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Michael Bada

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

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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. Santangelo B, Bada M, Hunter L, Lozupone C. Hypothesizing mechanistic links between microbes and disease using knowledge graphs. bioRxiv. 2023 Dec 04. PMID: 38106100.
      View in: PubMed
    2. Boguslav MR, Salem NM, White EK, Sullivan KJ, Bada M, Hernandez TL, Leach SM, Hunter LE. Creating an ignorance-base: Exploring known unknowns in the scientific literature. J Biomed Inform. 2023 07; 143:104405. PMID: 37270143.
      View in: PubMed
    3. Boguslav MR, Hailu ND, Bada M, Baumgartner WA, Hunter LE. Concept recognition as a machine translation problem. BMC Bioinformatics. 2021 Dec 17; 22(Suppl 1):598. PMID: 34920707.
      View in: PubMed
    4. 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
    5. 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
    6. 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
    7. Bada M, Vasilevsky N, Baumgartner WA, Haendel M, Hunter LE. Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. Database (Oxford). 2017 Jan 01; 2017. PMID: 31725864.
      View in: PubMed
    8. 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.
      View in: PubMed
    9. 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.
      View in: PubMed
    10. 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
    11. 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.
      View in: PubMed
    12. 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.
      View in: PubMed
    13. 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.
      View in: PubMed
    14. 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
    15. 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.
      View in: PubMed
    16. Bada M, Hunter L. Identification of OBO nonalignments and its implications for OBO enrichment. Bioinformatics. 2008 Jun 15; 24(12):1448-55. PMID: 18463117.
      View in: PubMed
    17. Bada M, Hunter L. Enrichment of OBO ontologies. J Biomed Inform. 2007 Jun; 40(3):300-15. PMID: 17011833.
      View in: PubMed
    18. 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.
      View in: PubMed
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