-
1
-
-
0037444724
-
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
-
Arkin AP, Rao CV (2003) Stochastic chemical kinetics and the quasi-steady-state assumption: application to the Gillespie algorithm. J Chem Phys 1:4999-5010
-
(2003)
J Chem Phys
, vol.1
, pp. 4999-5010
-
-
Arkin, A.P.1
Rao, C.V.2
-
3
-
-
85020041856
-
A calculus of looping sequences for modeling microbiological systems
-
Warsaw University, Warsaw
-
Barbuti R, Maggiolo-Schettini A, Milazzo P, Troina A (2005) A calculus of looping sequences for modeling microbiological systems. In: Proceedings of CS&P’05, 14th international workshop on concurrency specification and programming. Warsaw University, Warsaw, pp 29-40
-
(2005)
Proceedings of CS&P’05, 14Th International Workshop on Concurrency Specification and Programming
, pp. 29-40
-
-
Barbuti, R.1
Maggiolo-Schettini, A.2
Milazzo, P.3
Troina, A.4
-
4
-
-
10644250404
-
Evolving a lingua franca and associated software infrastructure for computational systems biology: The systems biology markup language (SBML) project
-
Bornstein BJ, Doyle JC, Finney A, Funahashi A, Hucka M, Keating SM, Kitano H, Kovitz BL, Matthews J, Shapiro BE, Schilstra MJ (2004) Evolving a lingua franca and associated software infrastructure for computational systems biology: the systems biology markup language (SBML) project. Syst Biol 1:41-53
-
(2004)
Syst Biol
, vol.1
, pp. 41-53
-
-
Bornstein, B.J.1
Doyle, J.C.2
Finney, A.3
Funahashi, A.4
Hucka, M.5
Keating, S.M.6
Kitano, H.7
Kovitz, B.L.8
Matthews, J.9
Shapiro, B.E.10
Schilstra, M.J.11
-
5
-
-
85020022176
-
Policriti A (2006) Modeling biological systems in stochastic concurrent constraint programming
-
Bortolussi L, Policriti A (2006) Modeling biological systems in stochastic concurrent constraint programming. In: Proceedings of WCB 2006
-
(2006)
Proceedings of WCB
-
-
Bortolussi, L.1
-
7
-
-
33746062738
-
Automatically deriving ODEs from process algebra models of signaling pathways
-
Calder M, Gilmore S, Hillston J (2005) Automatically deriving ODEs from process algebra models of signaling pathways. In: Proceedings of CMSB’05, pp 204-215
-
(2005)
In: Proceedings of CMSB’05
, pp. 204-215
-
-
Calder, M.1
Gilmore, S.2
Hillston, J.3
-
8
-
-
38549120134
-
Modeling the influence of RKIP on the ERK signaling pathway using the stochastic process algebra PEPA
-
Springer, Berlin
-
Calder M, Gilmore S, Hillston J (2006) Modeling the influence of RKIP on the ERK signaling pathway using the stochastic process algebra PEPA. In: Transactions on computational systems biology VII. Lecture notes in computer science, vol 4230. Springer, Berlin, 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
-
9
-
-
33845200552
-
Stronger computational modeling of signaling pathways using both continuous and discrete-space methods
-
Springer, Berlin
-
Calder M, Duguid A, Gilmore S, Hillston J (2006) Stronger computational modeling of signaling pathways using both continuous and discrete-space methods. In: Proceedings of CMSB’ 06. Lecture notes in computer science, vol 4210. Springer, Berlin, pp 63-77
-
(2006)
Proceedings of CMSB’ 06. Lecture Notes in Computer Science
, vol.4210
, pp. 63-77
-
-
Calder, M.1
Duguid, A.2
Gilmore, S.3
Hillston, J.4
-
10
-
-
33846185710
-
Accelerated stochastic simulation of the stiff enzymesubstrate reaction
-
Cao Y, Gillespie DT, Petzold L (2005) Accelerated stochastic simulation of the stiff enzymesubstrate reaction. J Chem Phys 123(14):144917-144929
-
(2005)
J Chem Phys
, vol.123
, Issue.14
, pp. 144917-144929
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.3
-
12
-
-
4444383325
-
BioAmbients: An abstraction for biological compartments
-
Cardelli L, Panina EM, Regev A, Shapiro E, Silverman W(2004) BioAmbients: an abstraction for biological compartments. Theor Comput Sci 325(1):141-167
-
(2004)
Theor Comput Sci
, vol.325
, Issue.1
, pp. 141-167
-
-
Cardelli, L.1
Panina, E.M.2
Regev, A.3
Shapiro, E.4
Silverman, W.5
-
13
-
-
84862992167
-
-
Technical Report TR-08-2006, The Microsoft Research, University of Trento Centre for Computational and Systems Biology
-
Cardelli L (2006) Artificial biochemistry. Technical Report TR-08-2006, The Microsoft Research, University of Trento Centre for Computational and Systems Biology
-
(2006)
Artificial Biochemistry
-
-
Cardelli, L.1
-
14
-
-
38649092709
-
On process rate semantics
-
Cardelli L (2008) On process rate semantics. Theor Comput Sci 391(3):190-215
-
(2008)
Theor Comput Sci
, vol.391
, Issue.3
, pp. 190-215
-
-
Cardelli, L.1
-
15
-
-
20144377930
-
Modeling and querying interaction networks in the biochemical abstract machine BIOCHAM
-
Chabrier-Rivier N, Fages F, Soliman S (2004) Modeling and querying interaction networks in the biochemical abstract machine BIOCHAM. J Biol Phys Chem 4:64-73
-
(2004)
J Biol Phys Chem
, vol.4
, pp. 64-73
-
-
Chabrier-Rivier, N.1
Fages, F.2
Soliman, S.3
-
16
-
-
34848908013
-
A computational approach to the functional screening of genomes
-
Chiarugi D, Degano P, Marangoni R (2007) A computational approach to the functional screening of genomes. PLOS Comput Biol 9:1801-1806
-
(2007)
PLOS Comput Biol
, vol.9
, pp. 1801-1806
-
-
Chiarugi, D.1
Degano, P.2
Marangoni, R.3
-
17
-
-
0242574987
-
Investigations into the analysis and modeling of the TNFα-mediated NF-κB-signaling pathway
-
Cho K-H, Shin S-Y, Lee H-W, Wolkenhauer O (2003) Investigations into the analysis and modeling of the TNFα-mediated NF-κB-signaling pathway. Genome Res 13:2413-2422
-
(2003)
Genome Res
, vol.13
, pp. 2413-2422
-
-
Cho, K.-H.1
Shin, S.-Y.2
Lee, H.-W.3
Wolkenhauer, O.4
-
18
-
-
38649133815
-
Bio-PEPA: An extension of the process algebra PEPA for biochemical networks
-
Ciocchetta F, Hillston J (2008) Bio-PEPA: an extension of the process algebra PEPA for biochemical networks. Electron Notes Theor Comput Sci 194(3):103-117
-
(2008)
Electron Notes Theor Comput Sci
, vol.194
, Issue.3
, pp. 103-117
-
-
Ciocchetta, F.1
Hillston, J.2
-
20
-
-
34548105489
-
Stochastic process algebras
-
Bertinoro, June 2007. Lecture notes in computer science, Springer, Berlin
-
Clark A, Gilmore S, Hillston J, Tribastone M (2007) Stochastic process algebras. In: Formal methods in performance modeling, Bertinoro, June 2007. Lecture notes in computer science, vol 4486. Springer, Berlin, pp 132-179
-
(2007)
Formal Methods in Performance Modeling
, vol.4486
, pp. 132-179
-
-
Clark, A.1
Gilmore, S.2
Hillston, J.3
Tribastone, M.4
-
22
-
-
38149083357
-
Ruled-based modeling of cellular signaling
-
Springer, Berlin
-
Danos V, Feret J, Fontana W, Harmer R, Krivine J (2007) Ruled-based modeling of cellular signaling. In: Proceedings of CONCUR’ 07. Lecture notes in computer science, vol 4703. Springer, Berlin
-
(2007)
Proceedings of CONCUR’ 07. Lecture Notes in Computer Science
, vol.4703
-
-
Danos, V.1
Feret, J.2
Fontana, W.3
Harmer, R.4
Krivine, J.5
-
23
-
-
0036212767
-
Computational modeling of the dynamics of theMAP kinase cascade activated by surface and internalized EGF receptors
-
Eichler-Jonsson C, Gilles ED, Muller G, Schoeberl B (2002) Computational modeling of the dynamics of theMAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol 20:370-375
-
(2002)
Nat Biotechnol
, vol.20
, pp. 370-375
-
-
Eichler-Jonsson, C.1
Gilles, E.D.2
Muller, G.3
Schoeberl, B.4
-
24
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340-2361
-
(1977)
J Phys Chem
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
29
-
-
85020055521
-
-
NuMSV model checker. http://nusmv.irst.itc.it
-
-
-
-
31
-
-
84974715948
-
Stochastic π-calculus
-
Priami C (1995) Stochastic π-calculus. Comput J 38(6):578-589
-
(1995)
Comput J
, vol.38
, Issue.6
, pp. 578-589
-
-
Priami, C.1
-
32
-
-
0035888407
-
Application of a stochastic name-passing calculus to representation and simulation of molecular processes
-
Priami C, Regev A, Silverman W, Shapiro E (2001) Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inf Process Lett 80:25-31
-
(2001)
Inf Process Lett
, vol.80
, pp. 25-31
-
-
Priami, C.1
Regev, A.2
Silverman, W.3
Shapiro, E.4
-
34
-
-
0037179670
-
Cells as computation
-
Regev A, Shapiro E (2002) Cells as computation. Nature 419:343
-
(2002)
Nature
, vol.419
, pp. 343
-
-
Regev, A.1
Shapiro, E.2
-
35
-
-
4544321024
-
Modeling and simulation of intracellular dynamics: Choosing an appropriate framework
-
Wolkenhauer O, Ullah M, Kolch W, Cho KH (2004) Modeling and simulation of intracellular dynamics: choosing an appropriate framework. IEEE Trans Nanobiosci 3:200-207
-
(2004)
IEEE Trans Nanobiosci
, vol.3
, pp. 200-207
-
-
Wolkenhauer, O.1
Ullah, M.2
Kolch, W.3
Cho, K.H.4
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