Zwolak, J. W., J. J. Tyson, and L. T. Watson, ``Estimating rate constants in cell cycle models'', in Proc. High Performance Computing Symposium 2001, A. Tentner (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, 2001, 53-57.

Zwolak, Jason W. October 31, 2001. "Parameter Estimation In Biological Cell Cycle Models Using Deterministic Optimization". Masters Thesis. Virginia Tech.

Zwolak, Jason W., Tyson, J. J., and Watson, L. T. "Parameter Estimation In a Cell Cycle Model for Frog Egg Extracts", in Proc. High Performance Computing Symposium 2002, A. Tentner (ed.), Soc. For Modeling and Simulation Internat., San Diego, CA, 2002, 67-74.

Zwolak, J. W., J. J. Tyson, and L. T. Watson, ``Finding all steady state solutions of chemical kinetic models'' in Proc. High Performance Computing Symposium 2003, I. Banicescu (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, 2003, 47-53.

Allen N.A., Calzone L., Chen K.C., Ciliberto A., Ramakrishnan N., Shaffer C.A., Sible J.C., Tyson J.J., Vass M.T., Watson L.T. and Zwolak J.W. (2003). Modeling regulatory networks at Virginia Tech. OMICS 7:285-299.

Zwolak, J. W., J. J. Tyson, and L. T. Watson, ``Finding All Steady State Solutions of Chemical Kinetic Models.'' Nonlinear Analysis: Real World Applications, 5 (2004) 801-814

J. He, M. Sosonkina, C. A. Shaffer, J. J. Tyson, L. T. Watson, and J. W. Zwolak, ``A hierarchical parallel scheme for global parameter estimation in systems biology'', in Proc. 18th Internat. Parallel & Distributed Processing Symp., CD-ROM, IEEE Computer Soc., Los Alamitos, CA, 2004, 9 pages.

Zwolak, Jason W. December 2004. "Computational Tools for Modelling Molecular Networks in Biological Systems". Doctoral Dissertation. Virginia Tech.

Zwolak, J. W., J. J. Tyson, and L. T. Watson, ``Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs.'' Journal of Computational Biology, Feb 2005, Vol. 12, No. 1: 48-63

Zwolak, J. W., J. J. Tyson, and L. T. Watson, ``Globally Optimized Parameters for a Model of Mitotic Control in Frog Egg Extracts.'' IEE Systems Biology, June 2005, Vol. 152, Iss. 2: 81-92

J. W. Zwolak, P.T. Boggs, and L.T. Watson, ``Algorithm 869: ODRPACK95: A weighted orthogonal distance regression code with bound constraints'', ACM Transactions on Mathematical Software Vol. 33, Issue 4, August 2007.

C.A. Shaffer, J.W. Zwolak, R. Randhawa, and J.J. Tyson. ``Modeling Molecular Regulatory Networks with JigCell and PET'' chapter in ``Systems Biology'', ed Ivan Maly, Humana Press, Chapter 4, 2009.

Zwolak, J., Adjerid, N., Bagci, E. Z., Tyson, J. J., and Sible, J. C. (2009) ``A quantitative model of the effect of unreplicated DNA on cell cycle progression in frog egg extracts'', Journal of Theoretical Biology Vol. 260, Issue 1, pg 110-120.