| 2007 | 
| 8 | EE | Ranjit Randhawa,
Clifford A. Shaffer,
John J. Tyson:
Fusing and composing macromolecular regulatory network models.
SpringSim (2) 2007: 337-344 | 
| 2006 | 
| 7 | EE | Clifford A. Shaffer,
Ranjit Randhawa,
John J. Tyson:
The role of composition and aggregation in modeling macromolecular regulatory networks.
Winter Simulation Conference 2006: 1628-1636 | 
| 6 | EE | Herbert M. Sauro,
David Harel,
Marta Z. Kwiatkowska,
Clifford A. Shaffer,
Adelinde M. Uhrmacher,
Michael Hucka,
Pedro Mendes,
Lena Strömbäck,
John J. Tyson:
Challenges for modeling and simulation methods in systems biology.
Winter Simulation Conference 2006: 1720-1730 | 
| 5 | EE | Marc Vass,
Clifford A. Shaffer,
Naren Ramakrishnan,
Layne T. Watson,
John J. Tyson:
The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models.
IEEE/ACM Trans. Comput. Biology Bioinform. 3(2): 155-164 (2006) | 
| 2005 | 
| 4 | EE | Jason W. Zwolak,
John J. Tyson,
Layne T. Watson:
Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs.
Journal of Computational Biology 12(1): 48-63 (2005) | 
| 2004 | 
| 3 | EE | Jian He,
Masha Sosonkina,
Clifford A. Shaffer,
John J. Tyson,
Layne T. Watson,
Jason W. Zwolak:
A Hierarchical Parallel Scheme for Global Parameter Estimation in Systems Biology.
IPDPS 2004 | 
| 2 | EE | Marc Vass,
Nicholas Allen,
Clifford A. Shaffer,
Naren Ramakrishnan,
Layne T. Watson,
John J. Tyson:
The JigCell Model Builder and Run Manager.
Bioinformatics 20(18): 3680-3681 (2004) | 
| 1991 | 
| 1 |   | Jörg R. Weimar,
John J. Tyson,
Layne T. Watson:
Third Generation Cellular Automation for Modeling Excitable Media.
PPSC 1991: 376-381 |