Positions

Selected Publications

Academic Article

Year Title Altmetric
2023 Delirium Mediates Incidence of Hospital-Associated Disability Among Older Adults. 2023
2022 The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren.  Frontiers in Artificial Intelligence.  5. 2022
2022 Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science.  Clinical and Translational Science.  15:1848-1855. 2022
2022 Progress toward a universal biomedical data translator.  Clinical and Translational Science.  15:1838-1847. 2022
2022 Development and Validation of an Emergency Department Electronic Medical Record Gout Flare Alert.  Arthritis Care and Research.  2022
2018 CUILESS2016: A clinical corpus applying compositional normalization of text mentions.  Journal of Biomedical Semantics.  9. 2018
2018 Phenotype Detection Registry System (PheDRS) - Implementation of a Generalizable Single Institution Clinical Registry Architecture.  Proceedings / AMIA ... Annual Symposium. AMIA Symposium.  2018:847-856. 2018
2016 Efficient identification of nationally mandated reportable cancer cases using natural language processing and machine learning.  Journal of the American Medical Informatics Association.  23:1077-1084. 2016
2015 Comparative genome analysis of Mycoplasma pneumoniae.  BMC Genomics.  16. 2015
2014 Reduction of hydrogen peroxide accumulation and toxicity by a catalase from Mycoplasma iowae.  PLoS One.  9. 2014
2014 Draft genome sequence of Hymenobacter sp. strain IS2118, isolated from a freshwater lake in Schirmacher Oasis, Antarctica, reveals diverse genes for adaptation to cold ecosystems.  Microbiology Resource Announcements.  2. 2014
2013 Type 1 and type 2 strains of Mycoplasma pneumoniae form different biofilms.  Microbiology.  159:737-747. 2013
2009 Annotating the human genome with Disease Ontology.  BMC Genomics.  10. 2009
2007 Genomic differences of Vaccinia virus clones from Dryvax smallpox vaccine: The Dryvax-like ACAM2000 and the mouse neurovirulent Clone-3.  Vaccine.  25:8807-8832. 2007
2007 OBO-Edit - An ontology editor for biologists.  Bioinformatics.  23:2198-2200. 2007
2007 Other riffs on cooperation are already showing how well a wiki could work [1].  Nature.  446:856. 2007
2007 Interpreting microarray results with gene ontology and MeSH.  Methods in Molecular Biology.  377:223-241. 2007
2007 GeneChip resequencing of the smallpox virus genome can identify novel strains: A biodefense application.  Journal of Clinical Microbiology.  45:358-363. 2007
2007 Interpreting microarray results with gene ontology and MeSH..  Methods in Molecular Biology.  377:223-242. 2007
2007 Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS)..  Methods in Molecular Biology.  408:153-169. 2007
2006 Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.  Virology Journal.  3. 2006
2006 Genome sequence diversity and clues to the evolution of variola (smallpox) virus.  Science.  313:807-812. 2006
2002 Poxvirus Orthologous Clusters (POCs).  Bioinformatics.  18:1544-1545. 2002

Education And Training

  • Doctor of Philosophy in Computer and Information Sciences, University of Alabama at Birmingham 2016
  • Master's Level Degree in Genetics, University of Alberta 1998
  • Bachelor's Level Degree in Computer Science, University of Alberta 1994

    • Full Name

  • John Osborne