John Gennari, PhD

Graduate Program Director and Associate Professor, Biomedical Informatics and Medical Education



Ontologies, knowledge sharing, semantic web.


PhD (Computer Science) UC-Irvine. Experience: Protege developer at Stanford Medical Informatics.

Current research:

Primary focus on semantic web, knowledge representation and ontology development.  See web pages for other interests: reproducibility, synthetic biology, physics-based biosimulation, health-care guidelines / protocols, and cellular signaling pathways.


Currently accepting new students.

Representative publications:

  • Gennari JH, Musen MA, Fergerson RW, Grosso WE, Cruzbezy M, Eriksson H, Noy NF, and Tu SW (2003). The Evolution of Protege: An Environment for Knowledge-Based Systems Development. International Journal of Human-Computer Studies, 58, 89-123.
  • Gennari JH, Neal ML, Galdzicki M, and Cook DL. (2011). Multiple Ontologies in Action: Composite Annotations for Biosimulation Models. Journal of Biomedical Informatics 44(1):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.
  • Galdzicki, M., many SBOL-Developers, Gennari JH, Myers CJ, and Sauro, HM (2014). SBOL: A community standard for communicating designs in synthetic biology. Nature Biotechnology 32(6): pp. 545-550.
  • Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH (2014). A reappraisal of how to build modular, reusable models of biological systems. PLoS Computational Biology.