Dr. Gerard Cagney | UCD Conway

Research

Dr Gerard Cagney Ph.D., B.Sc.

Books:

Gerard Cagney and Andrew Emili (2011) Network Biology (Methods in Molecular Biology). New York London: Springer. [Details]

Peer Reviewed Journals:

Jäger S et al (2011) 'Global landscape of HIV-human protein complexes'. Nature, 481(7381):365-70 (481(7381):365-70):481(7381):365-70-481(7381):365-70. [Details]

Casey F, Krogan N, Shields DC, Cagney G (2011) 'Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs'. BMC systems biology, 5 . [DOI] [Details]

Ryan C, Greene D, Guenole A, van Attikum H, Krogan NJ, Cunningham P, Cagney G (2011) 'Improved functional overview of protein complexes using inferred epistatic relationships'. BMC systems biology, 5 (80).

[DOI] [Details]

Agbor TA, Cheong A, Comerford KM, Scholz CC, Bruning U, Clarke A, Cummins EP, Cagney G, Taylor CT (2010) 'Small ubiquitin-related modifier (SUMO)-1 protein modification promotes glycolysis in Hypoxia'. Journal of Biological Chemistry, . [DOI] [Details]

Ryan C, Greene D, Cagney G, Cunningham P (2010) 'Missing value imputation for epistatic MAPs'. BMC Bioinformatics, 11 . [DOI] [Details]

Walker E, Chang WY, Hunkapiller J, Cagney G, Garcha K, Torchia J, Krogan NJ, Reiter JF, Stanford WL (2010) 'Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation'. Cell, 6 (2):153-166. [DOI] [Details]

Beltrao P, Cagney G, Krogan NJ (2010) 'Quantitative genetic interactions reveal biological modularity'. Cell, 141 (5):739-745. [DOI] [Details]
Zheng J, Benschop JJ, Shales M, Kemmeren P, Greenblatt J, Cagney G, Holstege F, Li H, Krogan NJ (2010) 'Epistatic relationships reveal the functional organization of yeast transcription factors'. Molecular systems biology, 6 . [DOI] [Details]
Ryan, C,Greene, D,Cagney, G,Cunningham, P (2010) 'Missing value imputation for epistatic MAPs'. BMC Bioinformatics, 11 . [DOI] [Details]
O'Connor, R,Cryan, LM,Wynne, K,de Stefani, A,Fitzgerald, D,O'Brien, C,Cagney, G (2010) 'Proteomics Strategy for Identifying Candidate Bioactive Proteins in Complex Mixtures: Application to the Platelet Releasate'. Journal Of Biomedicine And Biotechnology, . [DOI] [Details]
Lenassi, M,Cagney, G,Liao, MF,Vaupotic, T,Bartholomeeusen, K,Cheng, YF,Krogan, NJ,Plemenitas, A,Peterlin, BM (2010) 'HIV Nef is Secreted in Exosomes and Triggers Apoptosis in Bystander CD4(+) T Cells'. Traffic, 11 :110-122. [DOI] [Details]
Cagney G, (2009) 'Interaction networks: Lessons from large-scale studies in yeast'. Proteomics, 9 (20):4799-4811. [DOI] [Details]
O'Connor KE, Nikodinovic-Runic J, Flanagan M, Hume AR, Cagney G, (2009) 'Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions'. Microbiology (Reading, England), 155 (Pt 10):3348-3361. [DOI] [Details]
Cagney G, Wong JW, McRedmond JP, (2009) 'Activity profiling of platelets by chemical proteomics'. Proteomics, 9 (1):40-50. [DOI] [Details]
Fiedler, D,Braberg, H,Mehta, M,Chechik, G,Cagney, G,Mukherjee, P,Silva, AC,Shales, M,Collins, SR,van Wageningen, S,Kemmeren, P,Holstege, FCP,Weissman, JS,Keogh, MC,Koller, D,Shokat, KM,Krogan, NJ (2009) 'Functional Organization of the S-cerevisiae Phosphorylation Network'. Cell, 136 :952-963. [DOI] [Details]
Behan, A. T.,Byrne, C.,Dunn, M. J.,Cagney, G.,Cotter, D. R. (2009) 'Proteomic analysis of membrane microdomain-associated proteins in the dorsolateral prefrontal cortex in schizophrenia and bipolar disorder reveals alterations in LAMP, STXBP1 and BASP1 protein expression'. Mol Psychiatry, 14 (6):601-13. [Details]
Wong, JWH,McRedmond, JP,Cagney, G (2009) 'Activity profiling of platelets by chemical proteomics'. Proteomics, 9 :40-50. [DOI] [Details]
O'Connor KE, Nikodinovic-Runic J, Flanagan M, Hume AR, Cagney G, (2009) 'Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions'. Microbiology (Reading, England), 155 (Pt 10):3348-3361. [DOI] [Details]
Cotter DR, Behan A, Byrne C, Dunn MJ, Cagney G, (2008) 'Proteomic analysis of membrane microdomain-associated proteins in the dorsolateral prefrontal cortex in schizophrenia and bipolar disorder reveals alterations in LAMP, STXBP1 and BASP1 protein expression'. Molecular psychiatry, (NA). [DOI] [Details]
O'Riordan, A,Johnston, O,McMorrow, T,Wynne, K,Maguire, P,Hegarty, JE,McCormick, A,Watson, AJ,Cagney, G,Gallagher, WM,Ryan, MR (2008) 'Identification of Apolipoprotein AI as a serum biomarker of chronic kidney disease in liver transplant recipients, using proteomic techniques'. Proteomics, 2 :1338-1348. [DOI] [Details]
Cagney, G., Krogan, N., Weissman, J., Emili, A., Greenblatt, J., (2007) 'Insight into cell biology from physical and genetic protein interactions'. Molecular & Cellular Proteomics, 6 (8):19-19. [Details]
Cedervall, T.,Lynch, I.,Foy, M.,Berggard, T.,Donnelly, S. C.,Cagney, G.,Linse, S.,Dawson, K. A. (2007) 'Detailed identification of plasma proteins adsorbed on copolymer nanoparticles'. Angew Chem Int Ed Engl, 46 (30):5754-6. [Details]
Cagney, G., Alvaro, D., Reid, R.J., Thorpe, P.H., Rothstein, R., Krogan, N.J. (2005) 'Functional genomics of the yeast DNA-damage response'. Genome Biology, 7 (9). [Details]
Fitzgerald DJ, Maguire PB, Moran N, Cagney G, (2004) 'Application of proteomics to the study of platelet regulatory mechanisms'. Trends in Cardiovascular Medicine, 14 (6):207-220. [DOI] [Details]
Wong, J. W. H., Sullivan, M. J., Cagney, G., (2008) 'Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments'. Briefings in bioinformatics, 9 (2):156-165. [Details]
O'Riordan A, Johnston O, McMorrow T, Wynne K, Maguire P, Hegarty JE, McCormick A, Watson AJ, Cagney G, Gallagher WM, Ryan MR (2008) 'Identification of Apolipoprotein AI as a serum biomarker of chronic kidney disease in liver transplant recipients, using proteomic techniques'. Proteomics Clinical Applications, 2 (9):1338-1348. [Details]
Mathivanan, S.,Ahmed, M.,Ahn, N. G.,Alexandre, H.,Amanchy, R.,Andrews, P. C.,Bader, J. S.,Balgley, B. M.,Bantscheff, M.,Bennett, K. L.,Bjorling, E.,Blagoev, B.,Bose, R.,Brahmachari, S. K.,Burlingame, A. S.,Bustelo, X. R.,Cagney, G.,Cantin, G. T.,Cardasis, H. L.,Celis, J. E.,Chaerkady, R.,Chu, F.,Cole, P. A.,Costello, C. E.,Cotter, R. J.,Crockett, D.,DeLany, J. P.,De Marzo, A. M.,DeSouza, L. V.,Deutsch, E. W.,Dransfield, E.,Drewes, G.,Droit, A.,Dunn, M. J.,Elenitoba-Johnson, K.,Ewing, R. M.,Van Eyk, J.,Faca, V.,Falkner, J.,Fang, X.,Fenselau, C.,Figeys, D.,Gagne, P.,Gelfi, C.,Gevaert, K.,Gimble, J. M.,Gnad, F.,Goel, R.,Gromov, P.,Hanash, S. M.,Hancock, W. S.,Harsha, H. C.,Hart, G.,Hays, F.,He, F.,Hebbar, P.,Helsens, K.,Hermeking, H.,Hide, W.,Hjerno, K.,Hochstrasser, D. F.,Hofmann, O. (2008) 'Human Proteinpedia enables sharing of human protein data'. Nat Biotechnol, 26 (2):164-7. [Details]
Casey, FP,Cagney, G,Krogan, NJ,Shields, DC (2008) 'Optimal stepwise experimental design for pairwise functional interaction studies'. Bioinformatics, 24 :2733-2739. [DOI] [Details]
Wilmes, GM,Bergkessel, M,Bandyopadhyay, S,Shales, M,Braberg, H,Cagney, G,Collins, SR,Whitworth, GB,Kress, TL,Weissman, JS,Ideker, T,Guthrie, C,Krogan, NJ (2008) 'A Genetic Interaction Map of RNA-Processing Factors Reveals Links between Sem1/Dss1-Containing Complexes and mRNA Export and Splicing'. Cell, 32 :735-746. [DOI] [Details]
Cunningham P, Greene D, Cagney G, Krogan N, (2008) 'Ensemble Non-negative Matrix Factorization Methods for Clustering Protein-Protein Interactions'. Bioinformatics, . [DOI] [Details]
Pandey A et al. (2008) 'Human Proteinpedia enables sharing of human protein data'. Nature biotechnology, 2 (NA):164-167. [DOI] [Details]
Cagney, G., McRedmond, J., (2008) 'A central resource for platelet proteomics'. Arteriosclerosis Thrombosis and Vascular Biology, 28 (7):1214-1215. [Details]
Shields DC, Casey FP, Cagney G, Krogan NJ, (2008) 'Optimal stepwise experimental design for pairwise functional interaction studies'. Bioinformatics, (NA). [DOI] [Details]
Maderna P, Scannell M, Flanagan MB, deStefani A, Wynne KJ, Cagney G, Godson C, (2007) 'Annexin-1 and peptide derivatives are released by apoptotic cells and stimulate phagocytosis of apoptotic neutrophils by macrophages'. Immunology, 178 (7):4595-4605. [Details]
Wong, JWH, Sullivan, MJ, Cartwright, HM, Cagney, G, (2007) 'msmsEval: tandem mass spectral quality assignment for high-throughput proteomics'. BMC Bioinformatics, 8 . [Details]
Krogan NJ, Cagney G, Alvaro D, Reid RJ, Thorpe PH, Rothstein R, (2006) 'Functional genomics of the yeast DNA-damage response'. Genome Biology, 7 (9). [DOI] [Details]
Coppinger, JA, OConnor, R, Wynne, K, Flanagan, M, Sullivan, M, Maguire, PB, Fitzgerald, DJ, Cagney, G, (2007) 'Moderation of the platelet releasate response by aspirin'. Blood, 109 :4786-4792. [Details]
Wong, JWH,Cagney, G,Cartwright, HM (2005) 'SpecAlign - processing and alignment of mass spectra datasets'. Bioinformatics, 21 :2088-2090. [DOI] [Details]
Coppinger JA, Cagney G, Toomey S, Kislinger T, Belton O, McRedmond JP, Cahill DJ, Emili A, Fitzgerald DJ, McGuire PB. (2004) 'Characterisation of the proteins released from activated platelets leads to localization of novel platelet proteins in human atherosclerotic lesions'. Blood, 103 (6):2096-2104. [Details]
Lambkin, I., Cagney, G., Kinsella, BT. & O'Mahony, DJ. (1997) 'Identification of peptide mimetics from phage display libraries which bind to recombinant forms of the human thromboxane A2 receptor'. Journal of Controlled Release, 46 (1-2):190-191. [Details]
Krogan, NJ; Cagney, G; Yu, HY; Zhong, GQ; Guo, XH; Ignatchenko, A; Li, J; Pu, SY; Datta, N; Tikuisis, AP; Punna, T; Peregrin-Alvarez, JM; Shales, M; Zhang, X; Davey, M; Robinson, MD; Paccanaro, A; Bray, JE; Sheung, A; Beattie, B; Richards, DP; Canadien, V; Lalev, A; Mena, F; Wong, P; Starostine, A; Canete, MM; Vlasblom, J; Wu, S; Orsi, C; Collins, SR; Chandran, S; Haw, R; Rilstone, JJ; Gandi, K; Thompson, NJ; Musso, G; St Onge, P; Ghanny, S; Lam, MHY; Butland, G; Altaf-Ui, AM; Kanaya, S; Shilatifard, A; O'Shea, E; Weissman, JS; Ingles, CJ; Hughes, TR; Parkinson, J; Gerstein, M; Wodak, SJ; Emili, A; Greenblatt, JF; (2006) 'Global landscape of protein complexes in the yeast Saccharomyces cerevisiae'. NATURE, 440 (7084):637-643. [Details]
Cagney, G., Park, S., Chung, C., Tong, B., O'Dushlaine, C., Shields, D.C., Emili, A. (2005) 'Human Tissue Profiling with Multidimensional Protein Identification Technology'. J. Proteome Research, . [Details]
Measday V, Hailey DW, Pot I, Givan SA, Hyland KM, Cagney G, Fields S, Davis TN, Hieter P (2002) 'Ctf3p, the Mis6 budding yeast homolog, interacts with Mcm22p and Mcm16p at the yeast outer kinetochore'. Gene, 16 (1):101-113. [DOI] [Details]
Cagney G, Amiri S, Premawaradena T, Lindo M, Emili A (2003) 'In silico proteome analysis to facilitate proteomics experiments using mass spectrometry'. Proteome science, 1 (1). [DOI] [Details]
Cagney G, Emili A (2002) 'De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging'. Nature biotechnology, 20 (2):163-170. [DOI] [Details]
Cagney G, Uetz P, Fields S (2001) 'Two-hybrid analysis of the Saccharomyces cerevisiae 26S proteasome'. Genomics, 7 (1):27-34. [Details]
Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM (2000) 'A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae'. Nature, 403 (6770):623-627. [DOI] [Details]
Emili AQ, Cagney G (2000) 'Large-scale functional analysis using peptide or protein arrays'. Nature biotechnology, 18 (4):393-397. [DOI] [Details]
Ghavidel, A; Cagney, G; Emili, A; (2005) 'A skeleton of the human protein interactome'. Cell, 122 (6):830-832. [Details]
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Editorial

Ghavidel, A,Cagney, G,Emili, A (2005) A skeleton of the human protein interactome. Editorial [Details]