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2020 – today
- 2021
[j29]Chiara E. Cotroneo, Isobel Claire Gormley
, Denis C. Shields, Michael Salter-Townshend:
Computational modelling of chromosomally clustering protein domains in bacteria. BMC Bioinform. 22(1): 593 (2021)
2010 – 2019
- 2016
- [j28]Peter Jehl, Jean Manguy, Denis C. Shields, Desmond G. Higgins, Norman E. Davey:
ProViz - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. Nucleic Acids Res. 44(Webserver-Issue): W11-W15 (2016) - 2015
- [j27]Fergal J. Duffy, Darragh O'Donovan, Marc Devocelle, Niamh Moran, David J. O'Connell, Denis C. Shields:
Virtual Screening Using Combinatorial Cyclic Peptide Libraries Reveals Protein Interfaces Readily Targetable by Cyclic Peptides. J. Chem. Inf. Model. 55(3): 600-613 (2015) - [j26]Federica Lombardi, Kalyan Golla, Darren J. Fitzpatrick, Fergal P. Casey, Niamh Moran, Denis C. Shields:
Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies. PLoS Comput. Biol. 11(4) (2015) - [i1]Emily Olorin, Kevin T. O'Brien, Nicolas Palopoli, Åsa Pérez-Bercoff, Denis C. Shields, Richard J. Edwards:
SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks. F1000Research 4: 477 (2015) - 2014
- [j25]Fergal J. Duffy, Marc Devocelle, David R. Croucher, Denis C. Shields:
Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions. BMC Bioinform. 15: 305 (2014) - 2013
- [j24]Catherine Mooney, Niall J. Haslam, Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields:
PeptideLocator: prediction of bioactive peptides in protein sequences. Bioinform. 29(9): 1120-1126 (2013) - [j23]Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields, Catherine Mooney:
CPPpred: prediction of cell penetrating peptides. Bioinform. 29(23): 3094-3096 (2013) - [j22]Kevin T. O'Brien, Niall J. Haslam, Denis C. Shields:
SLiMScape: a protein short linear motif analysis plugin for Cytoscape. BMC Bioinform. 14: 224 (2013) - 2012
- [j21]Niall J. Haslam, Denis C. Shields:
Profile-based short linear protein motif discovery. BMC Bioinform. 13: 104 (2012) - 2011
- [j20]Fergal P. Casey, Nevan J. Krogan, Denis C. Shields, Gerard Cagney:
Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs. BMC Syst. Biol. 5: 133 (2011) - [j19]Fergal J. Duffy, Mélanie Verniere, Marc Devocelle, Elise Bernard, Denis C. Shields, Anthony J. Chubb:
CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids. J. Chem. Inf. Model. 51(4): 829-836 (2011) - [j18]Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards:
SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Res. 39(Web-Server-Issue): 56-60 (2011) - 2010
- [j17]Norman E. Davey, Richard J. Edwards, Denis C. Shields:
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. BMC Bioinform. 11: 14 (2010) - [j16]Praveen Surendran, Alice V. Stanton, Denis C. Shields:
Genome wide association study of nonsynonymous Single Nucleotide Polymorphisms for seven common diseases. BMC Bioinform. 11(S-10): O6 (2010) - [j15]Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards:
SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Res. 38(Web-Server-Issue): 534-539 (2010) - [c3]Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards:
SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context. PRIB 2010: 50-61
2000 – 2009
- 2009
- [j14]Norman E. Davey, Denis C. Shields, Richard J. Edwards:
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinform. 25(4): 443-450 (2009) - [j13]Fergal P. Casey, Emilie Pihan, Denis C. Shields:
Discovery of Small Molecule Inhibitors of Protein-Protein Interactions Using Combined Ligand and Target Score Normalization. J. Chem. Inf. Model. 49(12): 2708-2717 (2009) - 2008
- [j12]Richard J. Edwards, Norman E. Davey, Denis C. Shields:
CompariMotif: quick and easy comparisons of sequence motifs. Bioinform. 24(10): 1307-1309 (2008) - [j11]Fergal P. Casey, Gerard Cagney, Nevan J. Krogan, Denis C. Shields:
Optimal stepwise experimental design for pairwise functional interaction studies. Bioinform. 24(23): 2733-2739 (2008) - [j10]Fergal P. Casey, Norman E. Davey, Ivan Baran, Radka Svobodová Vareková, Denis C. Shields:
Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO). J. Chem. Inf. Model. 48(7): 1524-1529 (2008) - [j9]Laavanya Parthasarathi, Fergal P. Casey, Amelie Stein, Patrick Aloy, Denis C. Shields:
Approved Drug Mimics of Short Peptide Ligands from Protein Interaction Motifs. J. Chem. Inf. Model. 48(10): 1943-1948 (2008) - 2007
- [j8]Ivan Baran, Radka Svobodová Vareková, Laavanya Parthasarathi, Simon Suchomel, Fergal P. Casey, Denis C. Shields:
Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins. J. Chem. Inf. Model. 47(2): 464-474 (2007) - [j7]Norman E. Davey, Richard J. Edwards, Denis C. Shields:
The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res. 35(Web-Server-Issue): 455-459 (2007) - 2006
- [j6]Laavanya Parthasarathi, Marc Devocelle, Chresten R. Søndergaard, Ivan Baran, Colm O'Dushlaine, Norman E. Davey, Richard J. Edwards, Niamh Moran, Dermot Kenny, Denis C. Shields:
Absolute Net Charge and the Biological Activity of Oligopeptides. J. Chem. Inf. Model. 46(5): 2183-2190 (2006) - 2005
- [j5]Richard J. Edwards, Denis C. Shields:
BADASP: predicting functional specificity in protein families using ancestral sequences. Bioinform. 21(22): 4190-4191 (2005) - 2004
- [j4]Richard J. Edwards, Denis C. Shields:
GASP: Gapped Ancestral Sequence Prediction for proteins. BMC Bioinform. 5: 123 (2004) - [c2]Itizar Frades, Richard J. Edwards, Denis C. Shields:
Investigating the 3D Conformation of N-Terminally Constrained Oligopeptides. Spanish Bioinformatics Conference 2004: 122-123 - 2003
- [j3]Karsten Hokamp, Denis C. Shields, Kenneth H. Wolfe, Daniel R. Caffrey:
Wrapping up BLAST and other applications for use on Unix clusters. Bioinform. 19(3): 441-442 (2003) - 2002
- [j2]Philip J. Cotter, Daniel R. Caffrey, Denis C. Shields:
Improved database searches for orthologous sequences by conditioning on outgroup sequences. Bioinform. 18(1): 83-91 (2002)
1990 – 1999
- 1997
- [c1]Cathal Seoighe, Denis C. Shields, Kenneth H. Wolfe:
Genome duplication and the evolution of gene Order and chromosome number in yeast. German Conference on Bioinformatics 1997: 61-63 - 1992
- [j1]Denis C. Shields, Desmond G. Higgins, P. M. Sharp:
GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content. Comput. Appl. Biosci. 8(5): 521-523 (1992)
Coauthor Index
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