Richard J Edwards

Summary

Country: UK

Publications

  1. pmc SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:W534-9. 2010
  2. doi request reprint Interactome-wide prediction of short, disordered protein interaction motifs in humans
    Richard J Edwards
    Centre for Biological Sciences, University of Southampton, Southampton, UK
    Mol Biosyst 8:282-95. 2012
  3. doi request reprint CompariMotif: quick and easy comparisons of sequence motifs
    Richard 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
  4. doi request reprint Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
    Norman 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
  5. pmc The SLiMDisc server: short, linear motif discovery in proteins
    Norman E Davey
    UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
    Nucleic Acids Res 35:W455-9. 2007
  6. pmc SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins
    Richard J Edwards
    University College Dublin Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    PLoS ONE 2:e967. 2007
  7. pmc SLiMSearch 2.0: biological context for short linear motifs in proteins
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 39:W56-60. 2011
  8. pmc Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins
    Norman E Davey
    UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    BMC Bioinformatics 11:14. 2010
  9. ncbi request reprint Computational identification and analysis of protein short linear motifs
    Norman E Davey
    UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    Front Biosci (Landmark Ed) 15:801-25. 2010
  10. pmc SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden Württemberg 69117, Germany
    Nucleic Acids Res 40:10628-41. 2012

Collaborators

Detail Information

Publications18

  1. pmc SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:W534-9. 2010
    ..Returned motifs can also be compared with known SLiMs from the literature using CompariMotif. All results are available for download. The SLiMFinder server is available at: http://bioware.ucd.ie/slimfinder.html...
  2. doi request reprint Interactome-wide prediction of short, disordered protein interaction motifs in humans
    Richard 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...
  3. doi request reprint CompariMotif: quick and easy comparisons of sequence motifs
    Richard 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
    ..Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs...
  4. doi request reprint Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
    Norman 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...
  5. pmc The SLiMDisc server: short, linear motif discovery in proteins
    Norman 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/...
  6. pmc SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins
    Richard 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...
  7. pmc SLiMSearch 2.0: biological context for short linear motifs in proteins
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 39:W56-60. 2011
    ..Users can search motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html...
  8. pmc Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins
    Norman 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...
  9. ncbi request reprint Computational identification and analysis of protein short linear motifs
    Norman E Davey
    UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    Front Biosci (Landmark Ed) 15:801-25. 2010
    ..g. of physical protein interactions) as input for computational discovery...
  10. pmc SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions
    Norman 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...
  11. pmc Responses of the Emiliania huxleyi proteome to ocean acidification
    Bethan M Jones
    Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
    PLoS ONE 8:e61868. 2013
    ..huxleyi strain possesses some acclimation mechanisms to tolerate future CO2 scenarios, although the observed decline in growth rate may be an overriding factor affecting the success of this ecotype in future oceans...
  12. pmc SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent
    Norman 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...
  13. ncbi request reprint Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication
    Catrióna R Johnston
    UCD Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
    Mol Biol Evol 24:315-23. 2007
    ....
  14. doi request reprint Shotgun proteomic analysis of Emiliania huxleyi, a marine phytoplankton species of major biogeochemical importance
    Bethan 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...
  15. ncbi request reprint Absolute net charge and the biological activity of oligopeptides
    Laavanya 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...
  16. pmc ELM--the database of eukaryotic linear motifs
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 40:D242-51. 2012
    ..The motif discovery portion of the ELM resource has added conservation, and structural attributes have been incorporated to aid users to discriminate biologically relevant motifs from stochastically occurring non-functional instances...
  17. ncbi request reprint BADASP: predicting functional specificity in protein families using ancestral sequences
    Richard 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...
  18. pmc GASP: Gapped Ancestral Sequence Prediction for proteins
    Richard 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...