Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Last Name
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Michael Bada

TitleAffiliate
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 BE, Bada M, Hunter LE, Lozupone C. Hypothesizing mechanistic links between microbes and disease using knowledge graphs. Sci Rep. 2025 Feb 26; 15(1):6905. PMID: 40011529.
      View in: PubMed
    2. Callahan TJ, Tripodi IJ, Stefanski AL, Cappelletti L, Taneja SB, Wyrwa JM, Casiraghi E, Matentzoglu NA, Reese J, Silverstein JC, Hoyt CT, Boyce RD, Malec SA, Unni DR, Joachimiak MP, Robinson PN, Mungall CJ, Cavalleri E, Fontana T, Valentini G, Mesiti M, Gillenwater LA, Santangelo B, Vasilevsky NA, Hoehndorf R, Bennett TD, Ryan PB, Hripcsak G, Kahn MG, Bada M, Baumgartner WA, Hunter LE. An open source knowledge graph ecosystem for the life sciences. Sci Data. 2024 Apr 11; 11(1):363. PMID: 38605048.
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    3. 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
    4. 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.
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    5. Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ. Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci. 2022 08; 15(8):1848-1855. PMID: 36125173.
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    6. 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.
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    7. 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.
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    8. 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.
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    9. 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.
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    10. 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.
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    11. 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.
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    12. 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.
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    13. Bada M. Mapping of biomedical text to concepts of lexicons, terminologies, and ontologies. Methods Mol Biol. 2014; 1159:33-45. PMID: 24788260.
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    14. 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.
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    15. 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.
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    16. 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.
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    17. 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.
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    18. 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.
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    19. Bada M, Hunter L. Identification of OBO nonalignments and its implications for OBO enrichment. Bioinformatics. 2008 Jun 15; 24(12):1448-55. PMID: 18463117.
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    20. Bada M, Hunter L. Enrichment of OBO ontologies. J Biomed Inform. 2007 Jun; 40(3):300-15. PMID: 17011833.
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    21. 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.
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