A cellular automaton model for the study of DNA sequence evolution

Computers in Biology and Medicine

Volumn 33, Issue 5, 2003, Pages 439-453

  Sirakoulis, G Ch ^a   Karafyllidis, I ^b   Mizas, Ch ^a   Mardiris, V ^a   Thanailakis, A ^b   Tsalides, Ph ^b  

^a Ulysses Ltd   (Greece)

^b DEMOCRITUS UNIVERSITY OF THRACE   (Greece)

Author keywords

Bioinformatics; Cellular automata; DNA; Modeling; Nanotechnology; Simulation

Indexed keywords

CELLS; COMPUTER SIMULATION; DNA; MATHEMATICAL MODELS; USER INTERFACES;

CELLULAR AUTOMATION;

AUTOMATION;

DNA; DNA BASE;

ARTICLE; CELLULAR AUTOMATA; COMPUTER INTERFACE; COMPUTER SIMULATION; DEVICE; DNA SEQUENCE; DNA STRUCTURE; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN FUNCTION; SIMULATOR;

EID: 0038304965     PISSN: 00104825     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0010-4825(03)00017-9     Document Type: Article

References (26)

1. Moore S.K. Understanding the human genome. Inst. Electr. Electron. Eng. (IEEE) Spectrum. 37:2000;33.
2. Moore S.K. Making chips to probe genes. Inst. Electr. Electron. Eng. (IEEE) Spectrum. 38:2001;54.
3. Baxevanis A.D., Ouellette B.F., Bioinformatics, A Practical Guide to the Analysis of Genes and Proteins. 1998;Wiley-Interscience, New York.
4. Durbin R., Eddy S., Krogh A., Mitchison G. Biological Sequence Analysis, Probabilistic Models of Proteins and Nucleic Acids. 2000;Cambridge University Press, Cambridge.
5. von Neumann J. Theory of Self-reproducing Automata. 1966;University of Illinois Press, Urbana.
6. Wolfram S. Cellular Automata and Complexity. 1994;Addison-Wesley, New York.
7. Manneville P., Boccara N., Vichniac G.Y., Bidaux R. Cellular Automata and Modeling of Complex Physical Systems. 1990;Springer, Berlin.
8. Chopard B., Droz M. Cellular Automata Modeling of Physical Systems. 1998;Cambridge University Press, Cambridge, MA.
9. Gaylord R.J., Nishidate K. Modeling Nature, Cellular Automata Simulations with Mathematica. 1996;Telos Springer, Berlin.
10. Karafyllidis I., Thanailakis A. A model for predicting forest fire spreading using Cellular Automata. Ecol. Modeling. 99:1997;87.
11. Karafyllidis I. A model for the prediction of oil slick movement and spreading using Cellular Automata. Environ. Int. 23:1997;839.
12. Karafyllidis I. A model for the influence of the greenhouse effect on insect and microorganism geographical distribution and population dynamics. BioSystems. 45:1998;1.
13. Sirakoulis G.Ch., Karafyllidis I., Thanailakis A. A Cellular Automaton model for the effects of population movement and vaccination on epidemic propagation. Ecol. Modeling. 133:2000;209.
14. Kansal A.R., Torquato S., Harsh IV G.R., Chiocca E.A., Deisboeck T.S. Simulated brain tumor growth dynamics using a three-dimensional cellular automaton. J. Theoret. Biol. 203:2000;367.
15. Patel A.A., Gawlinski E.T., Lemieux S.K., Gatenby R.A. A cellular automaton model of early tumor growth and invasion. the effects of native tissue vascularity and increased anaerobic tumor metabolism J. Theoret. Biol. 213:2001;315.
16. R.M.Z. dos Santos, On the dynamics of the evolution of HIV infection, http://arXiv.org/pdf/cond-mat/0008081 (2000).
17. Bernadres A.T., dos Santos R.M.Z. Immune network at the edge of chaos. J. Theoret. Biol. 186:1997;173.
18. Bernaschi M., Castiglione F., Succi S. A high performance simulator of the immune system. Future Gen. Comput. Systems. 15:1999;333.
19. Ulam S. Some ideas and prospects in biomathematics. Ann. Rev. Bio. 12:1974;255.
20. McFadden J., Al-Khalili J. A quantum mechanical model of adaptive mutation. BioSystems. 50:1999;203.
21. Schwefel H.P. Deep insight from simple models of evolution. BioSystems. 64:2002;189.
22. P.F. Arndt, C.B. Burge, T. Hwa, DNA sequence evolution with neighbor-dependent mutation, http://arXiv.org/pdf/physics/0112029 (2001).
23. Jones M.E., Thomas S.M., Clarke K. The application of a linear algebra to the analysis of mutation rates. J. Theoret. Biol. 199:1999;11.
24. Adamatzky A. Identification of Cellular Automata. 1994;Taylor & Francis, London.
25. Voorhees B.H. Computational Analysis of One-dimensional Cellular Automata. 1996;World Scientific, Singapore.
26. Archilla J.F.R., Christiansen P.L., Gaididei Yu.B. Interplay of nonlinearity and geometry in a DNA-related, Klein-Gordon model with long-range dipole-dipole interaction. Phys. Rev. E (Stat. Nonlinear, Soft Matter Phys.). 65:2002;016609/1 Georgios Ch. Sirakoulis was born in Athens, Greece in 1973. He received the Diploma and Ph.D. degrees in Electrical and Computer Engineering from the Democritus University of Thrace, Greece, in 1996 and 2001, respectively. For his Diploma Thesis, he received a prize of distinction from the Technical Chamber of Greece (TEE). His current research emphasis is on cellular automata theory and applications, bioinformatics, modeling and simulation of microelectronic devices and processes, TCAD, VLSI design applications using VHDL, VLSI physical design, and genetic algorithms. He is with Ulysses Ltd. from 2001. The R&D Department of Ulysses Ltd. is focused on providing integrated customized software solutions for the emerging demands of the Life Sciences. He is a member of the IEEE and of the TEE. Ioannis Karafyllidis was born in Thessaloniki, Greece in 1959. He received the Diploma in Engineering and Ph.D. degrees in Electrical Engineering from the Aristotle University of Thessaloniki, Greece, in 1983 and 1991, respectively. In 1992, he joined the Department of Electrical and Computer Engineering, Democritus University of Thrace, Greece, as a faculty member, where he is currently an Associate Professor. He has published more than 70 papers in refereed journals and conferences and acts as a referee for several international journals. His current research emphasis is on nanoelectronics, nanotechnology, quantum computing, and cellular automata theory and applications. He is a fellow of the Institute of Nanotechnology, a member of the IEEE and a member of the Technical Chamber of Greece (TEE). Charilaos Mizas was born in Thessaloniki, Greece in 1971. He received the Diploma degree in Electrical and Computer Engineering from the Democritus University of Thrace, Greece, in 1996. His current research emphasis is on bioinformatics, low power design, parallel architectures, computer arithmetic, and VLSI signal processing. In 2000, he received an award from Intel and IBM for the Low Power Design project LPGD ESPRIT IV #25256. He is with Ulysses Ltd. from 2001. The R&D Department of Ulysses Ltd. is focused on providing integrated customized software solutions for the emerging demands of the Life Sciences. He is a member of the TEE. Vassilios Mardiris was born in Kavala, Greece in 1969. He received the Diploma degree in Electrical and Computer Engineering from the Democritus University of Thrace, Greece, in 1996. His current research emphasis is on cellular automata theory and applications, bioinformatics, neural networks and applications, parallel architectures and computer arithmetic. In 2000, he received an award from Intel and IBM for the Low Power Design project LPGD ESPRIT IV #25256. He is with Ulysses Ltd. from 2001. The R&D Department of Ulysses Ltd. is focused on providing integrated customized software solutions for the emerging demands of the Life Sciences. He is a member of the TEE. Adonios Thanailakis was born in Greece in 1940. He received B.Sc. degrees in Physics and Electrical Engineering from the University of Thessaloniki, Greece, in 1964 and 1968, respectively, and the M.Sc. and Ph.D. degrees in electrical engineering and electronics from UMIST, Manchester, England, UK, in 1968 and 1971, respectively.