Evolution of biological regulation networks under complex environmental constraints

Amit D (1992) Modeling brain function, 2nd edn. Cambridge University Press, Cambridge, UK Ando A, Fisher FM (1962) Two theorems on Ceteris Paribus in the analysis of dynamic systems. Am Pol Sci Rev 61:103–113 Bagley RJ, Farmer JD, Kauffman SA, Packard NH, Perelson AS, Stadnyk IM (1989) Modeling adaptive biological systems. BioSystems 23:113–138 Belew RK, McInerney J, Schraudolph NN (1992) Evolving networks: using the genetic algorithm with connectionist learning. In: Artificial life II. Addison-Wesley, New York Berridge MJ (1985) The molecular basis of communication with the cell. Sci Am 253:142–152 Calakos N, Bennett M, Peterson K, Scheller R (1994) Protein-protein interactions contributing to the specificity of intracellular vesicular trafficking. Science 263:1146–1149 Clark SC, Kamen R (1987) The human hematopoietic colony stimulating factors. Science 236:1229–1237 Cormier F, Dieterlen-Lièvre F (1988) The walls of the chick aorta harbours M-CFC, G-CFC, GM-CFC and BFU-E. Development 102:279–285 Cyert MS, Thorner J (1989) Putting it on and taking it off: phosphoprotein phosphatase involvement in cell cycle regulation. Cell 57:891–893 Derrida B, Stauffer D (1986) Phase-transitions in two-dimensional Kauffman cellular automata. Europhys Lett 2:739–745 Endo YG, Lee MA, Kopf GS (1987) Evidence for the role of a guanosine nucleotide-binding regulatory protein in the zona pellucida-induced mouse sperm acrosome reaction. Dev Biol 119:210–216 Farmer JD, Kauffman SA, Packard NH, Perelson AS (1989) Adaptive dynamic networks as models for the immune system and autocatalytic sets. Ann NY Acad Sci 118–130 Fothergill-Gilmore LA (1986) The evolution of the glycolytic pathway. Trends Biochem Sci 11:47–51 Gardner E (1988) The space of interactions in neural network models. J Phys A: Math Gen 21:257–270 Gardner E, Derrida D (1988) Optimal storage properties of neural network models. J Phys A: Math Gen 21:271–284 Goldberg DE (1989) Genetic algorithms in search, optimization and machine learning. Addison-Wesley, Reading Hassoun MH (1991) Dynamic associative memories. In: Sethi IK, Jain AK (eds) Artificial neural networks and statistical pattern recognition, old and new connections, pp 195–218 Hopfield JJ (1982) Neural networks and physical systems with emergent collective computational abilities. Proc Natl Acad Sci USA 79:2554–2558 Hopfield JJ (1984) Neurons with graded responses have collective computational properties like those of two-state neurons. Proc Natl Acad Sci USA 81:3088–3092 Jacobson H (1955) Information, reproduction and the origin of life. Am Sci 43:119–127 Kauffman SA (1989) Principles of adaptation in complex systems. In: Stein D (eds) Lectures in the science of complexity, vol 1, pp 619–712 Kauffman SA (1990) Requirement for evolvability in complex systems, orderly dynamics and frozen components. Physica D 42:135–152 Kauffman SA (1992) Origins of order: self-organization and selection in evolution. Oxford University Press, Oxford Kauffman SA (1994) Whispers from Carnot. In: Cowan G, Pines D, Meltzer D (eds) Complexity: metaphors, models and reality. (SFI studies in the science of complexity, Proc Vol. XIX), Addison-Wesley, New York, pp 83–160 Kauffman SA, Levin S (1987) Towards a general theory of adaptive walks on rugged landscapes. J Theor Biol 128:11–45 Kohonen T (1984) Self-organization and associative memory. Springer, Berlin Heidelberg New York Langton CG (1990) Computation at the edge of chaos, phase transitions and emergent computation. Physica D 42:12–37 Langton CG (1992) Life on the edge of chaos. In: Artificial life II. Addison-Wesley, New York pp 41–91 Le Douarin NM (1986) Cell line segregation during peripheral nervous system ontogeny. Science 231:1515–1522 Linsker R (1988) Self-organization in a perceptual network. Computer 21:105–117 Marchionni M, Gilbert W (1986) The triosephosphate isomerase gene from maize: introns antedate the plant-animal divergences. Cell 46:133–141 Minai A, Levy W (1993) The dynamics of sparse random networks. Biol. Cybern. 70:177–187 Mitchell M, Hraber PT, Crutchfield JP (1993) Revisiting the edge of chaos: evolving cellular automata to perform computations. Complex systems 7:89–130 Rabilloud T, Vincens P, Tarroux P (1985) A new tool to study genetic expression using 2-D electrophoresis data: the functional map concept. FEBS Lett 189:171–178 Rabilloud T, Pennetier JL, Hibner U, Vincens P, Tarroux P, Rougeon F (1991) Stage transitions in B-lymphocytes differentiation correlate with limited variations in nuclear proteins. Proc Natl Acad Sci USA 88:1830–1834 Rammal R, Toulouse G, Virasoro MA (1986) Ultrametricity for physicists. Rev Mod Phys 58:765–788 Simon HA (1962) Architecture of complexity. Proc Am Philos Soc 106:467–482 Sompolinsky H, Crisanti A (1988) Chaos in random neural networks. Phys Rev Lett 61:259–262 Spears WM, De Jong KA (1991) On the virtues of parameterized uniform crossover. In: Belew RK, Booker LB (eds) Proceeding of the Fourth International Conference on Genetic Algorithms. Morgan Kauffman, San Mateo, pp 230–236 Syswerda G (1989) Uniform crossover in genetic algorithms, In: Schaffer JD (ed) Proceeding of the Third International Conference on Genetic Algorithms. Morgan Kauffman, San Mateo, pp 2–9 Tarroux P (1983) Analysis of protein patterns during differentiation using 2-D electrophoresis and computer multidimensional classification. Electrophoresis 4:63–70 Tarroux P, Vincens P, Rabilloud T (1987) HERMeS: a second generation approach to the automatic analysis of two-dimensional electrophoresis gels. Part V. Data analysis. Electrophoresis 8:187–199 Wagner A (1994) Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. Proc Natl Acad Sci USA 91:4387–4391 Weisbuch G, Stauffer D (1987) Phase transition in cellular random Booleannets. J Phys 48:11–18