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Volumn , Issue , 2011, Pages 195-231

Interaction-based simulations for integrative spatial systems biology

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EID: 84890456492     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4419-7964-3_10     Document Type: Chapter
Times cited : (10)

References (50)
  • 1
    • 84976826673 scopus 로고
    • Voronoi diagrams-A survey of a fundamental geometric data structure
    • F. Aurenhammer. Voronoi diagrams-A survey of a fundamental geometric data structure. ACM Comput Surv, 23(3):345-405, 1991
    • (1991) ACM Comput Surv , vol.23 , Issue.3 , pp. 345-405
    • Aurenhammer, F.1
  • 3
    • 0027347704 scopus 로고
    • Programming by multiset transformation
    • ACM
    • J.-P. Banatre and D. LeMetayer. Programming by multiset transformation. Comm ACM, 36(1):98, 1993
    • (1993) Comm , vol.36 , Issue.1 , pp. 98
    • Banatre, J.-P.1    Lemetayer, D.2
  • 4
    • 33750743748 scopus 로고    scopus 로고
    • Generalised multisets for chemical programming
    • J.-P. Banatre, P. Fradet, and Y. Radenac. Generalised multisets for chemical programming. Math Struct Comput Sci, 16(4):557-580, 2006
    • (2006) Math Struct Comput Sci , vol.16 , Issue.4 , pp. 557-580
    • Banatre, J.-P.1    Fradet, P.2    Radenac, Y.3
  • 5
    • 31944445648 scopus 로고    scopus 로고
    • Computer simulations reveal novel properties of the cell-cell signaling network at the shoot apex in Arabidopsis
    • P. Barbier de Reuille, I. Bohn-Courseau, K. Ljung, H. Morin, N. Carraro, C. Godin, and J. Traas. Computer simulations reveal novel properties of the cell-cell signaling network at the shoot apex in Arabidopsis. Proc Natl Acad Sc USA, 103(5):1627-1632, 2006a
    • (2006) Proc Natl Acad Sc USA , vol.103 , Issue.5 , pp. 1627-1632
    • De Barbier, R.P.1    Bohn-Courseau, I.2    Ljung, K.3    Morin, H.4    Carraro, N.5    Godin, C.6    Traas, J.7
  • 7
    • 0028248821 scopus 로고
    • The importance of being discrete (and spatial)
    • R. Durrett and S. Levin. The importance of being discrete (and spatial). Theor Popul Biol, 46(3): 363-394, 1994
    • (1994) Theor Popul Biol , vol.46 , Issue.3 , pp. 363-394
    • Durrett, R.1    Levin, S.2
  • 10
    • 28544451327 scopus 로고    scopus 로고
    • Foundations for engineering biology
    • D. Endy. Foundations for engineering biology. Nature, 438:449-453, 2005
    • (2005) Nature , vol.438 , pp. 449-453
    • Endy, D.1
  • 11
    • 0000595654 scopus 로고
    • Studies of nonlinear problems LASL Report LA-1940 (5) Technical report 1965
    • E. Fermi, J. Pasta, and S. Ulam. Studies of nonlinear problems, LASL Report LA-1940 (5). Technical report, 1965. Reprinted in the collected work of E. Fermi, Vol. 2, pp. 977-988, 1965
    • (1965) Reprinted in the Collected Work of E. Fermi , vol.2 , pp. 977-988
    • Fermi, E.1    Pasta, J.2    Ulam, S.3
  • 12
    • 0034064199 scopus 로고    scopus 로고
    • Spatio-logical processes in intracellular signalling
    • M. Fisher, G. Malcolm, and R. Paton. Spatio-logical processes in intracellular signalling. BioSystems, 55:83-92, 2000
    • (2000) BioSystems , vol.55 , pp. 83-92
    • Fisher, M.1    Malcolm, G.2    Paton, R.3
  • 13
    • 0000575425 scopus 로고
    • Algorithmic chemistry
    • In C. G. Langton, C. Taylor, J. D. Farmer, and S. Rasmussen, editors
    • W. Fontana. Algorithmic chemistry. In C. G. Langton, C. Taylor, J. D. Farmer, and S. Rasmussen, editors, Proceedings of the Workshop on Artificial Life (ALIFE90), Vol. 5, pages 159-210, 1992
    • (1992) Proceedings of the Workshop on Artificial Life (ALIFE90) , vol.5 , pp. 159-210
    • Fontana, W.1
  • 14
    • 0028003496 scopus 로고
    • The arrival of the fittest: Toward a theory of biological organization
    • W. Fontana and L.W. Buss. The arrival of the fittest: Toward a theory of biological organization. Bull Math Biol, 1994
    • (1994) Bull Math Biol
    • Fontana, W.1    Buss, L.W.2
  • 15
    • 84947754668 scopus 로고    scopus 로고
    • Topological collections, transformations and their application to the modeling and the simulation of dynamical systems
    • J.-L. Giavitto. Topological collections, transformations and their application to the modeling and the simulation of dynamical systems. In Rewriting Techniques and Applications (RTA03), LNCS 2706, pages 208-233, 2003
    • (2003) Rewriting Techniques and Applications (RTA03), LNCS , vol.2706 , pp. 208-233
    • Giavitto, J.-L.1
  • 18
    • 0036986616 scopus 로고    scopus 로고
    • Pattern-matching and rewriting rules for group indexed data structures
    • J.-L. Giavitto and O. Michel. Pattern-matching and rewriting rules for group indexed data structures. ACM SIGPLAN Not, 37(12):76-87, 2002b
    • (2002) ACM SIGPLAN Not , vol.37 , Issue.12 , pp. 76-87
    • Giavitto, J.-L.1    Michel, O.2
  • 19
    • 0036190735 scopus 로고    scopus 로고
    • The topological structures of membrane computing
    • J.-L. Giavitto and O.Michel. The topological structures of membrane computing. Fundam Inform, 49:107-129, 2002c
    • (2002) Fundam Inform , vol.49 , pp. 107-129
    • Giavitto, J.-L.1    Michel, O.2
  • 20
    • 0043027097 scopus 로고    scopus 로고
    • Modeling the topological organization of cellular processes
    • J.-L. Giavitto and O. Michel. Modeling the topological organization of cellular processes. BioSystems, 70(2):149-163, 2003
    • (2003) BioSystems , vol.70 , Issue.2 , pp. 149-163
    • Giavitto, J.-L.1    Michel, O.2
  • 22
    • 44449105506 scopus 로고    scopus 로고
    • Topological rewriting and the geometrization of programming
    • J.-L. Giavitto and A. Spicher. Topological rewriting and the geometrization of programming. Physica D, 237:1302-1314, 2008b
    • (2008) Physica , vol.237 , pp. 1302-1314
    • Giavitto, J.-L.1    Spicher, A.2
  • 24
    • 0036986616 scopus 로고    scopus 로고
    • Pattern-matching and rewriting rules for group indexed data structures
    • J.-L. Giavitto, O. Michel, and J. Cohen. Pattern-matching and rewriting rules for group indexed data structures. In ACM Sigplan Workshop (RULE02), pages 55-66, 2002b
    • (2002) ACM Sigplan Workshop (RULE02 , pp. 55-66
    • Giavitto, J.-L.1    Michel, O.2    Cohen, J.3
  • 25
    • 2942587003 scopus 로고    scopus 로고
    • Rewriting systems and the modelling of biological systems
    • J.-L. Giavitto, G. Malcolm, and O. Michel. Rewriting systems and the modelling of biological systems. Comp Funct Genomics, 5:95-99, 2004
    • (2004) Comp Funct Genomics , vol.5 , pp. 95-99
    • Giavitto, J.-L.1    Malcolm, G.2    Michel, O.3
  • 26
    • 33748313224 scopus 로고    scopus 로고
    • The emergence of geometric order in proliferating metazoan epithelia
    • M. C. Gibson, A. B. Patel, R. Nagpal, and N. Perrimon. The emergence of geometric order in proliferating metazoan epithelia. Nature, 442:1038-1041, 2006
    • (2006) Nature , vol.442 , pp. 1038-1041
    • Gibson, M.C.1    Patel, A.B.2    Nagpal, R.3    Perrimon, N.4
  • 27
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • D. T. Gillespie. Exact stochastic simulation of coupled chemical reactions. J Phys Chem, 81(25): 2340-2361, 1977
    • (1977) J Phys Chem , vol.81 , Issue.25 , pp. 2340-2361
    • Gillespie, D.T.1
  • 28
    • 0001129177 scopus 로고
    • Spatial patterns for discrete models of diffusion in excitable media
    • J. Greenberg and S. Hastings. Spatial patterns for discrete models of diffusion in excitable media. SIAM J Appl Math, pages 515-523, 1978
    • (1978) SIAM J Appl Math , pp. 515-523
    • Greenberg, J.1    Hastings, S.2
  • 30
    • 0030651808 scopus 로고    scopus 로고
    • PolyP - A polytypic programming language extension
    • ACM
    • P. Jansson and J. Jeuring. PolyP - A polytypic programming language extension. In Principles of programming languages, pages 470-482. ACM, 1997
    • (1997) Principles of Programming Languages , pp. 470-482
    • Jansson, P.1    Jeuring, J.2
  • 31
    • 84900103776 scopus 로고
    • Idempotent vector design for standard assembly of biobricks
    • 2006. MIT Synthetic Biology Working Group A. Lindenmayer. Mathematical models for cellular interaction in development, Parts I and II
    • T. Knight. Idempotent vector design for standard assembly of biobricks, 2006. MIT Synthetic Biology Working Group A. Lindenmayer. Mathematical models for cellular interaction in development, Parts I and II. J Theor Biol, 18:280-315, 1968a
    • (1968) J Theor Biol , vol.18 , pp. 280-315
    • Knight, T.1
  • 32
    • 0037291744 scopus 로고    scopus 로고
    • Autopoiesis: A review and a reappraisal
    • P. L. Luisi. Autopoiesis: A review and a reappraisal. Naturwissenschaften, 90:49-59, 2003
    • (2003) Naturwissenschaften , vol.90 , pp. 49-59
    • Luisi, P.L.1
  • 34
    • 0029028963 scopus 로고
    • Circuit simulation of genetic networks
    • H. McAdams and L. Shapiro. Circuit simulation of genetic networks. Science, 269(5224):650, 1995
    • (1995) Science , vol.269 , Issue.5224 , pp. 650
    • McAdams, H.1    Shapiro, L.2
  • 35
    • 76849092686 scopus 로고    scopus 로고
    • Rule-based programming for integrative biological modeling - Application to the modeling of the - Phage genetic switch
    • O. Michel, A. Spicher, and J.-L Giavitto. Rule-based programming for integrative biological modeling - Application to the modeling of the - phage genetic switch. Nat Comput, 8(4):865-889, 2009
    • (2009) Nat Comput , vol.8 , Issue.4 , pp. 865-889
    • Michel, O.1    Spicher, A.2    Giavitto, J.-L.3
  • 37
    • 0035053070 scopus 로고    scopus 로고
    • From cells to computers: Computing with membranes (P systems)
    • G. P?aun. From cells to computers: Computing with membranes (P systems). Biosystems, 59(3): 139-158, 2001
    • (2001) Biosystems , vol.59 , Issue.3 , pp. 139-158
    • Paun, G.1
  • 38
    • 0034641717 scopus 로고    scopus 로고
    • The importance of being discrete: Life always wins on the surface
    • N.M. Shnerb, Y. Louzoun, E. Bettelheim, and S. Solomon. The importance of being discrete: Life always wins on the surface. PNAS, 97(19):10322-10324, 2000
    • (2000) PNAS , vol.97 , Issue.19 , pp. 10322-10324
    • Shnerb, N.M.1    Louzoun, Y.2    Bettelheim, E.3    Solomon, S.4
  • 40
    • 25144481338 scopus 로고    scopus 로고
    • Using rewriting techniques in the simulation of dynamical systems: Application to the modeling of sperm crawling
    • A. Spicher and O. Michel. Using rewriting techniques in the simulation of dynamical systems: Application to the modeling of sperm crawling. In Fifth International Conference on Computational Science (ICCS05), Part I, Vol. 3514 of LNCS, pages 820-827, 2005
    • (2005) Fifth International Conference on Computational Science (ICCS05), Part i of LNCS , vol.3514 , pp. 820-827
    • Spicher, A.1    Michel, O.2
  • 41
    • 33846092206 scopus 로고    scopus 로고
    • Declarative modeling of a neurulation-like process
    • A. Spicher and O. Michel. Declarative modeling of a neurulation-like process. BioSystems, 87 (2-3):281-288, 2007.
    • (2007) BioSystems , vol.87 , Issue.2-3 , pp. 281-288
    • Spicher, A.1    Michel, O.2
  • 43
    • 0002011401 scopus 로고
    • The chemical basis of morphogenesis, Series B: Biological Sciences
    • A.M. Turing. The chemical basis of morphogenesis, Series B: Biological Sciences. Phil Trans R Soc Lond, 237:37-72, 1952
    • (1952) Phil Trans R Soc Lond , vol.237 , pp. 37-72
    • Turing, A.M.1
  • 44
    • 85028881989 scopus 로고
    • Generating textures for arbitrary surfaces using reaction-diffusion
    • in T.W. Sederberg, editor
    • G. Turk. Generating textures for arbitrary surfaces using reaction-diffusion. In T.W. Sederberg, editor, Computer Graphics (SIGGRAPH 91 Proceedings), pages 289-298, 1991
    • (1991) Computer Graphics (SIGGRAPH 91 Proceedings) , pp. 289-298
    • Turk, G.1
  • 45
    • 34548860810 scopus 로고
    • Autopoiesis: The organization of living systems, its characterization and a model
    • F.J. Varela, H.R. Maturana, and R. Uribe. Autopoiesis: The organization of living systems, its characterization and a model. BioSystems, 5:187-196, 1974
    • (1974) BioSystems , vol.5 , pp. 187-196
    • Varela, F.J.1    Maturana, H.R.2    Uribe, R.3
  • 46
    • 0034644270 scopus 로고    scopus 로고
    • The segment polarity network is a robust developmental module
    • G. Von Dassow, E. Meir, E. M. Munro, and G. Odell. The segment polarity network is a robust developmental module. Nature, 406(6792):188-192, 2000
    • (2000) Nature , vol.406 , Issue.6792 , pp. 188-192
    • Von Dassow, G.1    Meir, E.2    Munro, E.M.3    Odell, G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.