메뉴 건너뛰기




Volumn 8, Issue 4, 2009, Pages 865-889

Rule-based programming for integrative biological modeling : AAApplication to the modeling of thλe phage genetic switch

Author keywords

Domain specific languages; Rule based modeling; Spatial systems biology

Indexed keywords

ARTICLE; BACTERIAL INFECTION; BACTERIOPHAGE; CHEMICAL REACTION; COMPUTER LANGUAGE; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; COMPUTER SYSTEM; ESCHERICHIA COLI; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; SYSTEMS BIOLOGY;

EID: 76849092686     PISSN: 15677818     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11047-008-9105-9     Document Type: Article
Times cited : (14)

References (45)
  • 1
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells
    • A Arkin J Ross HH McAdams 1998 Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells Genetics 149 1633 1648
    • (1998) Genetics , vol.149 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3
  • 2
    • 84875463332 scopus 로고    scopus 로고
    • Gamma and the chemical reaction model: Fifteen years after
    • 10.1007/3-540-45523-X-2
    • J-P Banâtre P Fradet DL Métayer 2001 Gamma and the chemical reaction model: fifteen years after Lect Notes in Comput Sci 2235 17 44 10.1007/3-540-45523-X-2
    • (2001) Lect Notes in Comput Sci , vol.2235 , pp. 17-44
    • Banâtre, J.-P.1    Fradet, P.2    Métayer, D.L.3
  • 5
    • 38549120134 scopus 로고    scopus 로고
    • Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA
    • Priami C, Ingólfsdóttir A, Mishra B, Nielson HR (eds) Springer
    • Calder M, Gilmore S, Hillston J (2006) Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA. In: Priami C, Ingólfsdóttir A, Mishra B, Nielson HR (eds) Transactions on Computational Systems Biology VII, Lecture Notes in Computer Science, vol 4230. Springer, pp 1-23
    • (2006) Transactions on Computational Systems Biology VII, Lecture Notes in Computer Science , vol.4230 , pp. 1-23
    • Calder, M.1    Gilmore, S.2    Hillston, J.3
  • 6
    • 33745647409 scopus 로고    scopus 로고
    • Brane calculi
    • Danos V, Schächter V (eds) Springer
    • Cardelli L (2004) Brane calculi. In: Danos V, Schächter V (eds) CMSB, Lecture Notes in Computer Science, vol 3082. Springer, pp 257-278
    • (2004) CMSB, Lecture Notes in Computer Science , vol.3082 , pp. 257-278
    • Cardelli, L.1
  • 7
    • 38149083357 scopus 로고    scopus 로고
    • Rule-based modelling of cellular signaling
    • Springer, Berlin doi: 10.1007/978-3-540-74407-83
    • Danos V, Feret J, Fontana W, Harmer R, Krivine J (2007) Rule-based modelling of cellular signalling. In: CONCUR'07. Springer, Berlin, pp 17-41. doi: 10.1007/978-3-540-74407-83
    • (2007) CONCUR'07 , pp. 17-41
    • Danos, V.1    Feret, J.2    Fontana, W.3    Harmer, R.4    Krivine, J.5
  • 12
    • 0027415226 scopus 로고
    • Cellular automata approaches to biological modeling
    • 10.1006/jtbi.1993.1007
    • GB Ermentrout L Edelstein-Keshet 1993 Cellular automata approaches to biological modeling J Theor Biol 160 1 97 133 10.1006/jtbi.1993.1007
    • (1993) J Theor Biol , vol.160 , Issue.1 , pp. 97-133
    • Ermentrout, G.B.1    Edelstein-Keshet, L.2
  • 13
    • 0041423614 scopus 로고    scopus 로고
    • Mechanical induction of Twist in the Drosophila foregut/stomodeal primordium
    • DOI 10.1016/S0960-9822(03)00576-1
    • E Farge 2003 Mechanical induction of twist in the Drosophila foregut/stomodeal primordium Curr Biol 13 16 1365 1377 10.1016/S0960-9822(03) 00576-1 (Pubitemid 37029426)
    • (2003) Current Biology , vol.13 , Issue.16 , pp. 1365-1377
    • Farge, E.1
  • 14
    • 0034064199 scopus 로고    scopus 로고
    • Spatio-logical processes in intracellular signalling
    • DOI 10.1016/S0303-2647(99)00086-6, PII S0303264799000866
    • M Fisher G Malcolm R Paton 2000 Spatio-logical processes in intracellular signalling BioSystems 55 83 92 10.1016/S0303-2647(99)00086-6 (Pubitemid 30162944)
    • (2000) BioSystems , vol.55 , Issue.1-3 , pp. 83-92
    • Fisher, M.J.1    Malcolm, G.2    Paton, R.C.3
  • 15
    • 84947754668 scopus 로고    scopus 로고
    • Topological collections, transformations and their application to the modeling and the simulation of dynamical systems
    • LNCS, vol LNCS 2706. Springer, Valencia
    • Giavitto J-L (2003) Topological collections, transformations and their application to the modeling and the simulation of dynamical systems. In: Rewriting technics and applications (RTA'03), LNCS, vol LNCS 2706. Springer, Valencia, pp 208-233
    • (2003) Rewriting Technics and Applications (RTA'03) , pp. 208-233
    • Giavitto, J.-L.1
  • 17
    • 0036190735 scopus 로고    scopus 로고
    • The topological structures of membrane computing
    • 2016433
    • J-L Giavitto O Michel 2002 The topological structures of membrane computing Fundam Inform 49 107 129 2016433
    • (2002) Fundam Inform , vol.49 , pp. 107-129
    • Giavitto, J.-L.1    Michel, O.2
  • 19
    • 44449105506 scopus 로고    scopus 로고
    • Topological rewriting and the geometrization of programming
    • doi: 10.1016/j.physd.2008.03.039
    • Giavitto J-L, Spicher A (2008) Topological rewriting and the geometrization of programming. Physica D 237:1302-1314. doi: 10.1016/j.physd.2008.03.039
    • (2008) Physica D , vol.237 , pp. 1302-1314
    • Giavitto, J.-L.1    Spicher, A.2
  • 21
    • 0036986616 scopus 로고    scopus 로고
    • Pattern-matching and rewriting rules for group indexed data structures
    • ACM, Pittsburgh
    • Giavitto J-L, Michel O, Cohen J (2002b) Pattern-matching and rewriting rules for group indexed data structures. In: ACM Sigplan Workshop RULE'02. ACM, Pittsburgh, pp 55-66
    • (2002) ACM Sigplan Workshop RULE'02 , pp. 55-66
    • Giavitto, J.-L.1    Michel, O.2    Cohen, J.3
  • 22
    • 2942587003 scopus 로고    scopus 로고
    • Rewriting systems and the modelling of biological systems
    • DOI 10.1002/cfg.363
    • J-L Giavitto G Malcolm O Michel 2004 Rewriting systems and the modelling of biological systems Comp Funct Genomics 5 95 99 10.1002/cfg.363 (Pubitemid 38744645)
    • (2004) Comparative and Functional Genomics , vol.5 , Issue.1 , pp. 95-99
    • Giavitto, J.-L.1    Malcolm, G.2    Michel, O.3
  • 23
    • 33748313224 scopus 로고    scopus 로고
    • The emergence of geometric order in proliferating metazoan epithelia
    • DOI 10.1038/nature05014, PII NATURE05014
    • MC Gibson AB Patel R Nagpal N Perrimon 2006 The emergence of geometric order in proliferating metazoan epithelia Nature 442 1038 1041 10.1038/nature05014 (Pubitemid 44330260)
    • (2006) Nature , vol.442 , Issue.7106 , pp. 1038-1041
    • Gibson, M.C.1    Patel, A.B.2    Nagpal, R.3    Perrimon, N.4
  • 24
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • 10.1021/j100540a008
    • DT Gillespie 1977 Exact stochastic simulation of coupled chemical reactions J Phys Chem 81 25 2340 2361 10.1021/j100540a008
    • (1977) J Phys Chem , vol.81 , Issue.25 , pp. 2340-2361
    • Gillespie, D.T.1
  • 26
    • 84867691396 scopus 로고    scopus 로고
    • IGEM: Modeling a synthetic multicellular bacterium
    • iGEM: Modeling a synthetic multicellular bacterium. Modeling page of the Paris team wiki at iGEM'07 (2007). http://parts.mit.edu/igem07/index.php/Paris/ Modeling
    • (2007) Modeling Page of the Paris Team Wiki at iGEM'07
  • 27
    • 38149103597 scopus 로고    scopus 로고
    • Gene regulation in the pi calculus: Simulation coperativity at the lambda switch
    • Kuttler C, Niehren J (2005) Gene regulation in the pi calculus: simulation coperativity at the lambda switch. Transactions on Computational Systems Biology VII: 24-55
    • (2005) Transactions on Computational Systems Biology , vol.8 , pp. 24-55
    • Kuttler, C.1    Niehren, J.2
  • 29
    • 34147185608 scopus 로고    scopus 로고
    • A quantitative study of λ-phage SWITCH and its components
    • DOI 10.1529/biophysj.106.097089
    • C Lou X Yang X Liu B He Q Ouyang 2007 A quantitative study of λ-phage switch and its components Biophys J 92 2685 2693 10.1529/biophysj.106.097089 (Pubitemid 46557844)
    • (2007) Biophysical Journal , vol.92 , Issue.8 , pp. 2685-2693
    • Lou, C.1    Yang, X.2    Liu, X.3    He, B.4    Ouyang, Q.5
  • 30
    • 0034903816 scopus 로고    scopus 로고
    • Logical string rewriting
    • 0972.68100 10.1016/S0304-3975(00)00212-7 1843496
    • V Manca 2001 Logical string rewriting Theor Comput Sci 264 25 51 0972.68100 10.1016/S0304-3975(00)00212-7 1843496
    • (2001) Theor Comput Sci , vol.264 , pp. 25-51
    • Manca, V.1
  • 33
    • 0035053070 scopus 로고    scopus 로고
    • From cells to computers: Computing with membranes (P systems)
    • DOI 10.1016/S0303-2647(00)00143-X, PII S030326470000143X
    • G Pǎun 2001 From cells to computers: computing with membranes (P systems) Biosystems 59 3 139 158 10.1016/S0303-2647(00)00143-X (Pubitemid 32318528)
    • (2001) BioSystems , vol.59 , Issue.3 , pp. 139-158
    • Pun, G.1
  • 34
    • 26444448026 scopus 로고    scopus 로고
    • Beta binders for biological interactions
    • Danos V, Schächter V (eds) Springer
    • Priami C, Quaglia P (2004) Beta binders for biological interactions. In: Danos V, Schächter V (eds) CMSB, Lecture Notes in Computer Science, vol 3082. Springer, pp 20-33
    • (2004) CMSB, Lecture Notes in Computer Science , vol.3082 , pp. 20-33
    • Priami, C.1    Quaglia, P.2
  • 36
    • 0035235039 scopus 로고    scopus 로고
    • Representation and simulation of biochemical processes using the π-calculus process algebra
    • Altman RB, Dunker AK, Hunter L, Klein TE (eds)
    • Regev A, Silverman W, Shapiro E (2001) Representation and simulation of biochemical processes using the π-calculus process algebra. In: Altman RB, Dunker AK, Hunter L, Klein TE (eds) Pacific symposium on biocomputing, pp 459-470
    • (2001) Pacific Symposium on Biocomputing , pp. 459-470
    • Regev, A.1    Silverman, W.2    Shapiro, E.3
  • 39
    • 0034641717 scopus 로고    scopus 로고
    • The importance of being discrete - Life always wins on the surface
    • Shnerb NM, Louzoun Y, Bettelheim E, Solomon S (1999) The importance of being discrete - life always wins on the surface. Proc Natl Acad Sci 97:10322-10324
    • (1999) Proc Natl Acad Sci , vol.97 , pp. 10322-10324
    • Shnerb, N.M.1    Louzoun, Y.2    Bettelheim, E.3    Solomon, S.4
  • 40
    • 33646037893 scopus 로고    scopus 로고
    • Local specification of surface subdivision algorithms
    • Pfaltz JL, Nagl M, Böhlen B (eds) Springer
    • Smith C, Prusinkiewicz P, Samavati FF (2003) Local specification of surface subdivision algorithms. In: Pfaltz JL, Nagl M, Böhlen B (eds) AGTIVE, Lecture Notes in Computer Science, vol 3062. Springer, pp 313-327
    • (2003) AGTIVE, Lecture Notes in Computer Science , vol.3062 , pp. 313-327
    • Smith, C.1    Prusinkiewicz, P.2    Samavati, F.F.3
  • 41
    • 38949179852 scopus 로고    scopus 로고
    • Stochastic P systems and the simulation of biochemical processes with dynamic compartments
    • DOI 10.1016/j.biosystems.2006.12.009, PII S030326470700113X
    • A Spicher O Michel M Cieslak J-L Giavitto P Prusinkiewicz 2008 Stochastic P systems and the simulation of biochemical processes with dynamic compartments BioSystems 91 3 458 472 10.1016/j.biosystems.2006.12.009 (Pubitemid 351215718)
    • (2008) BioSystems , vol.91 , Issue.3 , pp. 458-472
    • Spicher, A.1    Michel, O.2    Cieslak, M.3    Giavitto, J.-L.4    Prusinkiewicz, P.5
  • 42
    • 0008507891 scopus 로고
    • On some mathematical problems connected with patterns of growth of figures
    • SM Ulam 1962 On some mathematical problems connected with patterns of growth of figures Proc Symposia Appl Math 14 215 224
    • (1962) Proc Symposia Appl Math , vol.14 , pp. 215-224
    • Ulam, S.M.1
  • 44
    • 0141877349 scopus 로고    scopus 로고
    • Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL
    • Wilensky U (1999) Netlogo. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL. http://ccl.northwestern.edu/netlogo
    • (1999) Netlogo
    • Wilensky, U.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.