Ontology-Based Representation of Simulation Models of Physiology. - Daniel L. Rubin; David Grossman; Maxwell Lewis Neal; Daniel L. Cook; James B. Bassingthwaighte; Mark A. Musen (AMIA, 2006)

Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology. - Daniel L. Cook; José L. V. Mejino Jr.; Maxwell Lewis Neal; John H. Gennari (AMIA, 2008)

Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics. - John H. Gennari; Maxwell Lewis Neal; Brian E. Carlson; Daniel L. Cook (Pacific Symposium on Biocomputing, 2008)

Advances in Semantic Representation for Multiscale Biosimulation: A Case Study in Merging Models. - Maxwell Lewis Neal; John H. Gennari; Theo Arts; Daniel L. Cook (Pacific Symposium on Biocomputing, 2009)

Current progress in patient-specific modeling. - Maxwell Lewis Neal; Roy Kerckhoffs (Briefings Bioinform., 2010)

HeartCyc: A Cardiac Cycle Process Ontology Based in the Ontology of Physics for Biology. - Daniel L. Cook; Michal Galdzicki; Maxwell Lewis Neal; José L. V. Mejino Jr.; John H. Gennari (ICBO, 2011)

Multiple ontologies in action: Composite annotations for biosimulation models. - John H. Gennari; Maxwell Lewis Neal; Michal Galdzicki; Daniel L. Cook (J. Biomed. Informatics, 2011)

Innovative Use of Ontologies: Association of Physiological Pathways to Corresponding Computational Models and Disparate Data Types. - Nazanin Tabesh-Saleki; Brian E. Carlson; Christopher T. Thompson; Maxwell Lewis Neal; Daniel L. Cook; Mary Shimoyama (AMIA, 2013)

An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome. - Maxwell Lewis Neal; Daniel L. Cook; John H. Gennari (ICBO, 2013)

Ontology of physics for biology: representing physical dependencies as a basis for biological processes. - Daniel L. Cook; Maxwell Lewis Neal; Fred L. Bookstein; John H. Gennari (J. Biomed. Semant., 2013)

Representing physiological processes and their participants with PhysioMaps. - Daniel L. Cook; Maxwell Lewis Neal; Robert Hoehndorf; Georgios V. Gkoutos; John H. Gennari (J. Biomed. Semant., 2013)

JSim, an open-source modeling system for data analysis. - Erik Butterworth; Bartholomew Jardine; Gary M. Raymond; Maxwell Lewis Neal; James B. Bassingthwaighte (F1000Research, 2013)

A C library for retrieving specific reactions from the BioModels database. - Maxwell Lewis Neal; Michal Galdzicki; J. T. Gallimore; Herbert M. Sauro (Bioinform., 2014)

A Reappraisal of How to Build Modular, Reusable Models of Biological Systems. - Maxwell Lewis Neal; Michael T. Cooling; Lucian P. Smith; Christopher T. Thompson; Herbert M. Sauro; Brian E. Carlson; Daniel L. Cook; John H. Gennari (PLoS Comput. Biol., 2014)

Qualitative Causal Analyses of Biosimulation Models. - Maxwell Lewis Neal; John H. Gennari; Daniel L. Cook (ICBO/BioCreative, 2016)

Extending the Ontology of Physics for Biology with Thermodynamics. - Daniel L. Cook; John H. Gennari; Maxwell Lewis Neal (ICBO, 2017)

The Ontology of Physics for Biology - A Companion to Basic Formal Ontology. - Daniel L. Cook; John H. Gennari; Maxwell Lewis Neal (ICBO, 2019)

Harmonizing semantic annotations for computational models in biology. - Maxwell Lewis Neal; Matthias König 003; David P. Nickerson; Goksel Misirli; Reza Kalbasi; Andreas Dräger; Koray Atalag; Vijayalakshmi Chelliah; Michael T. Cooling; Daniel L. Cook; Sharon M. Crook; Miguel de Alba; et al. (Briefings Bioinform., 2019)

SemGen: a tool for semantics-based annotation and composition of biosimulation models. - Maxwell Lewis Neal; Christopher T. Thompson; Karam G. Kim; Ryan C. James; Daniel L. Cook; Brian E. Carlson; John H. Gennari (Bioinform., 2019)

Model annotation and discovery with the Physiome Model Repository. - Dewan M. Sarwar; Reza Kalbasi; John H. Gennari; Brian E. Carlson; Maxwell Lewis Neal; Bernard de Bono; Koray Atalag; Peter J. Hunter; David P. Nickerson (BMC Bioinform., 2019)

Open modeling and exchange (OMEX) metadata specification version 1.0. - Maxwell Lewis Neal; John H. Gennari; Dagmar Waltemath; David P. Nickerson; Matthias König 003 (J. Integr. Bioinform., 2020)

libOmexMeta: enabling semantic annotation of models to support FAIR principles. - Ciaran M. Welsh; David P. Nickerson; Anand K. Rampadarath; Maxwell Lewis Neal; Herbert M. Sauro; John H. Gennari (Bioinform., 2021)

OMEX metadata specification (version 1.2). - John H. Gennari; Matthias König 003; Goksel Misirli; Maxwell Lewis Neal; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2021)