Suzanna E Lewis

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Reactome: a knowledge base of biologic pathways and processes
    Imre Vastrik
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Genome Biol 8:R39. 2007
  2. pmc Calling on a million minds for community annotation in WikiProteins
    Barend Mons
    Erasmus Medical Centre, Department of Medical Informatics, Rotterdam, The Netherlands
    Genome Biol 9:R89. 2008
  3. pmc Apollo: a sequence annotation editor
    S E Lewis
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0082. 2002
  4. pmc Gene Ontology: looking backwards and forwards
    Suzanna E Lewis
    Department of Molecular and Cell Biology, University of California, 539 Life Sciences Addition, Berkeley, CA 94720 3200, USA
    Genome Biol 6:103. 2005
  5. pmc Uberon, an integrative multi-species anatomy ontology
    Christopher J Mungall
    Genomics Division, Lawrence Berkeley National Laboratory, 1 Cycltotron Road MS 64 121, Berkeley, CA 94720, USA
    Genome Biol 13:R5. 2012
  6. pmc Integrating phenotype ontologies across multiple species
    Christopher J Mungall
    Genome Dynamics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 11:R2. 2010
  7. pmc The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details
    Nicole L Washington
    Lawrence Berkeley National Laboratory, Genomics Division, 1 Cyclotron Road MS64 121, Berkeley, CA 94720, USA
    Database (Oxford) 2011:bar023. 2011
  8. pmc Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
    Sima Misra
    Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0083. 2002
  9. pmc The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
    Sebastian Kohler
    Institute for Medical Genetics and Human Genetics, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Lawrence Berkeley National Laboratory, Mail Stop 84R0171, Berkeley, CA 94720, USA, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Department of Medical Genetics, Cambridge University Addenbrooke s Hospital, Cambridge CB2 2QQ, UK, Universite Paul Sabatier, Faculte de Chirurgie Dentaire, CHU Toulouse, France, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre MAHSC, Manchester, UK, Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK, Institute of Genetic Medicine Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK, Department of Computer Science, University of Toronto, Ontario, Canada
    Nucleic Acids Res 42:D966-74. 2014
  10. pmc Linking human diseases to animal models using ontology-based phenotype annotation
    Nicole L Washington
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS Biol 7:e1000247. 2009

Detail Information

Publications19

  1. pmc Reactome: a knowledge base of biologic pathways and processes
    Imre Vastrik
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Genome Biol 8:R39. 2007
    ..Finally, we describe the use of Reactome both as a learning resource and as a computational tool to aid in the interpretation of microarrays and similar large-scale datasets...
  2. pmc Calling on a million minds for community annotation in WikiProteins
    Barend Mons
    Erasmus Medical Centre, Department of Medical Informatics, Rotterdam, The Netherlands
    Genome Biol 9:R89. 2008
    ..We call on a 'million minds' to annotate a 'million concepts' and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org...
  3. pmc Apollo: a sequence annotation editor
    S E Lewis
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0082. 2002
    ..FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects...
  4. pmc Gene Ontology: looking backwards and forwards
    Suzanna E Lewis
    Department of Molecular and Cell Biology, University of California, 539 Life Sciences Addition, Berkeley, CA 94720 3200, USA
    Genome Biol 6:103. 2005
    ..Its most significant achievement lies in uniting many independent biological database efforts into a cooperative force...
  5. pmc Uberon, an integrative multi-species anatomy ontology
    Christopher J Mungall
    Genomics Division, Lawrence Berkeley National Laboratory, 1 Cycltotron Road MS 64 121, Berkeley, CA 94720, USA
    Genome Biol 13:R5. 2012
    ..It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org...
  6. pmc Integrating phenotype ontologies across multiple species
    Christopher J Mungall
    Genome Dynamics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 11:R2. 2010
    ..We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology...
  7. pmc The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details
    Nicole L Washington
    Lawrence Berkeley National Laboratory, Genomics Division, 1 Cyclotron Road MS64 121, Berkeley, CA 94720, USA
    Database (Oxford) 2011:bar023. 2011
    ..modENCODE data can be found at http://www.modencode.org...
  8. pmc Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
    Sima Misra
    Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0083. 2002
    ....
  9. pmc The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
    Sebastian Kohler
    Institute for Medical Genetics and Human Genetics, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Lawrence Berkeley National Laboratory, Mail Stop 84R0171, Berkeley, CA 94720, USA, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Department of Medical Genetics, Cambridge University Addenbrooke s Hospital, Cambridge CB2 2QQ, UK, Universite Paul Sabatier, Faculte de Chirurgie Dentaire, CHU Toulouse, France, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre MAHSC, Manchester, UK, Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK, Institute of Genetic Medicine Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK, Department of Computer Science, University of Toronto, Ontario, Canada
    Nucleic Acids Res 42:D966-74. 2014
    ..We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online. ..
  10. pmc Linking human diseases to animal models using ontology-based phenotype annotation
    Nicole L Washington
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS Biol 7:e1000247. 2009
    ....
  11. pmc Systematic determination of patterns of gene expression during Drosophila embryogenesis
    Pavel Tomancak
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0088. 2002
    ..Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription...
  12. pmc The Sequence Ontology: a tool for the unification of genome annotations
    Karen Eilbeck
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
    Genome Biol 6:R44. 2005
    ....
  13. pmc The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective
    Joshua S Kaminker
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Genome Biol 3:RESEARCH0084. 2002
    ..We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species...
  14. pmc EGASP: the human ENCODE Genome Annotation Assessment Project
    Roderic Guigo
    Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
    Genome Biol 7:S2.1-31. 2006
    ..These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment...
  15. pmc Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Chris F Taylor
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 26:889-96. 2008
  16. pmc The RNA Ontology Consortium: an open invitation to the RNA community
    Neocles B Leontis
    RNA 12:533-41. 2006
    ....
  17. pmc The minimum information about a genome sequence (MIGS) specification
    Dawn Field
    Natural Environmental Research Council Centre for Ecology and Hydrology, Oxford OX1 3SR, UK
    Nat Biotechnol 26:541-7. 2008
    ..As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases...
  18. ncbi request reprint National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge
    Daniel L Rubin
    Stanford Medical Informatics, Stanford University, Stanford, California 94305, USA
    OMICS 10:185-98. 2006
    ....
  19. ncbi request reprint Modelling data across labs, genomes, space and time
    Jason R Swedlow
    Division of Gene Regulation and Expression, Wellcome Trust Biocentre, Faculty of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Nat Cell Biol 8:1190-4. 2006
    ..Here, we use imaging applications to illustrate the purpose of the various implementations of data specifications and the requirement for open, standardized, data formats to facilitate the sharing of critical digital data and metadata...