Research Topics
| Richard J EdwardsSummaryCountry: UK Publications
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Detail Information
Publications
CompariMotif: quick and easy comparisons of sequence motifsRichard J Edwards
UCD Complex and Adaptive Systems Laboratory and UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
Bioinformatics 24:1307-9. 2008..ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/..- Interactome-wide prediction of short, disordered protein interaction motifs in humansRichard J Edwards
Centre for Biological Sciences, University of Southampton, Southampton, UK
Mol Biosyst 8:282-95. 2012..Whether this is due to ascertainment bias or a true functional composition bias of SLiMs is not clear and warrants further investigation... - Masking residues using context-specific evolutionary conservation significantly improves short linear motif discoveryNorman E Davey
UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
Bioinformatics 25:443-50. 2009..Their short and degenerate nature presents a challenge for computational discovery. We sought to improve SLiM discovery by incorporating evolutionary information, since SLiMs are more conserved than surrounding residues... 
SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteinsRichard J Edwards
University College Dublin Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
PLoS ONE 2:e967. 2007..Incorporating ambiguous amino acid positions and/or variable-length wildcard spacers between defined residues further complicates the matter...- The SLiMDisc server: short, linear motif discovery in proteinsNorman E Davey
UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
Nucleic Acids Res 35:W455-9. 2007..Returned motifs can also be compared with known SLiMs from the literature. SLiMDisc is available at: http://bioware.ucd.ie/~slimdisc/... - Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteinsNorman E Davey
UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
BMC Bioinformatics 11:14. 2010..Here, we develop more exact methods and explore the potential biases of computationally efficient approximations... 
Computational identification and analysis of protein short linear motifsNorman E Davey
UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
Front Biosci 15:801-25. 2010..g. of physical protein interactions) as input for computational discovery...- SLiMDisc: short, linear motif discovery, correcting for common evolutionary descentNorman E Davey
Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
Nucleic Acids Res 34:3546-54. 2006..An implementation of Multiple Spanning Tree weighting outperformed two other weighting schemes, in a variety of settings... - Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplicationCatrióna R Johnston
UCD Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
Mol Biol Evol 24:315-23. 2007.... - Shotgun proteomic analysis of Emiliania huxleyi, a marine phytoplankton species of major biogeochemical importanceBethan M Jones
School of Ocean and Earth Science, National Oceanography Centre, Southampton, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, UK
Mar Biotechnol (NY) 13:496-504. 2011..The proteomic and bioinformatic approaches developed in this study are of wider applicability, particularly to the oceanographic community where genomic sequence data for species of interest are currently scarce... - SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regionsNorman E Davey
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden Württemberg 69117, Germany
Nucleic Acids Res 40:10628-41. 2012..Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E... - Absolute net charge and the biological activity of oligopeptidesLaavanya Parthasarathi
UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Republic of Ireland
J Chem Inf Model 46:2183-90. 2006..We conclude that the design of biologically active peptides should consider favoring those with a higher absolute net charge... - BADASP: predicting functional specificity in protein families using ancestral sequencesRichard J Edwards
Clinical Pharmacology, The Royal College of Surgeons in Ireland, Dublin
Bioinformatics 21:4190-1. 2005..Statistics are output along with subfamily groupings and ancestral sequences for an easy analysis with other packages. AVAILABILITY: BADASP is freely available from http://www.bioinformatics.rcsi.ie/~redwards/badasp/.. - GASP: Gapped Ancestral Sequence Prediction for proteinsRichard J Edwards
Bioinformatics Core, Clinical Pharmacology, Royal College of Surgeons in Ireland, 123 St Stephen s Green, Dublin 2, Ireland
BMC Bioinformatics 5:123. 2004..Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments...