Denis C. Shields

37 papers A* 1Journal 33Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	A*	`conf`	A new framework for evaluating model out-of-distribution generalisation for the biochemical domain. ICLR Raúl Fernández-Díaz, Hoang Thanh Lam, Vanessa López, Denis C. Shields
2025	J	`jnl`	How to build machine learning models able to extrapolate from standard to modified peptides. J. Cheminformatics Raúl Fernández-Díaz, Rodrigo Ochoa, Thanh Lam Hoang, Vanessa López, Denis C. Shields
2025	J	`jnl`	Open and Sustainable AI: challenges, opportunities and the road ahead in the life sciences. CoRR Gavin Farrell, Eleni S. 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, Raúl Fernández-Díaz, Styliani-Christina Fragkouli, Carole A. Goble, Wei Gu, John M. Hancock, Alireza Khanteymoori, Tom Lenaerts, Fabio G. Liberante, Peter Maccallum, Alexander Miguel Monzon, Magnus Palmblad, Lucy Poveda, Ovidiu Radulescu, Denis C. Shields, Shoaib Sufi, Thanasis Vergoulis, Fotis E. Psomopoulos, Silvio C. E. Tosatto
2024	J	`jnl`	AutoPeptideML: a study on how to build more trustworthy peptide bioactivity predictors. Bioinform. Raúl Fernández-Díaz, Rodrigo Cossio-Pérez, Clement Agoni, Hoang Thanh Lam, Vanessa López, Denis C. Shields
2021	J	`jnl`	Computational modelling of chromosomally clustering protein domains in bacteria. BMC Bioinform. Chiara E. Cotroneo, Isobel Claire Gormley, Denis C. Shields, Michael Salter-Townshend
2016	J	`jnl`	ProViz - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. Nucleic Acids Res. Peter Jehl, Jean Manguy, Denis C. Shields, Desmond G. Higgins, Norman E. Davey
2015	J	`jnl`	Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies. PLoS Comput. Biol. Federica Lombardi, Kalyan Golla, Darren J. Fitzpatrick, Fergal P. Casey, Niamh Moran, Denis C. Shields
2015	J	`jnl`	SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks. F1000Research Emily Olorin, Kevin T. O'Brien, Nicolas Palopoli, Åsa Pérez-Bercoff, Denis C. Shields, Richard J. Edwards
2015	J	`jnl`	Virtual Screening Using Combinatorial Cyclic Peptide Libraries Reveals Protein Interfaces Readily Targetable by Cyclic Peptides. J. Chem. Inf. Model. Fergal J. Duffy, Darragh O'Donovan, Marc Devocelle, Niamh Moran, David J. O'Connell, Denis C. Shields
2014	J	`jnl`	Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions. BMC Bioinform. Fergal J. Duffy, Marc Devocelle, David R. Croucher, Denis C. Shields
2013	J	`jnl`	CPPpred: prediction of cell penetrating peptides. Bioinform. Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields, Catherine Mooney
2013	J	`jnl`	PeptideLocator: prediction of bioactive peptides in protein sequences. Bioinform. Catherine Mooney, Niall J. Haslam, Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields
2013	J	`jnl`	SLiMScape: a protein short linear motif analysis plugin for Cytoscape. BMC Bioinform. Kevin T. O'Brien, Niall J. Haslam, Denis C. Shields
2012	J	`jnl`	Profile-based short linear protein motif discovery. BMC Bioinform. Niall J. Haslam, Denis C. Shields
2011	J	`jnl`	CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids. J. Chem. Inf. Model. Fergal J. Duffy, Mélanie Verniere, Marc Devocelle, Elise Bernard, Denis C. Shields, Anthony J. Chubb
2011	J	`jnl`	Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs. BMC Syst. Biol. Fergal P. Casey, Nevan J. Krogan, Denis C. Shields, Gerard Cagney
2011	J	`jnl`	SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Res. Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards
2010	J	`jnl`	Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. BMC Bioinform. Norman E. Davey, Richard J. Edwards, Denis C. Shields
2010	J	`jnl`	Genome wide association study of nonsynonymous Single Nucleotide Polymorphisms for seven common diseases. BMC Bioinform. Praveen Surendran, Alice V. Stanton, Denis C. Shields
2010	J	`jnl`	SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Res. Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards
2010	—	`conf`	SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context. PRIB Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards
2009	J	`jnl`	Discovery of Small Molecule Inhibitors of Protein-Protein Interactions Using Combined Ligand and Target Score Normalization. J. Chem. Inf. Model. Fergal P. Casey, Emilie Pihan, Denis C. Shields
2009	J	`jnl`	Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinform. Norman E. Davey, Denis C. Shields, Richard J. Edwards
2008	J	`jnl`	Approved Drug Mimics of Short Peptide Ligands from Protein Interaction Motifs. J. Chem. Inf. Model. Laavanya Parthasarathi, Fergal P. Casey, Amelie Stein, Patrick Aloy, Denis C. Shields
2008	J	`jnl`	CompariMotif: quick and easy comparisons of sequence motifs. Bioinform. Richard J. Edwards, Norman E. Davey, Denis C. Shields
2008	J	`jnl`	Optimal stepwise experimental design for pairwise functional interaction studies. Bioinform. Fergal P. Casey, Gerard Cagney, Nevan J. Krogan, Denis C. Shields
2008	J	`jnl`	Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO). J. Chem. Inf. Model. Fergal P. Casey, Norman E. Davey, Ivan Baran, Radka Svobodová Vareková, Denis C. Shields
2007	J	`jnl`	Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins. J. Chem. Inf. Model. Ivan Baran, Radka Svobodová Vareková, Laavanya Parthasarathi, Simon Suchomel, Fergal P. Casey, Denis C. Shields
2007	J	`jnl`	The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res. Norman E. Davey, Richard J. Edwards, Denis C. Shields
2006	J	`jnl`	Absolute Net Charge and the Biological Activity of Oligopeptides. J. Chem. Inf. Model. 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
2005	J	`jnl`	BADASP: predicting functional specificity in protein families using ancestral sequences. Bioinform. Richard J. Edwards, Denis C. Shields
2004	J	`jnl`	GASP: Gapped Ancestral Sequence Prediction for proteins. BMC Bioinform. Richard J. Edwards, Denis C. Shields
2004	—	`conf`	Investigating the 3D Conformation of N-Terminally Constrained Oligopeptides. Spanish Bioinformatics Conference Itizar Frades, Richard J. Edwards, Denis C. Shields
2003	J	`jnl`	Wrapping up BLAST and other applications for use on Unix clusters. Bioinform. Karsten Hokamp, Denis C. Shields, Kenneth H. Wolfe, Daniel R. Caffrey
2002	J	`jnl`	Improved database searches for orthologous sequences by conditioning on outgroup sequences. Bioinform. Philip J. Cotter, Daniel R. Caffrey, Denis C. Shields
1997	—	`conf`	Genome duplication and the evolution of gene Order and chromosome number in yeast. German Conference on Bioinformatics Cathal Seoighe, Denis C. Shields, Kenneth H. Wolfe
1992	J	`jnl`	GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content. Comput. Appl. Biosci. Denis C. Shields, Desmond G. Higgins, P. M. Sharp