Professor Denis Shields

Research

Professor Denis Shields B.A.Mod., PhD.

Contact Details

Address	Complex & Adaptive Systems Laboratory 2m
Telephone:	7165344

Title	Professor of Clinical Bioinformatics
Address	Conway Institute of Biomolecular & Biomedical Research 2m Complex and Adaptive Systems Laboratory University College Dublin Belfield Dublin 4
Telephone:	Ext. 5344
Email:	ei.dcu@sdleihs.sined
Homepage:	Web Page

Address

Complex & Adaptive Systems Laboratory

Address

School of Medicine & Medical Science

Title	Professor of Clinical Bioinformatics
Address	School of Medicine & Medical Science Belfield Office Park - 8 Belfield Dublin 4
Telephone:	Ext. 5344
Email:	ei.dcu@sdleihs.sined

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

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 two disease areas: cardiovascular disease, and autism. We have particular interests in the identification of structural re-arrangements associated with disease, and in the role of functional amino acid changes that do not simply weaken protein structure.

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.

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

RESEARCH GROUP:

Postdoc: Nora Khaldi (Jan 08): Computer analysis to identify milk bioactive peptides, and analysing the evolution of milk proteins
Postdoc: Niall Haslam (Oct 09): motif discovery and peptide analysis

Postdoc: Catherine Mooney: peptidomimetics and protein interaction inhibition
Postdoc: Anthony Chubb (PhD programme Manager and cheminformatics research group leader)

Current PhD students are:
Ravindra Pushker: short motifs and other determinants of viral pathogenicity
Naisha Shah: Bioinformatics applied to the genetics of autism (copy number variation, and systems analysis)
Ilias Stavrapoulos: Bioinformatic prediction and experimental evaluation of short oligopeptides influencing epithelial to mesenchymal transition
Federica Lombardi: Hyper-aggregable platelets: computer prediction and analysis of short oligopeptides and other reagents involved in pathway interaction (Jan 08)
Praveen Surendran: Bioinformatic analyses of cardiovascular genetic variation (co-supervisor Alice Stanton RCSI)

Kevin O'Brien: chimeric palmitylated peptides in platelet signalling (co-supervisor Niamh Moran RCSI)

Fergal Duffy: constrained peptides virtual library: modelling and testing (co-supervisor Marc Devocelle RCSI)

Eanna O'Keeffe: Evolution of motifs and disordered regions of proteins

Gian Luca Negri: integration of physical and functional information in biological networks (co-supervisor Ger Cagney, part of the CLIQUE SFI research cluster)

Darren Fitzpatrick: genetic interactions and gene expression, a network approach (co-supervisor Dr Derek Greene, part of CLIQUE SFI research cluster)

Research Projects

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-13

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-13

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
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Book Chapters

Mooney, C. and Davey, N. and Martin, AJ and Walsh, I. and Shields, D.C. and Pollastri, G.; (2011) 'In Silico Protein Motif Discovery and Structural Analysis' In: Bing Yu and Marcus Hinchcliffe (eds). In Silico Tools in Gene Discovery. Humana Press.

[DOI] [Details]

Shields DC, Johnston CR, Wallace IM, Edwards RJ; (2007) 'Evolution of specificity and diversity' In: DA Liberles (eds). Ancestral Sequence Reconstruction. Oxford: *. [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. [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

Mooney C, Pollastri G, Shields DC, Haslam NJ; (2011) 'Prediction of short linear protein binding regions'. Journal of molecular biology, .

[DOI] [Details]

Mooney C, Davey N, Martin AJ, Walsh I, Shields DC, Pollastri G; (2011) 'In silico protein motif discovery and structural analysis'. Methods, 760 :341-353. [DOI] [Details]

Casey JP, Magalhaes T, Conroy JM, Regan R, Shah N, Anney R, Shields DC, Abrahams BS, Almeida J, Bacchelli E, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bolton PF, 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 BA, Folstein SE, Foley S, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Green J, Guter SJ, Hakonarson H, Holt R, Hughes G, Hus V, 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 JA, 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 DH, Haines JL, Hallmayer J, Monaco AP, Nurnberger JI Jr, Pericak-Vance MA, Schellenberg GD, Scherer SW, Sutcliffe JS, Szatmari P, Vieland VJ, Wijsman EM, Green A, Gill M, Gallagher L, Vicente A, Ennis S.; (2011) 'A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder'. Human Genetics, . [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. [DOI] [Details]

Khaldi, N,Shields, DC; (2011) 'Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species'. Biology Direct, 6 . [DOI] [Details]

Montanari, F,Shields, DC,Khaldi, N; (2011) 'Differences in the Number of Intrinsically Disordered Regions between Yeast Duplicated Proteins, and Their Relationship with Functional Divergence'. PLoS ONE, 6 . [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]
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]
Fitzgerald DJ, Maree AO, Vangjeli C, Jneid H, Ryan J, Cox D, Cannon CP, Shields DC, ; (2010) 'G-Protein beta3 subunit Polymorphism and Bleeding in the Orbofiban in Patients with Unstable Coronary Syndromes-Thrombolysis In Myocardial Infarction (OPUS-TIMI) 16 Trial'. Journal of Thrombosis and Haemostasis, (NA). [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'. Journal of Virology, 84 (7):3644-3653. [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 Suppl :1-9. [DOI] [Details]
Davey NE, Edwards RJ, Shields DC; (2010) 'Computational identification and analysis of protein short linear motifs'. FRONT BIOSCI, 15 :801-825. [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]
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]
Pushker, R,Jacque, JM,Shields, DC; (2010) 'Meta-Analysis To Test the Association of HIV-1 nef Amino Acid Differences and Deletions with Disease Progression'. Virology, 84 :3644-3653. [DOI] [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'. Gene, 85 :628-642. [DOI] [Details]
Casey, FP,Pihan, E,Shields, DC; (2009) 'Discovery of Small Molecule Inhibitors of Protein-Protein Interactions Using Combined Ligand and Target Score Normalization'. J CHEM INF MODEL, 49 :2708-2717. [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. [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]
Parthasarathi, L,Casey, F,Stein, A,Aloy, P,Shields, DC; (2008) 'Approved Drug Mimics of Short Peptide Ligands from Protein Interaction Motifs'. J CHEM INF MODEL, 48 :1943-1948. [DOI] [Details]
Edwards, RJ,Davey, NE,Shields, DC; (2008) 'CompariMotif: quick and easy comparisons of sequence motifs'. Bioinformatics, 24 :1307-1309. [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]
Casey, FP,Cagney, G,Krogan, NJ,Shields, DC; (2008) 'Optimal stepwise experimental design for pairwise functional interaction studies'. Bioinformatics, 24 :2733-2739. [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]
Shields DC, Casey FP, Cagney G, Krogan NJ, ; (2008) 'Optimal stepwise experimental design for pairwise functional interaction studies'. Bioinformatics, . [DOI] [Details]
Shields DC, Casey FP, Cagney G, Krogan NJ, ; (2008) 'Optimal stepwise experimental design for pairwise functional interaction studies'. Bioinformatics, (NA). [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. [Details]
Moore, N,Dicker, P,O'Brien, JK,Stojanovic, M,Conroy, RM,Treumann, A,O'Brien, ET,Fitzgerald, D,Shields, D,Stanton, AV; (2007) 'Renin gene polymorphisms and haplotypes, blood pressure, and responses to renin-angiotensin system inhibition'. Hypertension, 50 :340-347. [DOI] [Details]
Lavin, PJ,Laing, ME,O'Kelly, P,Moloney, FJ,Gopinathan, D,Al Aradi, A,Shields, DC,Murphy, GM,Conlon, PJ; (2007) 'Improved renal allograft survival with vitamin D receptor polymorphism'. Renal failure, 29 :785-789. [DOI] [Details]
Edwards, RJ,Davey, NE,Shields, DC; (2007) 'SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins'. PLoS ONE, 2 . [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]
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. [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]
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 and Evolution, 24 (1):315-323. [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 and Evolution, 24 (1):315-323. [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'. Journal of 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'. NAT CHEM BIOL, 3 :108-112. [DOI] [Details]
Baran, I,Varekova, RS,Parthasarathi, L,Suchomel, S,Casey, F,Shields, DC; (2007) 'Identification of potential small molecule peptidomimetics similar to motifs in proteins'. J CHEM INF MODEL, 47 :464-474. [DOI] [Details]
Laing, ME,Dicker, P,Moloney, FJ,Ho, WL,Murphy, GM,Conlon, P,Whitehead, AS,Shields, DC; (2007) 'Association of methylenetetrahydrofolate reductase polymorphism and the risk of squamous cell carcinoma in renal transplant patients'. Planta, 84 :113-116. [DOI] [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'. Journal of Medical Genetics, 43 (NA):85-85. [DOI] [Details]
Parthasarathi, L; Devocelle, M; Sondergaard, C; Baran, I; O'Dushlaine, CT; Davey, NE; Edwards, RJ; Moran, N; Kenny, D; Shields, DC; ; (2006) 'Absolute net charge and the biological activity of oligopeptides'. Journal of Chemical Information and Modeling, 46 (5):2183-2190. [Details]
Davey, NE; Shields, DC; Edwards, RJ; ; (2006) 'SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent'. Nucleic Acids Research, 34 (12):3546-3554. [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. [DOI] [Details]
Davey, NE,Shields, DC,Edwards, RJ; (2006) 'SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent'. Nucleic Acids Research, 34 :3546-3554. [DOI] [Details]
O'Dushlaine, CT,Shields, DC; (2006) 'Tools for the identification of variable and potentially variable tandem repeats'. Genomics, 7 . [DOI] [Details]
Parthasarathi, L,Devocelle, M,Sondergaard, C,Baran, I,O'Dushlaine, CT,Davey, NE,Edwards, RJ,Moran, N,Kenny, D,Shields, DC; (2006) 'Absolute net charge and the biological activity of oligopeptides'. J CHEM INF MODEL, 46 :2183-2190. [DOI] [Details]
C.J. Shields, D.C. Winter. ; (2006) 'Infliximab For Ulcerative Colitis'. New England Journal of Medicine, 354 (13):1424-1426. [Details]
Moran N, Kiernan A, Dunne E, Edwards RJ, Shields DC & Kenny D; (2006) 'Monitoring Modulators of Platelet Aggregation in a Microtitre Plate Assay'. ANALYTICAL BIOCHEMISTRY, 357 (1):77-84. [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 PlA2 expression bias and GPIIb/IIIa receptor density in platelets'. BRITISH JOURNAL OF HAEMATOLOGY, . [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. [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]
Edwards RJ and Shields DC; (2005) 'BADASP: predicting functional specificity in protein families using ancestral sequences'. BIOINFORMATICS, 21 (22):4190-4191. [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]
O'Dushlaine CT, Edwards RJ, Park SD and Shields DC ; (2005) 'Tandem repeat copy-number variation in protein-coding regions of human genes'. GENOME BIOLOGY, 6 . [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'. European Journal of Human Genetics, 13 (4):500-502. [Details]
Cagney, G, Park, S, Chung, C, Tong, B, O'Dushlaine, C, Shields, DC, Emili, A, ; (2005) 'Human tissue profiling with multidimensional protein identification technology'. Journal of Proteome Research, 4 (5):1757-1767. [DOI] [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]
Cagney, G,Park, S,Chung, C,Tong, B,O'Dushlaine, C,Shields, DC,Emili, A; (2005) 'Human tissue profiling with multidimensional protein identification technology'. Journal of Proteome Research, 4 :1757-1767. [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'. European Journal of Human Genetics, 13 (4):500-502. [Details]
Emili A, Cagney G, Park S, Chung C, Tong B, O'Dushlaine C, Shields DC, ; (2005) 'Human tissue profiling with multidimensional protein identification technology'. Journal of Proteome Research, 4 (5):1757-1767. [DOI] [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, . [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]
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'. European Journal of Human Genetics, 13 (4):500-502. [Details]
Dolan, C,Shields, DC,Stanton, A,O'Brien, E,Lambert, DM,O'Brien, JK,Treacy, EP; (2005) 'Polymorphisms of the Flavin containing monooxygenase 3 (FMO3) gene do not predispose to essential hypertension in Caucasians'. Gene, 6 . [DOI] [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'. European Journal of Human Genetics, 13 (4):500-502. [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'. Mol Cell Proteomics, 3 (2):133-44. [Details]
McRedmond JP, Park SD, Reilly DF, Coppinger JA, Maguire PB, Shields DC & Fitzgerald DJ; (2004) 'Integration of proteomics and genomics in platelets: a profile of platelet proteins and platelet-specific genes'. Mol Cell Proteomics, (3):133-144. [Details]
Edwards, RJ & Shields DC; (2004) 'GASP: Gapped Ancestral Sequence Prediction for proteins'. BMC Bioinformatics, 5 (1). [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., Fitzgerald, A. P., O'Neill, P. A., Muckian, C., Kenny, D., Moran, B., Cannon, C. P., Byrne, C. E., Fitzgerald, D. J.; (2002) 'The contribution of genetic factors to thrombotic and bleeding outcomes in coronary patients randomised to IIb/IIIa antagonists'. Pharmacogenomics J, 2 (3):182-90. [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]
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]
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]
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]
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]
Cunnane G, Grehan S, Shields D, McCormack C, Whitehead A, Bresnihan B, FitzGerald O; (2000) 'Serum amyloid A in the assessment of early inflammatory arthritis'. Journal of Rheumatology, 27 (1):58-63. [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'. J Obstet Gynaecol, 20 (3):250-5. [Details]
Maree AO, Vangjeli C, Jneid H, Ryan J, Cox D, Cannon CP, Shields DC, Fitzgerald DJ.; (2010) 'G-Protein beta3 subunit Polymorphism and Bleeding in the Orbofiban in Patients with Unstable Coronary Syndromes-Thrombolysis In Myocardial Infarction (OPUS-TIMI) 16 Trial'. Journal of Thrombosis and Haemostasis, . [DOI] [Details]
Pushker R, Jacque JM, Shields DC; (2010) 'Meta-analysis to test the association of HIV-1 nef amino acid differences and deletions with disease progression'. Virology, . [DOI] [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 (1). [DOI] [Details]
Edwards RJ, Davey NE, Shields DC, ; (2009) 'Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery'. Bioinformatics, 25 (4):443-450. [DOI] [Details]
Hingorani AD, 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, ; (2009) 'Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip'. American Journal of Human Genetics, 85 (5):628-642. [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]
Hunt SW 3rd, Miller J, Agarwal A, Devi LA, Fontanini K, Hamilton JA, Pin JP, Shields DC, Spek CA, Sakmar TP, Kuliopulos A, ; (2009) 'Insider access: pepducin symposium explores a new approach to GPCR modulation'. Annals of the New York Academy of Sciences, 1180 Suppl 1 :1-12. [DOI] [Details]
Casey FP, Pihan E, Shields DC; (2009) 'Discovery of small molecule inhibitors of protein-protein interactions using combined ligand and target score normalization'. Journal of Chemical Information and Modeling, 49 (12):2708-2717. [DOI] [Details]
Bernard E, Parthasarathi L, Cho MK, Aylward K, Raab M, Daxecker H, O'Dushlaine CT, Shields DC, Devocelle M, Keyes T, Cosgrave L, O'Neill S, Mok KH, Moran N.; (2009) 'Ligand switching in cell-permeable peptides: manipulation of the alpha-integrin signature motif'. ACS Chemical Biology, 4 (6):457-471. [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]
Shields DC, Casey FP, Cagney G, Krogan NJ, ; (2008) 'Optimal stepwise experimental design for pairwise functional interaction studies'. Bioinformatics, . [DOI] [Details]
Shields DC, Casey FP, Davey NE, Baran I, Varekova RS, ; (2008) 'Web server to identify similarity of amino acid motifs to compounds (SAAMCO)'. Journal of Chemical Information and Modeling, 48 (7):1524-1529. [DOI] [Details]
Edwards, R. J., Davey, N. E., Shields, D. C., ; (2008) 'CompariMotif: quick and easy comparisons of sequence motifs'. Bioinformatics, 24 (10):1307-1309. [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]
Shields DC, O'Halloran AM, Patterson CC, Horan P, Maree A, Curtin R, Stanton A, McKeown PP, ; (2008) '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, . [DOI] [Details]
O'Dushlaine CT, Shields DC; (2008) 'Marked variation in predicted and observed variability of tandem repeat loci across the human genome'. BMC Genomics, 9 . [Details]
Shields DC, Edwards RJ, Davey NE, ; (2008) 'CompariMotif: quick and easy comparisons of sequence motifs'. Bioinformatics, 10 (NA):1307-1309. [DOI] [Details]
Ryan, A. W., 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 (1):465-466. [Details]
Laing, ME, Dicker, P, Moloney, FJ, Ho, WL, Murphy, GM, Conlon, P, Whitehead, AS, Shields, DC, ; (2007) 'Association of methylenetetrahydrofolate reductase polymorphism and the risk of squamous cell carcinoma in renal transplant patients'. Transplantation, 84 :113-116. [Details]
Baran, I, Varekova, RS, Parthasarathi, L, Suchomel, S, Casey, F, Shields, DC, ; (2007) 'Identification of potential small molecule peptidomimetics similar to motifs in proteins'. J CHEM INF MODEL, 47 :464-474. [Details]
Johnston, CR, ODushlaine, 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 and Evolution, 24 :315-323. [Details]
Conlon PJ, Lavin PJ, Laing ME, O'Kelly P, Moloney FJ, Gopinathan D, Aradi AA, Shields DC, Murphy GM, ; (2007) 'Improved renal allograft survival with vitamin D receptor polymorphism'. Renal failure, 29 (7):785-789. [DOI] [Details]
Parthasarathi, L, Devocelle, M, Sondergaard, C, Baran, I, O'Dushlaine, CT, Davey, NE, Edwards, RJ, Moran, N, Kenny, D, Shields, DC, ; (2006) 'Absolute net charge and the biological activity of oligopeptides'. J CHEM INF MODEL, 46 (5):2183-2190. [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. [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'. Eur J Anaesthesiol, 24 (11):912-9. [Details]
Davey, N. E.,Edwards, R. J.,Shields, D. C.; (2007) 'The SLiMDisc server: short, linear motif discovery in proteins'. Nucleic Acids Res, 35 (Web Server issue):W455-9. [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). [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. [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]
Cagney, G; Park, S; Chung, C; Tong, B; O'Dushlaine, C; Shields, DC; Emili, A; ; (2005) 'Human tissue profiling with multidimensional protein identification technology'. Journal of Proteome Research, 4 (5):1757-1767. [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 and Evolution, 24 (1):315-323. [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]
Davey, N., Shields, D.C. Edwards, R.J.; (2006) 'SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent'. NUCLEIC ACIDS RESEARCH, . [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'. BRITISH JOURNAL OF DERMATOLOGY, . [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 PlA2 expression bias and GPIIb/IIIa receptor density in platelets'. BRITISH JOURNAL OF HAEMATOLOGY, . [Details]
Moran N, Kiernan A, Dunne E, Edwards RJ, Shields DC, Kenny D; (2006) 'Monitoring modulators of platelet aggregation in a microtiter plate assay'. ANALYTICAL BIOCHEMISTRY, 357 :77-84. [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'. Journal of Medical Genetics, 43 (NA):85-85. [Details]
Davey, NE; Shields, DC; Edwards, RJ; ; (2006) 'SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent'. Nucleic Acids Research, 34 (12):3546-3554. [Details]
Parthasarathi, L; Devocelle, M; Sondergaard, C; Baran, I; O'Dushlaine, CT; Davey, NE; Edwards, RJ; Moran, N; Kenny, D; Shields, DC; ; (2006) 'Absolute net charge and the biological activity of oligopeptides'. Journal of Chemical Information and Modeling, 46 (5):2183-2190. [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'. Annals of Human Genetics, 70 (NA):934-945. [Details]
O'Halloran, A.M., Stanton, A., O'Brien, E. Shields, D.C.; (2006) 'The impact on coronary artery disease of common polymorphisms known to modulate responses to pathogens'. Ann Hum Genet, . [Details]
O'Dushlaine, CT; Shields, DC; ; (2006) 'Tools for the identification of variable and potentially variable tandem repeats'. BMC Genomics, 7 (NA). [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'. Journal of Proteome Research, . [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]
Dolan C, O'Halloran A, Bradley DG, Croke DT, Evans A, O'Brien JK, Dicker P , Shields DC ; (2005) 'Genetic stratification of pathogen-response related and other variants within a homogeneous Caucasian Irish population'. EUROPEAN JOURNAL OF HUMAN GENETICS, 13 :798-806. [Details]
Dolan, C; Shields, DC; Stanton, A; O'Brien, E; Lambert, DM; O'Brien, JK; Treacy, EP; ; (2005) 'Polymorphisms of the Flavin containing monooxygenase 3 (FMO3) gene do not predispose to essential hypertension in Caucasians'. BMC Medical Genetics, 6 (NA). [Details]
Johnston CR, Shields DC ; (2005) 'A sequence sub-sampling algorithm increases the power to detect distant homologues'. NUCLEIC ACIDS RESEARCH, 32 :3772-3778. [Details]
Molony CM, Fitzgerald AJ, Shields DC ; (2005) 'Over-Dispersion of Allele Frequency Differences Between Populations: Implications for Meta-Analyses of Genotypic Disease Associations'. EUROPEAN JOURNAL OF HUMAN GENETICS, 13 :79-85. [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, . [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'. European Journal of Human Genetics, 13 (4):500-502. [Details]
Byrne CE, Fitzgerald A, Cannon CP, Fitzgerald DJ, Shields DC. ; (2004) 'Elevated white cell count in acute coronary syndromes: relationship to variants in inflammatory and thrombotic genes'. BMC MED. GENET, 5 (13). [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'. BNC BIOINFORMATICS, 5 (123). [Details]
Edwards RJ, Shields DC ; (2004) 'GASP: Gapped Ancestral Sequence Prediction for Proteins'. BMC BIOINFORMATICS, 5 (123). [Details]
McRedmond JP, Park SD, Reilly DF, Coppinger JA, Maguire PB, Shields DC, Fitzgerald DJ.; (2004) 'Integration of proteomics and genomics in platelets: a profile of platelet proteins and platelet-specific genes'. Molecular and Cellular Proteomics, (3):133-144. [Details]
Martin K, Meade G, Moran N, Shields DC, Kenny D; (2003) 'A palmitylated peptide derived from the glycoprotein Ibbeta cytoplasmic tail inhibits platelet activation'. THROMBOSIS AND HAEMOSTASIS, (1):2643-2652. [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 DC, Wolfe KH, Caffrey DC; (2002) 'Wrapping up BLAST and other applications for use on Unix clusters'. BIOINFORMATICS, (19):441-442. [Details]
Cotter P, Caffrey DC, Shields DC; (2002) 'Improved database searches for orthologous sequences by conditioning on outgroup searches'. BIOINFORMATICS, (18):83-91. [Details]
Shields DC, O'Halloran A; (2002) 'Integrating genotypic data with transcriptomic and proteomic data'. Comp Funct. Genomics, (3):22-27. [Details]
Dermot Kenny, Clare Muckian, Desmond J Fitzgerald, Christopher P Cannon, Denis C Shields ; (2002) 'Platelet glycoprotein Ib alpha receptor polymorphisms and recurrent ischaemic events in acute coronary syndrome patients'. J Thrombos. Thrombolys, (13):13-19. [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, (2):182-190. [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]
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]
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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]

Associations

Association: Irish Society of Human Genetics (2007-2009), Function/Role: President

Association: Irish Society of Human Genetics (2001-2004), Function/Role: Council Member

Association: Irish Society of Human Genetics (2005-2007), Function/Role: Secretary

Association: Royal Statistical Society, Function/Role: Member (Fellow)

Association: MORGAM European cardiovascular genetics study Management Group, Function/Role: Member

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.
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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

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Education

Year 1989 Institution: Trinity College Dublin
Qualification: PhD Subject:

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

Outreach Activities

Our website has activities and ideas for anyone interested in exploring the use of computers in making sense of biology:

http://bioinformatics.ucd.ie/shields/kjohnston/eo.html contact denis.shields@ucd.ie for more information

Internal Collaborators

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

Jens Nielsen, UCD Conway Institute
structural biology
http://www.ucd.ie/conway/cv_79.html

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

Jean-Marc Jacque, UCD Centre for Research in Infectious Diseases (CRID)
Oligopeptides/motifs in HIV nef

Mike O'Neill, UCD CASL
Genetic programming for motif discovery

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

External Collaborators

The MORGAM consortium
www.ktl.fi/morgam

Alun Evans, QUB (Queen's University Belfast)
Cardiovascular genetics

Louise Gallagher, Trinity College
Psychiatric genetics

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

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

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

Alice Stanton, RCSI
Cardiovascular genetics

Rob Russell, Heidelberg.

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
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