R R Copley

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. ncbi request reprint Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways
    R R Copley
    Biocomputing, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
    J Mol Biol 303:627-41. 2000
  2. ncbi request reprint Genome and protein evolution in eukaryotes
    Richard R Copley
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Curr Opin Chem Biol 6:39-45. 2002
  3. ncbi request reprint Eukaryotic domain evolution inferred from genome comparisons
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    Curr Opin Genet Dev 13:623-8. 2003
  4. pmc SMART 4.0: towards genomic data integration
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 32:D142-4. 2004
  5. pmc The animal in the genome: comparative genomics and evolution
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
    Philos Trans R Soc Lond B Biol Sci 363:1453-61. 2008
  6. pmc Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes
    Martin S Taylor
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
    Genome Res 14:555-66. 2004
  7. ncbi request reprint Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
    Evol Dev 6:164-9. 2004
  8. ncbi request reprint Evolutionary convergence of alternative splicing in ion channels
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Trends Genet 20:171-6. 2004
  9. ncbi request reprint Analysis of the human VPS13 gene family
    Antonio Velayos-Baeza
    Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, OX3 7BN Oxford, UK
    Genomics 84:536-49. 2004
  10. pmc The EH1 motif in metazoan transcription factors
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
    BMC Genomics 6:169. 2005

Collaborators

Detail Information

Publications30

  1. ncbi request reprint Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways
    R R Copley
    Biocomputing, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
    J Mol Biol 303:627-41. 2000
    ..The results favour widespread recruitment of enzymes between pathways, rather than a "backwards evolution" model, and support the idea that modern proteins may have arisen from common ancestors that bound key metabolites...
  2. ncbi request reprint Genome and protein evolution in eukaryotes
    Richard R Copley
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Curr Opin Chem Biol 6:39-45. 2002
    ..The overall picture is of a huge diversity of gene content within eukaryotic genomes, reflecting different functional demands in different species...
  3. ncbi request reprint Eukaryotic domain evolution inferred from genome comparisons
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    Curr Opin Genet Dev 13:623-8. 2003
    ..If such families are evidence of past adaptation, then their functions must relate to the underlying mechanism of selection: competition among organisms...
  4. pmc SMART 4.0: towards genomic data integration
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 32:D142-4. 2004
    ..Other improvements include the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries...
  5. pmc The animal in the genome: comparative genomics and evolution
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
    Philos Trans R Soc Lond B Biol Sci 363:1453-61. 2008
    ..I examine progress being made in linking genome content to the pattern of animal evolution, and argue that the gap between genomic and phenotypic complexity can only be understood through the totality of interacting components...
  6. pmc Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes
    Martin S Taylor
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
    Genome Res 14:555-66. 2004
    ..There is a specific enrichment of CpG dinucleotides in close proximity to insertion events, and both insertions and deletions are more common in higher G+C content sequences...
  7. ncbi request reprint Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
    Evol Dev 6:164-9. 2004
    ..We conclude that the results from the intensively sampled ribosomal RNA genes supporting the Ecdysozoa hypothesis provide the most credible current estimates of metazoan phylogeny...
  8. ncbi request reprint Evolutionary convergence of alternative splicing in ion channels
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Trends Genet 20:171-6. 2004
    ..The result has important implications for the analysis of regulation of alternative splicing using comparative genomics and our understanding of molecular evolution...
  9. ncbi request reprint Analysis of the human VPS13 gene family
    Antonio Velayos-Baeza
    Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, OX3 7BN Oxford, UK
    Genomics 84:536-49. 2004
    ..Protein sequence comparisons suggest that intramolecular duplications have played an important role in the evolution of this gene family...
  10. pmc The EH1 motif in metazoan transcription factors
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
    BMC Genomics 6:169. 2005
    ..The small size of the motif makes its reliable identification by computational means difficult. I have systematically searched the predicted proteomes of Drosophila, C. elegans and human for further instances of the motif...
  11. pmc Functional conservation of Rel binding sites in drosophilid genomes
    Richard R Copley
    Wellcome Trust Centre for Human Genetics, Oxford University, Oxford OX3 7BN, United Kingdom
    Genome Res 17:1327-35. 2007
    ..We discuss how two types of conservation may contribute to the stabilization and optimization of a functional gene regulatory code in evolution...
  12. pmc The InterPro Database, 2003 brings increased coverage and new features
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 31:315-8. 2003
    ..The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)...
  13. ncbi request reprint Getting the most from your protein sequence
    Richard R Copley
    EMBL, Heidelberg, Germany
    Methods Mol Biol 211:411-30. 2003
  14. pmc Systematic identification of novel protein domain families associated with nuclear functions
    Tobias Doerks
    European Molecular Biology Laboratory, 69114 Heidelberg, Germany
    Genome Res 12:47-56. 2002
    ....
  15. ncbi request reprint CASH--a beta-helix domain widespread among carbohydrate-binding proteins
    Francesca D Ciccarelli
    Max Delbrueck Centrum, PO Box 740238, D 13092 Berlin, Germany
    Trends Biochem Sci 27:59-62. 2002
    ..The CASH domain is characterized by internal repetitions of glycines and hydrophobic residues that correspond to the repetitive units of a predicted or observed right-handed beta-helix structure of the pectate lyase superfamily...
  16. ncbi request reprint Protein domain analysis in the era of complete genomes
    Richard R Copley
    EMBL, Meyerhofstrasse 1, Heidelberg, Germany
    FEBS Lett 513:129-34. 2002
    ....
  17. pmc Recent improvements to the SMART domain-based sequence annotation resource
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 30:242-4. 2002
    ..SMART output can now be easily included in users' documents. A SMART mirror has been created at http://smart.ox.ac.uk...
  18. ncbi request reprint Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster
    Evgeny M Zdobnov
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 298:149-59. 2002
    ....
  19. ncbi request reprint Sequence analysis of multidomain proteins: past perspectives and future directions
    Richard R Copley
    Adv Protein Chem 61:75-98. 2002
  20. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  21. pmc A high-resolution single nucleotide polymorphism genetic map of the mouse genome
    Sagiv Shifman
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Biol 4:e395. 2006
    ..Genetic maps are available from http://gscan.well.ox.ac.uk/#genetic_map and as supporting information to this publication...
  22. ncbi request reprint Mitogenomics and phylogenomics reveal priapulid worms as extant models of the ancestral Ecdysozoan
    Bonnie L Webster
    Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
    Evol Dev 8:502-10. 2006
    ....
  23. ncbi request reprint Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida
    Sarah J Bourlat
    Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
    Nature 444:85-8. 2006
    ..As such, Xenoturbella is shown to be an independent phylum, Xenoturbellida, bringing the number of living deuterostome phyla to four...
  24. ncbi request reprint Broad taxon and gene sampling indicate that chaetognaths are protostomes
    David Q Matus
    Curr Biol 16:R575-6. 2006
  25. pmc SMART 5: domains in the context of genomes and networks
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 34:D257-60. 2006
    ..Furthermore, intrinsically disordered protein regions can be identified and displayed. The network context is now displayed in the results page for more than 350 000 proteins, enabling easy analyses of domain interactions...
  26. pmc Variation in structural location and amino acid conservation of functional sites in protein domain families
    Birgit Pils
    Department of Bioinformatics, University of Wurzburg, Biocenter, Am Hubland, 97074 Wurzburg, Germany
    BMC Bioinformatics 6:210. 2005
    ..In the analysis presented here, we have investigated the conservation of location and type of amino acids at functional sites, and compared the behaviour of functional sites between different protein domains...
  27. ncbi request reprint Animal phylogeny: fatal attraction
    Maximilian J Telford
    Department of Biology, University College London, Darwin Building, UK
    Curr Biol 15:R296-9. 2005
    ..MPhylogenetic analyses of hundreds of genes from model animals have placed flies closer to vertebrates than to nematodes; recent work suggests this may be due to an artefact known as long branch attraction...
  28. ncbi request reprint Functional organization of the yeast proteome by systematic analysis of protein complexes
    Anne Claude Gavin
    Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 415:141-7. 2002
    ..This higher-order map contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery...
  29. ncbi request reprint Common exon duplication in animals and its role in alternative splicing
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Hum Mol Genet 11:1561-7. 2002
    ..The common nature of recent exon duplication indicates that it might have a significant role in the fast evolution of eukaryotic genes. It also provides a general mechanism for the regulation of protein function...
  30. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....