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John Gennari, PhD

  • Professor
  • Graduate Program Director
  • Primary
  • BHI



Ontologies, knowledge representation, reproducibility, FAIR, and knowledge sharing.


PhD in Computer Science, UC-Irvine. Research scientist at Stanford for 6 yrs, Professor here at UW > 20 yrs.

Current research:

Broad range of interests, from imaging informatics to synthetic biology to health-care guidelines to physics-based biosimulation models. Expertise in ontology building and standards development.


Mentoring: Accepting graduate students. Classroom: Undergraduate: intro to BHI. Graduate: knowledge representation course, Professionalism in BHI.

Current projects:

Center for Reproducibility of Biomedical Modeling.

Representative publications:

  • Gennari, J.H., Musen, M.A., Fergerson, R.W., Grosso, W.E., Crubezy, M., Eriksson, H., Noy, N.F., and Tu, S.W. (2003). The Evolution of Protégé: An Environment for Knowledge-Based Systems Development. International Journal of Human-Computer Studies, 58, 89–123.
  • Gennari, J.H., Neal, M.L., Galdzicki, M. and Cook, D.L. (2011). Multiple Ontologies in Action: Composite Annotations for Biosimulation Models. Journal of Biomedical Informatics, v 44(1), pp. 146-154.
  • Cook, DL, Neal, ML, Bookstein, FL, and Gennari, JH (2013). Ontology of Physics for Biology: representing physical dependencies as a basis for biological processes, Journal of Biomedical Semantics. 4:41 doi: 10.1186/2041-1480-4-41.
  • Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn J, Rodriquez CA, Roener N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grunberg R, Hallinan J, Peccoud J, Plahar HA, Sirin E, Stan GB, Villalobos A, Wipat A, Gennari JH, Myers CJ, & Sauro HM (2014). SBOL: A community standard for communicating designs in synthetic biology. Nature Biotechnology.
  • Neal ML, Thompson CT, Kim KG, James RC, Cook DL, Carlson BE, and Gennari JH (2019). SemGen: a tool for semantics-based annotation and composition of biosimulation models. doi:10.1093/bioinformatics/bty829.
  • Blinov ML, Gennari JH, Karr JR, Moraru II, Nickerson DP, and Sauro HM (2021). Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology. Current Opinion in Systems Biology, v27,