Joel E Richardson

Summary

Affiliation: The Jackson Laboratory
Country: USA

Publications

  1. ncbi request reprint fjoin: simple and efficient computation of feature overlaps
    Joel E Richardson
    The Jackson Laboratory, Mouse Genome Informatics, Bar Harbor, Maine 04609, USA
    J Comput Biol 13:1457-64. 2006
  2. pmc The mouse genome database (MGD): new features facilitating a model system
    Janan T Eppig
    The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 35:D630-7. 2007
  3. pmc The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse
    Judith A Blake
    Bioinformatics and Computational Biology, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 42:D810-7. 2014
  4. pmc The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse
    Janan T Eppig
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 40:D881-6. 2012
  5. doi request reprint GXD: a community resource of mouse Gene Expression Data
    Constance M Smith
    The Jackson Laboratory, Bar Harbor, ME, 04609, USA
    Mamm Genome 26:314-24. 2015
  6. doi request reprint The mouse gene expression database: New features and how to use them effectively
    Jacqueline H Finger
    The Jackson Laboratory, Bar Harbor, Maine
    Genesis 53:510-22. 2015
  7. pmc The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology
    Janan T Eppig
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 33:D471-5. 2005
  8. pmc The mouse genome database: genotypes, phenotypes, and models of human disease
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
    Nucleic Acids Res 41:D885-91. 2013
  9. pmc The Mouse Genome Database (MGD): integrating biology with the genome
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 32:D476-81. 2004
  10. doi request reprint Orthology for comparative genomics in the mouse genome database
    Mary E Dolan
    The Jackson Laboratory, Bar Harbor, ME, 04609, USA
    Mamm Genome 26:305-13. 2015

Collaborators

Detail Information

Publications35

  1. ncbi request reprint fjoin: simple and efficient computation of feature overlaps
    Joel E Richardson
    The Jackson Laboratory, Mouse Genome Informatics, Bar Harbor, Maine 04609, USA
    J Comput Biol 13:1457-64. 2006
    ..The reference implementation is a stand-alone Python program; it implements the basic algorithm and a number of useful extensions, which are also discussed in this paper...
  2. pmc The mouse genome database (MGD): new features facilitating a model system
    Janan T Eppig
    The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 35:D630-7. 2007
    ....
  3. pmc The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse
    Judith A Blake
    Bioinformatics and Computational Biology, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 42:D810-7. 2014
    ..All MGD resources are freely available to the research community. ..
  4. pmc The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse
    Janan T Eppig
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 40:D881-6. 2012
    ....
  5. doi request reprint GXD: a community resource of mouse Gene Expression Data
    Constance M Smith
    The Jackson Laboratory, Bar Harbor, ME, 04609, USA
    Mamm Genome 26:314-24. 2015
    ..Thus, GXD can provide researchers with critical insights into the functions of genes and the molecular mechanisms of development, differentiation, and disease...
  6. doi request reprint The mouse gene expression database: New features and how to use them effectively
    Jacqueline H Finger
    The Jackson Laboratory, Bar Harbor, Maine
    Genesis 53:510-22. 2015
    ....
  7. pmc The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology
    Janan T Eppig
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 33:D471-5. 2005
    ....
  8. pmc The mouse genome database: genotypes, phenotypes, and models of human disease
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
    Nucleic Acids Res 41:D885-91. 2013
    ....
  9. pmc The Mouse Genome Database (MGD): integrating biology with the genome
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 32:D476-81. 2004
    ..Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data...
  10. doi request reprint Orthology for comparative genomics in the mouse genome database
    Mary E Dolan
    The Jackson Laboratory, Bar Harbor, ME, 04609, USA
    Mamm Genome 26:305-13. 2015
    ..Here, we describe current comparative data in MGD and review the history and refinement of orthology representation in this resource. ..
  11. pmc Mouse Tumor Biology (MTB): a database of mouse models for human cancer
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
    Nucleic Acids Res 43:D818-24. 2015
    ....
  12. doi request reprint Mouse Genome Database: From sequence to phenotypes and disease models
    Janan T Eppig
    The Jackson Laboratory, Bar Harbor, Maine
    Genesis 53:458-73. 2015
    ..Here, we describe the data acquisition process, specifics about MGD's key data areas, methods to access and query MGD data, and outreach and user help facilities...
  13. doi request reprint Mouse Genome Informatics (MGI): reflecting on 25 years
    Janan T Eppig
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, 04609, USA
    Mamm Genome 26:272-84. 2015
    ..Here, we review some of the major changes in research approaches over that last quarter century, how these changes are reflected in the MGI resource you use today, and what may be around the next corner. ..
  14. pmc The mouse Gene Expression Database (GXD): 2014 update
    Constance M Smith
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 42:D818-24. 2014
    ..At present, GXD includes >1.4 million expression results and 250,000 images that are accessible to our search tools...
  15. pmc The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics
    Judith A Blake
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 39:D842-8. 2011
    ....
  16. doi request reprint Mouse genome database 2016
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 44:D840-7. 2016
    ....
  17. pmc The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips
    Constance M Smith
    The Jackson Laboratory, Bar Harbor, Maine
    Dev Dyn 243:1176-86. 2014
    ....
  18. pmc The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease
    Janan T Eppig
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 43:D726-36. 2015
    ..MGD resources are freely available to the scientific community. ..
  19. pmc The Mouse Genome Database (MGD): the model organism database for the laboratory mouse
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 30:113-5. 2002
    ....
  20. pmc Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies
    David P Hill
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Genome Res 12:1982-91. 2002
    ..The combination of concepts from orthogonal vocabularies provides a robust representation of relevant terms and an opportunity for evaluation of hypothetical concepts...
  21. pmc MGD: the Mouse Genome Database
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 31:193-5. 2003
    ..Recent developments include a general implementation of database structures for controlled vocabularies and the integration of a phenotype classification system...
  22. pmc Connecting sequence and biology in the laboratory mouse
    Richard M Baldarelli
    Mouse Genome Informatics Group, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Genome Res 13:1505-19. 2003
    ..In particular, we describe the methods and results of integration of 60,770 FANTOM2 mouse cDNAs with gene records in the databases of MGI and LocusLink...
  23. pmc The mouse Gene Expression Database (GXD): updates and enhancements
    David P Hill
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 32:D568-71. 2004
    ..GXD is accessible through the MGI website at http://www.informatics.jax.org/ or directly at http://www. informatics.jax.org/menus/expression_menu.shtml...
  24. pmc The Mouse Genome Database (MGD): updates and enhancements
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 34:D562-7. 2006
    ..informatics.jax.org. Recent improvements in MGD described here include the incorporation of an interactive genome browser, the enhancement of phenotype resources and the further development of functional annotation resources...
  25. pmc The mouse Gene Expression Database (GXD): 2007 update
    Constance M Smith
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 35:D618-23. 2007
    ..GXD is available through the MGI web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu.shtml...
  26. pmc The Mouse Genome Database genotypes::phenotypes
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 37:D712-9. 2009
    ..Recent improvements in MGD described here include the unified mouse gene catalog for NCBI Build 37 of the reference genome assembly, and improved representation of mouse mutants and phenotypes...
  27. pmc The Mouse Genome Database (MGD): mouse biology and model systems
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 36:D724-8. 2008
    ..Recent improvements in MGD described here include the association of gene trap data with mouse genes and a new batch query capability for customized data access and retrieval...
  28. pmc Disease model curation improvements at Mouse Genome Informatics
    Susan M Bello
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Database (Oxford) 2012:bar063. 2012
    ..Here we describe our evaluation of the CTD application, the extensions made by MGI and discuss the strengths and weaknesses of this approach. DATABASE URL: http://www.informatics.jax.org/..
  29. ncbi request reprint Mouse genome informatics (MGI) resources for pathology and toxicology
    Janan T Eppig
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Toxicol Pathol 35:456-7. 2007
  30. doi request reprint The International Mouse Strain Resource (IMSR): cataloging worldwide mouse and ES cell line resources
    Janan T Eppig
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, 04609, USA
    Mamm Genome 26:448-55. 2015
    ....
  31. pmc Identifying mouse models for skin cancer using the Mouse Tumor Biology Database
    Dale A Begley
    Department of Research and Development, The Jackson Laboratory, Bar Harbor, ME, USA
    Exp Dermatol 23:761-3. 2014
    ..In this report, we detail MTB's contents and capabilities, together with instructions on how to use MTB to search for skin-related tumor models and associated data. ..
  32. pmc The Mouse Genome Database: enhancements and updates
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
    Nucleic Acids Res 38:D586-92. 2010
    ....
  33. pmc The mouse Gene Expression Database (GXD): 2011 update
    Jacqueline H Finger
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 39:D835-41. 2011
    ..GXD is available through the MGI web site (www.informatics.jax.org), or directly at www.informatics.jax.org/expression.shtml...
  34. pmc A mouse model of conditional lipodystrophy
    Suyeon Kim
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Proc Natl Acad Sci U S A 104:16627-32. 2007
    ..Thus, the Pparg(ldi/+) mouse provides a conditional animal model for studying lipodystrophy and its associated physiology and gene expression...
  35. doi request reprint Visual annotation display (VLAD): a tool for finding functional themes in lists of genes
    Joel E Richardson
    Mouse Genome Informatics MGI Database Consortium, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
    Mamm Genome 26:567-73. 2015
    ..VLAD is available as a web-based application from the MGI web site (http://proto.informatics.jax.org/prototypes/vlad/)...