9 in Esophageal Squamous Cell Carcinoma. ScientificWorldJournal. 2015; 2015:325721 Epub 2015 Dec 14
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223. Renuse S, Madugundu AK, Kumar P, Nair BG, Gowda H, Prasad TS, Pandey A. Proteomic analysis and genome annotation of Pichia pastoris, a recombinant protein expression host. Proteomics. 2014 Dec; 14 (23-24):2769-79 Epub 2014 Nov 20
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224. Tong Z, Kim MS, Pandey A, Espenshade PJ. Identification of candidate substrates for the Golgi Tul1 E3 ligase using quantitative diGly proteomics in yeast. Mol Cell Proteomics. 2014 Nov; 13 (11):2871-82 Epub 2014 July 30
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225. Kim MS, Zhong Y, Yachida S, Rajeshkumar NV, Abel ML, Marimuthu A, Mudgal K, Hruban RH, Poling JS, Tyner JW, Maitra A, Iacobuzio-Donahue CA, Pandey A. Heterogeneity of pancreatic cancer metastases in a single patient revealed by quantitative proteomics. Mol Cell Proteomics. 2014 Nov; 13 (11):2803-11 Epub 2014 June 03
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226. Kelkar DS, Provost E, Chaerkady R, Muthusamy B, Manda SS, Subbannayya T, Selvan LD, Wang CH, Datta KK, Woo S, Dwivedi SB, Renuse S, Getnet D, Huang TC, Kim MS, Pinto SM, Mitchell CJ, Madugundu AK, Kumar P, Sharma J, Advani J, Dey G, Balakrishnan L, Syed N, Nanjappa V, Subbannayya Y, Goel R, Prasad TS, Bafna V, Sirdeshmukh R, Gowda H, Wang C, Leach SD, Pandey A. Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Mol Cell Proteomics. 2014 Nov; 13 (11):3184-98 Epub 2014 July 24
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227. Wu X, Renuse S, Sahasrabuddhe NA, Zahari MS, Chaerkady R, Kim MS, Nirujogi RS, Mohseni M, Kumar P, Raju R, Zhong J, Yang J, Neiswinger J, Jeong JS, Newman R, Powers MA, Somani BL, Gabrielson E, Sukumar S, Stearns V, Qian J, Zhu H, Vogelstein B, Park BH, Pandey A. Activation of diverse signalling pathways by oncogenic PIK3CA mutations. Nat Commun. 2014 Sep 23; 5:4961.
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228. Luo W, Lin B, Wang Y, Zhong J, O'Meally R, Cole RN, Pandey A, Levchenko A, Semenza GL. PHD3-mediated prolyl hydroxylation of nonmuscle actin impairs polymerization and cell motility. Mol Biol Cell. 2014 Sep 15; 25 (18):2788-96 Epub 2014 July 30
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229. Marimuthu A, Huang TC, Selvan LDN, Renuse S, Nirujogi RS, Kumar P, Rajagopalan S, Pandey A, Harsha HC, Chatterjee A. Identification of targets of miR-200b by a SILAC-based quantitative proteomic approach EuPA Open Proteomics. 2014; 4:10-17.
     
230. Sahasrabuddhe NA, Huang TC, Ahmad S, Kim MS, Yang Y, Ghosh B, Leach SD, Gowda H, Somani BL, Chaerkady R, Pandey A. Regulation of PPAR-alpha pathway by Dicer revealed through proteomic analysis. J Proteomics. 2014 Aug 28; 108:306-15 Epub 2014 Apr 24
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231. Pawar H, Renuse S, Khobragade SN, Chavan S, Sathe G, Kumar P, Mahale KN, Gore K, Kulkarni A, Dixit T, Raju R, Prasad TS, Harsha HC, Patole MS, Pandey A. Neglected tropical diseases and omics science: proteogenomics analysis of the promastigote stage of Leishmania major parasite. OMICS. 2014 Aug; 18 (8):499-512 Epub 2014 June 17
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232. Gupta MK, Jayaram S, Madugundu AK, Chavan S, Advani J, Pandey A, Thongboonkerd V, Sirdeshmukh R. Chromosome-centric human proteome project: deciphering proteins associated with glioma and neurodegenerative disorders on chromosome 12. J Proteome Res. 2014 Jul 3; 13 (7):3178-90 Epub 2014 June 24
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233. Manda SS, Nirujogi RS, Pinto SM, Kim MS, Datta KK, Sirdeshmukh R, Prasad TS, Thongboonkerd V, Pandey A, Gowda H. Identification and characterization of proteins encoded by chromosome 12 as part of chromosome-centric human proteome project. J Proteome Res. 2014 Jul 3; 13 (7):3166-77 Epub 2014 June 24
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234. Dwivedi SB, Muthusamy B, Kumar P, Kim MS, Nirujogi RS, Getnet D, Ahiakonu P, De G, Nair B, Gowda H, Prasad TS, Kumar N, Pandey A, Okulate M. Brain proteomics of Anopheles gambiae. OMICS. 2014 Jul; 18 (7):421-37 Epub 2014 June 17
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235. Pinto SM, Manda SS, Kim MS, Taylor K, Selvan LD, Balakrishnan L, Subbannayya T, Yan F, Prasad TS, Gowda H, Lee C, Hancock WS, Pandey A. Functional annotation of proteome encoded by human chromosome 22. J Proteome Res. 2014 Jun 6; 13 (6):2749-60 Epub 2014 Apr 29
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236. Subbannayya Y, Anuja K, Advani J, Ojha UK, Nanjappa V, George B, Sonawane A, Kumar RV, Ramaswamy G, Pandey A, Somani BL, Raju R. A network map of the gastrin signaling pathway. J Cell Commun Signal. 2014 Jun; 8 (2):165-70 Epub 2014 Mar 02
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237. Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A. A draft map of the human proteome. Nature. 2014 May 29; 509 (7502):575-81
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238. Chi Z, Byrne ST, Dolinko A, Harraz MM, Kim MS, Umanah G, Zhong J, Chen R, Zhang J, Xu J, Chen L, Pandey A, Dawson TM, Dawson VL. Botch is a gamma-glutamyl cyclotransferase that deglycinates and antagonizes Notch. Cell Rep. 2014 May 8; 7 (3):681-8 Epub 2014 Apr 24
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239. Sahasrabuddhe NA, Barbhuiya MA, Bhunia S, Subbannayya T, Gowda H, Advani J, Shrivastav BR, Navani S, Leal P, Roa JC, Chaerkady R, Gupta S, Chatterjee A, Pandey A, Tiwari PK. Identification of prosaposin and transgelin as potential biomarkers for gallbladder cancer using quantitative proteomics. Biochem Biophys Res Commun. 2014 Apr 18; 446 (4):863-9 Epub 2014 Mar 20
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240. Martin I, Kim JW, Lee BD, Kang HC, Xu JC, Jia H, Stankowski J, Kim MS, Zhong J, Kumar M, Andrabi SA, Xiong Y, Dickson DW, Wszolek ZK, Pandey A, Dawson TM, Dawson VL. Ribosomal protein s15 phosphorylation mediates LRRK2 neurodegeneration in Parkinson's disease. Cell. 2014 Apr 10; 157 (2):472-485
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241. Haeusler AR, Donnelly CJ, Periz G, Simko EA, Shaw PG, Kim MS, Maragakis NJ, Troncoso JC, Pandey A, Sattler R, Rothstein JD, Wang J. C9orf72 nucleotide repeat structures initiate molecular cascades of disease. Nature. 2014 Mar 13; 507 (7491):195-200 Epub 2014 Mar 05
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242. Balakrishnan L, Nirujogi RS, Ahmad S, Bhattacharjee M, Manda SS, Renuse S, Kelkar DS, Subbannayya Y, Raju R, Goel R, Thomas JK, Kaur N, Dhillon M, Tankala SG, Jois R, Vasdev V, Ramachandra Y, Sahasrabuddhe NA, Prasad TsK, Mohan S, Gowda H, Shankar S, Pandey A. Proteomic analysis of human osteoarthritis synovial fluid. Clin Proteomics. 2014 Feb 17; 11 (1):6
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243. Heydarian M, Luperchio TR, Cutler J, Mitchell CJ, Kim MS, Pandey A, Sollner-Webb B, Reddy K. Prediction of Gene Activity in Early B Cell Development Based on an Integrative Multi-Omics Analysis. J Proteomics Bioinform. 2014 Feb 17; 7
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244. Nagarajha Selvan LD, Kaviyil JE, Nirujogi RS, Muthusamy B, Puttamallesh VN, Subbannayya T, Syed N, Radhakrishnan A, Kelkar DS, Ahmad S, Pinto SM, Kumar P, Madugundu AK, Nair B, Chatterjee A, Pandey A, Ravikumar R, Gowda H, Prasad TS. Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry. Clin Proteomics. 2014 Feb 3; 11 (1):5 Epub 2014 Feb 03
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245. Selvan LD, Renuse S, Kaviyil JE, Sharma J, Pinto SM, Yelamanchi SD, Puttamallesh VN, Ravikumar R, Pandey A, Prasad TS, Harsha HC. Phosphoproteome of Cryptococcus neoformans. J Proteomics. 2014 Jan 31; 97:287-95 Epub 2013 July 11
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246. Nirujogi RS, Pawar H, Renuse S, Kumar P, Chavan S, Sathe G, Sharma J, Khobragade S, Pande J, Modak B, Prasad TS, Harsha HC, Patole MS, Pandey A. Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani. J Proteomics. 2014 Jan 31; 97:48-61 Epub 2013 May 09
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247. Vega-Rodriguez J, Ghosh AK, Kanzok SM, Dinglasan RR, Wang S, Bongio NJ, Kalume DE, Miura K, Long CA, Pandey A, Jacobs-Lorena M. Multiple pathways for Plasmodium ookinete invasion of the mosquito midgut. Proc Natl Acad Sci U S A. 2014 Jan 28; 111 (4):E492-500 Epub 2014 Jan 13
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248. Balakrishnan L, Bhattacharjee M, Ahmad S, Nirujogi RS, Renuse S, Subbannayya Y, Marimuthu A, Srikanth SM, Raju R, Dhillon M, Kaur N, Jois R, Vasudev V, Ramachandra Y, Sahasrabuddhe NA, Prasad TsK, Mohan S, Gowda H, Shankar S, Pandey A. Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients. Clin Proteomics. 2014 Jan 6; 11 (1):1 Epub 2014 Jan 06
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249. Ahn JM, Kim MS, Kim YI, Jeong SK, Lee HJ, Lee SH, Paik YK, Pandey A, Cho JY. Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues. J Proteome Res. 2014 Jan 3; 13 (1):137-46 Epub 2013 Dec 06
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250. Raju R, Palapetta SM, Sandhya VK, Sahu A, Alipoor A, Balakrishnan L, Advani J, George B, Kini KR, Geetha NP, Prakash HS, Prasad TS, Chang YJ, Chen L, Pandey A, Gowda H. A Network Map of FGF-1/FGFR Signaling System. J Signal Transduct. 2014; 2014:962962 Epub 2014 Apr 16
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251. Murthy KR, Goel R, Subbannayya Y, Jacob HK, Murthy PR, Manda SS, Patil AH, Sharma R, Sahasrabuddhe NA, Parashar A, Nair BG, Krishna V, Prasad TK, Gowda H, Pandey A. Proteomic analysis of human vitreous humor. Clin Proteomics. 2014; 11 (1):29 Epub 2014 July 14
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252. Khan AA, Sandhya VK, Singh P, Parthasarathy D, Kumar A, Advani J, Gattu R, Ranjit DV, Vaidyanathan R, Mathur PP, Prasad TS, Mac Gabhann F, Pandey A, Raju R, Gowda H. Signaling Network Map of Endothelial TEK Tyrosine Kinase. J Signal Transduct. 2014; 2014:173026 Epub 2014 Oct 13
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253. Sahu A, Kumar S, Sreenivasamurthy SK, Selvan LD, Madugundu AK, Yelamanchi SD, Puttamallesh VN, Dey G, Anil AK, Srinivasan A, Mukherjee KK, Gowda H, Satishchandra P, Mahadevan A, Pandey A, Prasad TS, Shankar SK. Host response profile of human brain proteome in toxoplasma encephalitis co-infected with HIV. Clin Proteomics. 2014; 11 (1):39 Epub 2014 Nov 01
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254. Zhong J, Sharma J, Raju R, Palapetta SM, Prasad TS, Huang TC, Yoda A, Tyner JW, van Bodegom D, Weinstock DM, Ziegler SF, Pandey A. TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling. Database (Oxford). 2014; 2014:bau007 Epub 2014 Feb 25
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255. Wu X, Zahari MS, Renuse S, Jacob HK, Sakamuri S, Singal M, Gabrielson E, Sukumar S, Pandey A. A breast cancer cell microarray (CMA) as a rapid method to characterize candidate biomarkers. Cancer Biol Ther. 2014; 15 (12):1593-9
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256. Nanjappa V, Thomas JK, Marimuthu A, Muthusamy B, Radhakrishnan A, Sharma R, Ahmad Khan A, Balakrishnan L, Sahasrabuddhe NA, Kumar S, Jhaveri BN, Sheth KV, Kumar Khatana R, Shaw PG, Srikanth SM, Mathur PP, Shankar S, Nagaraja D, Christopher R, Mathivanan S, Raju R, Sirdeshmukh R, Chatterjee A, Simpson RJ, Harsha HC, Pandey A, Prasad TS. Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic Acids Res. 2014 Jan; 42 (Database issue):D959-65 Epub 2013 Dec 03
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257. Sandhya VK, Raju R, Verma R, Advani J, Sharma R, Radhakrishnan A, Nanjappa V, Narayana J, Somani BL, Mukherjee KK, Pandey A, Christopher R, Prasad TS. A network map of BDNF/TRKB and BDNF/p75NTR signaling system. J Cell Commun Signal. 2013 Dec; 7 (4):301-7 Epub 2013 Apr 20
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258. Marimuthu A, Chavan S, Sathe G, Sahasrabuddhe NA, Srikanth SM, Renuse S, Ahmad S, Radhakrishnan A, Barbhuiya MA, Kumar RV, Harsha HC, Sidransky D, Califano J, Pandey A, Chatterjee A. Identification of head and neck squamous cell carcinoma biomarker candidates through proteomic analysis of cancer cell secretome. Biochim Biophys Acta. 2013 Nov; 1834 (11):2308-16 Epub 2013 May 07
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259. Puttamallesh VN, Sreenivasamurthy SK, Singh PK, Harsha HC, Ganjiwale A, Broor S, Pandey A, Narayana J, Prasad TSK. Proteomic profiling of serum samples from chikungunya-infected patients provides insights into host response. Clin Proteomics. 2013 Oct 14; 10 (1):14
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260. Bhattacharjee M, Sharma R, Goel R, Balakrishnan L, Renuse S, Advani J, Gupta ST, Verma R, Pinto SM, Sekhar NR, Nair B, Prasad TSK, Harsha HC, Jois R, Shankar S, Pandey A. A multilectin affinity approach for comparative glycoprotein profiling of rheumatoid arthritis and spondyloarthropathy. Clin Proteomics. 2013 Sep 6; 10 (1):11 Epub 2013 Sept 06
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261. Goel R, Murthy KR, Srikanth SM, Pinto SM, Bhattacharjee M, Kelkar DS, Madugundu AK, Dey G, Mohan SS, Krishna V, Prasad TK, Chakravarti S, Harsha HC, Pandey A. Characterizing the normal proteome of human ciliary body. Clin Proteomics. 2013 Aug 1; 10 (1):9 Epub 2013 Aug 01
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262. Balakrishnan L, Soman S, Patil YB, Advani J, Thomas JK, Desai DV, Kulkarni-Kale U, Harsha HC, Prasad TS, Raju R, Pandey A, Dimitriadis E, Chatterjee A. IL-11/IL11RA receptor mediated signaling: a web accessible knowledgebase. Cell Commun Adhes. 2013 Aug; 20 (3-4):81-6 Epub 2013 Apr 30
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263. Prasad TS, Verma R, Kumar S, Nirujogi RS, Sathe GJ, Madugundu AK, Sharma J, Puttamallesh VN, Ganjiwale A, Myneedu VP, Chatterjee A, Pandey A, Harsha H, Narayana J. Proteomic analysis of purified protein derivative of Mycobacterium tuberculosis. Clin Proteomics. 2013 Jul 19; 10 (1):8 Epub 2013 July 19
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264. Ambekar AS, Nirujogi RS, Srikanth SM, Chavan S, Kelkar DS, Hinduja I, Zaveri K, Prasad TS, Harsha HC, Pandey A, Mukherjee S. Proteomic analysis of human follicular fluid: a new perspective towards understanding folliculogenesis. J Proteomics. 2013 Jul 11; 87:68-77 Epub 2013 May 24
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265. Chaerkady R, Shao H, Scott SG, Pandey A, Jun AS, Chakravarti S. The keratoconus corneal proteome: loss of epithelial integrity and stromal degeneration. J Proteomics. 2013 Jul 11; 87:122-31 Epub 2013 May 29
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266. Polisetty RV, Gautam P, Gupta MK, Sharma R, Uppin MS, Challa S, Ankathi P, Purohit AK, Renu D, Harsha HC, Pandey A, Sirdeshmukh R. Heterogeneous nuclear ribonucleoproteins and their interactors are a major class of deregulated proteins in anaplastic astrocytoma: a grade III malignant glioma. J Proteome Res. 2013 Jul 5; 12 (7):3128-38 Epub 2013 June 06
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267. Patel K, Scrimieri F, Ghosh S, Zhong J, Kim MS, Ren YR, Morgan RA, Iacobuzio-Donahue CA, Pandey A, Kern SE. FAM190A deficiency creates a cell division defect. Am J Pathol. 2013 Jul; 183 (1):296-303 Epub 2013 May 10
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268. Sreenivasamurthy SK, Dey G, Ramu M, Kumar M, Gupta MK, Mohanty AK, Harsha HC, Sharma P, Kumar N, Pandey A, Kumar A, Prasad TS. A compendium of molecules involved in vector-pathogen interactions pertaining to malaria. Malar J. 2013 Jun 26; 12:216 Epub 2013 June 26
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269. Marimuthu A, Subbannayya Y, Sahasrabuddhe NA, Balakrishnan L, Syed N, Sekhar NR, Katte TV, Pinto SM, Srikanth SM, Kumar P, Pawar H, Kashyap MK, Maharudraiah J, Ashktorab H, Smoot DT, Ramaswamy G, Kumar RV, Cheng Y, Meltzer SJ, Roa JC, Chaerkady R, Prasad TS, Harsha HC, Chatterjee A, Pandey A. SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics Clin Appl. 2013 Jun; 7 (5-6):355-66 Epub 2013 May 21
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270. Dey G, Radhakrishnan A, Syed N, Thomas JK, Nadig A, Srikumar K, Mathur PP, Pandey A, Lin SK, Raju R, Prasad TS. Signaling network of Oncostatin M pathway. J Cell Commun Signal. 2013 Jun; 7 (2):103-8 Epub 2012 Dec 20
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271. Venugopal AK, Ghantasala SS, Selvan LD, Mahadevan A, Renuse S, Kumar P, Pawar H, Sahasrabhuddhe NA, Suja MS, Ramachandra YL, Prasad TS, Madhusudhana SN, Hc H, Chaerkady R, Satishchandra P, Pandey A, Shankar SK. Quantitative proteomics for identifying biomarkers for Rabies. Clin Proteomics. 2013 Mar 22; 10 (1):3
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272. Soman S, Raju R, Sandhya VK, Advani J, Khan AA, Harsha HC, Prasad TS, Sudhakaran PR, Pandey A, Adishesha PK. A multicellular signal transduction network of AGE/RAGE signaling. J Cell Commun Signal. 2013 Mar; 7 (1):19-23 Epub 2012 Nov 19
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273. Pawar H, Maharudraiah J, Kashyap MK, Sharma J, Srikanth SM, Choudhary R, Chavan S, Sathe G, Manju HC, Kumar KV, Vijayakumar M, Sirdeshmukh R, Harsha HC, Prasad TS, Pandey A, Kumar RV. Downregulation of cornulin in esophageal squamous cell carcinoma. Acta Histochem. 2013 Mar; 115 (2):89-99 Epub 2012 May 05
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274. Huang TC, Pinto SM, Pandey A. Proteomics for understanding miRNA biology. Proteomics. 2013 Feb; 13 (3-4):558-67 Epub 2012 Dec 27
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275. Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Jeong JS, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J. Construction of human activity-based phosphorylation networks. Mol Syst Biol. 2013; 9:655
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276. Harsha HC, Pinto SM, Pandey A. Proteomic strategies to characterize signaling pathways. Methods Mol Biol. 2013; 1007:359-77
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277. Hansen AM, Chaerkady R, Sharma J, Diaz-Mejia JJ, Tyagi N, Renuse S, Jacob HK, Pinto SM, Sahasrabuddhe NA, Kim MS, Delanghe B, Srinivasan N, Emili A, Kaper JB, Pandey A. The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathog. 2013; 9 (6):e1003403 Epub 2013 June 13
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278. Luo W, Chang R, Zhong J, Pandey A, Semenza GL. Histone demethylase JMJD2C is a coactivator for hypoxia-inducible factor 1 that is required for breast cancer progression. Proc Natl Acad Sci U S A. 2012 Dec 4; 109 (49):E3367-76 Epub 2012 Nov 05
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279. Kumar GS, Venugopal AK, Mahadevan A, Renuse S, Harsha HC, Sahasrabuddhe NA, Pawar H, Sharma R, Kumar P, Rajagopalan S, Waddell K, Ramachandra YL, Satishchandra P, Chaerkady R, Prasad TS, Shankar K, Pandey A. Quantitative proteomics for identifying biomarkers for tuberculous meningitis. Clin Proteomics. 2012 Nov 30; 9 (1):12
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280. Kim MS, Kuppireddy SV, Sakamuri S, Singal M, Getnet D, Harsha HC, Goel R, Balakrishnan L, Jacob HK, Kashyap MK, Tankala SG, Maitra A, Iacobuzio-Donahue CA, Jaffee E, Goggins MG, Velculescu VE, Hruban RH, Pandey A. Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs). J Proteome Res. 2012 Nov 2; 11 (11):5556-63 Epub 2012 Oct 11
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281. Ren YR, Chaerkady R, Hu S, Wan J, Qian J, Zhu H, Pandey A, Kern SE. Unbiased discovery of interactions at a control locus driving expression of the cancer-specific therapeutic and diagnostic target, mesothelin. J Proteome Res. 2012 Nov 2; 11 (11):5301-10 Epub 2012 Oct 12
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282. Renuse S, Harsha HC, Kumar P, Acharya PK, Sharma J, Goel R, Kumar GS, Raju R, Prasad TS, Slotta T, Pandey A. Proteomic analysis of an unsequenced plant--Mangifera indica. J Proteomics. 2012 Oct 22; 75 (18):5793-6 Epub 2012 Aug 10
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283. van Bodegom D, Zhong J, Kopp N, Dutta C, Kim MS, Bird L, Weigert O, Tyner J, Pandey A, Yoda A, Weinstock DM. Differences in signaling through the B-cell leukemia oncoprotein CRLF2 in response to TSLP and through mutant JAK2. Blood. 2012 Oct 4; 120 (14):2853-63 Epub 2012 Aug 20
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284. Radhakrishnan A, Raju R, Tuladhar N, Subbannayya T, Thomas JK, Goel R, Telikicherla D, Palapetta SM, Rahiman BA, Venkatesh DD, Urmila KK, Harsha HC, Mathur PP, Prasad TS, Pandey A, Shemanko C, Chatterjee A. A pathway map of prolactin signaling. J Cell Commun Signal. 2012 Aug; 6 (3):169-73 Epub 2012 June 09
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285. Ferrando IM, Chaerkady R, Zhong J, Molina H, Jacob HK, Herbst-Robinson K, Dancy BM, Katju V, Bose R, Zhang J, Pandey A, Cole PA. Identification of targets of c-Src tyrosine kinase by chemical complementation and phosphoproteomics. Mol Cell Proteomics. 2012 Aug; 11 (8):355-69 Epub 2012 Apr 12
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286. Do Vale LH, Gomez-Mendoza DP, Kim MS, Pandey A, Ricart CA, Ximenes F Filho E, Sousa MV. Secretome analysis of the fungus Trichoderma harzianum grown on cellulose. Proteomics. 2012 Aug; 12 (17):2716-28 Epub 2012 Aug 01
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287. Telikicherla D, Marimuthu A, Kashyap MK, Ramachandra YL, Mohan S, Roa JC, Maharudraiah J, Pandey A. Overexpression of ribosome binding protein 1 (RRBP1) in breast cancer. Clin Proteomics. 2012 Jun 18; 9 (1):7 Epub 2012 June 18
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288. Polisetty RV, Gautam P, Sharma R, Harsha HC, Nair SC, Gupta MK, Uppin MS, Challa S, Puligopu AK, Ankathi P, Purohit AK, Chandak GR, Pandey A, Sirdeshmukh R. LC-MS/MS analysis of differentially expressed glioblastoma membrane proteome reveals altered calcium signaling and other protein groups of regulatory functions. Mol Cell Proteomics. 2012 Jun; 11 (6):M111.013565 Epub 2012 Jan 04
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289. Zhong J, Kim MS, Chaerkady R, Wu X, Huang TC, Getnet D, Mitchell CJ, Palapetta SM, Sharma J, O'Meally RN, Cole RN, Yoda A, Moritz A, Loriaux MM, Rush J, Weinstock DM, Tyner JW, Pandey A. TSLP signaling network revealed by SILAC-based phosphoproteomics. Mol Cell Proteomics. 2012 Jun; 11(6):M112.017764. Epub 2012 Feb 16.
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290. Huang TC, Sahasrabuddhe NA, Kim MS, Getnet D, Yang Y, Peterson JM, Ghosh B, Chaerkady R, Leach SD, Marchionni L, Wong GW, Pandey A. Regulation of lipid metabolism by Dicer revealed through SILAC mice. J Proteome Res. 2012 Apr 6; 11 (4):2193-205 Epub 2012 Feb 28
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291. Nagaraj SH, Harsha HC, Reverter A, Colgrave ML, Sharma R, Andronicos N, Hunt P, Menzies M, Lees MS, Sekhar NR, Pandey A, Ingham A. Proteomic analysis of the abomasal mucosal response following infection by the nematode, Haemonchus contortus, in genetically resistant and susceptible sheep. J Proteomics. 2012 Apr 3; 75 (7):2141-52 Epub 2012 Jan 25
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292. Pawar H, Sahasrabuddhe NA, Renuse S, Keerthikumar S, Sharma J, Kumar GS, Venugopal A, Sekhar NR, Kelkar DS, Nemade H, Khobragade SN, Muthusamy B, Kandasamy K, Harsha HC, Chaerkady R, Patole MS, Pandey A. A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani. Proteomics. 2012 Mar; 12(6):832-44.
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293. Kim MS, Pandey A. Electron transfer dissociation mass spectrometry in proteomics. Proteomics. 2012 Feb; 12 (4-5):530-42 Epub 2012 Jan 23
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294. Agyeman AS, Chaerkady R, Shaw PG, Davidson NE, Visvanathan K, Pandey A, Kensler TW. Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane-treated human breast epithelial cells reveals common expression profiles. Breast Cancer Res Treat. 2012 Feb; 132 (1):175-87 Epub 2011 May 20
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295. Goel R, Harsha HC, Pandey A, Prasad TS. Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Mol Biosyst. 2012 Feb; 8 (2):453-63 Epub 2011 Dec 08
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296. Kalra H, Simpson RJ, Ji H, Aikawa E, Altevogt P, Askenase P, Bond VC, Borras FE, Breakefield X, Budnik V, Buzas E, Camussi G, Clayton A, Cocucci E, Falcon-Perez JM, Gabrielsson S, Gho YS, Gupta D, Harsha HC, Hendrix A, Hill AF, Inal JM, Jenster G, Kramer-Albers EM, Lim SK, Llorente A, Lotvall J, Marcilla A, Mincheva-Nilsson L, Nazarenko I, Nieuwland R, Nolte-'t Hoen EN, Pandey A, Patel T, Piper MG, Pluchino S, Prasad TS, Rajendran L, Raposo G, Record M, Reid GE, Sanchez-Madrid F, Schiffelers RM, Siljander P, Stensballe A, Stoorvogel W, Taylor D, Thery C, Valadi H, van Balkom BW, Vazquez J, Vidal M, Wauben MH, Yanez-Mo M, Zoeller M, Mathivanan S. Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PLoS Biol. 2012; 10 (12):e1001450 Epub 2012 Dec 18
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297. Bhattacharjee M, Raju R, Radhakrishnan A, Nanjappa V, Muthusamy B, Singh K, Kuppusamy D, Lingala BT, Pan A, Mathur PP, Harsha HC, Prasad TS, Atkins GJ, Pandey A, Chatterjee A. A Bioinformatics Resource for TWEAK-Fn14 Signaling Pathway. J Signal Transduct. 2012; 2012:376470 Epub 2012 May 09
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298. Prasad TS, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LD, Kumar P, Pinto SM, Muthusamy B, Subbannayya Y, Renuse S, Chaerkady R, Mathur PP, Ravikumar R, Pandey A. Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry. J Proteome Res. 2012 Jan 1; 11 (1):247-60 Epub 2011 Dec 13
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299. Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Mol Cell Proteomics. 2011 Dec; 10 (12):O111.015446 Epub 2011 Nov 03
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300. Barbhuiya MA, Sahasrabuddhe NA, Pinto SM, Muthusamy B, Singh TD, Nanjappa V, Keerthikumar S, Delanghe B, Harsha HC, Chaerkady R, Jalaj V, Gupta S, Shrivastav BR, Tiwari PK, Pandey A. Comprehensive proteomic analysis of human bile. Proteomics. 2011 Dec; 11 (23):4443-53 Epub 2011 Nov 04
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301. Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav AK, Shrivastava P, Marimuthu A, Anand S, Sundaram H, Kingsbury R, Harsha HC, Nair B, Prasad TS, Chauhan DS, Katoch K, Katoch VM, Kumar P, Chaerkady R, Ramachandran S, Dash D, Pandey A. Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics. 2011 Dec; 10 (12):M111.011627 Epub 2011 Oct 03
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302. Chaerkady R, Kelkar DS, Muthusamy B, Kandasamy K, Dwivedi SB, Sahasrabuddhe NA, Kim MS, Renuse S, Pinto SM, Sharma R, Pawar H, Sekhar NR, Mohanty AK, Getnet D, Yang Y, Zhong J, Dash AP, MacCallum RM, Delanghe B, Mlambo G, Kumar A, Keshava Prasad TS, Okulate M, Kumar N, Pandey A. A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Res. 2011 Nov; 21(11):1872-81. Epub 2011 Jul 27.
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303. Goel R, Raju R, Maharudraiah J, Sameer Kumar GS, Ghosh K, Kumar A, Lakshmi TP, Sharma J, Sharma R, Balakrishnan L, Pan A, Kandasamy K, Christopher R, Krishna V, Mohan SS, Harsha HC, Mathur PP, Pandey A, Keshava Prasad TS. A Signaling Network of Thyroid-Stimulating Hormone. J Proteomics Bioinform. 2011 Oct 29; 4
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304. Telikicherla D, Ambekar A, Palapetta SM, Dwivedi SB, Raju R, Sharma J, Prasad TsK, Ramachandra Y, Mohan SS, Maharudraiah J, Mukherjee S, Pandey A. A comprehensive curated resource for follicle stimulating hormone signaling. BMC Res Notes. 2011 Oct 13; 4:408
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305. Pawar H, Kashyap MK, Sahasrabuddhe NA, Renuse S, Harsha HC, Kumar P, Sharma J, Kandasamy K, Marimuthu A, Nair B, Rajagopalan S, Maharudraiah J, Premalatha CS, Kumar KV, Vijayakumar M, Chaerkady R, Prasad TS, Kumar RV, Kumar RV, Pandey A. Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biol Ther. 2011 Sep 15; 12(6):510-22.
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306. Shao H, Chaerkady R, Chen S, Pinto SM, Sharma R, Delanghe B, Birk DE, Pandey A, Chakravarti S. Proteome profiling of wild type and lumican-deficient mouse corneas. J Proteomics. 2011 Sep 6; 74 (10):1895-905 Epub 2011 May 17
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307. Nanjappa V, Raju R, Muthusamy B, Sharma J, Thomas JK, Nidhina PAH, Harsha HC, Pandey A. A comprehensive curated reaction map of leptin signaling pathway Journal of Proteomics and Bioinformatics. 2011; 4:184-189.
     
308. Hyland EM, Molina H, Poorey K, Jie C, Xie Z, Dai J, Qian J, Bekiranov S, Auble DT, Pandey A, Boeke JD. An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae. Genes Dev. 2011 Jun 15; 25 (12):1306-19
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309. Marimuthu A, O'Meally RN, Chaerkady R, Subbannayya Y, Nanjappa V, Kumar P, Kelkar DS, Pinto SM, Sharma R, Renuse S, Goel R, Christopher R, Delanghe B, Cole RN, Harsha HC, Pandey A. A comprehensive map of the human urinary proteome. J Proteome Res. 2011 Jun 3; 10 (6):2734-43 Epub 2011 May 09
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310. Kim MS, Zhong J, Kandasamy K, Delanghe B, Pandey A. Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides. Proteomics. 2011 Jun; 11(12):2568-72. Epub 2011 May 20.
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311. Luo W, Hu H, Chang R, Zhong J, Knabel M, O'Meally R, Cole RN, Pandey A, Semenza GL. Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1. Cell. 2011 May 27; 145 (5):732-44
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312. Zachara NE, Molina H, Wong KY, Pandey A, Hart GW. The dynamic stress-induced "O-GlcNAc-ome" highlights functions for O-GlcNAc in regulating DNA damage/repair and other cellular pathways. Amino Acids. 2011 Mar; 40 (3):793-808 Epub 2010 July 31
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313. Zhong J, Chaerkady R, Kandasamy K, Gucek M, Cole RN, Pandey A. The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. J Proteomics. 2011 Mar 01; 74(3):294-303. Epub 2010 Nov 13.
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314. Wang Q, Chaerkady R, Wu J, Hwang HJ, Papadopoulos N, Kopelovich L, Maitra A, Matthaei H, Eshleman JR, Hruban RH, Kinzler KW, Pandey A, Vogelstein B. Mutant proteins as cancer-specific biomarkers. Proc Natl Acad Sci U S A. 2011 Feb 8; 108 (6):2444-9 Epub 2011 Jan 19
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315. Renuse S, Chaerkady R, Pandey A. Proteogenomics. Proteomics. 2011 Feb; 11 (4):620-30 Epub 2011 Jan 18
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316. Raju R, Balakrishnan L, Nanjappa V, Bhattacharjee M, Getnet D, Muthusamy B, Kurian Thomas J, Sharma J, Rahiman BA, Harsha HC, Shankar S, Prasad TS, Mohan SS, Bader GD, Wani MR, Pandey A. A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway. Database (Oxford). 2011; 2011:bar021 Epub 2011 July 08
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317. Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M, Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y, Telikicherla D, Bhattacharjee M, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S, Chavan SN, Kumar GS, Marimuthu A, Prasad TS, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A. NetSlim: high-confidence curated signaling maps. Database (Oxford). 2011; 2011:bar032 Epub 2011 Sept 29
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318. Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A. Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome. J Proteomics Bioinform. 2011; 4 (2):22-35
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319. Harsha HC, Pandey A. Phosphoproteomics in cancer. Mol Oncol. 2010 Dec; 4 (6):482-95 Epub 2010 Sept 26
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320. Hector A, Montgomery EA, Karikari C, Canto M, Dunbar KB, Wang JS, Feldmann G, Hong SM, Haffner MC, Meeker AK, Holland SJ, Yu J, Heckrodt TJ, Zhang J, Ding P, Goff D, Singh R, Roa JC, Marimuthu A, Riggins GJ, Eshleman JR, Nelkin BD, Pandey A, Maitra A. The Axl receptor tyrosine kinase is an adverse prognostic factor and a therapeutic target in esophageal adenocarcinoma. Cancer Biol Ther. 2010 Nov 15; 10 (10):1009-18
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321. Chen H, Pimienta G, Gu Y, Sun X, Hu J, Kim MS, Chaerkady R, Gucek M, Cole RN, Sukumar S, Pandey A. Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 2010 Nov; 10 (21):3800-10
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322. Kashyap MK, Harsha HC, Renuse S, Pawar H, Sahasrabuddhe NA, Kim MS, Marimuthu A, Keerthikumar S, Muthusamy B, Kandasamy K, Subbannayya Y, Prasad TS, Mahmood R, Chaerkady R, Meltzer SJ, Kumar RV, Rustgi AK, Pandey A. SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biol Ther. 2010 Oct 15; 10(8):796-810.
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323. Prasad, Keerthikumar S, Chaerkady R, Kandasamy K, Renuse S, Marimuthu A, Venugopal AK, Thomas JK, Jacob, Goel R, Pawar H, Sahasrabuddhe NA, Krishna V, Nair BG, Gucek M, Cole RN, Ravikumar R, Harsha HC, Pandey A. Comparative proteomic analysis of Candida albicans and Candida glabrata Clinical Proteomics. 2010; 6:163-173.
     
324. Yang Y, Chaerkady R, Kandasamy K, Huang TC, Selvan LD, Dwivedi SB, Kent OA, Mendell JT, Pandey A. Identifying targets of miR-143 using a SILAC-based proteomic approach. Mol Biosyst. 2010 Oct; 6(10):1873-82. Epub 2010 Jun 14.
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325. Zhong J, Krawczyk SA, Chaerkady R, Huang H, Goel R, Bader JS, Wong GW, Corkey BE, Pandey A. Temporal profiling of the secretome during adipogenesis in humans. J Proteome Res. 2010 Oct 01; 9(10):5228-38.
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326. Demir E, Cary MP, 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 AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, 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 KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep; 28(9):935-42. Epub 2010 Sep 09.
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327. Kim MS, Kandasamy K, Chaerkady R, Pandey A. Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer. J Am Soc Mass Spectrom. 2010 Sep; 21(9):1606-11. Epub 2010 Apr 24.
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328. Chaerkady R, Kerr CL, Kandasamy K, Marimuthu A, Gearhart JD, Pandey A. Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics. 2010 Apr; 10(7):1359-73.
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329. Kashyap MK, Marimuthu A, Peri S, Kumar GS, Jacob HK, Prasad TS, Mahmood R, Kumar KV, Kumar MV, Meltzer SJ, Montgomery EA, Kumar RV, Pandey A. Overexpression of periostin and lumican in esophageal squamous cell carcinoma. Cancers (Basel). 2010 Mar 1; 2 (1):133-42 Epub 2010 Mar 01
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330. Zhong J, Liu X, Pandey A. Effects of transmembrane and juxtamembrane domains on proliferative ability of TSLP receptor. Mol Immunol. 2010 Mar; 47 (6):1207-15 Epub 2010 Jan 21
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331. Zhou Q, Chaerkady R, Shaw PG, Kensler TW, Pandey A, Davidson NE. Screening for therapeutic targets of vorinostat by SILAC-based proteomic analysis in human breast cancer cells. Proteomics. 2010 Mar; 10 (5):1029-39
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332. Zhong J, Pandey A. Site-directed mutagenesis reveals a unique requirement for tyrosine residues in IL-7Ralpha and TSLPR cytoplasmic domains in TSLP-dependent cell proliferation. BMC Immunol. 2010 Feb 8; 11:5 Epub 2010 Feb 08
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333. Luo W, Zhong J, Chang R, Hu H, Pandey A, Semenza GL. Hsp70 and CHIP selectively mediate ubiquitination and degradation of hypoxia-inducible factor (HIF)-1alpha but Not HIF-2alpha. J Biol Chem. 2010 Feb 5; 285 (6):3651-63 Epub 2009 Nov 23
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334. Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A. NetPath: a public resource of curated signal transduction pathways. Genome Biol. 2010 Jan 12; 11(1):R3.
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335. Keerthikumar S, Bhadra S, Kandasamy K, Raju R, Ramachandra YL, Bhattacharyya C, Imai K, Ohara O, Mohan S, Pandey A. Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach. DNA Res. 2009 Dec; 16(6):345-51. Epub 2009 Oct 03.
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336. Amanchy R, Zhong J, Hong R, Kim JH, Gucek M, Cole RN, Molina H, Pandey A. Identification of c-Src tyrosine kinase substrates in platelet-derived growth factor receptor signaling. Mol Oncol. 2009 Dec; 3(5-6):439-50. Epub 2009 Jul 10.
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337. Kandasamy K, Keerthikumar S, Raju R, Keshava Prasad TS, Ramachandra YL, Mohan S, Pandey A. PathBuilder--open source software for annotating and developing pathway resources. Bioinformatics. 2009 Nov 01; 25(21):2860-2. Epub 2009 Jul 23.
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338. Kandasamy K, Pandey A, Molina H. Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Anal Chem. 2009 Sep 01; 81(17):7170-80.
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339. Parikh K, Diks SH, Tuynman JH, Verhaar A, Lowenberg M, Hommes DW, Joore J, Pandey A, Peppelenbosch MP. Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8. PLoS One. 2009 Jul 30; 4 (7):e6440 Epub 2009 July 30
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340. Li X, Molina H, Huang H, Zhang YY, Liu M, Qian SW, Slawson C, Dias WB, Pandey A, Hart GW, Lane MD, Tang QQ. O-linked N-acetylglucosamine modification on CCAAT enhancer-binding protein beta: role during adipocyte differentiation. J Biol Chem. 2009 Jul 17; 284 (29):19248-54 Epub 2009 May 28
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341. Harsha HC, Kandasamy K, Ranganathan P, Rani S, Ramabadran S, Gollapudi S, Balakrishnan L, Dwivedi SB, Telikicherla D, Selvan LD, Goel R, Mathivanan S, Marimuthu A, Kashyap M, Vizza RF, Mayer RJ, Decaprio JA, Srivastava S, Hanash SM, Hruban RH, Pandey A. A compendium of potential biomarkers of pancreatic cancer. PLoS Med. 2009 Apr 07; 6(4):e1000046.
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342. Cooper EM, Cutcliffe C, Kristiansen TZ, Pandey A, Pickart CM, Cohen RE. K63-specific deubiquitination by two JAMM/MPN+ complexes: BRISC-associated Brcc36 and proteasomal Poh1. EMBO J. 2009 Mar 18; 28 (6):621-31 Epub 2009 Feb 12
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343. Chaerkady R, Kerr CL, Marimuthu A, Kelkar DS, Kashyap MK, Gucek M, Gearhart JD, Pandey A. Temporal analysis of neural differentiation using quantitative proteomics. J Proteome Res. 2009 Mar; 8 (3):1315-26
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344. Yang Y, Chaerkady R, Beer MA, Mendell JT, Pandey A. Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics. 2009 Mar; 9 (5):1374-84
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345. Ranganathan P, Harsha HC, Pandey A. Molecular alterations in exocrine neoplasms of the pancreas. Arch Pathol Lab Med. 2009 Mar; 133 (3):405-12
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346. Venugopal A, Chaerkady R, Pandey A. Application of mass spectrometry-based proteomics for biomarker discovery in neurological disorders. Ann Indian Acad Neurol. 2009 Jan; 12 (1):3-11
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347. Keerthikumar S, Raju R, Kandasamy K, Hijikata A, Ramabadran S, Balakrishnan L, Ahmed M, Rani S, Selvan LD, Somanathan DS, Ray S, Bhattacharjee M, Gollapudi S, Ramachandra YL, Bhadra S, Bhattacharyya C, Imai K, Nonoyama S, Kanegane H, Miyawaki T, Pandey A, Ohara O, Mohan S. RAPID: Resource of Asian Primary Immunodeficiency Diseases. Nucleic Acids Res. 2009 Jan; 37 (Database issue):D863-7 Epub 2008 Oct 08
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348. Prasad TS, Kandasamy K, Pandey A. Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol. 2009; 577:67-79.
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349. Kashyap MK, Marimuthu A, Kishore CJ, Peri S, Keerthikumar S, Prasad TS, Mahmood R, Rao S, Ranganathan P, Sanjeeviah RC, Vijayakumar M, Kumar KV, Montgomery EA, Kumar RV, Pandey A. Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biol Ther. 2009 Jan; 8 (1):36-46 Epub 2009 Jan 01
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350. Ghosh AK, Devenport M, Jethwaney D, Kalume DE, Pandey A, Anderson VE, Sultan AA, Kumar N, Jacobs-Lorena M. Malaria parasite invasion of the mosquito salivary gland requires interaction between the Plasmodium TRAP and the Anopheles saglin proteins. PLoS Pathog. 2009 Jan; 5 (1):e1000265 Epub 2009 Jan 16
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351. Molina H, Yang Y, Ruch T, Kim JW, Mortensen P, Otto T, Nalli A, Tang QQ, Lane MD, Chaerkady R, Pandey A. Temporal profiling of the adipocyte proteome during differentiation using a five-plex SILAC based strategy. J Proteome Res. 2009 Jan; 8 (1):48-58
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352. Pimienta G, Chaerkady R, Pandey A. SILAC for global phosphoproteomic analysis. Methods Mol Biol. 2009; 527:107-16, x
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353. Kandasamy K, Keerthikumar S, Goel R, Mathivanan S, Patankar N, Shafreen B, Renuse S, Pawar H, Ramachandra YL, Acharya PK, Ranganathan P, Chaerkady R, Keshava Prasad TS, Pandey A. Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Res. 2009 Jan; 37(Database issue):D773-81. Epub 2008 Oct 23.
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354. Keshava Prasad TS, 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 DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A. Human Protein Reference Database--2009 update. Nucleic Acids Res. 2009 Jan; 37(Database issue):D767-72. Epub 2008 Nov 06.
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355. Harsha HC, Jimeno A, Molina H, Mihalas AB, Goggins MG, Hruban RH, Schulick RD, Kamath U, Maitra A, Hidalgo M, Pandey A. Activated epidermal growth factor receptor as a novel target in pancreatic cancer therapy. J Proteome Res. 2008 Nov; 7 (11):4651-8 Epub 2008 Sept 27
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356. Kristiansen TZ, Harsha HC, Gronborg M, Maitra A, Pandey A. Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma. J Proteome Res. 2008 Nov; 7 (11):4670-7 Epub 2008 Oct 08
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357. Dixon SJ, Fedyshyn Y, Koh JL, Prasad TS, Chahwan C, Chua G, Toufighi K, Baryshnikova A, Hayles J, Hoe KL, Kim DU, Park HO, Myers CL, Pandey A, Durocher D, Andrews BJ, Boone C. Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A. 2008 Oct 28; 105 (43):16653-8 Epub 2008 Oct 17
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358. Chaerkady R, Harsha HC, Nalli A, Gucek M, Vivekanandan P, Akhtar J, Cole RN, Simmers J, Schulick RD, Singh S, Torbenson M, Pandey A, Thuluvath PJ. A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma. J Proteome Res. 2008 Oct; 7 (10):4289-98 Epub 2008 Aug 21
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359. Mathivanan S, Pandey A. Human Proteinpedia as a resource for clinical proteomics. Mol Cell Proteomics. 2008 Oct; 7 (10):2038-47 Epub 2008 June 23
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360. Song D, Chaerkady R, Tan AC, Garcia-Garcia E, Nalli A, Suarez-Gauthier A, Lopez-Rios F, Zhang XF, Solomon A, Tong J, Read M, Fritz C, Jimeno A, Pandey A, Hidalgo M. Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer. Mol Cancer Ther. 2008 Oct; 7 (10):3275-84
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361. Guha U, Chaerkady R, Marimuthu A, Patterson AS, Kashyap MK, Harsha HC, Sato M, Bader JS, Lash AE, Minna JD, Pandey A, Varmus HE. Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proc Natl Acad Sci U S A. 2008 Sep 16; 105 (37):14112-7 Epub 2008 Sept 05
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362. Sarker R, Gronborg M, Cha B, Mohan S, Chen Y, Pandey A, Litchfield D, Donowitz M, Li X. Casein kinase 2 binds to the C terminus of Na+/H+ exchanger 3 (NHE3) and stimulates NHE3 basal activity by phosphorylating a separate site in NHE3. Mol Biol Cell. 2008 Sep; 19 (9):3859-70 Epub 2008 July 09
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363. Zhong L, Roybal J, Chaerkady R, Zhang W, Choi K, Alvarez CA, Tran H, Creighton CJ, Yan S, Strieter RM, Pandey A, Kurie JM. Identification of secreted proteins that mediate cell-cell interactions in an in vitro model of the lung cancer microenvironment. Cancer Res. 2008 Sep 1; 68 (17):7237-45
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364. Luo W, Slebos RJ, Hill S, Li M, Brabek J, Amanchy R, Chaerkady R, Pandey A, Ham AJ, Hanks SK. Global impact of oncogenic Src on a phosphotyrosine proteome. J Proteome Res. 2008 Aug; 7 (8):3447-60 Epub 2008 June 19
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365. Chaerkady R, Thuluvath PJ, Kim MS, Nalli A, Vivekanandan P, Simmers J, Torbenson M, Pandey A. O Labeling for a Quantitative Proteomic Analysis of Glycoproteins in Hepatocellular Carcinoma. Clin Proteomics. 2008 Jul 18; 4 (3-4):137-155
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366. Molina H, Matthiesen R, Kandasamy K, Pandey A. Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Anal Chem. 2008 Jul 01; 80(13):4825-35. Epub 2008 Jun 10.
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367. Karanjawala ZE, Illei PB, Ashfaq R, Infante JR, Murphy K, Pandey A, Schulick R, Winter J, Sharma R, Maitra A, Goggins M, Hruban RH. New markers of pancreatic cancer identified through differential gene expression analyses: claudin 18 and annexin A8. Am J Surg Pathol. 2008 Feb; 32 (2):188-96
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368. Chaerkady R, Pandey A. Applications of proteomics to lab diagnosis. Annu Rev Pathol. 2008; 3:485-98
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369. Harsha HC, Molina H, Pandey A. Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nat Protoc. 2008; 3 (3):505-16
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370. Okulate MA, Kalume DE, Reddy R, Kristiansen T, Bhattacharyya M, Chaerkady R, Pandey A, 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 Mol Biol. 2007 Dec; 16 (6):711-22
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371. Zhong J, Molina H, Pandey A. Phosphoproteomics. Curr Protoc Protein Sci. 2007 Nov; Chapter 24:Unit 24.4.
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372. Lucito R, Suresh S, Walter K, Pandey A, Lakshmi B, Krasnitz A, Sebat J, Wigler M, Klein AP, Brune K, Palmisano E, Maitra A, Goggins M, Hruban RH. Copy-number variants in patients with a strong family history of pancreatic cancer. Cancer Biol Ther. 2007 Oct; 6 (10):1592-9 Epub 2007 July 12
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373. 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. Protein pyrophosphorylation by inositol pyrophosphates is a posttranslational event. Proc Natl Acad Sci U S A. 2007 Sep 25; 104 (39):15305-10 Epub 2007 Sept 14
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374. Chaerkady R, Pandey A. Quantitative proteomics for identification of cancer biomarkers. Proteomics Clin Appl. 2007 Sep; 1 (9):1080-9 Epub 2007 Aug 17
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375. Dinglasan RR, Kalume DE, Kanzok SM, Ghosh AK, Muratova O, Pandey A, Jacobs-Lorena M. Disruption of Plasmodium falciparum development by antibodies against a conserved mosquito midgut antigen. Proc Natl Acad Sci U S A. 2007 Aug 14; 104 (33):13461-6 Epub 2007 Aug 02
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376. Wang Z, Pandey A, Hart GW. Dynamic interplay between O-linked N-acetylglucosaminylation and glycogen synthase kinase-3-dependent phosphorylation. Mol Cell Proteomics. 2007 Aug; 6 (8):1365-79 Epub 2007 May 16
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377. Kim JW, Monila H, Pandey A, Lane MD. Upstream stimulatory factors regulate the C/EBP alpha gene during differentiation of 3T3-L1 preadipocytes. Biochem Biophys Res Commun. 2007 Mar 9; 354 (2):517-21 Epub 2007 Jan 10
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378. Molina H, Horn DM, Tang N, Mathivanan S, Pandey A. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A. 2007 Feb 13; 104 (7):2199-204 Epub 2007 Feb 07
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379. Mathivanan S, Periaswamy B, Gandhi TK, Kandasamy K, Suresh S, Mohmood R, Ramachandra YL, Pandey A. An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics. 2006 Dec 18; 7 Suppl 5:S19.
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380. Liu B, Molina H, Kalume D, Pandey A, Griffith JD, Englund PT. Role of p38 in replication of Trypanosoma brucei kinetoplast DNA. Mol Cell Biol. 2006 Jul; 26 (14):5382-93
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381. Bose R, Molina H, Patterson AS, Bitok JK, Periaswamy B, Bader JS, Pandey A, Cole PA. Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc Natl Acad Sci U S A. 2006 Jun 27; 103 (26):9773-8 Epub 2006 June 19
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382. Wang D, Kalume D, Pickart C, Pandey A, Cotter RJ. Identification of protein ubiquitylation by electrospray ionization tandem mass spectrometric analysis of sulfonated tryptic peptides. Anal Chem. 2006 Jun 1; 78 (11):3681-7
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383. Lerin C, Rodgers JT, Kalume DE, Kim SH, Pandey A, Puigserver P. GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of PGC-1alpha. Cell Metab. 2006 Jun; 3 (6):429-38
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384. Moff SL, Clark DP, Maitra A, Pandey A, Thuluvath PJ. Utility of bile duct brushings for the early detection of cholangiocarcinoma in patients with primary sclerosing cholangitis. J Clin Gastroenterol. 2006 Apr; 40 (4):336-41
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385. Qiao Y, Molina H, Pandey A, Zhang J, Cole PA. Chemical rescue of a mutant enzyme in living cells. Science. 2006 Mar 3; 311 (5765):1293-7
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386. 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. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet. 2006 Mar; 38(3):285-93.
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387. Gronborg M, Kristiansen TZ, Iwahori A, Chang R, Reddy R, Sato N, Molina H, Jensen ON, Hruban RH, Goggins MG, Maitra A, Pandey A. Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol Cell Proteomics. 2006 Jan; 5 (1):157-71 Epub 2005 Oct 08
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388. Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, Menon S, Hanumanthu G, Gupta M, Upendran S, Gupta S, Mahesh M, Jacob B, Mathew P, Chatterjee P, Arun KS, Sharma S, Chandrika KN, Deshpande N, Palvankar K, Raghavnath R, Krishnakanth R, Karathia H, Rekha B, Nayak R, Vishnupriya G, Kumar HG, Nagini M, Kumar GS, Jose R, Deepthi P, Mohan SS, Gandhi TK, Harsha HC, Deshpande KS, Sarker M, Prasad TS, Pandey A. Human protein reference database--2006 update. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D411-4.
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389. Suresh S, Sujatha Mohan S, Mishra G, Hanumanthu GR, Suresh M, Reddy R, Pandey A. Proteomic resources: integrating biomedical information in humans. Gene. 2005 Dec 30; 364:13-8 Epub 2005 Oct 03
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390. Bala P, Georgantas RW 3rd, Sudhir D, Suresh M, Shanker K, Vrushabendra BM, Civin CI, Pandey A. TAGmapper: a web-based tool for mapping SAGE tags. Gene. 2005 Dec 30; 364:123-9 Epub 2005 Aug 19
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391. Hyland EM, Cosgrove MS, Molina H, Wang D, Pandey A, Cottee RJ, Boeke JD. Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Mol Cell Biol. 2005 Nov; 25 (22):10060-70
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392. Kalume DE, Peri S, Reddy R, Zhong J, Okulate M, Kumar N, Pandey A. Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics. 2005 Sep 19; 6:128 Epub 2005 Sept 19
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393. Amanchy R, Kalume DE, Iwahori A, Zhong J, Pandey A. Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). J Proteome Res. 2005 Sep-Oct; 4 (5):1661-71
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394. Kalume DE, Okulate M, Zhong J, Reddy R, Suresh S, Deshpande N, Kumar N, Pandey A. A proteomic analysis of salivary glands of female Anopheles gambiae mosquito. Proteomics. 2005 Sep; 5 (14):3765-77
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395. Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM. Probabilistic model of the human protein-protein interaction network. Nat Biotechnol. 2005 Aug; 23 (8):951-9
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396. Muthusamy B, Hanumanthu G, Suresh S, Rekha B, Srinivas D, Karthick L, Vrushabendra BM, Sharma S, Mishra G, Chatterjee P, Mangala KS, Shivashankar HN, Chandrika KN, Deshpande N, Suresh M, Kannabiran N, Niranjan V, Nalli A, Prasad TS, Arun KS, Reddy R, Chandran S, Jadhav T, Julie D, Mahesh M, John SL, Palvankar K, Sudhir D, Bala P, Rashmi NS, Vishnupriya G, Dhar K, Reshma S, Chaerkady R, Gandhi TK, Harsha HC, Mohan SS, Deshpande KS, Sarker M, Pandey A. Plasma Proteome Database as a resource for proteomics research. Proteomics. 2005 Aug; 5 (13):3531-6
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397. Ping P, Vondriska TM, Creighton CJ, Gandhi TK, Yang Z, Menon R, Kwon MS, Cho SY, Drwal G, Kellmann M, Peri S, Suresh S, Gronborg M, Molina H, Chaerkady R, Rekha B, Shet AS, Gerszten RE, Wu H, Raftery M, Wasinger V, Schulz-Knappe P, Hanash SM, Paik YK, Hancock WS, States DJ, Omenn GS, Pandey A. A functional annotation of subproteomes in human plasma. Proteomics. 2005 Aug; 5 (13):3506-19
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398. Tang QQ, Gronborg M, Huang H, Kim JW, Otto TC, Pandey A, Lane MD. Sequential phosphorylation of CCAAT enhancer-binding protein beta by MAPK and glycogen synthase kinase 3beta is required for adipogenesis. Proc Natl Acad Sci U S A. 2005 Jul 12; 102 (28):9766-71 Epub 2005 June 28
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399. Molina H, Bunkenborg J, Reddy GH, Muthusamy B, Scheel PJ, Pandey A. A proteomic analysis of human hemodialysis fluid. Mol Cell Proteomics. 2005 May; 4 (5):637-50 Epub 2005 Feb 20
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400. Molina H, Parmigiani G, Pandey A. Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. Anal Chem. 2005 May 1; 77 (9):2739-44
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401. Amanchy R, Kalume DE, Pandey A. Stable isotope labeling with amino acids in cell culture (SILAC) for studying dynamics of protein abundance and posttranslational modifications. Sci STKE. 2005 Jan 18; 2005 (267):pl2
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402. Gandhi TK, Chandran S, Peri S, Saravana R, Amanchy R, Prasad TS, Pandey A. A bioinformatics analysis of protein tyrosine phosphatases in humans. DNA Res. 2005; 12 (2):79-89
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403. Raghothama C, Harsha HC, Prasad CK, Pandey A. Bioinformatics and proteomics approaches for aging research. Biogerontology. 2005; 6 (4):227-32
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404. Hustinx SR, Cao D, Maitra A, Sato N, Martin ST, Sudhir D, Iacobuzio-Donahue C, Cameron JL, Yeo CJ, Kern SE, Goggins M, Mollenhauer J, Pandey A, Hruban RH. Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression. Cancer Biol Ther. 2004 Dec; 3 (12):1254-61 Epub 2004 Dec 14
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405. Cao D, Hustinx SR, Sui G, Bala P, Sato N, Martin S, Maitra A, Murphy KM, Cameron JL, Yeo CJ, Kern SE, Goggins M, Pandey A, Hruban RH. Identification of novel highly expressed genes in pancreatic ductal adenocarcinomas through a bioinformatics analysis of expressed sequence tags. Cancer Biol Ther. 2004 Nov; 3 (11):1081-9; discussion 1090-1 Epub 2004 Nov 12
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406. Koopmann J, Thuluvath PJ, Zahurak ML, Kristiansen TZ, Pandey A, Schulick R, Argani P, Hidalgo M, Iacobelli S, Goggins M, Maitra A. Mac-2-binding protein is a diagnostic marker for biliary tract carcinoma. Cancer. 2004 Oct 1; 101 (7):1609-15
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407. Gronborg M, Bunkenborg J, Kristiansen TZ, Jensen ON, Yeo CJ, Hruban RH, Maitra A, Goggins MG, Pandey A. Comprehensive proteomic analysis of human pancreatic juice. J Proteome Res. 2004 Sep-Oct; 3 (5):1042-55
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408. Kristiansen TZ, Nielsen MM, Blagoev B, Pandey A, Mann M. Mouse embryonic fibroblasts derived from Odin deficient mice display a hyperproliiferative phenotype. DNA Res. 2004 Aug 31; 11 (4):285-92
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409. Al-Shami A, Spolski R, Kelly J, Fry T, Schwartzberg PL, Pandey A, Mackall CL, Leonard WJ. A role for thymic stromal lymphopoietin in CD4(+) T cell development. J Exp Med. 2004 Jul 19; 200 (2):159-68
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410. Kristiansen TZ, Bunkenborg J, Gronborg M, Molina H, Thuluvath PJ, Argani P, Goggins MG, Maitra A, Pandey A. A proteomic analysis of human bile. Mol Cell Proteomics. 2004 Jul; 3 (7):715-28 Epub 2004 Apr 14
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411. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A. 2004 Jun 22; 101 (25):9309-14 Epub 2004 June 07
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412. Navarro JD, Talreja N, Peri S, Vrushabendra BM, Rashmi BP, Padma N, Surendranath V, Jonnalagadda CK, Kousthub PS, Deshpande N, Shanker K, Pandey A. BioBuilder as a database development and functional annotation platform for proteins. BMC Bioinformatics. 2004 Apr 20; 5:43
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413. Ibarrola N, Molina H, Iwahori A, Pandey A. A novel proteomic approach for specific identification of tyrosine kinase substrates using [13C]tyrosine. J Biol Chem. 2004 Apr 16; 279 (16):15805-13 Epub 2004 Jan 21
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414. Navarro JD, Pandey A. Unraveling the human interactome: Lessons from the yeast Drug Discover Today: Targets. 2004; 3(2):79-84.
     
415. Tewari M, Hu PJ, Ahn JS, Ayivi-Guedehoussou N, Vidalain PO, Li S, Milstein S, Armstrong CM, Boxem M, Butler MD, Busiguina S, Rual JF, Ibarrola N, Chaklos ST, Bertin N, Vaglio P, Edgley ML, King KV, Albert PS, Vandenhaute J, Pandey A, Riddle DL, Ruvkun G, Vidal M. Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol Cell. 2004 Feb 27; 13 (4):469-82
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416. 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 SG, 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, Apweiler R. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol. 2004 Feb; 22 (2):177-83
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417. Ibarrola N, Kratchmarova I, Nakajima D, Schiemann WP, Moustakas A, Pandey A, Mann M. Cloning of a novel signaling molecule, AMSH-2, that potentiates transforming growth factor beta signaling. BMC Cell Biol. 2004 Jan 19; 5:2
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418. Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi TK, Chandrika KN, Deshpande N, Suresh S, Rashmi BP, Shanker K, Padma N, Niranjan V, Harsha HC, Talreja N, Vrushabendra BM, Ramya MA, Yatish AJ, Joy M, Shivashankar HN, Kavitha MP, Menezes M, Choudhury DR, Ghosh N, Saravana R, Chandran S, Mohan S, Jonnalagadda CK, Prasad CK, Kumar-Sinha C, Deshpande KS, Pandey A. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res. 2004 Jan 1; 32 (Database issue):D497-501
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419. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia. 2004 Jan-Feb; 6 (1):1-6
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420. Ibarrola N, Kalume DE, Gronborg M, Iwahori A, Pandey A. A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture. Anal Chem. 2003 Nov 15; 75 (22):6043-9
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421. Raghothama C, Pandey A. Absolute systems biology--measuring dynamics of protein modifications. Trends Biotechnol. 2003 Nov; 21 (11):467-70
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422. 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. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003 Oct; 13 (10):2363-71
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423. Navarro JD, Niranjan V, Peri S, Jonnalagadda CK, Pandey A. From biological databases to platforms for biomedical discovery. Trends Biotechnol. 2003 Jun; 21 (6):263-8
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424. Steen H, Fernandez M, Ghaffari S, Pandey A, Mann M. Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanning. Mol Cell Proteomics. 2003 Mar; 2 (3):138-45 Epub 2003 Feb 25
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425. Kalume DE, Molina H, Pandey A. Tackling the phosphoproteome: tools and strategies. Curr Opin Chem Biol. 2003 Feb; 7 (1):64-9
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426. Pandey A, Peri S, Thacker C, Whipple CA, Collins JJ, Mann M. Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome. Bioinformatics. 2003 Jan 22; 19 (2):169-72
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427. Deshpande KS, Harsha HC, Pandey A. Microarrays and mass spectrometry: The future of proteomics Current Genomics. 2003; 4(7):605-613.
     
428. Pandey A, Blagoev B, Kratchmarova I, Fernandez M, Nielsen M, Kristiansen TZ, Ohara O, Podtelejnikov AV, Roche S, Lodish HF, Mann M. Cloning of a novel phosphotyrosine binding domain containing molecule, Odin, involved in signaling by receptor tyrosine kinases. Oncogene. 2002 Nov 14; 21 (52):8029-36
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429. Blagoev B, Kratchmarova I, Nielsen MM, Fernandez MM, Voldby J, Andersen JS, Kristiansen K, Pandey A, Mann M. Inhibition of adipocyte differentiation by resistin-like molecule alpha. Biochemical characterization of its oligomeric nature. J Biol Chem. 2002 Nov 1; 277 (44):42011-6 Epub 2002 Aug 19
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430. Steen H, Pandey A, Andersen JS, Mann M. Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning method. Sci STKE. 2002 Oct 15; 2002 (154):pl16
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431. Steen H, Pandey A. Proteomics goes quantitative: measuring protein abundance. Trends Biotechnol. 2002 Sep; 20 (9):361-4
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432. Jebanathirajah JA, Peri S, Pandey A. Toll and interleukin-1 receptor (TIR) domain-containing proteins in plants: a genomic perspective. Trends Plant Sci. 2002 Sep; 7 (9):388-91
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433. Schiemann WP, Blobe GC, Kalume DE, Pandey A, Lodish HF. Context-specific effects of fibulin-5 (DANCE/EVEC) on cell proliferation, motility, and invasion. Fibulin-5 is induced by transforming growth factor-beta and affects protein kinase cascades. J Biol Chem. 2002 Jul 26; 277 (30):27367-77 Epub 2002 May 20
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434. Dan I, Watanabe NM, Kajikawa E, Ishida T, Pandey A, Kusumi A. Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution. Nucleic Acids Res. 2002 Jul 1; 30 (13):2906-10
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435. Gronborg M, Kristiansen TZ, Stensballe A, Andersen JS, Ohara O, Mann M, Jensen ON, 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. Mol Cell Proteomics. 2002 Jul; 1 (7):517-27
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436. Mann M, Ong SE, Gronborg M, Steen H, Jensen ON, Pandey A. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol. 2002 Jun; 20 (6):261-8
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437. Pandey A, Dan I, Kristiansen TZ, Watanabe NM, Voldby J, Kajikawa E, Khosravi-Far R, Blagoev B, Mann M. Cloning and characterization of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain. Oncogene. 2002 May 30; 21 (24):3939-48
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438. Pandey A, Ibarrola N, Kratchmarova I, Fernandez MM, Constantinescu SN, Ohara O, Sawasdikosol S, Lodish HF, Mann M. A novel Src homology 2 domain-containing molecule, Src-like adapter protein-2 (SLAP-2), which negatively regulates T cell receptor signaling. J Biol Chem. 2002 May 24; 277 (21):19131-8 Epub 2002 Mar 12
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439. Kristiansen TZ, Pandey A. Resources for full-length cDNAs. Trends Biochem Sci. 2002 May; 27 (5):266-7
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440. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002 May; 1 (5):376-86
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441. Kratchmarova I, Kalume DE, Blagoev B, Scherer PE, Podtelejnikov AV, Molina H, Bickel PE, Andersen JS, Fernandez MM, Bunkenborg J, Roepstorff P, Kristiansen K, Lodish HF, Mann M, Pandey A. A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes. Mol Cell Proteomics. 2002 Mar; 1 (3):213-22
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442. Dan I, Ong SE, Watanabe NM, Blagoev B, Nielsen MM, Kajikawa E, Kristiansen TZ, Mann M, Pandey A. Cloning of MASK, a novel member of the mammalian germinal center kinase III subfamily, with apoptosis-inducing properties. J Biol Chem. 2002 Feb 22; 277 (8):5929-39 Epub 2001 Dec 06
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443. Blagoev B, Nielsen MM, Angrist M, Chakravarti A, Pandey A. Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene. Gene. 2002 Feb 6; 284 (1-2):161-8
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444. Steen H, Kuster B, Fernandez M, Pandey A, Mann M. Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. J Biol Chem. 2002 Jan 11; 277 (2):1031-9 Epub 2001 Oct 30
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445. Peri S, Pandey A. A reassessment of the translation initiation codon in vertebrates. Trends Genet. 2001 Dec; 17 (12):685-7
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446. Peri S, Steen H, Pandey A. GPMAW--a software tool for analyzing proteins and peptides. Trends Biochem Sci. 2001 Nov; 26 (11):687-9
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447. Ong SE, Pandey A. An evaluation of the use of two-dimensional gel electrophoresis in proteomics. Biomol Eng. 2001 Nov; 18 (5):195-205
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448. Peri S, Ibarrola N, Blagoev B, Mann M, Pandey A. Common pitfalls in bioinformatics-based analyses: look before you leap. Trends Genet. 2001 Sep; 17 (9):541-5
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449. Steen H, Kuster B, Fernandez M, Pandey A, Mann M. Detection of tyrosine phosphorylated peptides by precursor ion scanning quadrupole TOF mass spectrometry in positive ion mode. Anal Chem. 2001 Apr 1; 73 (7):1440-8
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450. Kratchmarova I, Sosinowski T, Weiss A, Witter K, Vincenz C, Pandey A. Characterization of promoter region and genomic structure of the murine and human genes encoding Src like adapter protein. Gene. 2001 Jan 10; 262 (1-2):267-73
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451. Mann M, Pandey A. Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. Trends Biochem Sci. 2001 Jan; 26 (1):54-61
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452. Mann M, Hendrickson RC, Pandey A. Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem. 2001; 70:437-73
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453. Pandey A, Fernandez MM, Steen H, Blagoev B, Nielsen MM, Roche S, Mann M, Lodish HF. Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways. J Biol Chem. 2000 Dec 8; 275 (49):38633-9
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454. Pandey A, Ozaki K, Baumann H, Levin SD, Puel A, Farr AG, Ziegler SF, Leonard WJ, Lodish HF. Cloning of a receptor subunit required for signaling by thymic stromal lymphopoietin. Nat Immunol. 2000 Jul; 1 (1):59-64
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455. Pandey A, Andersen JS, Mann M. Use of mass spectrometry to study signaling pathways. Sci STKE. 2000 Jun 20; 2000 (37):pl1 Epub 2000 June 20
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456. Pandey A, Mann M. Proteomics to study genes and genomes. Nature. 2000 Jun 15; 405 (6788):837-46
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457. Sosinowski T, Pandey A, Dixit VM, Weiss A. Src-like adaptor protein (SLAP) is a negative regulator of T cell receptor signaling. J Exp Med. 2000 Feb 7; 191 (3):463-74
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458. Pandey A, Podtelejnikov AV, Blagoev B, Bustelo XR, Mann M, Lodish HF. Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. Proc Natl Acad Sci U S A. 2000 Jan 4; 97 (1):179-84
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459. Pandey A, Lewitter F. Nucleotide sequence databases: a gold mine for biologists. Trends Biochem Sci. 1999 Jul; 24 (7):276-80
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460. Roche S, Alonso G, Kazlauskas A, Dixit VM, Courtneidge SA, Pandey A. Src-like adaptor protein (Slap) is a negative regulator of mitogenesis. Curr Biol. 1998 Aug 27; 8 (17):975-8
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461. Pandey A, Liu X, Dixon JE, Di Fiore PP, Dixit VM. Direct association between the Ret receptor tyrosine kinase and the Src homology 2-containing adapter protein Grb7. J Biol Chem. 1996 May 3; 271 (18):10607-10
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462. Angrist M, Wells DE, Chakravarti A, Pandey A. Chromosomal localization of the mouse Src-like adapter protein (Slap) gene and its putative human homolog SLA. Genomics. 1995 Dec 10; 30 (3):623-5
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463. Pandey A, Duan H, Di Fiore PP, Dixit VM. The Ret receptor protein tyrosine kinase associates with the SH2-containing adapter protein Grb10. J Biol Chem. 1995 Sep 15; 270 (37):21461-3
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464. Pandey A, Lindberg RA, Dixit VM. Cell signalling. Receptor orphans find a family. Curr Biol. 1995 Sep 1; 5 (9):986-9
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465. Pandey A, Duan H, Dixit VM. Characterization of a novel Src-like adapter protein that associates with the Eck receptor tyrosine kinase. J Biol Chem. 1995 Aug 18; 270 (33):19201-4
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466. Pandey A, Shao H, Marks RM, Polverini PJ, Dixit VM. Role of B61, the ligand for the Eck receptor tyrosine kinase, in TNF-alpha-induced angiogenesis. Science. 1995 Apr 28; 268 (5210):567-9
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467. Shao H, Pandey A, O'Shea KS, Seldin M, Dixit VM. Characterization of B61, the ligand for the Eck receptor protein-tyrosine kinase. J Biol Chem. 1995 Mar 10; 270 (10):5636-41
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468. Shao H, Lou L, Pandey A, Verderame MF, Siever DA, Dixit VM. cDNA cloning and characterization of a Cek7 receptor protein-tyrosine kinase ligand that is identical to the ligand (ELF-1) for the Mek-4 and Sek receptor protein-tyrosine kinases. J Biol Chem. 1995 Feb 24; 270 (8):3467-70
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469. Pandey A, Lazar DF, Saltiel AR, Dixit VM. Activation of the Eck receptor protein tyrosine kinase stimulates phosphatidylinositol 3-kinase activity. J Biol Chem. 1994 Dec 2; 269 (48):30154-7
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470. Shao H, Lou L, Pandey A, Pasquale EB, Dixit VM. cDNA cloning and characterization of a ligand for the Cek5 receptor protein-tyrosine kinase. J Biol Chem. 1994 Oct 28; 269 (43):26606-9
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471. Pandey A, Tjoelker LW, Thompson CB. Restricted immunoglobulin junctional diversity in neonatal B cells results from developmental selection rather than homology-based V(D)J joining. J Exp Med. 1993 Feb 1; 177 (2):329-37
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