J B Bard

Summary

Affiliation: University of Edinburgh
Country: UK

Publications

  1. ncbi Ontologies in biology: design, applications and future challenges
    Jonathan B L Bard
    Bioinformatics, Biomedical Sciences University of Edinburgh, Edinburgh EH8 9XD, UK
    Nat Rev Genet 5:213-22. 2004
  2. ncbi Ontologies: Formalising biological knowledge for bioinformatics
    Jonathan Bard
    Dept of Biomedical Sciences, Edinburgh University, EH8 9XD, UK
    Bioessays 25:501-6. 2003
  3. ncbi A systems biology representation of developmental anatomy
    Jonathan Bard
    Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
    J Anat 218:591-9. 2011
  4. ncbi Anatomics: the intersection of anatomy and bioinformatics
    Jonathan B L Bard
    Division of Biomedical Science, University of Edinburgh, UK
    J Anat 206:1-16. 2005
  5. ncbi An ontology for cell types
    Jonathan Bard
    Department of Biomedical Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
    Genome Biol 6:R21. 2005
  6. ncbi Systems developmental biology: the use of ontologies in annotating models and in identifying gene function within and across species
    Jonathan Bard
    School of Biomedical Sciences, Edinburgh University, Edinburgh, EH8 9XD, UK
    Mamm Genome 18:402-11. 2007
  7. ncbi A bioinformatics approach for identifying candidate transcriptional regulators of mesenchyme-to-epithelium transitions in mouse embryos
    Jonathan B L Bard
    Computational Biology, Research Group, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
    Dev Dyn 237:2748-54. 2008
  8. ncbi Growth and death in the developing mammalian kidney: signals, receptors and conversations
    Jonathan B L Bard
    Department of Biomedical Science, Edinburgh University, Edinburgh EH8 9XD, Scotland, UK
    Bioessays 24:72-82. 2002
  9. ncbi Early nephron formation in the developing mouse kidney
    J B Bard
    Department of Biomedical Sciences, University of Edinburgh, UK
    J Anat 199:385-92. 2001
  10. ncbi Ontologies of developmental anatomy: their current and future roles
    J Bard
    Department of Biomedical Sciences, University of Edinburgh, UK
    Brief Bioinform 2:289-99. 2001

Collaborators

Detail Information

Publications24

  1. ncbi Ontologies in biology: design, applications and future challenges
    Jonathan B L Bard
    Bioinformatics, Biomedical Sciences University of Edinburgh, Edinburgh EH8 9XD, UK
    Nat Rev Genet 5:213-22. 2004
  2. ncbi Ontologies: Formalising biological knowledge for bioinformatics
    Jonathan Bard
    Dept of Biomedical Sciences, Edinburgh University, EH8 9XD, UK
    Bioessays 25:501-6. 2003
    ..This article considers the production, formulation and types of bio-ontologies together with the reasons why they are so useful...
  3. ncbi A systems biology representation of developmental anatomy
    Jonathan Bard
    Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
    J Anat 218:591-9. 2011
    ....
  4. ncbi Anatomics: the intersection of anatomy and bioinformatics
    Jonathan B L Bard
    Division of Biomedical Science, University of Edinburgh, UK
    J Anat 206:1-16. 2005
    ..It is suggested that the appropriate term for the analysis, computer formulation and use of the anatome is anatomics...
  5. ncbi An ontology for cell types
    Jonathan Bard
    Department of Biomedical Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
    Genome Biol 6:R21. 2005
    ..The ontology is freely available at http://obo.sourceforge.net/ and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA...
  6. ncbi Systems developmental biology: the use of ontologies in annotating models and in identifying gene function within and across species
    Jonathan Bard
    School of Biomedical Sciences, Edinburgh University, Edinburgh, EH8 9XD, UK
    Mamm Genome 18:402-11. 2007
    ..Second, Boolean analysis of the G-E profiles of the mesenchyme-to-epithelium transitions that take place during mouse development suggest Lhx1, Foxc1, and Meox1 as candidate transcription factors for mediating this process...
  7. ncbi A bioinformatics approach for identifying candidate transcriptional regulators of mesenchyme-to-epithelium transitions in mouse embryos
    Jonathan B L Bard
    Computational Biology, Research Group, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
    Dev Dyn 237:2748-54. 2008
    ..GXD-search is downloadable from http://www.aiai.ed.ac.uk/project/biosphere/GXD-search.html...
  8. ncbi Growth and death in the developing mammalian kidney: signals, receptors and conversations
    Jonathan B L Bard
    Department of Biomedical Science, Edinburgh University, Edinburgh EH8 9XD, Scotland, UK
    Bioessays 24:72-82. 2002
    ..It also points to some unanswered questions, the most intriguing being what role does apoptosis play during normal kidney development?..
  9. ncbi Early nephron formation in the developing mouse kidney
    J B Bard
    Department of Biomedical Sciences, University of Edinburgh, UK
    J Anat 199:385-92. 2001
    ..These observations revise our knowledge of the timing and process of nephron initiation...
  10. ncbi Ontologies of developmental anatomy: their current and future roles
    J Bard
    Department of Biomedical Sciences, University of Edinburgh, UK
    Brief Bioinform 2:289-99. 2001
    ....
  11. ncbi A bioinformatics approach to investigating developmental pathways in the kidney and other tissues
    J B Bard
    Department of Biomedical Science, Edinburgh University, United Kingdom
    Int J Dev Biol 43:397-403. 1999
    ..This paper also considers both the types of tools that will be necessary and the databases on which they will operate...
  12. ncbi Expression and genomic characterization of protein phosphatase inhibitor-1: a novel marker for mesothelium in the mouse
    L McLaren
    Department of Biomedical Sciences and Centre for Developmental Biology, Hugh Robson Building, University of Edinburgh, EH8 9XD, Edinburgh, UK
    Mech Dev 96:237-41. 2000
    ..The blast cells of the kidney do not express I-1. We conclude that I-1 is a marker for mesothelium...
  13. ncbi A three-dimensional model of the mouse at embryonic day 9
    R M Brune
    Anatomy Section, University of Edinburgh, United Kingdom
    Dev Biol 216:457-68. 1999
    ..This reconstruction and its associated anatomy are available in a variety of data formats with some supporting software from http:@genex.hgu.mrc.ac.uk/...
  14. ncbi OBO Explorer: an editor for Open Biomedical Ontologies in OWL
    Stuart Aitken
    School of Informatics, University of Edinburgh, 11 Crichton Street, Edinburgh, UK
    Bioinformatics 24:443-4. 2008
    ..We present an ontology editor that allows end users to work directly with this OWL representation of OBO format ontologies. AVAILABILITY: http://www.aiai.ed.ac.uk/project/cobra-ct...
  15. ncbi COBrA: a bio-ontology editor
    Stuart Aitken
    School of Informatics, The University of Edinburgh, Edinburgh EH8 9LE, UK
    Bioinformatics 21:825-6. 2005
    ..In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL...
  16. ncbi The expression of the Wilms' tumour gene, WT1, in the developing mammalian embryo
    J F Armstrong
    MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
    Mech Dev 40:85-97. 1993
    ..The data indicate that WT1 plays a role in mediating some cases of the mesenchyme-to-epithelial transition, but its expression elsewhere argues that it has other tissue-specific roles in development...
  17. ncbi The mouse 14-3-3 epsilon isoform, a kinase regulator whose expression pattern is modulated in mesenchyme and neuronal differentiation
    J E McConnell
    MRC Human Genetics Unit, Edinburgh, United Kingdom
    Dev Biol 169:218-28. 1995
    ..The results as a whole thus argue for the 14-3-3 epsilon isoform playing roles in neural development and in early mesenchyme, with this latter function being lost or replaced as the tissue differentiates...
  18. ncbi EMAP and EMAGE: a framework for understanding spatially organized data
    Richard A Baldock
    MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, UK
    Neuroinformatics 1:309-25. 2003
    ....
  19. ncbi Pathbase: a new reference resource and database for laboratory mouse pathology
    Paul N Schofield
    Department of Anatomy, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
    Radiat Prot Dosimetry 112:525-8. 2004
    ..The database currently has over 1000 images on-line with 2000 more under curation and presents a paradigm for the development of future databases dedicated to aspects of experimental biology...
  20. ncbi Pathbase: a database of mutant mouse pathology
    Paul N Schofield
    Department of Anatomy, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
    Nucleic Acids Res 32:D512-5. 2004
    ..The database interface is designed to have optimal browser and platform compatibility and to interact directly with other web-based mouse genetic resources...
  21. ncbi Apoptosis in the cortex of the developing mouse kidney
    Jonathan G D Foley
    Department of Biomedical Sciences, Edinburgh University, Edinburgh EH8 9XD, UK
    J Anat 201:477-84. 2002
    ....
  22. ncbi Using bioinformatics to identify kidney genes
    Jonathan B L Bard
    Department of Biomedical Sciences, Edinburgh University, Edinburgh EH8 9XD, UK
    Nephrol Dial Transplant 17:62-4. 2002
    ..Future databases will also include graphical data, and this knowledge will provide a further level of insight. These databases and tools are discussed here...
  23. ncbi The growth and morphogenesis of the early mouse mandible: a quantitative analysis
    Thaya Ramaesh
    Department of Biomedical Sciences, Edinburgh University, Edinburgh EH8 9XD, UK
    J Anat 203:213-22. 2003
    ....
  24. ncbi An ontology of human developmental anatomy
    Amy Hunter
    Bioinformatics Group, Division of Biomedical Sciences, Hugh Robson Building, University of Edinburgh, UK
    J Anat 203:347-55. 2003
    ..The third gives the second version in GO ontology syntax (with standard IDs for each tissue) and can be downloaded from both the genex and the Open Biological Ontology sites (http://obo.sourceforge.net/)...