GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content. - Denis C. Shields; Desmond G. Higgins; P. M. Sharp (Comput. Appl. Biosci., 1992)

Genome duplication and the evolution of gene Order and chromosome number in yeast. - Cathal Seoighe; Denis C. Shields; Kenneth H. Wolfe (German Conference on Bioinformatics, 1997)

Improved database searches for orthologous sequences by conditioning on outgroup sequences. - Philip J. Cotter; Daniel R. Caffrey; Denis C. Shields (Bioinform., 2002)

Wrapping up BLAST and other applications for use on Unix clusters. - Karsten Hokamp; Denis C. Shields; Kenneth H. Wolfe; Daniel R. Caffrey (Bioinform., 2003)

Investigating the 3D Conformation of N-Terminally Constrained Oligopeptides. - Itizar Frades; Richard J. Edwards; Denis C. Shields (Spanish Bioinformatics Conference, 2004)

GASP: Gapped Ancestral Sequence Prediction for proteins. - Richard J. Edwards; Denis C. Shields (BMC Bioinform., 2004)

BADASP: predicting functional specificity in protein families using ancestral sequences. - Richard J. Edwards; Denis C. Shields (Bioinform., 2005)

Absolute Net Charge and the Biological Activity of Oligopeptides. - 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 (J. Chem. Inf. Model., 2006)

Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins. - Ivan Baran; Radka Svobodová Vareková; Laavanya Parthasarathi; Simon Suchomel; Fergal P. Casey; Denis C. Shields (J. Chem. Inf. Model., 2007)

The SLiMDisc server: short, linear motif discovery in proteins. - Norman E. Davey; Richard J. Edwards; Denis C. Shields (Nucleic Acids Res., 2007)

Optimal stepwise experimental design for pairwise functional interaction studies. - Fergal P. Casey; Gerard Cagney; Nevan J. Krogan; Denis C. Shields (Bioinform., 2008)

CompariMotif: quick and easy comparisons of sequence motifs. - Richard J. Edwards; Norman E. Davey; Denis C. Shields (Bioinform., 2008)

Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO). - Fergal P. Casey; Norman E. Davey; Ivan Baran; Radka Svobodová Vareková; Denis C. Shields (J. Chem. Inf. Model., 2008)

Approved Drug Mimics of Short Peptide Ligands from Protein Interaction Motifs. - Laavanya Parthasarathi; Fergal P. Casey; Amelie Stein; Patrick Aloy; Denis C. Shields (J. Chem. Inf. Model., 2008)

Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. - Norman E. Davey; Denis C. Shields; Richard J. Edwards (Bioinform., 2009)

Discovery of Small Molecule Inhibitors of Protein-Protein Interactions Using Combined Ligand and Target Score Normalization. - Fergal P. Casey; Emilie Pihan; Denis C. Shields (J. Chem. Inf. Model., 2009)

SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context. - Norman E. Davey; Niall J. Haslam; Denis C. Shields; Richard J. Edwards (PRIB, 2010)

Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. - Norman E. Davey; Richard J. Edwards; Denis C. Shields (BMC Bioinform., 2010)

Genome wide association study of nonsynonymous Single Nucleotide Polymorphisms for seven common diseases. - Praveen Surendran; Alice V. Stanton; Denis C. Shields (BMC Bioinform., 2010)

SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. - Norman E. Davey; Niall J. Haslam; Denis C. Shields; Richard J. Edwards (Nucleic Acids Res., 2010)

Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs. - Fergal P. Casey; Nevan J. Krogan; Denis C. Shields; Gerard Cagney (BMC Syst. Biol., 2011)

CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids. - Fergal J. Duffy; Mélanie Verniere; Marc Devocelle; Elise Bernard; Denis C. Shields; Anthony J. Chubb (J. Chem. Inf. Model., 2011)

SLiMSearch 2.0: biological context for short linear motifs in proteins. - Norman E. Davey; Niall J. Haslam; Denis C. Shields; Richard J. Edwards (Nucleic Acids Res., 2011)

Profile-based short linear protein motif discovery. - Niall J. Haslam; Denis C. Shields (BMC Bioinform., 2012)

CPPpred: prediction of cell penetrating peptides. - Thérèse A. Holton; Gianluca Pollastri; Denis C. Shields; Catherine Mooney (Bioinform., 2013)

PeptideLocator: prediction of bioactive peptides in protein sequences. - Catherine Mooney; Niall J. Haslam; Thérèse A. Holton; Gianluca Pollastri; Denis C. Shields (Bioinform., 2013)

SLiMScape: a protein short linear motif analysis plugin for Cytoscape. - Kevin T. O'Brien; Niall J. Haslam; Denis C. Shields (BMC Bioinform., 2013)

Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions. - Fergal J. Duffy; Marc Devocelle; David R. Croucher; Denis C. Shields (BMC Bioinform., 2014)

SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks. - Emily Olorin; Kevin T. O'Brien; Nicolas Palopoli; Åsa Pérez-Bercoff; Denis C. Shields; Richard J. Edwards (F1000Research, 2015)

Virtual Screening Using Combinatorial Cyclic Peptide Libraries Reveals Protein Interfaces Readily Targetable by Cyclic Peptides. - Fergal J. Duffy; Darragh O'Donovan; Marc Devocelle; Niamh Moran; David J. O'Connell; Denis C. Shields (J. Chem. Inf. Model., 2015)

Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies. - Federica Lombardi; Kalyan Golla; Darren J. Fitzpatrick; Fergal P. Casey; Niamh Moran; Denis C. Shields (PLoS Comput. Biol., 2015)

ProViz - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. - Peter Jehl; Jean Manguy; Denis C. Shields; Desmond G. Higgins; Norman E. Davey (Nucleic Acids Res., 2016)

Computational modelling of chromosomally clustering protein domains in bacteria. - Chiara E. Cotroneo; Isobel Claire Gormley; Denis C. Shields; Michael Salter-Townshend (BMC Bioinform., 2021)

A new framework for evaluating model out-of-distribution generalisation for the biochemical domain. - Raúl Fernandez-Diaz; Hoang Thanh Lam; Vanessa López; Denis C. Shields (ICLR, 2025)

Open and Sustainable AI: challenges, opportunities and the road ahead in the life sciences. - Gavin Farrell; Eleni Adamidi; Rafael Andrade Buono; Mihail Anton; Omar Abdelghani Attafi; Salvador Capella-Gutiérrez; Emidio Capriotti; Leyla Jael Castro; Davide Cirillo; Lisa C. Crossman; Christophe Dessimoz; Alexandros C. Dimopoulos; et al. (CoRR, 2025)