For the complete list of my publications, please see my Google Scholar listing.
In addition, below find a brief list of my favorite or most representative publications. (Some of these are new, some are quite old.)
Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology (2021) ML Blinov, JH Gennari, JR Karr, II Moraru, DP Nickerson, HM Sauro. Current Opinion in Systems Biology 27, 100350
SemGen: a tool for semantics-based annotation and composition of biosimulation models (2019) ML Neal, CT Thompson, KG Kim, RC James, DL Cook, BE Carlson. Bioinformatics 35 (9), 1600-1602
Predicting instances of pathway ontology classes for pathway integration (2019) LL Wang, G Thomas Hayman, JR Smith, M Tutaj, ME Shimoyama, JH Gennari. Journal of biomedical semantics 10, 1-11
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology (2014) M Galdzicki, KP Clancy, E Oberortner, M Pocock, and many others (including me!). Nature biotechnology 32 (6), 545-550
Ontology of physics for biology: Representing physical dependencies as a basis for biological processes (2013) DL Cook, ML Neal, FL Bookstein, JH Gennari. Journal of biomedical semantics 4, 1-8
The evolution of Protégé: an environment for knowledge-based systems development (2003) JH Gennari, MA Musen, RW Fergerson, WE Grosso, M Crubézy, Henrik Eriksson, Natalya F Noy, Samson W Tu. International Journal of Human-computer studies 58 (1), 89-123
Also, with Dan Cook leading, I have co-authored a textbook on the Ontology of Physics for Biology:
Cook DL, Gennari, JH and Neal, ML (2023). The Ontology of Physics for Biology: Semantic modeling of multiscale, multidomain physiological systems. CRC Press. ISBN 9781138598058
You can buy (or view more about the book) from the publisher's page , or (of course) from Amazon