Arkin, A., and Ross, J. 1995. Statistical construction of chemical reaction mechanisms from measured time-series. J. Phys. Chem. 99, 970–979.

Arkin, A., Ross, J., and McAdams, H.A. 1998. Stochastic kinetic analysis of developmental pathway bifurcation in phage ¸-infected Escherichia coli cells. Genetics 149, 1633–1648.

Arkin, A., Shen, P., and Ross, J. 1997. A test case of correlation metric construction of a reaction pathway from measurements. Science 277, 1275–1279.

Brown. et al (1999). Knowledge-based analysis of microarray gene expression data.  Proceedings of National Academy of Sciences, 1997, 262-267.

de Jong, H., Page, M., Hernandez, C., and Geiselmann, J. 2001. Qualitative simulation of genetic regulatory networks: Method and application. In B. Nebel, ed. Proc. 17th Int. Joint Conf. Artif. Intell. (IJCAI-01), 67–73, San Mateo,CA. Morgan Kaufmann.

de Jong, H., and Rip, A. 1997. The computer revolution in science: Steps towards the realization of computer-supported discovery environments. Artif. Intell. 91, 225–256.

DeRise et al (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680 - 686.

Eisen (1995). Cluster analysis and display of genome-wide expression patterns. Proceedings of National Academy of Sciences, 1995, 14863-14868.

Friedman, N., Linial, M., Nachman, I., and Pe’er, D. 2000. Using Bayesian networks to analyze expression data. J. Comput. Biol. 7, 601–620.

Gillespie, D.T. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81(25), 2340–2361.

Gillespie, D.T. 1992. A rigorous derivation of the chemical master equation. Physica D 188, 404–425.

Iyer, V.R., Eisen, M.B., Ross, D.T., Schuler, G., Moore, T., Lee, J.C.F., Trent, J.M., Staudt, L.M., Hudson, J. Jr., Boguski, M.S., Lashkari, D., Shalon, D., Botstein, D. and Brown, P.O. (1999) The transcriptional program in the response of human fibroblasts to serum. Science 283, 83-87.

Karp, P.D. (1991) Hypothesis formation as design. In J. Shrager and P. Langley, eds. ComputationalModels of Scienti. cDiscovery and Theory Formation, 275–317, Morgan Kaufmann, San Mateo, CA.

Kauffman, S.A. 1969a. Homeostasis and differentiation in random genetic control networks. Nature 224, 177–178.

Kauffman, S.A. 1969. Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22, 437–467.

Kauffman, S.A. 1974. The large-scale structure and dynamics of gene control circuits: An ensemble approach. J. Theor. Biol. 44, 167–190.

Kauffman, S.A. 1977. Gene regulation networks: A theory for their global structure and behaviors. In Current Topics in Developmental Biology, vol. 6, 145–182, Academic Press, New York.

Lander E.S (1996). The new genomics: global view of biology, Science 274, 536-539.

McAdams, H.M., and Arkin, A. 1997. Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. USA 94, 814–819.

McAdams, H.H., and Arkin, A. 1998. Simulation of prokaryotic genetic circuits. Ann. Rev. Biophys. Biomol. Struct. 27, 199–224.

McAdams, H.H., and Arkin, A. 1999. It’s a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 15(2), 65–69.

McAdams, H.H., and Shapiro, L. 1995. Circuit simulation of genetic networks. Science 269, 650–656.

Pathfinder, (Z solutions, LLC 1998, http://www.zsolutions.com/pathfind.htm).

Shatkay, H., Edwards, S., Wilbur, W.J., and Boguski, M. (2000) Genes, themes, and microarray: using information retrieval for large-scale gene analysis. In Proceedings of 8^th International Conference on Intelligent Systems for Molecular Biology (ISMB). AAAI Press, 317-328.

Schena, M., Shalon, D., Davis, R.W. and Brown, P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470.

Samsonova, M.G., Savostyanova, E.G., Serov, V.N., Spirov, A.V., and Reinitz, J. (1998) GeNet: A database of genetic networks. In Proc. First Int. Conf. Bioinformatics Genome Regul. Struct., BGRS’98, Novosibirsk, ICG.

Samsonova, M., and Serov, V.N. (1999) NetWork: An interactive interface to the tools for analysis of genetic network structure and dynamics. In R.B. Altman, K. Lauderdale, A.K. Dunker, L. Hunter, and T.E. Klein, eds. Proc. Pac. Symp. Biocomput. (PSB’99), vol. 4, 102–111, Singapore,World Scientific Publishing.

Sanchez, C., Lachaize, C., Janody, F., Bellon, B., Röder, L., Euzenat, J., Rechenmann, F., and Jacq, B. (1999) Grasping at molecular interactions and genetic networks in Drosophila melanogaster. Nucleic Acids Res. 27(1), 89–94.

Sánchez, L., and Thieffry, D. (2001) A logical analysis of the Drosophila gap genes. J. Theor. Biol. 211, 115–141.

Sánchez, L., van Helden, J., and Thieffry, D. (1997) Establishment of the dorso-ventral pattern during embryonic development of Drosophila melanogaster: A logical analysis. J. Theor. Biol. 189, 377–389.

Sugita, M. 1961. Functional analysis of chemical systems in vivo using a logical circuit equivalent. J. Theor. Biol. 1, 179–192.

.Sugita, M. 1963. Functional analysis of chemical systems in vivo using a logical circuit equivalent: II. The idea of a molecular automaton. J. Theor. Biol. 4, 179–192.

Somogyi, R., and Sniegoski, C.A. 1996. Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation. Complexity 1(6), 45–63.

Tavazoie, S., Huges, J.D., Campbell, M.J., Cho, R.J. and Church, G.M. (1999) Systematic determination of genetic network architecture. Nat. Genet. 22, 281-285.

Walter, C., Parker, R., and YÏas, M. 1967. A model for binary logic in biochemical systems. J. Theor. Biol. 15, 208–217.