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JHU Proteomics Publications

Complete Publication Listing


  • Vidal M, Chan DW, Gerstein M, Mann M, Omenn GS, Tagle D, et al. The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. Clin Proteomics. 2012 May 14; 9(1): 6.
  • Huang TC, Sahasrabuddhe NA, Kim MS, Getnet D, Yang Y, Peterson JM, et al. Regulation of lipid metabolism by dicer revealed through SILAC mice. J Proteome Res. 2012 Apr 6; 11(4): 2193-205.
  • Kim MS, Pandey A. Electron transfer dissociation mass spectrometry in proteomics. Proteomics. 2012 Feb; 12(4-5): 530-42.
  • Marimuthu A, O'Meally RN, Chaerkady R, Subbannayya Y, Nanjappa V, Kumar P, et al. A comprehensive map of the human urinary proteome. J Proteome Res. 2011 Jun 3; 10(6): 2734-43.
  • 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 1; 74(3): 294-303.
  • 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.
  • Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, et al. Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome. J Proteomics Bioinform. 2011; 4(2): 22-35.
  • Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics Clin Appl. 2011 Dec; 5(11-12): 580-9.
  • Chaerkady R, Kelkar DS, Muthusamy B, Kandasamy K, Dwivedi SB, Sahasrabuddhe NA, et al. A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Res. 2011 Nov; 21(11): 1872-81.
  • Zhang PB, Kirk JA, Ji W, dos Remedios CG, Kass DA, Van Eyk JE, et al. Multiple reaction monitoring to identify site-specific troponin I phosphorylated residues in the failing human heart. In review. 2012.
  • Akimoto Y, Miura Y, Toda T, Wolfert MA, Wells L, Boons GJ, et al. Morphological changes in diabetic kidney are associated with increased O-GlcNAcylation of cytoskeletal proteins including alpha-actinin 4. Clin Proteomics. 2011; 8(1): 15.
  • Alfaro JF, Gong CX, Monroe ME, Aldrich JT, Clauss TR, Purvine SO, et al. Tandem mass spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets. Proc Natl Acad Sci U S A. 2012 May 8; 109(19): 7280-5.
  • Allison DF, Wamsley JJ, Kumar M, Li D, Gray LG, Hart GW, et al. Modification of RelA by O-linked N-Acetylglucosamine Links Glucose Metabolism to NF-κB Acetylation and Transcription. 2012; Submitted.
  • Bullen JW, Balsbaugh J, Neumann D, Shabanowitz J, Hunt DF, Hart GW. Dynamic Crosstalk between two essential nutrient-sensitive enzymes: O-GlcNAc Transferase (OGT) and AMP-activated protein kinase (AMPK). . 2012; Submitted.
  • Dias WB, Cheung WD, Hart GW. O-GlcNAcylation of kinases. Biochem Biophys Res Commun. 2012 Jun 1; 422(2): 224-8.
  • Ramirez-Correa G, Slawson C, Zeidan Q, Shen X, Gao WD, Caceres V, et al. Increased O-GlcNAc in Diabetic Cardiac Sarcomeres Leads to Myofilament Ca2+ Desensitization and Contractile Dysfunction 2012; in revision.
  • Ranuncolo SM, Ghosh S, Hanover JA, Hart GW, Lewis BA. Evidence of the involvement of O-GlcNAc-modified human RNA polymerase II CTD in transcription in vitro and in vivo. J Biol Chem. 2012 May 17.
  • Slawson C, Hart GW. O-GlcNAc signaling: implications for cancer cell biology. Nat Rev Cancer. 2011 Sept; 11(9): 678-84.
  • Tarrant MK, Rho HS, Xie Z, Jiang YL, Gross C, Culhane JC, et al. Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis. Nat Chem Biol. 2011 Mar; 8(3): 262-9.
  • Zachara NE, Vosseller K, Hart GW. Detection and analysis of proteins modified by O-linked N-acetylglucosamine. Curr Protoc Protein Sci. 2011 Nov; Chapter 12: Unit12 8.
  • Akimoto Y, Fuwa TJ, Ichimiya T, Ueyama M, Matsuda M, Ueda R, et al. O-GlcNAcylation accelerates transcription in the interband region of chromosomes. 2012; Submitted.
  • Murray CI, Kane LA, Uhrigshardt H, Wang SB, Van Eyk JE. Site-Mapping of In Vitro S-nitrosation in Cardiac Mitochondria: Implications for Cardioprotection. Mol Cell Proteomics. 2011 Mar; 10(3): M110 004721.
  • Hersman E, Nelson DM, Griffith WP, Jelinke C, Cotter RJ. Analysis of Histone Modifications from Tryptic Peptides of Deuteroacetylated Isoforms. Int J Mass Spectrom. 2012; 47: 644-54.
  • Osula O, Swatkoski S, Cotter RJ. Identification of protein SUMOylation sites by mass spectrometry using combined microwave-assisted aspartic acid cleavage and tryptic digestion. J Mass Spectrom. 2012 May; 47(5): 644-54.
  • Gundry RL, Riordon DR, Tarasova Y, Chuppa S, Bhattacharya S, Juhasz O, et al. A Cell Surfaceome Map for Immunophenotyping and Sorting Pluripotent Stem Cells. Mol Cell Proteomics. 2012 Apr 6.
  • Stastna M, Van Eyk JE. Investigating the secretome: lessons about the cells that comprise the heart. Circ Cardiovasc Genet. 2012 Feb 1; 5(1): o8-o18.
  • Stastna M, Van Eyk JE. Secreted proteins as a fundamental source for biomarker discovery. Proteomics. 2012 Feb; 12(4-5): 722-35.
  • Li Y, De Marzo AM, Bova GS, Chan DW, Zhang H. Identification of glycosylation on specific glycosites using lectin and chemical immobilizations and mass spectrometry. 2012; Submitted.
  • Yang SJ, Zhang H. Glycan analysis by reversible reaction to hydrazide beads and mass spectrometry. Anal Chem. 2012 Mar 6; 84(5): 2232-8.
  • Zhang M, Takimoto E, Lee D, Santos CXC, Nakamura T, Hsu S, et al. Pathological Cardiac Hypertrophy Alters Intracellular Targeting of PDE5 from Nitric Oxide Synthase-3 to Natriuretic Peptide Signaling  Circ Res. 2012; In press.
  • Foster DB, Liu T, Rucker J, O'Meally R, Hitt L, Cole RN, et al. The cardiac acetyl-lysine proteome. In Preparation. 2012.
  • Giles JT, Fert-Bober J, Park JK, Bingham CO, 3rd, Andrade F, Fox-Talbot K, et al. Myocardial citrullination in rheumatoid arthritis: a correlative histopathologic study. Arthritis Res Ther. 2012 Feb 24; 14(1): R39.
  • Husberg C, Agnetti G, Holewinski RJ, Christensen G, Van Eyk JE. Dephosphorylation of cardiac proteins in vitro - a matter of phosphatase specificity. Proteomics. 2012 Apr; 12(7): 973-8.
  • Van Eyk JE. Maximizing the utility of proteomics: an educational series. Circ Cardiovasc Genet. 2011 Oct; 4(5): 574.
  • Aon MA, Stanley BA, Sivakumaran V, Kembro JM, O'Rourke B, Paolocci N, et al. Glutathione/thioredoxin systems modulate mitochondrial H2O2 emission: An experimental-computational study. J Gen Physiol. 2012 Jun; 139(6): 479-91.
  • Cortassa S, Aon MA, O'Rourke B, Winslow RL. Metabolic control analysis applied to mitochondrial networks. Conf Proc IEEE Eng Med Biol Soc. 2011; 2011: 4673-6.
  • Wei AC, Aon MA, O'Rourke B, Winslow RL, Cortassa S. Mitochondrial energetics, pH regulation, and ion dynamics: a computational-experimental approach. Biophys J. 2011 Jun 22; 100(12): 2894-903.
  • Wei AC, Liu T, Winslow RL, O'Rourke B. Dynamics of matrix-free Ca2+ in cardiac mitochondria: two components of Ca2+ uptake and role of phosphate buffering. J Gen Physiol. 2012 Jun; 139(6): 465-78.
  • Winslow RL, Cortassa S, O'Rourke B, Hashambhoy YL, Rice JJ, Greenstein JL. Integrative modeling of the cardiac ventricular myocyte. Wiley Interdiscip Rev Syst Biol Med. 2011 Jul-Aug; 3(4): 392-413.
  • Zhou L, O'Rourke B. Cardiac mitochondrial network excitability: insights from computational analysis. Am J Physiol Heart Circ Physiol. 2012 Jun; 302(11): H2178-89.
  • Parish LA, Colquhoun DR, Ubaida Mohien C, Lyashkov AE, Graham DR, Dinglasan RR. Ookinete-interacting proteins on the microvillar surface are partitioned into detergent resistant membranes of Anopheles gambiae midguts. J Proteome Res. 2011 Nov 4; 10(11): 5150-62.
  • Ubaida Mohien C, Colquhoun DR, Mathias DK, Gibbons JG, Armistead JS, del Carmen-Rodriguez M, et al. Comparative Proteomic Analyses of Model and Non-sequenced Anopheline Vectors of Human Malaria Parasites Using a Bioinformatics Platform to Integrate Transcriptomics and Proteomics Data. Submitted. 2012.
  • Baycin D, Tabb DL, Chaerkady R, Chen L, Lewis N, Nagarajan H, et al. Proteomic and Glycoproteomic Analysis of Chinese Hamster Ovary Cells. Submitted. 2012.
  • Kadam SD, Gucek M, Cole RN, Watkins PA, Comi AM. Cell proliferation and oxidative stress pathways are modified in fibroblasts from Sturge-Weber syndrome patients. Arch Dermatol Res. 2012 Apr; 304(3): 229-35.
  • Ratovitski T, Chighladze E, Arbez N, Boronina T, Herbrich S, Cole RN, et al. Huntingtin protein interactions altered by polyglutamine expansion as determined by quantitative proteomic analysis. Cell Cycle. 2012 May 15; 11(10): 2006-21.
  • Ruczinski I, Cole RN, Schulze K, Christian P, Herbrich S, Wu L, et al. Mining the Plasma Proteome to Assess Micronutrient Status in Undernourished Nepalese Children. Submitted. 2012.
  • Scholl PF, Cole RN, Ruczinski I, Gucek M, Diez R, Rennie A, et al. Maternal serum proteome changes between the first and third trimester of pregnancy in rural southern Nepal. Placenta. 2012 May; 33(5): 424-32.
  • Zhong J, Kim MS, Chaerkady R, Wu X, Huang TC, Getnet D, et al. TSLP Signaling Network Revealed by SILAC-Based Phosphoproteomics. Mol Cell Proteomics. 2012 Jun; 11(6): M112 017764.
  • Houser SR, Margulies KB, Murphy AM, Spinale FG, Francis GS, Prabhu SD, et al. Animal Models of Heart Failure: A Scientific Statement From the American Heart Association. Circ Res. 2012 May 17.
  • Agnetti G, Husberg C, Van Eyk JE. Divide and conquer: the application of organelle proteomics to heart failure. Circ Res. 2011 Feb 18; 108(4): 512-26.
  • Ashley EA, Hershberger RE, Caleshu C, Ellinor PT, Garcia JG, Herrington DM, et al. Genetics and Cardiovascular Disease: A Policy Statement From the American Heart Association. Circulation. 2012 May 29.
  • Cammarato A, Ahrens CH, Alayari NN, Qeli E, Rucker J, Reedy MC, et al. A mighty small heart: the cardiac proteome of adult Drosophila melanogaster. PLoS One. 2011; 6(4): e18497.
  • Chakir K, Depry C, Dimaano VL, Zhu WZ, Vanderheyden M, Bartunek J, et al. Gαs-Biased β2-Adrenergic Signaling from Restoring Synchronous Contraction in the Failing Heart. Science Translational Medicine. 2011; 3(100): 100ra88.
  • Chakir K, Kass DA. Rethinking Resynch: Exploring Mechanisms of Cardiac Resynchroniztion Beyond Wall Motion Control. Drug Discov Today Dis Mech. 2010 Summer; 7(2): e103-e7.
  • Chakir K, Zhu W, Tsang S, Woo AY, Yang D, Wang X, et al. RGS2 is a primary terminator of beta(2)-adrenergic receptor-mediated G(i) signaling. J Mol Cell Cardiol. 2011 Feb 1.
  • Chen H, Pimienta G, Gu Y, Sun X, Hu J, Kim MS, et al. Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 2010 Nov; 10(21): 3800-10.
  • Ellenbogen KA, Gold MR, Meyer TE, Fernndez Lozano I, Mittal S, Waggoner AD, et al. Primary results from the SmartDelay determined AV optimization: a comparison to other AV delay methods used in cardiac resynchronization therapy (SMART-AV) trial: a randomized trial comparing empirical, echocardiography-guided, and algorithmic atrioventricular delay programming in cardiac resynchronization therapy. Circulation. 2010 Dec 21; 122(25): 2660-8.
  • Frazier AH, Ramirez-Correa GA, Murphy AM. Molecular mechanisms of sarcomere dysfunction in dilated and hypertrophic cardiomyopathy. Prog Pediatr Cardiol. 2011 Jan 1; 31(1): 29-33.
  • Goel R, Muthusamy B, Pandey A, Prasad TS. Human Protein Reference Database and Human Proteinpedia as Discovery Resources for Molecular Biotechnology. Mol Biotechnol. 2010 Oct 7.
  • Harsha HC, Pandey A. Phosphoproteomics in cancer. Mol Oncol. 2010 Dec; 4(6): 482-95.
  • Hart GW, Copeland RJ. Glycomics hits the big time. Cell. 2010 Nov 24; 143(5): 672-6.
  • Hart GW, Slawson C, Ramirez-Correa G, Lagerlof O. Crosstalk Between O-GlcNAcylation and Phosphorylation:  Roles in Signaling, Transcription and Chronic Disease. Ann Rev Biochem. 2011; 80: 825-58.
  • Hu P, Shimoji S, Hart GW. Site-specific interplay between O-GlcNAcylation and phosphorylation in cellular regulation. FEBS Lett. 2010 Jun 18; 584(12): 2526-38.
  • Hubbi ME, Luo W, Baek JH, Semenza GL. MCM proteins are negative regulators of hypoxia-inducible factor 1. Mol Cell. 2011 Jun 10; 42(5): 700-12.
  • Jokela TA, Makkonen KM, Oikari S, Karna R, Koli E, Hart GW, et al. Cellular content of UDP-N-Acetylhexosamines controls hyaluronan synthase 2 expression and correlates with O-GlcNAc modification of transcription factors YY1 and SP1. J Biol Chem. 2011 Jul 27.
  • 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.
  • Lam MP, Vivanco F, Scholten A, Hermjakob H, Van Eyk J, Ping P. HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease. Proteomics. 2012 Mar; 12(6): 749-51.
  • Lin Y, Fu Q, Zhu J, Miller JM, Van Eyk JE. Development of a qualitative sequential immunoassay for characterizing the intrinsic properties of circulating cardiac troponin I. Clin Chem. 2010 Aug; 56(8): 1307-19.
  • Luo W, Hu H, Chang R, Zhong J, Knabel M, O'Meally R, et al. Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1. Cell. 2011 May 27; 145(5): 732-44.
  • Luo W, Semenza GL. Pyruvate kinase M2 regulates glucose metabolism by functioning as a coactivator for hypoxia-inducible factor 1 in cancer cells. Oncotarget. 2011 Jul; 2(7): 551-6.
  • O'Rourke B, Van Eyk JE, Foster DB. Mitochondrial protein phosphorylation as a regulatory modality: implications for mitochondrial dysfunction in heart failure. Congest Heart Fail. 2012 Nov-Dec; 17(6): 269-82.
  • Patterson SD, Van Eyk JE, Banks RE. Report from the Wellcome Trust/EBA "Perspectives in Clinical Proteomics" retreat--a strategy to implement next-generation proteomic analyses to the clinic for patient benefit: pathway to translation. Proteomics Clin Appl. 2010 Dec; 4(12): 883-7.
  • Ramirez-Correa GA, Cortassa S, Stanley B, Gao WD, Murphy AM. Calcium sensitivity, force frequency relationship and cardiac troponin I: critical role of PKA and PKC phosphorylation sites. J Mol Cell Cardiol. 2010 May; 48(5): 943-53.
  • Rotty JD, Hart GW, Coulombe PA. Stressing the role of O-GlcNAc: linking cell survival to keratin modification. Nat Cell Biol. 2010 Sep; 12(9): 847-9.
  • Sakabe K, Hart GW. O-GlcNAc transferase regulates mitotic chromatin dynamics. J Biol Chem. 2010 Nov 5; 285(45): 34460-8.
  • Sakabe K, Hart GW. Sweet-talking the Histone Code: O-GlcNAcylation of Histones. Cell Cycle In Press. 2011.
  • Sakabe K, Wang Z, Hart GW. Beta-N-acetylglucosamine (O-GlcNAc) is part of the histone code. Proc Natl Acad Sci U S A. 2010 Nov 16; 107(46): 19915-20.
  • Semenza GL. Oxygen sensing, homeostasis, and disease. N Engl J Med. 2011 Aug 11; 365(6): 537-47.
  • Sheng S, Skalnikova H, Meng A, Tra J, Fu Q, Everett A, et al. Intact protein separation by one- and two-dimensional liquid chromatography for the comparative proteomic separation of partitioned serum or plasma. Methods Mol Biol. 2011; 728: 29-46.
  • Slawson C, Copeland RJ, Hart GW. O-GlcNAc signaling: a metabolic link between diabetes and cancer? Trends Biochem Sci. 2010 Oct; 35(10): 547-55.
  • Stanley BA, Graham DR, James J, Mitsak M, Tarwater PM, Robbins J, et al. Altered myofilament stoichiometry in response to heart failure in a cardioprotective alpha-myosin heavy chain transgenic rabbit model. Proteomics Clin Appl. 2011 Feb 16.
  • Stastna M, Chimenti I, Marban E, Van Eyk JE. Identification and functionality of proteomes secreted by rat cardiac stem cells and neonatal cardiomyocytes. Proteomics. 2010 Jan; 10(2): 245-53.
  • Tocchetti CG, Stanley BA, Murray CI, Sivakumaran V, Donzelli S, Mancardi D, et al. Playing with Cardiac "Redox Switches": The "HNO Way" to Modulate Cardiac Function. Antioxid Redox Signal. 2011 Mar 3.
  • Van Eyk JE. Overview: the maturing of proteomics in cardiovascular research. Circ Res. 2011 Feb 18; 108(4): 490-8.
  • Wang J, Torii M, Liu H, Hart GW, Hu Z-Z. dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation  Biomed Central Bioinformatics In press. 2011; 12: 91.
  • Wang SB, Foster DB, Rucker J, O'Rourke B, Kass DA, Van Eyk JE. Redox Regulation of Mitochondrial ATP Synthase: Implications for Cardiac Resynchronization Therapy. Circ Res. 2011 Aug 4.
  • Wells L, Slawson C, Hart GW. The E2F-1 associated retinoblastoma-susceptibility gene product is modified by O-GlcNAc. Amino Acids. 2011 Mar; 40(3): 877-83.
  • White MY, Brown DA, Sheng S, Cole RN, O'Rourke B, Van Eyk JE. Parallel Proteomics to Improve Coverage and Confidence in the Partially Annotated Oryctolagus cuniculus Mitochondrial Proteome. Mol Cell Proteomics. 2011 Feb; 10(2): M110 004291.
  • Yang Y, Chaerkady R, Kandasamy K, Huang TC, Selvan LD, Dwivedi SB, et al. Identifying targets of miR-143 using a SILAC-based proteomic approach. Mol Biosyst. 2010 Oct 1; 6(10): 1873-82.
  • Yu H, Mashtalir N, Daou S, Hammond-Martel I, Ross J, Sui G, et al. The ubiquitin carboxyl hydrolase BAP1 forms a ternary complex with YY1 and HCF-1 and is a critical regulator of gene expression. Mol Cell Biol. 2010 Nov; 30(21): 5071-85.
  • 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.
  • Zachara NE, Vosseller K, Hart GW. Detection and analysis of proteins modified by O-linked N-acetylglucosamine. Curr Protoc Mol Biol. 2011 Jul; Chapter 17: Unit 17 6.
  • Zeidan Q, Hart GW. The intersections between O-GlcNAcylation and phosphorylation: implications for multiple signaling pathways. J Cell Sci. 2011 Jan 1; 123(Pt 1): 13-22.