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Michael Bada

TitleResearch Associate
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM - Pharmacology

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Callahan TJ, Baumgartner WA, Bada M, Stefanski AL, Tripodi I, White EK, Hunter LE. OWL-NETS: Transforming OWL Representations for Improved Network Inference. Pac Symp Biocomput. 2018; 23:133-144. PMID: 29218876.
      View in: PubMed
    2. Cohen KB, Lanfranchi A, Choi MJ, Bada M, Baumgartner WA, Panteleyeva N, Verspoor K, Palmer M, Hunter LE. Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. BMC Bioinformatics. 2017 Aug 17; 18(1):372. PMID: 28818042.
      View in: PubMed
    3. Yadav P, Jezek E, Bouillon P, Callahan TJ, Bada M, Hunter LE, Cohen KB. Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement. Stud Health Technol Inform. 2017; 245:644-648. PMID: 29295175.
      View in: PubMed
    4. Livingston KM, Bada M, Baumgartner WA, Hunter LE. KaBOB: ontology-based semantic integration of biomedical databases. BMC Bioinformatics. 2015 Apr 23; 16:126. PMID: 25903923; PMCID: PMC4448321.
    5. Funk C, Baumgartner W, Garcia B, Roeder C, Bada M, Cohen KB, Hunter LE, Verspoor K. Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinformatics. 2014 Feb 26; 15:59. PMID: 24571547; PMCID: PMC4015610.
    6. Bada M. Mapping of biomedical text to concepts of lexicons, terminologies, and ontologies. Methods Mol Biol. 2014; 1159:33-45. PMID: 24788260.
      View in: PubMed
    7. Livingston KM, Bada M, Hunter LE, Verspoor K. Representing annotation compositionality and provenance for the Semantic Web. J Biomed Semantics. 2013; 4:38. PMID: 24268021; PMCID: PMC4129183.
    8. Verspoor K, Cohen KB, Lanfranchi A, Warner C, Johnson HL, Roeder C, Choi JD, Funk C, Malenkiy Y, Eckert M, Xue N, Baumgartner WA, Bada M, Palmer M, Hunter LE. A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. BMC Bioinformatics. 2012 Aug 17; 13:207. PMID: 22901054; PMCID: PMC3483229.
    9. Bada M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA, Cohen KB, Verspoor K, Blake JA, Hunter LE. Concept annotation in the CRAFT corpus. BMC Bioinformatics. 2012 Jul 09; 13:161. PMID: 22776079; PMCID: PMC3476437.
    10. Bada M, Hunter L. Desiderata for ontologies to be used in semantic annotation of biomedical documents. J Biomed Inform. 2011 Feb; 44(1):94-101. PMID: 20971216.
      View in: PubMed
    11. Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. Cross-product extensions of the Gene Ontology. J Biomed Inform. 2011 Feb; 44(1):80-6. PMID: 20152934; PMCID: PMC2910209.
    12. Bada M, Hunter L. Identification of OBO nonalignments and its implications for OBO enrichment. Bioinformatics. 2008 Jun 15; 24(12):1448-55. PMID: 18463117; PMCID: PMC2427163.
    13. Bada M, Hunter L. Enrichment of OBO ontologies. J Biomed Inform. 2007 Jun; 40(3):300-15. PMID: 17011833; PMCID: PMC2084396.
    14. Johnson HL, Cohen KB, Baumgartner WA, Lu Z, Bada M, Kester T, Kim H, Hunter L. Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. Pac Symp Biocomput. 2006; 28-39. PMID: 17094225; PMCID: PMC1810343.
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