Damian Smedley

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi TRACER: a resource to study the regulatory architecture of the mouse genome
    Chao Kung Chen
    European Bioinformatics Institute European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Genomics 14:215. 2013
  2. ncbi XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
    Morris A Swertz
    Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
    Genome Biol 11:R27. 2010
  3. ncbi Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
    Michael Gruenberger
    Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
    BMC Res Notes 3:16. 2010
  4. ncbi Solutions for data integration in functional genomics: a critical assessment and case study
    Damian Smedley
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Brief Bioinform 9:532-44. 2008
  5. ncbi BioMart--biological queries made easy
    Damian Smedley
    Ontario Institute for Cancer Research, MaRS Centre, 101 College Street, Toronto, Ontario, Canada
    BMC Genomics 10:22. 2009
  6. ncbi Finding and sharing: new approaches to registries of databases and services for the biomedical sciences
    Damian Smedley
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
    Database (Oxford) 2010:baq014. 2010
  7. ncbi Ensembl's 10th year
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D557-62. 2010
  8. ncbi EnsMart: a generic system for fast and flexible access to biological data
    Arek Kasprzyk
    European Bioinformatics Institute EBI, Hinxton, Cambridge CB10 1SH, UK
    Genome Res 14:160-9. 2004
  9. ncbi BioMart Central Portal--unified access to biological data
    Syed Haider
    EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
    Nucleic Acids Res 37:W23-7. 2009
  10. ncbi EMMA--mouse mutant resources for the international scientific community
    Phil Wilkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D570-6. 2010

Detail Information

Publications18

  1. ncbi TRACER: a resource to study the regulatory architecture of the mouse genome
    Chao Kung Chen
    European Bioinformatics Institute European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Genomics 14:215. 2013
    ..The mechanisms that control the integration of these diverse inputs into specific gene expression patterns are still poorly understood. New approaches enabling the dissection of these mechanisms in vivo are needed...
  2. ncbi XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
    Morris A Swertz
    Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
    Genome Biol 11:R27. 2010
    ..Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans...
  3. ncbi Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
    Michael Gruenberger
    Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
    BMC Res Notes 3:16. 2010
    ..abstract:..
  4. ncbi Solutions for data integration in functional genomics: a critical assessment and case study
    Damian Smedley
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Brief Bioinform 9:532-44. 2008
    ..Finally, we focus on the current impediments to adopting such an approach in a wider context, and strategies to overcome them...
  5. ncbi BioMart--biological queries made easy
    Damian Smedley
    Ontario Institute for Cancer Research, MaRS Centre, 101 College Street, Toronto, Ontario, Canada
    BMC Genomics 10:22. 2009
    ..This is not an efficient solution in terms of cost and time. Instead, it would be better if the biologist only had to learn one generic interface. BioMart provides such a solution...
  6. ncbi Finding and sharing: new approaches to registries of databases and services for the biomedical sciences
    Damian Smedley
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
    Database (Oxford) 2010:baq014. 2010
    ..We expect such approaches will result in improved discovery, uptake and utilization of data resources. Database URL: http://www.casimir.org.uk/casimir_ddf...
  7. ncbi Ensembl's 10th year
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D557-62. 2010
    ....
  8. ncbi EnsMart: a generic system for fast and flexible access to biological data
    Arek Kasprzyk
    European Bioinformatics Institute EBI, Hinxton, Cambridge CB10 1SH, UK
    Genome Res 14:160-9. 2004
    ..Both implementations and the database are freely available for local installation, and can be extended or adapted to 'non-Ensembl' data sets...
  9. ncbi BioMart Central Portal--unified access to biological data
    Syed Haider
    EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
    Nucleic Acids Res 37:W23-7. 2009
    ..The website is free and open to all users and there is no login requirement...
  10. ncbi EMMA--mouse mutant resources for the international scientific community
    Phil Wilkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D570-6. 2010
    ..g. Ensembl. Other resources are able to display EMMA data by accessing our Distributed Annotation System server. EMMA database access is publicly available at http://www.emmanet.org...
  11. ncbi Ensembl variation resources
    Yuan Chen
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Genomics 11:293. 2010
    ..Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics...
  12. ncbi BioMart Central Portal: an open database network for the biological community
    Jonathan M Guberman
    Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
    Database (Oxford) 2011:bar041. 2011
    ..Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities...
  13. ncbi BioMart as an integration solution for the International Knockout Mouse Consortium
    Darren J Oakley
    The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH
    Database (Oxford) 2011:bar028. 2011
    ..Here, we describe these datasets in more detail and illustrate the functionality of the portal using several examples...
  14. ncbi PhenoDigm: analyzing curated annotations to associate animal models with human diseases
    Damian Smedley
    Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Database (Oxford) 2013:bat025. 2013
    ..Furthermore, we provide guidance on how to browse the data with PhenoDigm's web interface and illustrate its usefulness in supporting research. Database URL: http://www.sanger.ac.uk/resources/databases/phenodigm...
  15. ncbi MouseFinder: Candidate disease genes from mouse phenotype data
    Chao Kung Chen
    Vertebrate Genomics Team, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Hum Mutat 33:858-66. 2012
    ..We demonstrate its use in identifying ARTN as a strong candidate gene within the 1p34.1-p32 mapped locus for a hereditary form of ptosis...
  16. ncbi Cre recombinase resources for conditional mouse mutagenesis
    Damian Smedley
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Methods 53:411-6. 2011
    ..The continuously changing landscape of these mouse resources reflects the rapid progression of research and development in conditional and inducible mouse mutagenesis...
  17. ncbi Post-publication sharing of data and tools
    Paul N Schofield
    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
    Nature 461:171-3. 2009
    ..Despite existing guidelines on access to data and bioresources, good practice is not widespread. A meeting of mouse researchers in Rome proposes ways to promote a culture of sharing...
  18. ncbi An overview of Ensembl
    Ewan Birney
    EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:925-8. 2004
    ....