CompuCell Publications 1. Cickovski, T., Huang, C., Chaturvedi, R., Glimm, T., Hentschel, H.G.E., Alber, M., Glazier, J.A., Newman, S.A., and Izaguirre, J.A. [2005], A framework for three-dimensional simulation of morphogenesis, ACM Transactions on Computational Biology and Bioinformatics 2(4), 273-288. (PDF) 2. Izaguirre, J.A., Chaturvedi, R., Huang, C., Cickovski, T., Coffland, J., Thomas, G., Forgacs, G., Alber, M., Hentschel, G., Newman, S.A., and Glazier, J.A. [2004], CompuCell, a multi-model framework for simulation of morphogenesis, Bioinformatics 20, 1129-1137 (PDF). 3. Cickovski, T., Matthey, T., and Izaguirre, J.A., Design Patterns for Scientific Software, Technical Report 29, University of Notre Dame, Department of Computer Science and Engineering, Nov. 2004 (PDF). Related Publications 1. Alber, M.S., Kiskowski, M.A., Glazier, J.A., and Jiang, Y., On Cellular Automaton Approaches to Modeling Biological Cells, in J. Rosenthal and D.S. Gilliam (Eds.), Mathematical Systems Theory in Biology, Communication and Finance, IMA Volume 134, Springer-Verlag, New York, 2003, p.1. 2. Chaturvedi, R., Izaguirre, J.A., Huang, C., Cickovski, T., Virtue, P., Thomas, G., Forgacs, G., Alber, M., Hentschel, G., Newman, S.A., and Glazier, J.A. [2003], Multi-model simulations of chicken limb morphogenesis, Lecture Notes in Computer Science, Volume 2659, Springer-Verlag, New York, 39-49. 3. Hentschel, H.G.E., Glimm, T., Glazier, J.A., and Newman, S.A., Dynamical mechanisms for skeletal pattern formation in the vertebrate limb. Proc. R. Soc. Lond: Bio. Sciences 271 (2004) 1713-1722. 4. Kiskowski, M.A., Alber, M.S., Thomas, G.L., Glazier, J.A., Bronstein, N., Pu, J., and Newman, S.A. [2004], Interaction between activator-inhibitor coupling and cell-matrix adhesion in a cellular automaton model for chondrogenic patterning, Developmental Biology 271, 372--387 (corresponding authors: M. Alber and S. Newman). 5. Alber, M.S., Jiang, Y., and Kiskowski, M.A. [2004], Lattice gas cellular automaton model for rippling and aggregation in myxobacteria, Physics D 191, 343-358. 6. Alber, M.S., Kiskowski, M.A., and Jiang, Y. [2004], Two-stage aggregate formation via streams in myxobacteria, Phys. Rev. Lett. 93 068301. 7. Alber, M., Glimm, T., Hentschel, H.G.E., Kazmierczak, B., and Newman, S. [2005], Stability of n-Dimensional Patterns in a Generalized Turing System: Implications for Biological Pattern Formation, Nonlinearity 18 125-138. 8. Kiskowski, M.A., Jiang, Y., and Alber, M.S. [2004], Role of Streams in Myxobacteria Aggregate Formation, Physical Biology 1 173-183. 9. Chaturvedi, R., Huang, C., Izaguirre, J.A., Newman, S.A., Glazier, J.A. and Alber, M. [2004], A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of Vertebrate Limb, Lecture Notes in Computer Science, Vol. 3305, Springer-Verlag, New York, 543-552. 10. Alber, M.S., Kiskowski, M.A., Jiang, Y., and Newman, S.A. [2004], Biological Lattice Gas Models, in Dynamics and Bifurcation of Patterns in Dissipative Systems, G. Dangelmayr and I. Oprea (eds.), World Scientific Series on Nonlinear Science, Vol. 12, World Scientific, Singapore, 2004, pp 274-291. 11. Alber, M., Hentschel, H.G.E., Kazmierczak, B., and Newman, S.A., Existence of Solutions to a New Model of Biological Pattern Formation, Journal of Mathematical Analysis and Applications (to appear). 12. Chaturvedi, R., Huang, C., Kazmiercazk, B., Schneider, T., Izaguirre, J.A., Glimm, T., Hentschel, H.G.E., Newman, S.A., Glazier, J.A., and Alber, M., On Multiscale Approaches to Three-Dimensional Modeling of Morphogenesis (submitted). 13. Zeng, W., Thomas, G.L., Newman, S.A., and Glazier, J.A., A Novel Mechanism for Mesenchymal Condensation During Limb Chondrogenesis In Vitro, Mathematical Modeling and Computing in Biology and Medicine: 5th Conference of the European Society of Mathematical and Theoretical Biology, Milan, V. Capasso and M. Ortisi, 2002. 14. Cickovski, T. and Izaguirre, J.A. BioLogo, A Domain-Specific Language for Morphogenesis, Preprint available: (PDF)