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Denis Shields

Professor of Clinical Bioinformatics

School Of Medicine & Medical Science
Conway Institute
Belfield
Dublin 4

Tel: +353 1 7166735
Email: denis.shields@ucd.ie

Biography

Oct 2005 - present      Professor of Clinical Bioinformatics, University College Dublin
2002-2005                   Senior Lecturer Clinical Pharmacology, RCSI
1998-2005                   Managing Director, Surgen Ltd. (pharmacogenomics), RCSI, Dublin.
1998-2001                   Lecturer in Clinical Pharmacology, RCSI
1994-1998                   Wellcome Bioinformatics Fellow, Genetics, Trinity College Dublin
1993-1994                   Biometrics Manager, Icon Clinical Research, Dublin.
1990-1992                   Research Fellow in Genetic Epidemiology, Univ of Southampton UK.
1989                            PhD Genetics, Trinity college Dublin
1986-1989                   Research Assistant, Irish National Centre for Bioinformatics, TCD
1985                            B.A (Mod), Natural Sciences, Trinity College, University of Dublin

Teaching interests: 

Developing new structured interdisciplinary research training opportunities to help researchers maximise their mastery of both computational and experimental approaches to biology.  

Research Interests:

Using computational methods to identify short peptide modulators of protein interactions alone or in combination, targeting cardiovascular disease (platelet function) and cancer.  

Analysing peptide combinations and gene combinations, to understand better how biological factors synergise, and to try and make use of that in furthering understanding of biological and disease processes, and how to target them.  


 


 
 

Professional

         

Conference Contributions

Pushker Ravindra and Shields Denis; (2009) Intrinsically disordered proteins in viral genomes. [Poster Presentation], 17th Annual International Conference on ISMB & 8th ECCB, Stockholm, Sweden , 27-JUN-09 - 02-JUL-09.
Denis Shields; (2009) Computational challenges in screens to discover novel bioactive peptides and peptidomimetics. [Invited Oral Presentation], Pepducin Symposium, Harvard, Boston MA, USA , 25-MAR-09 - 27-MAR-09.
Denis Shields; (2008) Bioinformatic discovery of novel bioactive peptides. [Invited Oral Presentation], Synthetic Biology, Synthetic Biology, Cambridge, UK , 05-MAR-08 - 07-MAR-08.
Shields, D.; (2006) 'Discovery of bioactive peptides in platelet proteins' EMBL Heidelberg. [Invited Lecture], 'Discovery of bioactive peptides in platelet proteins' EMBL Heidelberg, Heidelberg , 17-OCT-06.
Shields, D.; 'Ancestral reconstruction and the evolution of specificity and diversity' Ancestral Sequence Reconstruction Meeting, Mar 2005, Kristineberg, Sweden. [Invited Lecture], 'Ancestral reconstruction and the evolution of specificity and diversity' Ancestral Sequence Reconstruction Meeting, Kristineberg, Sweden .
Shields, D.; Platelet Pharmacogenomics. Italian Cardiologists Meeting, Dublin, Nov 2003. [Invited Lecture], Platelet Pharmacogenomics. Italian Cardiologists Meeting, Dublin .
Shields, D.; European Science Foundation Workshop, University of Ulster, November 2003 'Bioinformatics for the identification of drug targets.'. [Invited Lecture], European Science Foundation Workshop, University of Ulster, November 2003 'Bioinformatics for the identification of drug targets.', University of Ulster .
Shields, D.; (2003) Irish Association of Pharmacologists 14th Annual Meeting, 10th October 2003, 'Bioinformatic approaches to helping understand drug targets', Dublin. [Invited Lecture], Irish Association of Pharmacologists 14th Annual Meeting, 10th October 2003, 'Bioinformatic approaches to helping understand drug targets', Dublin, Dublin , 10-OCT-03.
Shields, D.; 'Bioinformatic design of transdominant peptides' SFI meeting, Killarney, 2003. [Invited Lecture], 'Bioinformatic design of transdominant peptides' SFI meeting, Killarney, 2003, Killarney .
Shields, D.; (2002) Irish Medicines Board, Dublin. 'Pharmacogenomics.' 2nd October 2002. [Invited Lecture], Irish Medicines Board, Dublin. 'Pharmacogenomics.', Dublin , 02-OCT-02.
Shields, D.; (2002) Pharmacogenomics meeting, Association of Clinical Biochemists, Cambridge, UK, 26-27th September 2002. 'Cardiovascular pharmacogenomics'. [Invited Lecture], Pharmacogenomics meeting, Association of Clinical Biochemists, Cambridge, UK, 26-27th September 2002. 'Cardiovascular pharmacogenomics', Cambridge UK , 26-SEP-02 - 27-SEP-02.
Shields, D.; Bioinformatics 2002 meeting, Bergen, Norway (March 2002). 'Evolution of protein function'. [Invited Lecture], Bioinformatics 2002 meeting, Bergen, Norway (March 2002). 'Evolution of protein function', Bergen, Norway .
Shields, D.; ESF Workshop: Data Integration in Functional Genomics and Proteomics, Geneva, October 2001. 'Integrating genotyping data with proteomics and expression data'. [Invited Lecture], ESF Workshop: Data Integration in Functional Genomics and Proteomics, Geneva, October 2001. 'Integrating genotyping data with proteomics and expression data', Geneva .
Shields, D.; (2001) XVIIIth Congress of the International Society of Thrombosis and Hemostasis, Paris, 'Genetics of Recurrent Acute Coronary Syndromes', 8 July 2001. [Invited Lecture], XVIIIth Congress of the International Society of Thrombosis and Hemostasis, Paris, 'Genetics of Recurrent Acute Coronary Syndromes', 8 July 2001, Paris , 08-JUL-01.
Shields, D.; European Cardiology Society Working Group on Thrombosis and Platelets, Lisbon, Portugal, Pharmacogenomics of the GPIIb/IIIa antagonists. (December 2000). [Invited Lecture], European Cardiology Society Working Group on Thrombosis and Platelets, Lisbon, Portugal, Pharmacogenomics of the GPIIb/IIIa antagonists, Lisbon, Portugal .
Shields, D.; (2006) 'Identification of diverse sets of bioactive oligopeptides from human proteins' Richard Edwards et al, poster Cold Spring Harbor Laboratory/Wellcome Trust Conference 'Interactome Networks' Hinxton. [Poster Presentation], 'Identification of diverse sets of bioactive oligopeptides from human proteins' Richard Edwards et al, poster Cold Spring Harbor Laboratory/Wellcome Trust Conference 'Interactome Networks' Hinxton, * , 30-AUG-06 - 03-SEP-06.
Shields, D.; (2006) 'Diverse sets of bioactive peptides from human proteins' Denis Shields et al, 3rd EMBL Biennial Symposium: From Functional Genomics to Systems Biology, Heidelberg. [Poster Presentation], 'Diverse sets of bioactive peptides from human proteins' Denis Shields et al, 3rd EMBL Biennial Symposium: From Functional Genomics to Systems Biology, Heidelberg, Heidelberg , 14-OCT-06 - 16-OCT-06.

Committees

Committee : ASCOT (18,000 patient cardiovascular outcome trial) genetics sub-study committee

Employment

Employer: University College Dublin
Position: Professor of Clinical Bioinformatics
Employer: RCSI
Position: Senior Lecturer Clinical Pharmacology
Employer: RCSI
Position: Lecturer in Clinical Pharmacology
Employer: Surgen Ltd. (pharmacogenomics), RCSI, Dublin
Position: Managing Director
Employer: Trinity College Dublin
Position: Wellcome Bioinformatics Fellow, Genetics
Employer: Icon Clinical Research, Dublin
Position: Biometrics Manager
Employer: University of Southampton, UK
Position: Research Fellow in Genetic Epidemiology
Employer: Research Assistant, Irish National Centre for Bioinformatics
Position: Trinity College Dublin

Education

Year 1989 Institution: Trinity College Dublin
Qualification: PhD Subject:
Year 1985 Institution: Trinity College Dublin
Qualification: BA (Mod) Subject:

Languages

Irish:
French:
 

Outreach Activities

I often am invited to visit schools to encourage an interest of students in science.
Contact denis.shields@ucd.ie for more information

 

   

Publications

 

Book Chapters

Shields, D.C., et al.; (2007) 'Evolution of Specificity and Diversity' In: Liberles, D.A (eds). Ancestral Sequence Reconstruction. Oxford: Oxford University Press. , pp.225-235 Available Online [Details]
Read A.F., P. Aaby, R. Antia, D. Ebert, P.W. Ewald, S. Gupta, E.C. Holmes, R. Moxon, A. Sasaki, D.C. Shields and F. Taddei ; (1999) 'What can evolutionary biology contribute to the understanding of virulence?' In: Stearns S.C (eds). Evolution in Health and Disease. Oxford: Oxford University Press. [Details]
Sharp, P.M., D.G. Higgins, D.C. Shields, and K.M. Devine; (1990) 'Protein-coding genes: DNA sequence database and codon usage' In: Harwood, C.R. & Cutting, S.M (eds). Molecular Biological Methods for Bacillus. *: John Wiley and Sons. , pp.557-569 [Details]
Sharp, P.M., D.G. Higgins, D.C. Shields, K.M. Devine, and J.A. Hoch; (1990) 'Bacillus subtilis gene sequences' In: Zukowski M.M., Ganesan, A.T. & Hoch, J.A (eds). Genetics and Biotechnology of Bacilli, Vol. III. San Diego: Academic Press. [Details]
 

Peer Reviewed Journals

Duffy, F.J. and O'Donovan, D. and Devocelle, M. and Moran, N. and O'Connell, D.J. and Shields, D.C. (2015) 'Virtual screening using combinatorial cyclic peptide libraries reveals protein interfaces readily targetable by cyclic peptides'. Journal of Chemical Information and Modeling, 55 (3):600-613. Available Online [DOI] [Details]
Johnson, T., Gaunt, T. R., Newhouse, S. J., Padmanabhan, S., Tomaszewski, M., Kumari, M., Morris, R. W., Tzoulaki, I., O'Brien, E. T., Poulter, N. R., Sever, P., Shields, D. C., Thom, S., Wannamethee, S. G., Whincup, P. H., Brown, M. J., Connell, J. M., Dobson, R. J., Howard, P. J., Mein, C. A., Onipinla, A., Shaw-Hawkins, S., Zhang, Y., Davey Smith, G., Day, I. N., Lawlor, D. A., Goodall, A. H., Fowkes, F. G., Abecasis, G. R., Elliott, P., Gateva, V., Braund, P. S., Burton, P. R., Nelson, C. P., Tobin, M. D., van der Harst, P., Glorioso, N., Neuvrith, H., Salvi, E., Staessen, J. A., Stucchi, A., Devos, N., Jeunemaitre, X., Plouin, P. F., Tichet, J., Juhanson, P., Org, E., Putku, M., Sober, S., Veldre, G., Viigimaa, M., Levinsson, A., Rosengren, A., Thelle, D. S., Hastie, C. E., Hedner, T (2011) 'Blood pressure loci identified with a gene-centric array'. American Journal of Human Genetics, 89 (6):688-700. Available Online [DOI] [Details]
Casey J, Magalhaes T, Conroy J, Regan R, Shah N, Anney R, Shields D, Abrahams BS, Almeida J, Bacchelli E, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bolton PF, Bourgeron T, Brennan A, Cali P, Correia A, Corsello A, Coutanche M, Dawson G, de Jonge M, Delorme R, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SA, Foley S, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Green J, Guter JT, Hakonarson H, Holt R, Hughes G, Hus A, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Lamb JA, Leboyer M, Le Couteur A, Leventhal BL, Lord C, Lund SC, Maestrini E, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Miller J, Minopoli F, Mirza GK, Munson J, Nelson SF, Nygren G, Oliveira G, Pagnamenta AT, Papanikolaou K, Parr JR, Parrini B, Pickles A, Pinto D, Piven J, Posey DJ, Poustka A, Poustka F, Ragoussis J, Roge B, Rutter ML, Sequeira AF, Soorya L, Sousa I, Sykes N, Stoppioni V, Tancredi R, Tauber M, Thompson AP, Thomson S, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Vorstman JAS, Wallace S, Wang K, Wassink TH, White K, Wing K, Wittemeyer K, Yaspan BL, Zwaigenbaum L, Betancur C, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Geschwind SH, Haines JL, Hallmayer J, Monaco AP, Nurnberger Jr. JI, Pericak-Vance MA, Schellenberg GD, Scherer SW, Sutcliffe JS, Szatmari P, Vieland V, Wijsman EM, Green A, Gill M, Gallagher L, Vicente A, Ennis S. (2012) 'A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder'. Human Genetics, 131 (4):565-579. Link to full text [Details]
Holton, T. A., Pollastri, G., Shields, D. C., Mooney, C. (2013) 'CPPpred: prediction of cell penetrating peptides'. Bioinformatics, . Available Online [Details]
Khan, W., Duffy, F., Pollastri, G., Shields, D. C., Mooney, C. (2013) 'Predicting binding within disordered protein regions to structurally characterised peptide-binding domains'. PLoS ONE, 8 (9). Available Online [DOI] [Details]
Ruhanen H, Hurley D, Ghosh A, O'Brien KT, Johnston CR, Shields DC (2014) 'Potential of known and short prokaryotic protein motifs as a basis for novel peptide-based antibacterial therapeutics: a computational survey'. Frontiers in Microbiology, 5 . [DOI] [Details]
Khaldi N, Vijayakumar V, Dallas DC, Guerrero A, Wickramasinghe S, Smilowitz JT, Medrano JF, Lebrilla CB, Shields DC, German JB (2014) 'Predicting the important enzymes in human breast milk digestion'. Journal of Agricultural and Food Chemistry, 62 (29):7225-7232. [DOI] [Details]
Nongonierma AB, Mooney C, Shields DC, FitzGerald RJ (2014) 'In silico approaches to predict the potential of milk protein-derived peptides as dipeptidyl peptidase IV (DPP-IV) inhibitors'. Peptides, 57 :43-51. [DOI] [Details]
Stavropoulos I, Golla K, Moran N, Martin F, Shields DC (journal name Bioarchitecture) (2014) 'Cadherin juxtamembrane region derived peptides inhibit TGFβ1 induced gene expression'. Bioarchitecture, 4 (3):103-110. [DOI] [Details]
Duffy FJ, Devocelle M, Croucher DR, Shields DC (2014) 'Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions'. BMC Bioinformatics, 15 . [DOI] [Details]
Postmus et al (2014) 'Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins'. Nature Communications, 5 . [DOI] [Details]
Therese Anne Holton , Vaishnavi Vijaykumar , David C. Dallas , Andrés Guerrero , Robyn C Borghese , Carlito B. Lebrilla , J. Bruce German , Daniela Barile , Mark A Underwood , Denis C Shields , and Nora Khaldi , Accepted DOI: 10.1021/pr5006907 (Web): Oct 23, 2014 (2014) 'Following the digestion of milk proteins from mother to baby'. Journal of Proteome Research, . [DOI] [Details]
Khaldi, N.*, Holton, T.A.*, Shields, D.C. (2014) 'Amino acid enrichment and compositional changes among mammalian milk proteins and the resulting nutritional consequences'. Journal of Dairy Science, . [Details]
Mooney, C., Cessieux, A., Shields, D. C., Pollastri, G. (2013) 'SCL-Epred: a generalised de novo eukaryotic protein subcellular localisation predictor'. Amino Acids, 45 (2):291-9. Available Online [DOI] [Details]
Mooney, C., Haslam, N. J., Holton, T. A., Pollastri, G., Shields, D. C. (2013) 'PeptideLocator: prediction of bioactive peptides in protein sequences'. Bioinformatics, 29 (9):1120-6. Available Online [DOI] [Details]
Nongonierma, A. B., Mooney, C., Shields, D. C., Fitzgerald, R. J. (2013) 'Inhibition of dipeptidyl peptidase IV and xanthine oxidase by amino acids and dipeptides'. Food Chemistry, 141 (1):644-53. Available Online [DOI] [Details]
O'Brien, K. T., Haslam, N. J., Shields, D. C. (2013) 'SLiMScape: a protein short linear motif analysis plugin for Cytoscape'. BMC Bioinformatics, 14 . Available Online [DOI] [Details]
Yadav, S., Cotlarciuc, I., Munroe, P. B., Khan, M. S., Nalls, M. A., Bevan, S., Cheng, Y. C., Chen, W. M., Malik, R., McCarthy, N. S., Holliday, E. G., Speed, D., Hasan, N., Pucek, M., Rinne, P. E., Sever, P., Stanton, A., Shields, D. C., Maguire, J. M., McEvoy, M., Scott, R. J., Ferrucci, L., Macleod, M. J., Attia, J., Markus, H. S., Sale, M. M., Worrall, B. B., Mitchell, B. D., Dichgans, M., Sudlow, C., Meschia, J. F., Rothwell, P. M., Caulfield, M., Sharma, P. (2013) 'Genome-wide analysis of blood pressure variability and ischemic stroke'. Stroke, 44 (10):2703-9. Available Online [DOI] [Details]
den Hoed, M., Eijgelsheim, M., Esko, T., Brundel, B. J., Peal, D. S., Evans, D. M., Nolte, I. M., Segre, A. V., Holm, H., Handsaker, R. E., Westra, H. J., Johnson, T., Isaacs, A., Yang, J., Lundby, A., Zhao, J. H., Kim, Y. J., Go, M. J., Almgren, P., Bochud, M., Boucher, G., Cornelis, M. C., Gudbjartsson, D., Hadley, D., van der Harst, P., Hayward, C., den Heijer, M., Igl, W., Jackson, A. U., Kutalik, Z., Luan, J., Kemp, J. P., Kristiansson, K., Ladenvall, C., Lorentzon, M., Montasser, M. E., Njajou, O. T., O'Reilly, P. F., Padmanabhan, S., St Pourcain, B., Rankinen, T., Salo, P., Tanaka, T., Timpson, N. J., Vitart, V., Waite, L., Wheeler, W., Zhang, W., Draisma, H. H., Feitosa, M. F., Kerr, K. F., Lind, P. A., Mihailov, E., Onland-Moret, N. C., Song, C., Weedon, M. N., Xie, W., Yengo, L. (2013) 'Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders'. Nature Genetics, 45 (6):621-31. Available Online [DOI] [Details]
Pushker, R,Mooney, C,Davey, NE,Jacque, JM,Shields, DC (2013) 'Marked Variability in the Extent of Protein Disorder within and between Viral Families'. PLoS ONE, 8 . [DOI] [Details]
O'Brien, R. P., Phelan, P. J., Conroy, J., O'Kelly, P., Green, A., Keogan, M., O'Neill, D., Jennings, S., Traynor, C., Casey, J., McCormack, M., Conroy, R., Chubb, A., Ennis, S., Shields, D. C., Cavalleri, G. L., Conlon, P. J. (2013) 'A genome-wide association study of recipient genotype and medium-term kidney allograft function'. Clinical Transplantation, 27 (3):379-87. Available Online [DOI] [Details]
Stavropoulos I, Khaldi N, Davey NE, O'Brien K, Martin F, Shields DC (2012) 'Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins'. PLoS ONE, 7 (9). [DOI] Link to full text [Details]
Vijayakumar, V,Guerrero, AN,Davey, N,Lebrilla, CB,Shields, DC,Khaldi, N (2012) 'EnzymePredictor: A Tool for Predicting and Visualizing Enzymatic Cleavages of Digested Proteins'. Journal of Proteome Research, 11 :6056-6065. [DOI] [Details]
Mooney, C. Haslam, NJ. Pollastri1, G. Shields, DC (2012) 'Towards the Improved Discovery and Design of Functional Peptides: Common Features of Diverse Classes Permit Generalized Prediction of Bioactivity'. PLoS ONE, 7 (10). [DOI] Link to full text [Details]
Lombardi, F,De Chaumont, C,Shields, DC,Moran, N (2012) 'Platelet signalling networks: Pathway perturbation demonstrates differential sensitivity of ADP secretion and fibrinogen binding'. Platelets, 23 :17-25. [DOI] [Details]
Haslam, NJ,Shields, DC (2012) 'Profile-based short linear protein motif discovery'. BMC Bioinformatics, 13 . [DOI] [Details]
Haslam, N. J., Shields, D. C. (2012) 'Peptide-binding domains: are limp handshakes safest?'. Science signaling, 5 (243). Available Online [DOI] [Details]
Edwards, R. J., Davey, N. E., O'Brien, K., Shields, D. C. (2012) 'Interactome-wide prediction of short, disordered protein interaction motifs in humans'. Molecular BioSystems, 8 (1):282-95. Available Online [DOI] [Details]
Deshmukh, HA,Colhoun, HM,Johnson, T,McKeigue, PM,Betteridge, DJ,Durrington, PN,Fuller, JH,Livingstone, S,Charlton-Menys, V,Neil, A,Poulter, N,Sever, P,Shields, DC,Stanton, AV,Chatterjee, A,Hyde, C,Calle, RA,DeMicco, DA,Trompet, S,Postmus, I,Ford, I,Jukema, JW,Caulfield, M,Hitman, GA (2012) 'Genome-wide association study of genetic determinants of LDL-c response to atorvastatin therapy: importance of Lp(a)'. Journal of Lipid Research, 53 :1000-1011. [DOI] [Details]
Davey, NE,Cowan, JL,Shields, DC,Gibson, TJ,Coldwell, MJ,Edwards, RJ (2012) 'SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions'. Nucleic Acids Research, 40 :10628-10641. [DOI] [Details]
Casey, J. P., Magalhaes, T., Conroy, J. M., Regan, R., Shah, N., Anney, R., Shields, D. C., Abrahams, B. S., Almeida, J., Bacchelli, E., Bailey, A. J., Baird, G., Battaglia, A., Berney, T., Bolshakova, N., Bolton, P. F., Bourgeron, T., Brennan, S., Cali, P., Correia, C., Corsello, C., Coutanche, M., Dawson, G., de Jonge, M., Delorme, R., Duketis, E., Duque, F., Estes, A., Farrar, P., Fernandez, B. A., Folstein, S. E., Foley, S., Fombonne, E., Freitag, C. M., Gilbert, J., Gillberg, C., Glessner, J. T., Green, J., Guter, S. J., Hakonarson, H., Holt, R., Hughes, G., Hus, V., Igliozzi, R., Kim, C., Klauck, S. M., Kolevzon, A., Lamb, J. A., Leboyer, M., Le Couteur, A., Leventhal, B. L., Lord, C., Lund, S. C., Maestrini, E., Mantoulan, C., Marshall, C. R., McConachie, H., McDougle, C. J., McGra (2012) 'A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder'. Human Genetics, 131 (4):565-79. Available Online [Details]
Saxena, R,Elbers, CC,Guo, YR,Peter, I,Gaunt, TR,Mega, JL,Lanktree, MB,Tare, A,Castillo, BA,Li, YR,Johnson, T,Bruinenberg, M,Gilbert-Diamond, D,Rajagopalan, R,Voight, BF,Balasubramanyam, A,Barnard, J,Bauer, F,Baumert, J,Bhangale, T,Bohm, BO,Braund, PS,Burton, PR,Chandrupatla, HR,Clarke, R,Cooper-DeHoff, RM,Crook, ED,Davey-Smith, G,Day, IN,de Boer, A,de Groot, MCH,Drenos, F,Ferguson, J,Fox, CS,Furlong, CE,Gibson, Q,Gieger, C,Gilhuijs-Pederson, LA,Glessner, JT,Goel, A,Gong, Y,Grant, SFA,Grobbee, DE,Hastie, C,Humphries, SE,Kim, CE,Kivimaki, M,Kleber, M,Meisinger, C,Kumari, M,Langaee, TY,Lawlor, DA,Li, MY,Lobmeyer, MT,Maitland-van der Zee, AH,Meijs, MFL,Molony, CM,Morrow, DA,Murugesan, G,Musani, SK,Nelson, CP,Newhouse, SJ,O'Connell, JR,Padmanabhan, S,Palmen, J,Patel, SR,Pepine, CJ,Pettinger, M (2012) 'Large-Scale Gene-Centric Meta-Analysis across 39 Studies Identifies Type 2 Diabetes Loci'. American Journal of Human Genetics, 90 :410-425. [DOI] [Details]
Rue-Albrecht, K., Shields, D. C., Khaldi, N. (2012) 'Correlation of disorder between S. cerevisiae interacting proteins'. Molecular BioSystems, 8 (1):417-25. Available Online [DOI] [Details]
Mooney C, Pollastri G, Shields DC, Haslam NJ; (2011) 'Prediction of short linear protein binding regions'. Journal of Molecular Biology, . Available Online [DOI] Link to full text [Details]
Norris, R,Casey, F,FitzGerald, RJ,Shields, D,Mooney, C (2012) 'Predictive modelling of angiotensin converting enzyme inhibitory dipeptides'. Food Chemistry, 133 :1349-1354. [DOI] [Details]
Davey, NE,Haslam, NJ,Shields, DC,Edwards, RJ; (2011) 'SLiMSearch 2.0: biological context for short linear motifs in proteins'. Nucleic Acids Research, 39 :56-60. Available Online [DOI] Link to full text [Details]
Khaldi, N., Shields, D. C. (2011) 'Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species'. Biology Direct, 6 . Available Online [DOI] [Details]
Alende, N., Nielsen, J. E., Shields, D. C., Khaldi, N. (2011) 'Evolution of the isoelectric point of mammalian proteins as a consequence of indels and adaptive evolution'. Proteins: Structure, Function, and Bioinformatics, 79 (5):1635-48. Available Online [DOI] [Details]
Lanktree, MB,Guo, YR,Murtaza, M,Glessner, JT,Bailey, SD,Onland-Moret, NC,Lettre, G,Ongen, H,Rajagopalan, R,Johnson, T,Shen, HQ,Nelson, CP,Klopp, N,Baumert, J,Padmanabhan, S,Pankratz, N,Pankow, JS,Shah, S,Taylor, K,Barnard, J,Peters, BJ,Maloney, CM,Lobmeyer, MT,Stanton, A,Zafarmand, MH,Romaine, SPR,Mehta, A,van Iperen, EPA,Gong, Y,Price, TS,Smith, EN,Kim, CE,Li, YR,Asselbergs, FW,Atwood, LD,Bailey, KM,Bhatt, D,Bauer, F,Behr, ER,Bhangale, T,Boer, JMA,Boehm, BO,Bradfield, JP,Brown, M,Braund, PS,Burton, PR,Carty, C,Chandrupatla, HR,Chen, W,Connell, J,Dalgeorgou, C,de Boer, A,Drenos, F,Elbers, CC,Fang, JC,Fox, CS,Frackelton, EC,Fuchs, B,Furlong, CE,Gibson, Q,Gieger, C,Goe, A,Grobbee, DE,Hastie, C,Howard, PJ,Huang, GH,Johnson, WC,Li, Q,Kleber, ME,Klein, BEK,Klein, R,Kooperberg, C,Ky, B,LaCroix,; (2011) 'Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height'. American Journal of Human Genetics, 88 :6-18. [DOI] [Details]
Vangjeli, C., Dicker, P., Tregouet, D. A., Shields, D. C., Evans, A., Stanton, A. V. (2011) 'A polymorphism in ACE2 is associated with a lower risk for fatal cardiovascular events in females: the MORGAM project'. Journal of the Renin-Angiotensin-Aldosterone System, 12 (4):504-9. Available Online [Details]
Mooney, C., Davey, N., Martin, A. J., Walsh, I., Shields, D. C., Pollastri, G. (2011) 'In silico protein motif discovery and structural analysis'. Methods in Molecular Biology, 760 :341-53. Available Online [Details]
Montanari, F., Shields, D. C., Khaldi, N. (2011) 'Differences in the number of intrinsically disordered regions between yeast duplicated proteins, and their relationship with functional divergence'. PLoS ONE, 6 (9). Available Online [DOI] [Details]
Duffy, FJ,Verniere, M,Devocelle, M,Bernard, E,Shields, DC,Chubb, AJ; (2011) 'CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids'. Journal of Chemical Information and Modeling, 51 :829-836. [DOI] [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]
Davey, NE,Edwards, RJ,Shields, DC; (2010) 'Computational identification and analysis of protein short linear motifs'. Frontiers in Bioscience, 15 :801-825. Available Online [DOI] [Details]
Padmanabhan, S,Melander, O,Johnson, T,Di Blasio, AM,Lee, WK,Gentilini, D,Hastie, CE,Menni, C,Monti, MC,Delles, C,Laing, S,Corso, B,Navis, G,Kwakernaak, AJ,van der Harst, P,Bochud, M,Maillard, M,Burnier, M,Hedner, T,Kjeldsen, S,Wahlstrand, B,Sjogren, M,Fava, C,Montagnana, M,Danese, E,Torffvit, O,Hedblad, B,Snieder, H,Connell, JMC,Brown, M,Samani, NJ,Farrall, M,Cesana, G,Mancia, G,Signorini, S,Grassi, G,Eyheramendy, S,Wichmann, HE,Laan, M,Strachan, DP,Sever, P,Shields, DC,Stanton, A,Vollenweider, P,Teumer, A,Volzke, H,Rettig, R,Newton-Cheh, C,Arora, P,Zhang, F,Soranzo, N,Spector, TD,Lucas, G,Kathiresan, S,Siscovick, DS,Luan, JA,Loos, RJF,Wareham, NJ,Penninx, BW,Nolte, IM,McBride, M,Miller, WH,Nicklin, SA,Baker, AH,Graham, D,McDonald, RA,Pell, JP,Sattar, N,Welsh, P,Munroe, P,Caulfield, MJ,Za; (2010) 'Genome-Wide Association Study of Blood Pressure Extremes Identifies Variant near UMOD Associated with Hypertension'. PLoS Genetics, 6 . [DOI] [Details]
Pushker R., Jacque J.M. and Shields D.C.; (2010) 'Meta-analysis to test the association of HIV-1 nef amino acid differences and deletions with disease progression'. Virology, 84 (7):3644-3653. Available Online [Details]
Maree, AO,Vangjeli, C,Jneid, H,Ryan, J,Cox, D,Cannon, CP,Shields, DC,Fitzgerald, DJ; (2010) 'G-protein beta 3 subunit polymorphism and bleeding in the orbofiban in patients with unstable coronary syndromes-thrombolysis in myocardial infarction 16 trial'. Journal of Thrombosis and Haemostasis, 8 :934-941. [DOI] [Details]
Davey, NE,Haslam, NJ,Shields, DC,Edwards, RJ; (2010) 'SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs'. Nucleic Acids Research, 38 :534-539. [DOI] Link to full text [Details]
Davey, NE,Edwards, RJ,Shields, DC; (2010) 'Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins'. BMC Bioinformatics, 11 . [DOI] [Details]
Davey, Norman E and Edwards, Richard J and Shields, Denis C (2010) 'Computational identification and analysis of protein short linear motifs'. Frontiers in Bioscience, 15 :801-825. [Details]
Talmud, PJ,Drenos, F,Shah, S,Shah, T,Palmen, J,Verzilli, C,Gaunt, TR,Pallas, J,Lovering, R,Li, K,Casas, JP,Sofat, R,Kumari, M,Rodriguez, S,Johnson, T,Newhouse, SJ,Dominiczak, A,Samani, NJ,Caulfield, M,Sever, P,Stanton, A,Shields, DC,Padmanabhan, S,Melander, O,Hastie, C,Delles, C,Ebrahim, S,Marmot, MG,Smith, GD,Lawlor, DA,Munroe, PB,Day, IN,Kivimaki, M,Whittaker, J,Humphries, SE,Hingorani, AD,ASCOT Investigators,NORDIL Investigators,BRIGHT Consortium; (2009) 'Gene-centric Association Signals for Lipids and Apolipoproteins Identified via the HumanCVD BeadChip'. American Journal of Human Genetics, 85 :628-642. Available Online [DOI] [Details]
O'Halloran, AM,Patterson, CC,Horan, P,Maree, A,Curtin, R,Stanton, A,McKeown, PP,Shields, DC; (2009) 'Genetic polymorphisms in platelet-related proteins and coronary artery disease: investigation of candidate genes, including N-acetylgalactosaminyltransferase 4 (GALNT4) and sulphotransferase 1A1/2 (SULT1A1/2)'. Journal of thrombosis and thrombolysis, 27 :175-184. Available Online [DOI] [Details]
Davey, NE,Shields, DC,Edwards, RJ; (2009) 'Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery'. Bioinformatics, 25 :443-450. [DOI] [Details]
Casey, F. P.,Pihan, E.,Shields, D. C.; (2009) 'Discovery of small molecule inhibitors of protein-protein interactions using combined ligand and target score normalization'. J CHEM INF MODEL, 49 (1212):2708-172708. Available Online [DOI] [Details]
Bernard, E., Parthasarathi, L., Cho, M. K., Aylward, K., Raab, M., Daxecker, H., O'Dushlaine, C. T., Shields, D. C., Devocelle, M., Keyes, T., Cosgrave, L., O'Neill, S., Mok, K. H., Moran, N. (2009) 'Ligand switching in cell-permeable peptides: manipulation of the alpha-integrin signature motif'. ACS Chemical Biology, 4 (6):457-71. Available Online [DOI] [Details]
Evans A, Karvanen J, Silander K, Kee F, Tiret L, Salomaa V, Kuulasmaa K, Wiklund PG, Virtamo J, Saarela O, Perret C, Perola M, Peltonen L, Cambien F, Erdmann J, Samani NJ, Schunkert H, ; (2009) 'The impact of newly identified loci on coronary heart disease, stroke and total mortality in the MORGAM prospective cohorts'. genetic epidemiology, 33 (3):237-246. [DOI] [Details]
O'Dushlaine, CT,Shields, DC; (2008) 'Marked variation in predicted and observed variability of tandem repeat loci across the human genome'. Genomics, 9 . [DOI] [Details]
Edwards, RJ,Davey, NE,Shields, DC; (2008) 'CompariMotif: quick and easy comparisons of sequence motifs'. Bioinformatics, 24 :1307-1309. [DOI] [Details]
Parthasarathi, L., Casey, F., Stein, A., Aloy, P., Shields, D. C. (2008) 'Approved drug mimics of short peptide ligands from protein interaction motifs'. J CHEM INF MODEL, 48 (10):1943-8. Available Online [DOI] [Details]
Casey, FP,Davey, NE,Baran, I,Varekova, RS,Shields, DC; (2008) 'Web server to identify similarity of amino acid motifs to compounds (SAAMCO)'. J CHEM INF MODEL, 48 :1524-1529. [DOI] [Details]
Casey, FP,Cagney, G,Krogan, NJ,Shields, DC; (2008) 'Optimal stepwise experimental design for pairwise functional interaction studies'. Bioinformatics, 24 :2733-2739. Available Online [DOI] [Details]
Ryan AW, O'Brien E, Shields D, McManus R. ; (2008) 'Lack of association between NFKBIL1/LTA polymorphisms and hypertension, myocardial infarct, unstable angina and stable angina in a large Irish population sample'. Atherosclerosis, 197 :465-466. Available Online [DOI] [Details]
Tregouet DA, Grisoni ML, Proust C, Alanne M, Desuremain M, Salomaa V, Kuulasmaa K, Cambien F, Nicaud V, Stegmayr B, Virtamo J, Shields D, Kee F, Tiret L, Evans A, ; (2008) 'Haplotypic analysis of tag SNPs of the interleukin-18 gene in relation to cardiovascular disease events: the MORGAM Project'. European Journal of Human Genetics, . [DOI] [Details]
Johnston, CR,O'Dushlaine, C,Fitzpatrick, DA,Edwards, RJ,Shields, DC; (2007) 'Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication'. Molecular Biology, 24 :315-323. [DOI] [Details]
Edwards, RJ; Moran, N; Devocelle, M; Kiernan, A; Meade, G; Signac, W; Foy, M; Park, SDE; Dunne, E; Kenny, D; Shields, DC; ; (2007) 'Bioinformatic discovery of novel bioactive peptides'. Nature Chemical Biology, 3 (2):108-112. [Details]
Edwards, R. J.,Davey, N. E.,Shields, D. C.; (2007) 'SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins'. PLoS ONE, 2 (10). [DOI] [Details]
Baran, I., Varekova, R. S., Parthasarathi, L., Suchomel, S., Casey, F., Shields, D. C. (2007) 'Identification of potential small molecule peptidomimetics similar to motifs in proteins'. J CHEM INF MODEL, 47 (2):464-74. Available Online [DOI] [Details]
Moore, N.,Dicker, P.,O'Brien, J. K.,Stojanovic, M.,Conroy, R. M.,Treumann, A.,O'Brien, E. T.,Fitzgerald, D.,Shields, D.,Stanton, A. V.; (2007) 'Renin gene polymorphisms and haplotypes, blood pressure, and responses to renin-angiotensin system inhibition'. Hypertension, 50 (2):340-7. [DOI] [Details]
Davey, NE,Edwards, RJ,Shields, DC; (2007) 'The SLiMDisc server: short, linear motif discovery in proteins'. Nucleic Acids Research, 35 :455-459. [DOI] [Details]
Lavin, P. J., Laing, M. E., O'Kelly, P., Moloney, F. J., Gopinathan, D., Aradi, A. A., Shields, D. C., Murphy, G. M., Conlon, P. J. (2007) 'Improved renal allograft survival with vitamin D receptor polymorphism'. Ren Fail, 29 (7):785-9. Available Online [Details]
Laing, M. E., Dicker, P., Moloney, F. J., Ho, W. L., Murphy, G. M., Conlon, P., Whitehead, A. S., Shields, D. C. (2007) 'Association of methylenetetrahydrofolate reductase polymorphism and the risk of squamous cell carcinoma in renal transplant patients'. Transplantation, 84 (1):113-6. Available Online [DOI] [Details]
Iohom, G.,Ni Chonghaile, M.,O'Brien J, K.,Cunningham, A. J.,Fitzgerald, D. F.,Shields, D. C.; (2007) 'An investigation of potential genetic determinants of propofol requirements and recovery from anaesthesia'. European Journal of Anaesthesiology, 24 (11):912-9. Available Online [Details]
O'Halloran, AM,Stanton, A,O'Brien, E,Shields, DC; (2006) 'The impact on coronary artery disease of common polymorphisms known to modulate responses to pathogens'. Gene, 70 :934-945. Available Online [DOI] [Details]
Davey, N. E., Shields, D. C., Edwards, R. J. (2006) 'SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent'. Nucleic Acids Res, 34 (12):3546-54. Available Online [DOI] [Details]
Parthasarathi, L., Devocelle, M., Sondergaard, C., Baran, I., O'Dushlaine, C. T., Davey, N. E., Edwards, R. J., Moran, N., Kenny, D., Shields, D. C. (2006) 'Absolute net charge and the biological activity of oligopeptides'. J CHEM INF MODEL, 46 (5):2183-90. Available Online [DOI] [Details]
C.J. Shields, D.C. Winter. ; (2006) 'Infliximab For Ulcerative Colitis'. New England Journal of Medicine, 354 (13):1424-1426. [Details]
O'Halloran, A. M.,Curtin, R.,O'Connor, F.,Dooley, M.,Fitzgerald, A.,O'Brien, J. K.,Fitzgerald, D. J.,Shields, D. C.; (2006) 'The impact of genetic variation in the region of the GPIIIa gene, on Pl expression bias and GPIIb/IIIa receptor density in platelets'. British Journal of Haematology, 132 (4):494-502. Available Online [Details]
C. J. Shields, D.C. Winter J.P. Geibel, G.C. O'Sullivan, J.H. Wang, H.P. Redmond; (2006) 'Hypertonic Saline Attenuates Colonic Tumor Cell Metastatic Potential By Activating Transmembrane Sodium Conductance'. Journal of Membrane Biology, 211 (1):35-42. [Details]
Moran, N., Kiernan, A., Dunne, E., Edwards, R. J., Shields, D. C., Kenny, D. (2006) 'Monitoring modulators of platelet aggregation in a microtiter plate assay'. Analytical Biochemistry, 357 (1):77-84. Available Online [Details]
Moloney, F. J., Dicker, P., Conlon, P. J., Shields, D. C., Murphy, G. M. (2006) 'The frequency and significance of thiopurine S-methyltransferase gene polymorphisms in azathioprine-treated renal transplant recipients'. Br J Dermatol, 154 (6):1199-200. Available Online [Details]
Hillmann AG, Harmon S, Park SDE, O'Brien J, Shields DC, Kenny D ; (2006) 'Comparative RNA expression analyses from small-scale, single-donor platelet samples'. Thrombosis and Haemostasis, 4 :349-356. [Details]
O'Dushlaine, CT; Shields, DC; ; (2006) 'Tools for the identification of variable and potentially variable tandem repeats'. BMC Genomics, 7 (NA). [Details]
Maree, A. O., Curtin, R. J., Chubb, A., Dolan, C., Cox, D., O'Brien, J., Crean, P., Shields, D. C., Fitzgerald, D. J.; (2005) 'Cyclooxygenase-1 haplotype modulates platelet response to aspirin'. Thrombosis and Haemostasis, 3 (10):2340-5. [Details]
Alun Evans A, Salomaa V, Kulathinal S, Asplund K, Cambien F, Ferrario M, Perola M, Peltonen L, Shields D, Tunstall-Pedoe H, Kuulasmaa K, for the MORGAM Project; (2005) 'An international pooling of cardiovascular cohorts'. INTERNATIONAL JOURNAL OF EPIDEMIOLOGY, 34 :21-27. [Details]
Hawi Z, Segurado R, Conroy J, Sheehan K, Lowe N, Kirley A, Shields D, Fitzgerald M, Gallagher L, Gill M; (2005) 'Preferential transmission of paternal alleles at risk genes in attention-deficit/hyperactivity disorder'. American Journal of Human Genetics, 77 (6):958-965. [DOI] [Details]
Thompson, J.,Hipwell, E.,Loo, H. V.,Bannigan, J.; (2005) 'Effects of cadmium on cell death and cell proliferation in chick embryos'. Reprod Toxicol, 20 (4):539-48. [DOI] [Details]
O'Dushlaine, C. T., Edwards, R. J., Park, S. D., Shields, D. C. (2005) 'Tandem repeat copy-number variation in protein-coding regions of human genes'. Genome Biol, 6 (8). Available Online [Details]
Molony, C. M., Fitzgerald, A. P., Shields, D. C. (2005) 'Overdispersion of allele frequency differences between populations: implications for meta-analyses of genotypic disease associations'. Eur J Hum Genet, 13 (1):79-85. Available Online [Details]
Kelly, H,Ennis, S,Yoneda, A,Bermingham, C,Shields, DC,Molony, C,Green, AJ,Puri, P,Barton, DE; (2005) 'Uroplakin III is not a major candidate gene for primary vesicoureteral reflux'. Gene, 13 :500-502. [DOI] [Details]
Johnston, C. R., Shields, D. C. (2005) 'A sequence sub-sampling algorithm increases the power to detect distant homologues'. Nucleic Acids Research, 33 (12):3772-8. Available Online [Details]
Hawi, Z., Segurado, R., Conroy, J., Sheehan, K., Lowe, N., Kirley, A., Shields, D., Fitzgerald, M., Gallagher, L., Gill, M. (2005) 'Preferential transmission of paternal alleles at risk genes in attention-deficit/hyperactivity disorder'. Am J Hum Genet, 77 (6):958-65. Available Online [Details]
Evans, A., Salomaa, V., Kulathinal, S., Asplund, K., Cambien, F., Ferrario, M., Perola, M., Peltonen, L., Shields, D., Tunstall-Pedoe, H., Kuulasmaa, K. (2005) 'MORGAM (an international pooling of cardiovascular cohorts)'. Int J Epidemiol, 34 (1):21-7. Available Online [Details]
Edwards, R. J., Shields, D. C. (2005) 'BADASP: predicting functional specificity in protein families using ancestral sequences'. Bioinformatics, 21 (22):4190-1. Available Online [Details]
Dolan, C., Shields, D. C., Stanton, A., O'Brien, E., Lambert, D. M., O'Brien, J. K., Treacy, E. P. (2005) 'Polymorphisms of the Flavin containing monooxygenase 3 (FMO3) gene do not predispose to essential hypertension in Caucasians'. BMC Med Genet, 6 . Available Online [DOI] [Details]
Dolan, C., O'Halloran, A., Bradley, D. G., Croke, D. T., Evans, A., O'Brien, J. K., Dicker, P., Shields, D. C. (2005) 'Genetic stratification of pathogen-response-related and other variants within a homogeneous Caucasian Irish population'. Eur J Hum Genet, 13 (7):798-806. Available Online [Details]
Kelly H, Ennis S, Yonedia A, Bermingham C, Shields D, Molony C, Green AJ, Puri P, Barton DE ; (2004) 'Uroplakin III Is Not a Major Candidate Gene for Primary Vesicoureteral Reflux'. EUROPEAN JOURNAL OF HUMAN GENETICS, 13 :500-502. [Details]
Edwards, RJ & Shields DC; (2004) 'GASP: Gapped Ancestral Sequence Prediction for proteins'. BMC Bioinformatics, 5 (1). Available Online [Details]
McRedmond J., Park S., Reilly, D., Coppinger J.A., Maguire, P.B., Shields, D. & Fitzgerald D.J. ; (2004) 'Integration of transcriptomics and genomics in platelets: a profile of platelet proteins and platelet-specific genes'. Molecular and Cellular Proteomics, 3 :133-144. [Details]
Byrne, C. E.,Fitzgerald, A.,Cannon, C. P.,Fitzgerald, D. J.,Shields, D. C.; (2004) 'Elevated white cell count in acute coronary syndromes: relationship to variants in inflammatory and thrombotic genes'. BMC Med Genet, 5 . [Details]
McRedmond, J. P.,Park, S. D.,Reilly, D. F.,Coppinger, J. A.,Maguire, P. B.,Shields, D. C.,Fitzgerald, D. J.; (2004) 'Integration of proteomics and genomics in platelets: a profile of platelet proteins and platelet-specific genes'. Molecular and Cellular Proteomics, 3 (2):133-44. [Details]
Seoighe C, Johnston CR, Shields DC ; (2003) 'Evolution of protein function after gene duplication'. Mol Biol Evol, (20):484-490. [Details]
Hokamp, K., Shields, D. C., Wolfe, K. H., Caffrey, D. R. (2003) 'Wrapping up BLAST and other applications for use on Unix clusters'. Bioinformatics, 19 (3):441-2. Available Online [Details]
Martin, K., Meade, G., Moran, N., Shields, D. C., Kenny, D. (2003) 'A palmitylated peptide derived from the glycoprotein Ib beta cytoplasmic tail inhibits platelet activation'. Journal of Thrombosis and Haemostasis, 1 (12):2643-52. Available Online [Details]
Shields, D. C. (2003) 'Molecular evolution of CXC chemokines and receptors'. Trends Immunol, 24 (7). Available Online [Details]
Seoighe, C., Johnston, C. R., Shields, D. C. (2003) 'Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation'. Mol Biol Evol, 20 (4):484-90. Available Online [Details]
Muckian, C., Fitzgerald, A., O'Neill, A., O'Byrne, A., Fitzgerald, D. J., Shields, D. C.; (2002) 'Genetic variability in the extracellular matrix as a determinant of cardiovascular risk: association of type III collagen COL3A1 polymorphisms with coronary artery disease'. Blood, 100 (4):1220-3. [Details]
Kenny, D.,Muckian, C.,Fitzgerald, D. J.,Cannon, C. P.,Shields, D. C.; (2002) 'Platelet glycoprotein Ib alpha receptor polymorphisms and recurrent ischaemic events in acute coronary syndrome patients'. J Thromb Thrombolysis, 13 (1):13-9. [Details]
Shields, D. C., O'Halloran, A. M. (2002) 'Integrating genotypic data with transcriptomic and proteomic data'. Comp Funct Genomics, 3 (1):22-7. Available Online [Details]
Cotter, P. J., Caffrey, D. R., Shields, D. C. (2002) 'Improved database searches for orthologous sequences by conditioning on outgroup sequences'. Bioinformatics, 18 (1):83-91. Available Online [Details]
Denis C. Shields, Anthony Fitzgerald, Anne O'Neill, Clare Muckian, Barry Moran, Dermot Kenny, Christopher C. Cannon, Connie Byrne, Desmond G. Fitzgerald; (2002) 'The contribution of genetic factors to thromobotic and bleeding outcomes in coronary patients randomised to IIb/IIIa antagonists'. Pharmacogenomics Journal, (2):182-190. [Details]
Yoneda, A; Kelly, S; Shields, D; Molony, C; Green, AJ; Puri, P; Barton, DE; ; (2001) 'No evidence for a role for the angiotensin II, type 2 receptor in primary vesicoureteral reflux'. Journal of Medical Genetics, 38 (NA):69-69. [Details]
Stanton, A., Fitzgerald, D., Hughes, A., Mayet, J., O'Brien, E., Poulter, N. R., Sever, P. S., Shields, D., Thom, S. (2001) 'An intensive phenotyping study to enable the future examination of genetic influences on hypertension-associated cardiovascular disease'. J Hum Hypertens, 15 Suppl 1 . Available Online [Details]
Murphy, V. E., Mynett-Johnson, L. A., Claffey, E., Shields, D. C., McKeon, P. (2001) 'No association between 5HT-2A and bipolar disorder irrespective of genomic imprinting'. Am J Med Genet, 105 (5):422-5. Available Online [Details]
Cahill, M., Karabatzaki, M., Donoghue, C., Meleady, R., Mynett-Johnson, L. A., Mooney, D., Graham, I. M., Whitehead, A. S., Shields, D. C. (2001) 'Thermolabile MTHFR genotype and retinal vascular occlusive disease'. Br J Ophthalmol, 85 (1):88-90. Available Online [Details]
Ennis, S; Bermingham, C; Kelly, H; Yoneda, A; Kelly, S; Shields, D; Molony, C; Green, AJ; Puri, P; Barton, DE; ; (2001) 'Exclusion of the candidate gene Uroplakin III in primary vesicoureteral reflux'. Journal of Medical Genetics, 38 (NA):67-67. [Details]
O'Connor, F. F., Shields, D. C., Fitzgerald, A., Cannon, C. P., Braunwald, E., Fitzgerald, D. J.; (2001) 'Genetic variation in glycoprotein IIb/IIIa (GPIIb/IIIa) as a determinant of the responses to an oral GPIIb/IIIa antagonist in patients with unstable coronary syndromes'. Blood, 98 (12):3256-60. [Details]
Shields, D. C., Ramsbottom, D., Donoghue, C., Pinjon, E., Kirke, P. N., Molloy, A. M., Edwards, Y. H., Mills, J. L., Mynett-Johnson, L., Weir, D. G., Scott, J. M., Whitehead, A. S. (2000) 'Association between historically high frequencies of neural tube defects and the human T homologue of mouse T (Brachyury)'. Am J Med Genet, 92 (3):206-11. Available Online [Details]
Shields, D. C. (2000) 'Gene conversion among chemokine receptors'. Gene, 246 (1-2):239-45. Available Online [Details]
Muckian, C., Hillmann, A., Kenny, D., Shields, D. C. (2000) 'A novel variant of the platelet glycoprotein Ibalpha macroglycopeptide region lacks any copies of the perfect 13 amino acid repeat'. Journal of Thrombosis and Haemostasis, 83 (3):513-4. Available Online [Details]
Malcuit, I., de Jong, W., Baulcombe, D. C., Shields, D. C., Kavanagh, T. A. (2000) 'Acquisition of multiple virulence/avirulence determinants by potato virus X (PVX) has occurred through convergent evolution rather than through recombination'. Virus Genes, 20 (2):165-72. Available Online [Details]
Cunnane, G., Grehan, S., Geoghegan, S., McCormack, C., Shields, D., Whitehead, A. S., Bresnihan, B., Fitzgerald, O. (2000) 'Serum amyloid A in the assessment of early inflammatory arthritis'. J Rheumatol, 27 (1):58-63. Available Online [Details]
Cahill, M., Karabatzaki, M., Meleady, R., Refsum, H., Ueland, P., Shields, D., Mooney, D., Graham, I. (2000) 'Raised plasma homocysteine as a risk factor for retinal vascular occlusive disease'. Br J Ophthalmol, 84 (2):154-7. Available Online [Details]
Caffrey, D. R., O'Neill, L. A., Shields, D. C. (2000) 'A method to predict residues conferring functional differences between related proteins: application to MAP kinase pathways'. PROTEIN SCI, 9 (4):655-70. Available Online [Details]
Hillmann, A.,Shields, D. C.,Fitzgerald, D. J.,Kenny, D.; (2000) 'Polymorphisms in glycoprotein (GP) lb alpha are not associated with adverse outcomes in primigravidae'. Journal of Obstetrics and Gynaecology, 20 (3):250-5. [Details]
Caffrey, D. R., O'Neill, L. A., Shields, D. C. (1999) 'The evolution of the MAP kinase pathways: coduplication of interacting proteins leads to new signaling cascades'. J Mol Evol, 49 (5):567-82. Available Online [Details]
Harmon, D. L., Shields, D. C., Woodside, J. V., McMaster, D., Yarnell, J. W., Young, I. S., Peng, K., Shane, B., Evans, A. E., Whitehead, A. S. (1999) 'Methionine synthase D919G polymorphism is a significant but modest determinant of circulating homocysteine concentrations'. Genet Epidemiol, 17 (4):298-309. Available Online [Details]
Harmon, D. L., Doyle, R. M., Meleady, R., Doyle, M., Shields, D. C., Barry, R., Coakley, D., Graham, I. M., Whitehead, A. S. (1999) 'Genetic analysis of the thermolabile variant of 5, 10-methylenetetrahydrofolate reductase as a risk factor for ischemic stroke'. Arterioscler Thromb Vasc Biol, 19 (2):208-11. Available Online [Details]
Hawi, Z., Mynett-Johnson, L., Gill, M., Murphy, V., Straubl, R. E., Kendler, K. S., Walsh, D., Machen, F., Connell, H., McKeon, P., Shields, D. (1999) 'Pseudoautosomal gene: possible association with bipolar males but not with schizophrenia'. Psychiatr Genet, 9 (3):129-34. Available Online [Details]
Shields, D. C., Kirke, P. N., Mills, J. L., Ramsbottom, D., Molloy, A. M., Burke, H., Weir, D. G., Scott, J. M., Whitehead, A. S. (1999) 'The thermolabile variant of methylenetetrahydrofolate reductase and neural tube defects: An evaluation of genetic risk and the relative importance of the genotypes of the embryo and the mother'. Am J Hum Genet, 64 (4):1045-55. Available Online [Details]
Mynett-Johnson, L., Murphy, V., McCormack, J., Shields, D. C., Claffey, E., Manley, P., McKeon, P. (1998) 'Evidence for an allelic association between bipolar disorder and a Na+, K+ adenosine triphosphatase alpha subunit gene (ATP1A3)'. Biol Psychiatry, 44 (1):47-51. Available Online [Details]
Mynett-Johnson, L. A., Murphy, V. E., Claffey, E., Shields, D. C., McKeon, P. (1998) 'Preliminary evidence of an association between bipolar disorder in females and the catechol-O-methyltransferase gene'. Psychiatr Genet, 8 (4):221-5. Available Online [Details]
Harmon, D. L., McMaster, D., McCluskey, D. R., Shields, D., Whitehead, A. S. (1997) 'A common genetic variant affecting folate metabolism is not over-represented in chronic fatigue syndrome'. Ann Clin Biochem, 34 ( Pt 4) :427-9. Available Online [Details]
Jensen, L. E., Hiney, M. P., Shields, D. C., Uhlar, C. M., Lindsay, A. J., Whitehead, A. S. (1997) 'Acute phase proteins in salmonids: evolutionary analyses and acute phase response'. Journal of Immunology, 158 (1):384-92. Available Online [Details]
Harmon, D. L., McMaster, D., Shields, D. C., Whitehead, A. S., Rea, I. M. (1997) 'MTHFR thermolabile genotype frequencies and longevity in Northern Ireland'. Atherosclerosis, 131 (1):137-8. Available Online [Details]
Mynett-Johnson, L. A., Murphy, V. E., Manley, P., Shields, D. C., McKeon, P. (1997) 'Lack of evidence for a major locus for bipolar disorder in the pericentromeric region of chromosome 18 in Irish pedigrees'. Biol Psychiatry, 42 (6):486-94. Available Online [Details]
Wolfe, K. H., Shields, D. C. (1997) 'Molecular evidence for an ancient duplication of the entire yeast genome'. Nature, 387 (6634):708-13. Available Online [Details]
Shields, D. C., Wolfe, K. H. (1997) 'Accelerated evolution of sites undergoing mRNA editing in plant mitochondria and chloroplasts'. Mol Biol Evol, 14 (3):344-9. Available Online [Details]
Gallagher, P. M., Meleady, R., Shields, D. C., Tan, K. S., McMaster, D., Rozen, R., Evans, A., Graham, I. M., Whitehead, A. S. (1996) 'Homocysteine and risk of premature coronary heart disease. Evidence for a common gene mutation'. Circulation Journal, 94 (9):2154-8. Available Online [Details]
Shields, D. C., Butler, A., Mosurski, K. R., Walsh, M. T., Whitehead, A. S. (1996) 'Mapping genes within a YAC by computer-assisted interpretation of partial restriction digestions'. Nucleic Acids Res, 24 (22):4495-500. Available Online [Details]
Uhlar, C. M., Black, I. L., Shields, D. C., Brack, C. M., Schreiber, G., Whitehead, A. S. (1996) 'Wallaby serum amyloid A protein: cDNA cloning, sequence and evolutionary analysis'. Scand J Immunol, 43 (3):271-6. Available Online [Details]
Shields, D. C., Harmon, D. L., Whitehead, A. S. (1996) 'Evolution of hemopoietic ligands and their receptors. Influence of positive selection on correlated replacements throughout ligand and receptor proteins'. Journal of Immunology, 156 (3):1062-70. Available Online [Details]
Houlston, R. S., Collins, A., Kee, F., Collins, B. J., Shields, D. C., Morton, N. E. (1995) 'Segregation analysis of colorectal cancer in Northern Ireland'. Hum Hered, 45 (1):41-8. Available Online [Details]
Shields, D. C., McDevitt, D., Foster, T. J. (1995) 'Evidence against concerted evolution in a tandem array in the clumping factor gene of Staphylococcus aureus'. Mol Biol Evol, 12 (5):963-5. Available Online [Details]
Shields, D. C., Harmon, D. L., Nunez, F., Whitehead, A. S. (1995) 'The evolution of haematopoietic cytokine/receptor complexes'. Cytokine, 7 (7):679-88. Available Online [Details]
Whitehead, A. S., Gallagher, P., Mills, J. L., Kirke, P. N., Burke, H., Molloy, A. M., Weir, D. G., Shields, D. C., Scott, J. M. (1995) 'A genetic defect in 5,10 methylenetetrahydrofolate reductase in neural tube defects'. Qjm-An International Journal Of Medicine, 88 (11):763-6. Available Online [Details]
Cook, J. T., Shields, D. C., Page, R. C., Levy, J. C., Hattersley, A. T., Shaw, J. A., Neil, H. A., Wainscoat, J. S., Turner, R. C. (1994) 'Segregation analysis of NIDDM in Caucasian families'. Diabetologia, 37 (12):1231-40. Available Online [Details]
Shields, D. C., Collins, A., Marlow, A. (1994) 'Coding of pointers in the segregation analysis program POINTER'. Genet Epidemiol, 11 (4):385-7. Available Online [Details]
Shields, D. C., Marlow, A. J., Houlston, R. S., Eccles, D. M., Morton, N. E. (1994) 'Prediction of genetic risks from segregation analyses of morbid risks'. Hum Hered, 44 (1):52-5. Available Online [Details]
Sham, P. C., Morton, N. E., Muir, W. J., Walker, M., Collins, A., Shields, D. C., St Clair, D. M., Blackwood, D. H. (1994) 'Segregation analysis of complex phenotypes: an application to schizophrenia and auditory P300 latency'. Psychiatr Genet, 4 (1):29-38. Available Online [Details]
McCarthy, M. I., Hitman, G. A., Shields, D. C., Morton, N. E., Snehalatha, C., Mohan, V., Ramachandran, A., Viswanathan, M. (1994) 'Family studies of non-insulin-dependent diabetes mellitus in South Indians'. Diabetologia, 37 (12):1221-30. Available Online [Details]
Shields, D. C., Ratanachaiyavong, S., McGregor, A. M., Collins, A., Morton, N. E. (1994) 'Combined segregation and linkage analysis of Graves disease with a thyroid autoantibody diathesis'. Am J Hum Genet, 55 (3):540-54. Available Online [Details]
Phillips, D. I., Shields, D. C., Dugoujon, J. M., Prentice, L., McGuffin, P., Ree Smith, B. (1993) 'Complex segregation analysis of thyroid autoantibodies: are they inherited as an autosomal dominant trait?'. Hum Hered, 43 (3):141-6. Available Online [Details]
Collins, A., Keats, B. J., Dracopoli, N., Shields, D. C., Morton, N. E. (1992) 'Integration of gene maps: chromosome 1'. Proceedings of the National Academy of Sciences of the United States of America, 89 (10):4598-602. Available Online [Details]
Morton, N. E., Collins, A., Lawrence, S., Shields, D. C. (1992) 'Algorithms for a location database'. Ann Hum Genet, 56 (Pt 3):223-32. Available Online [Details]
Spurr, N. K., Cox, S., Bryant, S. P., Attwood, J., Robson, E. B., Shields, D. C., Steinbrueck, T., Jenkins, T., Murray, J. C., Kidd, K. K., et al., (1992) 'The CEPH consortium linkage map of human chromosome 2'. Genomics, 14 (4):1055-63. Available Online [Details]
Shields, D. C., Higgins, D. G., Sharp, P. M. (1992) 'GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content'. Comput Appl Biosci, 8 (5):521-3. Available Online [Details]
Robinson, D., Lamont, M., Curtis, G., Shields, D. C., Phelps, P. (1992) 'A family with X-linked deafness showing linkage to the proximal Xq region of the X chromosome'. Hum Genet, 90 (3):316-8. Available Online [Details]
Morton, N. E., Shields, D. C., Collins, A. (1991) 'Genetic epidemiology of complex phenotypes'. Ann Hum Genet, 55 (Pt 4):301-14. Available Online [Details]
Shields, D. C., Collins, A., Buetow, K. H., Morton, N. E. (1991) 'Error filtration, interference, and the human linkage map'. Proceedings of the National Academy of Sciences of the United States of America, 88 (15):6501-5. Available Online [Details]
Shields, D. C. (1990) 'Switches in species-specific codon preferences: the influence of mutation biases'. J Mol Evol, 31 (2):71-80. Available Online [Details]
Sharp, P. M., Shields, D. C., Wolfe, K. H., Li, W. H. (1989) 'Chromosomal location and evolutionary rate variation in enterobacterial genes'. Science, 246 (4931):808-10. Available Online [Details]
Shields, D. C., Sharp, P. M. (1989) 'Evidence that mutation patterns vary among Drosophila transposable elements'. J Mol Biol, 207 (4):843-6. Available Online [Details]
Sharp, P. M., Cowe, E., Higgins, D. G., Shields, D. C., Wolfe, K. H., Wright, F. (1988) 'Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity'. Nucleic Acids Res, 16 (17):8207-11. Available Online [Details]
Shields, D. C., Sharp, P. M., Higgins, D. G., Wright, F. (1988) 'Silent sites in Drosophila genes are not neutral: evidence of selection among synonymous codons'. Mol Biol Evol, 5 (6):704-16. Available Online [Details]
Shields, D. C., Sharp, P. M. (1987) 'Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases'. Nucleic Acids Res, 15 (19):8023-40. Available Online [Details]

Other Journals

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]

Conference Publications

Gallagher HC, Clyne M, Shields DC and O'Connor C; (2009) Thematic PhD programmes at the UCD School of Medicine and Medical Science, Dublin, Ireland Orpheus Conference on PhD Education in Europe [Details]
O'Halloran, AM; Stanton, A; O'Brien, E; Shields, DC; ; (2006) ANNALS OF HUMAN GENETICS The impact on coronary artery disease of common polymorphisms known to modulate responses to pathogens , pp.934-945 [Details]
Dolan, C; Shields, DC; Stanton, A; O'Brien, E; Lambert, DM; O'Brien, JK; Treacy, EP; ; (2005) BMC MEDICAL GENETICS Polymorphisms of the Flavin containing monooxygenase 3 (FMO3) gene do not predispose to essential hypertension in Caucasians [Details]
                       

Abstract

Surendran, P,Vangjeli, C,McCarthy, N,Thom, S,Sever, P,O'Brien, E,Poulter, N,Mayet, J,Hughes, A,Caulfield, M,Munroe, P,Johnson, T,Shields, D,Stanton, A (2012) Genome-wide association analysis identifies the MTHFR-CLCN6-NPPA-NPPB gene cluster as an important influence on BNP levels-implications for the use of BNP levels in the diagnosis and therapeutic monitoring of heart failure-an ASCOT sub study. Abstract [Details]
McCarthy, N,Vangjeli, C,Surendran, P,Treumann, A,Rooney, C,Ho, E,Sever, P,Thom, S,Hughes, A,Munroe, P,Howard, P,Johnson, T,Caulfield, MJ,Shields, D,O'Brien, E,Fitzgerald, D,Stanton, A (2011) PPARGC1 beta is a genetic determinant of the cardiovascular risk factor, Thromboxane A2-an Anglo-Scandinavian Cardiac Outcomes Trial (ASCOT) sub-study. Abstract [Details]
Johnson, T,Shaw-Hawkins, S,Howard, P,Lathrop, M,Stanton, A,Shields, D,Poulter, N,Sever, P,Munroe, PB,Caulfield, M (2010) A novel gene locus for blood pressure variability identified by genomewide association scanning in the Anglo-Scandinavian Cardiac Outcome Trial. Abstract [Details]
Edwards, R,Moran, N,Devocelle, M,Kiernan, A,Dunne, E,Meade, G,Park, S,Foy, M,Kenny, D,Shields, D (2008) Identification of novel bioactive peptide sequences from human proteins for the development of potential therapeutics. Abstract [Details]
Barton, DE,Kelly, H,Yoneda, A,Darlow, JM,Shields, D,Molony, C,Puri, P (2006) A genome-wide scan for genes involved in vesicoureteral reflux. Abstract [Details]
Ennis, S,Bermingham, C,Kelly, H,Yoneda, A,Kelly, S,Shields, D,Molony, C,Green, AJ,Puri, P,Barton, DE (2001) Exclusion of the candidate gene Uroplakin III in primary vesicoureteral reflux. Abstract [Details]
Yoneda, A,Kelly, S,Shields, D,Molony, C,Green, AJ,Puri, P,Barton, DE (2001) No evidence for a role for the angiotensin II, type 2 receptor in primary vesicoureteral reflux. Abstract [Details]
                                                               

Research

Research Interests

RESEARCH INTERESTS:

Our group focuses on identifying functional regions of proteins and genes that impact on disease risk and therapy. This is focused on functional oligopeptides and polymorphism in disease.

GENETIC POLYMORPHISM AND DISEASE

Genome wide association technology and sequencing technology are revolutionising the discovery of genetic associations. We are interested in three disease areas: cardiovascular disease, autism and cancer. We have particular interests in gene combinations (epistasis or synergy) and in amino acid altering variants. 

TOWARDS THE DRUGGABLE INTERACTOME

The human genome sequence gives us a set of predicted protein sequences. Many of these proteins represent useful drug targets. However, simply knocking out or over-activating the primary enzymatic or signal transduction activity of such targets may not yield the most appropriate clinical response. For this reason, the pharmaceutical industry is increasingly focusing on targeting protein-protein interactions involved in more subtly modifying signalling in cells. There is strong evidence (www.elm.eu.org) that some short regions of proteins (<10 amino acids) have independent function, often involved in mediating transient protein interactions. These are attractive starting points for modulating protein interactions, since the interface between proteins is often relatively small, making it easier to modulate. Our group develop bioinformatic methods (link to references) to systematically survey and identify short peptides and motifs of most interest from human and viral proteins. With collaborators, we experimentally validate which of these are likely to be bioactive peptides. Such peptides/peptidomimetics may then be used to tease apart signalling pathways important in health and disease, and ultimately may themselves be lead therapeutics to target aspects of pathways. For this reason, we develop methods to identify non-peptide mimetic compounds that may be more powerful and clinically applicable modulators. The bioinformatic methods combine evolutionary modelling, structural modelling, chemical modelling and statistical modelling, and our researchers have been drawn from many backgrounds: biology, computer science, statistics, mathematics, chemistry, and engineering. Current focus is on cyclic peptides targeting cancer and cardiovascular disease (platelet function). 


See http://bioinformatics.ucd.ie/shields

RESEARCH GROUP

Postdoc: Anthony Chubb (PhD programme Manager and cheminformatics research group leader)
Postdoc: Therese Holton: Milk peptides and mass spectrometric analysis.  
Postdoc: Ilias Stavropoulos: peptide functional effects (experimental analysis) 
Postdoc: Kevin O'Brien: polyproline helix II prediction and analysis
Postdoc: Veranika Zobnina: designing lipidated compounds targeting integrin complex signalling

Current PhD students:

Darren Fitzpatrick: genetic interactions and gene expression, a network approach (co-supervisor Dr Derek Greene, part of CLIQUE SFI research cluster)
Alessandra Bianchin: cheminformatic and experimental investigation of malaria (supervised by Anthony Chubb).
Nikunj Mahashwari:  Wellcome Trust PhD programme: cyclic anti-Tb peptides, co-supervised with Steve Gordon).
Aoife Crowe: IRC fellowship studying membrane-permeable cyclic peptides (co-supervised with Vio Buchete, Physics)

Tilen Kranjc (primary supervisor Jez Simpson, studying localisation of proteins involved in cellular trafficking)

 

Research Projects

Sponsor : Science Foundation Ireland (SFI)
Title : Towards the druggable interactome: bioinformatic analysis of protein interactions and oligopeptide modulation of signalling networks
Start Date / End Date : 01-JAN-11 / 31-DEC-15
Sponsor : The Wellcome Trust (WT)
Title : Computational Infection Biology
Start Date / End Date : 01-OCT-11 / 30-SEP-15
Sponsor : University College Dublin (UCD)
Title : Genetic associations in determining cardiovascular risk prediction - Application for conference participation funding (Dissemination and Outputs)
Start Date / End Date : 01-MAY-12 / 31-OCT-13
Sponsor : Enterprise Ireland (EI)
Title : Computational Network Biology coordinator support
Start Date / End Date : 15-DEC-11 / 12-JAN-12
Sponsor : Enterprise Ireland (EI)
Title : Computational Cancer Network Biology coordinator support
Start Date / End Date : 23-AUG-12 / 22-NOV-12
Sponsor : Science Foundation Ireland (SFI)
Title : Computational Biology and Innovation 2013
Start Date / End Date : 01-OCT-13 / 31-MAR-14
Sponsor : Carbery Milk Products
Title : Matching samples using proteomics and bioinformatics technologies
Start Date / End Date : 17-JAN-14 / 27-FEB-14
Sponsor : Science Foundation Ireland (SFI)
Title : 5th Annual PhD Symposium in Computational Biology & Innovation
Start Date / End Date : 01-OCT-14 / 31-MAR-15
Sponsor : University College Dublin Foundation Ltd.
Title : ICON Newman Fellowship in Genomics
Start Date / End Date : 01-JUN-12 / 30-JUN-15
Sponsor : Science Foundation Ireland (SFI)
Title : Computational Biology and Innovation PhD Symposium 2012
Start Date / End Date : 01-NOV-12 / 30-APR-13
Sponsor : Irish Research Council (IRC)
Title : Structural and dynamic properties of peptides traversing lipid membranes: computational modelling of cell penetration and membrane anchoring
Start Date / End Date : 01-OCT-13 / 30-SEP-17
Sponsor : Food for Health Ireland - FHI2 UCD
Title : FHI-2 Technology
Start Date / End Date : 02-SEP-13 / 02-SEP-18
Sponsor : Irish Research Council for Science Engineering and Technology (IRCSET)
Title : The co-evolution of human, bifidobacteria, and milk as a means for the discovery of novel therapeutic strategies
Start Date / End Date : 10-SEP-10 / 31-JAN-14
Sponsor : Enterprise Ireland (EI)
Title : Functional Food Centre (WP1)
Start Date / End Date : 01-JUN-08 / 31-MAY-13
Sponsor : Science Foundation Ireland (SFI)
Title : Towards the druggable interactome: bioinformatic analysis of protein
Start Date / End Date : 01-JAN-09 / 31-DEC-15
Sponsor : Irish Research Council for Science Engineering and Technology (IRCSET)
Title : Unraveling the evolution of mammalian milk proteins and the detection of novel bioactive peptides.
Start Date / End Date : 15-JUL-08 / 14-JUL-10
Sponsor : Irish Research Council for Science Engineering and Technology (IRCSET)
Title : Bioinformatics and Computational Biomedicine PhD Programme
Start Date / End Date : 01-OCT-07 / 31-DEC-15
Sponsor : Irish Research Council for Science Engineering and Technology (IRCSET)
Title : "Bioinformatics & Computational Biomedicine PhD Programme"
Start Date / End Date : 01-OCT-07 / 30-SEP-12
Sponsor : Irish Research Council for Science Engineering and Technology (IRCSET)
Title : optimal experimental Design for Darwise Gene Interaction Datasets
Start Date / End Date : 01-AUG-07 / 31-JUL-09
Sponsor : Irish Research Council for the Humanities and Social Sciences (IRCHSS)
Irish Research Council for Science Engineering and Technology (IRCSET)
Title : Bioinformation and computational biomedicine PHD programme
Start Date / End Date : 18-NOV-06 / 31-JUL-07
Sponsor : Science Foundation Ireland (SFI)
Title : Functional Bio-informatics of protein MidroDomains and the Design of Biologically Active Peptides from Transmembrane Proteins
Start Date / End Date : 01-OCT-03 / 30-SEP-07
Sponsor : UCD Conway Institute
Title : Professor of Clinical Bioinformatics Start-up Funding
Start Date / End Date : 01-OCT-05 / 30-JUN-15
Sponsor : Science Foundation Ireland (SFI)
Title : Functional bioinformatics of protein micro-domains and the design of biologically active peptides from transmembrane proteins
Start Date / End Date : 01-JUL-04 / 31-DEC-05
Sponsor : Science Foundation Ireland (SFI)
Title : Pharmacophore Linkage of Oligopeptide Motifs to Drugs
Start Date / End Date : 01-FEB-06 / 31-JAN-07

Recent Postgraduates

Recent postgraduate students:
Norman Davey: discovery of short protein motifs (2009): postdoctoral fellow, UCSF
Ravindra Pushker: viral protein motifs (2010) next-gen sequencing company, Chennai, India.
Naisha Shah: genetics of autism (2012) John Zhang group, NIH, Bethesda, MD, USA
Ilias Stavrapoulos: short oligopeptides influencing EMT (2012), postdoctoral fellow, in my group.
Federica Lombardi: platelet pathways (2012) Postdoctoral fellow, IRB, Barcelona

Praveen Surendran: cardiovascular genetics (2013) Postdoctoral fellow, University of Cambridge UK.
Gianluca Negri. biological network analysis. (2013) postdoc, U  British Columbia 

Fergal Duffy (Oct 2013) seeking postdoctoral fellowship, US

Kevin O'Brien protein motifs and peptides in integrin signalling (viva Nov 2013) postdoc in my group.  

 

Current Postgraduate Students

Nikunj Maheshwari, Doctor of Philosophy (PhD)   -   Thesis Supervisor

Teaching

 

Modules Coordinated

201400   MEIN30240     Medical Informatics: Bioinformatics
201400   CNWY40070     Conway Institute: Bioinformatics Research Sem
       

Collaborators

Internal Collaborators

Des Higgins, UCD Conway Institute
Bioinformatics
http://www.ucd.ie/conway/cv_248.html


Ger Cagney, UCD Conway Institute
Protein interactions
http://www.ucd.ie/conway/cv_400.html


Finian Martin, UCD Conway Institute
Motifs, epidermal-mesenchymal transition

Gianluca Pollastri, UCD CASL
Neural nets for oligopeptide structure

Sean Ennis
Bioinformatic analysis of the genetics of autism

Vio Buchete, Physics UCD. Structural modelling of peptides near membranes.

Ulla Knaus, Medicine UCD. NOX signalling and inflammation.

Jez Simpson, UCD. Protein motifs and protein localisation.  

 David O'Connell, UCD, protein interaction studies (SPR)
 

 


External Collaborators


Niamh Moran, RCSI (Royal College of Surgeons in Ireland)
Platelet biology

Marc Devocelle, RCSI (Royal College of Surgeons in Ireland)
Peptide synthesis and function

Gianpiero Cavelleri/Peter Conlon, RCSI (Royal College of Surgeons in Ireland)
Genetics of renal transplant

Alice Stanton, RCSI Cardiovascular genetics

Mark Caulfield, St Barts, London (cardiovascular genetics)