Use of evolved artificial regulatory networks to simulate 3D cell differentiation

BioSystems

Volumn 102, Issue 1, 2010, Pages 41-48

  Chavoya, Arturo ^a   Andalon Garcia, Irma R ^a   Lopez Martin, Cuauhtemoc ^a   Meda Campana M E ^a  

^a UNIVERSITY OF GUADALAJARA   (Mexico)

Author keywords

Artificial regulatory network; Cell differentiation; Cellular automata; French flag problem; Genetic algorithm

Indexed keywords

ARTIFICIAL NEURAL NETWORK; CELLULAR AUTOMATON; CHROMOSOME; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENETIC ALGORITHM; INHIBITION; MORPHOGENESIS; SELECTION;

ARTICLE; CELL DIFFERENTIATION; CELL DIVISION; CELL GROWTH; CELL STRUCTURE; CHROMOSOME REPLICATION; GENE ACTIVATION; GENE REGULATORY NETWORK; GENETIC ALGORITHM; NONHUMAN; STRUCTURAL GENE; THREE DIMENSIONAL CELL DIFFERENTIATION;

EID: 77957277131     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2010.07.011     Document Type: Article

References (36)

1. Baker R.W., Herman G.T. Celia-a cellular linear iterative array simulator. Proceedings of the Fourth Annual Conference on Applications of Simulation: Winter Simulation Conference 1970, 64-73.
2. Banzhaf W. Artificial regulatory networks and genetic programming. Genetic Programming Theory and Practice 2003, 43-62. Kluwer, Ch. 4. R.L. Riolo, B. Worzel (Eds.).
3. Beurier G., Michel F., Ferber J. A morphogenesis model for multiagent embryogeny. Proceedings of the Tenth International Conference on the Simulation and Synthesis of Living Systems (ALife X) 2006, 84-90. L.M. Rocha, L.S. Yaeger, M.A. Bedau, D. Floreano, R.L. Goldstone, A. Vespignani (Eds.).
4. Bongard J. Evolving modular genetic regulatory networks. Proceedings of the 2002 Congress on Evolutionary Computation (CEC2002) 2002, 1872-1877. IEEE Press, Piscataway, NJ.
5. Bowers C. Simulating evolution with a computational model of embryogeny: Obtaining robustness from evolved individuals. Advances in Artificial Life Proceeding of the 8th European Conference on Artificial Life: ECAL 2005 2005, 149-158. Springer. M.S. Capcarrere, A.A. Freitas, P.J. Bentley, C.G. Johnson, J. Timmons (Eds.).
6. Breukelaar R., Bäck T. Using a genetic algorithm to evolve behavior in multi dimensional cellular automata: emergence of behavior. GECCO'05 2005, 107-114.
7. Carroll S.B., Grenier J.K., Weatherbee S.D. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design 2004, Blackwell Science. 2nd edition.
8. Chavoya A. Cell pattern generation in artificial development. Brain, Vision and AI 2008, 73-94. In-Teh, Croatia, Ch. 4. C. Rossi (Ed.).
9. Chavoya A. Artificial development. Foundations of Computational Intelligence. Volume 1: Learning and Approximation (Studies in Computational Intelligence) 2009, 185-215. Springer, Berlin/Heidelberg, Ch. 8.
10. Chavoya A., Duthen Y. Using a genetic algorithm to evolve cellular automata for 2D/3D computational development. GECCO'06: Proceedings of the 8th Annual Conference on Genetic and Evolutionary Computation 2006, 231-232. ACM Press, New York, NY, USA.
11. Chavoya A., Duthen Y. An artificial development model for cell pattern generation. ACAL'07: Proceedings of the 3rd Australian Conference on Artificial Life 2007, 61-71. Springer.
12. Chavoya A., Duthen Y. Evolving an artificial regulatory network for 2D cell patterning. Proceedings of the 2007 IEEE Symposium on Artificial Life (CI-ALife'07) IEEE Computational Intelligence Society 2007, 47-53.
13. Chavoya A., Duthen Y. A cell pattern generation model based on an extended artificial regulatory network. BioSystems 2008, 94(1):95-101.
14. Cickovski T., Aras K., Swat M., Merks R.M.H., Glimm T., Hentschel H.G.E., Alber M.S., Glazier J.A., Newman S.A., Izaguirre J.A. From genes to organisms via the cell: A problem-solving environment for multicellular development. Computing in Science and Engineering 2007, 9(4):50-60.
15. Davidson E.H. The Regulatory Genome: Gene Regulatory Networks in Development And Evolution 2006, Academic Press. 1st Edition.
16. de-Garis H. Artificial embryology and cellular differentiation. Evolutionary Design by Computers 1999, 281-295. Morgan Kaufmann Publishers Inc., San Francisco, USA. P.J. Bentley (Ed.).
17. Devert A., Bredeche N., Schoenauer M. Robust multi-cellular developmental design. GECCO'07: Proceedings of the 9th Annual Conference on Genetic and Evolutionary Computation 2007, 982-989. ACM, New York, NY, USA.
18. Eggenberger P. Evolving morphologies of simulated 3D organisms based on differential gene expression. Proceedings of the 4th European Conference on Artificial Life 1997, 205-213. Springer. I. Harvey, P. Husbands (Eds.).
19. Gordon T.G.W., Bentley P.J. Bias and scalability in evolutionary development. GECCO'05: Proceedings of the 2005 Conference on Genetic and Evolutionary Computation 2005, 83-90. ACM, New York, NY, USA.
20. Harding S.L., Miller J.F., Banzhaf W. Self-modifying cartesian genetic programming. GECCO'07: Proceedings of the 9th annual conference on Genetic and Evolutionary Computation 2007, 1021-1028. ACM, New York, NY, USA.
21. Herman G.T., Liu W.H. The daughter of celia the french flag and the firing squad. WSC'73: Proceedings of the 6th conference on Winter Simulation 1973, 870. ACM, New York, NY, USA.
22. Holland J.H. Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology Control and Artificial Intelligence 1992, MIT Press, Cambridge, MA, USA.
23. Joachimczak M., Wróbel B. Evo-devo in silico: a model of a gene network regulating multicellular development in 3D space with artificial physics. Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems 2008, 297-304. MIT Press, Cambridge, MA. S. Bullock, J. Noble, R. Watson, M.A. Bedau (Eds.).
24. Knabe J.F., Nehaniv C.L., Schilstra M.J. Evolution and morphogenesis of differentiated multicellular organisms: autonomously generated diffusion gradients for positional information. Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems 2008, 321-328. MIT Press.
25. Kuo P.D., Leier A., Banzhaf W. September Evolving dynamics in an artificial regulatory network model. Proceedings of the Parallel Problem Solving from Nature Conference (PPSN-04). LNCS 3242 2004, 571-580. Springer, Berlin, Birmingham, UK. X. Yao, E. Burke, J. Lozano, J. Smith, J. Merelo-Guervós, J. Bullinaria, J. Rowe, P. Tino, A. Kabán, H.-P. Schwefel (Eds.).
26. Lindenmayer A., Rozenberg G. Developmental systems and languages. STOC'72: Proceedings of the Fourth Annual ACM Symposium on Theory of Computing 1972, 214-221. ACM, New York, NY, USA.
27. Meinhardt H. Models of Biological Pattern Formation 1982, Academic Press, London.
28. Miller J.F., Banzhaf W. Evolving the program for a cell: from French flags to Boolean circuits. On Growth, Form and Computers Oct. 2003, 278-301. Academic Press. S. Kumar, P.J. Bentley (Eds.).
29. Mitchell M. An Introduction to Genetic Algorithms 1996, MIT Press, Cambridge, MA, USA.
30. Reil T. Dynamics of gene expression in an artificial genome - implications for biological and artificial ontogeny. Proceedings of the 5th European Conference on Artificial Life (ECAL) 1999, 457-466. Springer Verlag, New York, NY.
31. Turing A.M. The chemical basis of morphogenesis. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 1952, 237(641):37-72.
32. Tyrrell A.M., Greensted A.J. Evolving dependability. Journal of Emergency Technology Computer System 2007, 3(2):7.
33. Wilensky, U., 1999. NetLogo. http://ccl.northwestern.edu/netlogo/, center for Connected Learning and Computer-Based Modeling, Northwestern University. Evanston, IL.
34. Wolfram S. Statistical mechanics of cellular automata. Reviews of Modern Physics 1983, 55:601-644.
35. Wolpert L. The French flag problem: a contribution to the discussion on pattern development and regulation. Towards a Theoretical Biology 1968, 125-133. Edinburgh University Press, New York, NY, USA. C. Waddington (Ed.).
36. Wu P., Wu X., Wainer G.A. Applying cell-devs in 3D free-form shape modeling. Cellular Automata, 6th International Conference on Cellular Automata for Research and Industry, ACRI 2004 2004, 81-90.