-
1
-
-
0035235039
-
Representation and simulation of biochemical processes using the π-calculus process algebra
-
Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the π-calculus process algebra. In: Proceedings of Pacific Symposium on Bio-computing (PSB 2001), vol. 6, pp. 459-470 (2001)
-
(2001)
Proceedings of Pacific Symposium on Bio-computing (PSB
, vol.6
, pp. 459-470
-
-
Regev, A.1
Silverman, W.2
Shapiro, E.3
-
2
-
-
4444383325
-
BioAmbients: An Abstraction for Biological Compartments
-
Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.Y.: BioAmbients: an Abstraction for Biological Compartments. Theoretical Computer Science 325(1), 141-167 (2004)
-
(2004)
Theoretical Computer Science
, vol.325
, Issue.1
, pp. 141-167
-
-
Regev, A.1
Panina, E.M.2
Silverman, W.3
Cardelli, L.4
Shapiro, E.Y.5
-
3
-
-
26444592298
-
-
Cardelli, L.: Brane Calculi - Interactions of Biological Membranes. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), 3082, pp. 257-278. Springer, Heidelberg (2005)
-
Cardelli, L.: Brane Calculi - Interactions of Biological Membranes. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257-278. Springer, Heidelberg (2005)
-
-
-
-
4
-
-
33748915162
-
Operational patterns in Beta-binders
-
Priami, C, ed, Springer, Heidelberg
-
Priami, C., Quaglia, P.: Operational patterns in Beta-binders. In: Priami, C. (ed.) Transactions on Computational Systems Biology I. LNCS (LNBI), vol. 3380, pp. 50-65. Springer, Heidelberg (2005)
-
(2005)
Transactions on Computational Systems Biology I. LNCS (LNBI)
, vol.3380
, pp. 50-65
-
-
Priami, C.1
Quaglia, P.2
-
5
-
-
4444382239
-
Formal molecular biology. TCS
-
Danos, V., Laneve, C.: Formal molecular biology. TCS 325(1) (2004)
-
(2004)
, vol.325
, Issue.1
-
-
Danos, V.1
Laneve, C.2
-
6
-
-
0037179670
-
Cells as Computation
-
Regev, A., Shapiro, E.: Cells as Computation. Nature 419 (6905), 343 (2002)
-
(2002)
Nature
, vol.419
, Issue.6905
, pp. 343
-
-
Regev, A.1
Shapiro, E.2
-
7
-
-
43049179364
-
Bio-PEPA: An extension of the process algebra PEPA for biochemical networks
-
Ciocchetta, F., Hillston, J.: Bio-PEPA: An extension of the process algebra PEPA for biochemical networks. In: Proc. of FBTC 2007. ENTCS, vol. 194, pp. 103-117 (2008)
-
(2008)
Proc. of FBTC 2007. ENTCS
, vol.194
, pp. 103-117
-
-
Ciocchetta, F.1
Hillston, J.2
-
8
-
-
65549101937
-
-
Ciocchetta, F., Hillston, J.: Bio-PEPA: A Framework for the Modelling and Analysis of Biological Systems. Theoretical Computer Science 410(33-34), 3065-3084 (2009)
-
Ciocchetta, F., Hillston, J.: Bio-PEPA: A Framework for the Modelling and Analysis of Biological Systems. Theoretical Computer Science 410(33-34), 3065-3084 (2009)
-
-
-
-
10
-
-
45749134288
-
-
Ciocchetta, F., Hillston, J.: Calculi for Biological Systems. In: Formal Methods for Computational Systems Biology (SFM 2008). LNCS, 5016, pp. 265-312. Springer, Heidelberg (2008)
-
Ciocchetta, F., Hillston, J.: Calculi for Biological Systems. In: Formal Methods for Computational Systems Biology (SFM 2008). LNCS, vol. 5016, pp. 265-312. Springer, Heidelberg (2008)
-
-
-
-
11
-
-
70450149356
-
-
Home Page
-
Bio-PEPA Workbench Home Page: http://www.dcs.ed.ac.uk/home/stg/software/ biopepa/
-
Workbench
-
-
Bio-PEPA1
-
12
-
-
17644396339
-
Dizzy: Stochastic simulation of large-scale genetic regulatory networks
-
Ramsey, S., Orrell, D., Bolouri, H.: Dizzy: stochastic simulation of large-scale genetic regulatory networks. J. Bioinf. Comp. Biol. 3(2), 415-436 (2005)
-
(2005)
J. Bioinf. Comp. Biol
, vol.3
, Issue.2
, pp. 415-436
-
-
Ramsey, S.1
Orrell, D.2
Bolouri, H.3
-
13
-
-
70450147091
-
-
PRISM Home Page: http://www.prismmodelchecker.org
-
PRISM Home Page: http://www.prismmodelchecker.org
-
-
-
-
14
-
-
84941709469
-
Model-checking continuous-time Markov chains
-
Aziz, A., Sanwal, K., Singhal, V., Brayton, R.: Model-checking continuous-time Markov chains. ACM Trans. Comput. Logic 1(1), 162-170 (2000)
-
(2000)
ACM Trans. Comput. Logic
, vol.1
, Issue.1
, pp. 162-170
-
-
Aziz, A.1
Sanwal, K.2
Singhal, V.3
Brayton, R.4
-
15
-
-
33845339658
-
Oncostatin M (OSM) Cytostasis of Breast Tumor Cells: Characterization of an OSM Receptor β-Specific Kernel
-
Underhill-Day, N., Heath, J.: Oncostatin M (OSM) Cytostasis of Breast Tumor Cells: Characterization of an OSM Receptor β-Specific Kernel. Cancer Research 66(22), 10891-10901 (2006)
-
(2006)
Cancer Research
, vol.66
, Issue.22
, pp. 10891-10901
-
-
Underhill-Day, N.1
Heath, J.2
-
16
-
-
0041677606
-
Principles od interleukin (IL)-6-type cytokine signalling and its regulation
-
Heinrich, P., Behrmann, I., Haan, S., Hermanns, H., Müller-Newen, G., Schaper, F.: Principles od interleukin (IL)-6-type cytokine signalling and its regulation. Biochem. J. 374, 1-20 (2003)
-
(2003)
Biochem. J
, vol.374
, pp. 1-20
-
-
Heinrich, P.1
Behrmann, I.2
Haan, S.3
Hermanns, H.4
Müller-Newen, G.5
Schaper, F.6
-
17
-
-
0037138370
-
Signaling through the JAK/STAT pathway, recent advances and future challenges
-
Kisseleva, T., Bhattacharya, S., Braunstein, J., Schindler, C.: Signaling through the JAK/STAT pathway, recent advances and future challenges. Gene 285, 1-24 (2002)
-
(2002)
Gene
, vol.285
, pp. 1-24
-
-
Kisseleva, T.1
Bhattacharya, S.2
Braunstein, J.3
Schindler, C.4
-
18
-
-
0037417886
-
Identification of nucleocy-toplasmic cycling as a remote sensor in cellular signaling by databased modeling
-
Swameye, I., Müller, T., Timmer, J., Sandra, O., Klingmüller, U.: Identification of nucleocy-toplasmic cycling as a remote sensor in cellular signaling by databased modeling. PNAS 100, 1028-1033 (2003)
-
(2003)
PNAS
, vol.100
, pp. 1028-1033
-
-
Swameye, I.1
Müller, T.2
Timmer, J.3
Sandra, O.4
Klingmüller, U.5
-
19
-
-
34547570814
-
Sensitivity Analysis of In-tracellular Signaling Pathway Kinetics Predicts Targets for Stem Cell Fate Control
-
Mahdavi, A., Davey, R.E., Bhola, P., Yin, T., Zandstra, P.W.: Sensitivity Analysis of In-tracellular Signaling Pathway Kinetics Predicts Targets for Stem Cell Fate Control. PLoS Computational Biology 3(7), 1257-1267 (2007)
-
(2007)
PLoS Computational Biology
, vol.3
, Issue.7
, pp. 1257-1267
-
-
Mahdavi, A.1
Davey, R.E.2
Bhola, P.3
Yin, T.4
Zandstra, P.W.5
-
20
-
-
33751543926
-
Modeling Regulatory Mechanisms in IL-6 Transduction in Hepatocytes
-
Singh, A., Jayaraman, A., Hahn, J.: Modeling Regulatory Mechanisms in IL-6 Transduction in Hepatocytes. Biotechnology and Bioengineering 95(5), 850-862 (2006)
-
(2006)
Biotechnology and Bioengineering
, vol.95
, Issue.5
, pp. 850-862
-
-
Singh, A.1
Jayaraman, A.2
Hahn, J.3
-
21
-
-
65549137015
-
Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway
-
Guerriero, M.L., Dudka, A., Underhill-Day, N., Heath, J.K., Priami, C.: Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway. BMC Systems Biology 3(1), 40 (2009)
-
(2009)
BMC Systems Biology
, vol.3
, Issue.1
, pp. 40
-
-
Guerriero, M.L.1
Dudka, A.2
Underhill-Day, N.3
Heath, J.K.4
Priami, C.5
-
22
-
-
70450140853
-
-
Home Page
-
Bio-PEPA Home Page: http://www.biopepa.org/
-
Bio-PEPA
-
-
-
23
-
-
33745802027
-
PRISM: A tool for automatic verification of probabilistic systems
-
Hermanns, H, Palsberg, J, eds, TACAS 2006, Springer, Heidelberg
-
Hinton, A., Kwiatkowska, M., Norman, G., Parker, D.: PRISM: A tool for automatic verification of probabilistic systems. In: Hermanns, H., Palsberg, J. (eds.) TACAS 2006. LNCS, vol. 3920, pp. 441-444. Springer, Heidelberg (2006)
-
(2006)
LNCS
, vol.3920
, pp. 441-444
-
-
Hinton, A.1
Kwiatkowska, M.2
Norman, G.3
Parker, D.4
-
24
-
-
70450127850
-
-
Home Page
-
Dizzy Home Page: http://magnet.systemsbiology.net/software/Dizzy
-
Dizzy
-
-
-
25
-
-
84957369657
-
-
Aziz, A., Kanwal, K., Singhal, V., Brayton, V.: Verifying continuous time Markov chains. In: Alur, R., Henzinger, T.A. (eds.) CAV 1996. LNCS, 1102, pp. 269-276. Springer, Heidelberg (1996)
-
Aziz, A., Kanwal, K., Singhal, V., Brayton, V.: Verifying continuous time Markov chains. In: Alur, R., Henzinger, T.A. (eds.) CAV 1996. LNCS, vol. 1102, pp. 269-276. Springer, Heidelberg (1996)
-
-
-
-
26
-
-
41149144239
-
Approximate Symbolic Model Checking of Continuous-Time Markov Chains
-
Baeten, J.C.M, Mauw, S, eds, CONCUR 1999, Springer, Heidelberg
-
Baier, C., Katoen, J.P., Hermanns, H.: Approximate Symbolic Model Checking of Continuous-Time Markov Chains. In: Baeten, J.C.M., Mauw, S. (eds.) CONCUR 1999. LNCS, vol. 1664, pp. 146-161. Springer, Heidelberg (1999)
-
(1999)
LNCS
, vol.1664
, pp. 146-161
-
-
Baier, C.1
Katoen, J.P.2
Hermanns, H.3
-
27
-
-
15744394108
-
Dissecting the puzzle of life: Modularization of signal transduction networks
-
Saez-Rodriguez, J., Kremling, A., Gilles, E.: Dissecting the puzzle of life: modularization of signal transduction networks. Computers and Chemical Engineering 29, 619-629 (2005)
-
(2005)
Computers and Chemical Engineering
, vol.29
, pp. 619-629
-
-
Saez-Rodriguez, J.1
Kremling, A.2
Gilles, E.3
-
28
-
-
20444419234
-
Reduction of mathematical models of signal transduction networks: Simulation-based approach applied to EGF receptor signalling
-
Conzelmann, H., Saez-Rodriguez, J., Sauter, T., Bullinger, E., Allgöwer, F., Gilles, E.: Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling. Systems Biology 1(1), 159-169 (2004)
-
(2004)
Systems Biology
, vol.1
, Issue.1
, pp. 159-169
-
-
Conzelmann, H.1
Saez-Rodriguez, J.2
Sauter, T.3
Bullinger, E.4
Allgöwer, F.5
Gilles, E.6
-
29
-
-
49549083532
-
Temporal logic patterns for querying dynamic models of cellular interaction networks
-
Monteiro, P., Ropers, D., Mateescu, R., Freitas, A., de Jong, H.: Temporal logic patterns for querying dynamic models of cellular interaction networks. ECCB 24, 227-233 (2008)
-
(2008)
ECCB
, vol.24
, pp. 227-233
-
-
Monteiro, P.1
Ropers, D.2
Mateescu, R.3
Freitas, A.4
de Jong, H.5
-
30
-
-
0001144902
-
Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels
-
Gibson, M., Bruck, J.: Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels. The Journal of Chemical Physics 104, 1876-1889 (2000)
-
(2000)
The Journal of Chemical Physics
, vol.104
, pp. 1876-1889
-
-
Gibson, M.1
Bruck, J.2
-
31
-
-
49949112078
-
The Beta Workbench: A computational tool to study the dynamics of biological systems
-
Dematté, L., Priami, C., Romanel, A.: The Beta Workbench: a computational tool to study the dynamics of biological systems. Briefings in Bioinformatics 9(5), 437-449 (2008), http://www.cosbi.eu/Rpty-Soft-BetaWB.php
-
(2008)
Briefings in Bioinformatics
, vol.9
, Issue.5
, pp. 437-449
-
-
Dematté, L.1
Priami, C.2
Romanel, A.3
-
32
-
-
45749111042
-
-
Dematté, L., Priami, C., Romanel, A.: The BlenX Language: A Tutorial. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, 5016, pp. 313-365. Springer, Heidelberg (2008)
-
Dematté, L., Priami, C., Romanel, A.: The BlenX Language: A Tutorial. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 313-365. Springer, Heidelberg (2008)
-
-
-
-
33
-
-
38649122071
-
Probabilistic Model Checking of Complex Biological Pathways
-
Heath, J., Kwiatkowska, M., Norman, G., Parker, D., Tymchyshyn, O.: Probabilistic Model Checking of Complex Biological Pathways. Theoretical Computer Science 319, 239-257 (2008)
-
(2008)
Theoretical Computer Science
, vol.319
, pp. 239-257
-
-
Heath, J.1
Kwiatkowska, M.2
Norman, G.3
Parker, D.4
Tymchyshyn, O.5
-
34
-
-
38549120134
-
Modelling the Influence of RKIP on the ERK Signalling Pathway Using the Stochastic Process Algebra PEPA
-
Priami, C, Ingólfsdóttir, A, Mishra, B, Riis Nielson, H, eds, Springer, Heidelberg
-
Calder, M., Gilmore, S., Hillston, J.: Modelling the Influence of RKIP on the ERK Signalling Pathway Using the Stochastic Process Algebra PEPA. In: Priami, C., Ingólfsdóttir, A., Mishra, B., Riis Nielson, H. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol. 4230, pp. 1-23. Springer, Heidelberg (2006)
-
(2006)
Transactions on Computational Systems Biology VII. LNCS (LNBI)
, vol.4230
, pp. 1-23
-
-
Calder, M.1
Gilmore, S.2
Hillston, J.3
-
35
-
-
33845385005
-
Analysis of signalling pathways using continuous time Markov chains
-
Priami, C, Plotkin, G, eds, Springer, Heidelberg
-
Calder, M., Vyshemirsky, V., Gilbert, D., Orton, R.: Analysis of signalling pathways using continuous time Markov chains. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 44-67. Springer, Heidelberg (2006)
-
(2006)
Transactions on Computational Systems Biology VI. LNCS (LNBI)
, vol.4220
, pp. 44-67
-
-
Calder, M.1
Vyshemirsky, V.2
Gilbert, D.3
Orton, R.4
-
36
-
-
70450149348
-
-
Home Page
-
The Idd-CSL Home Page: http://www-dssz.informatik.tu-cottbus.de/software/ software.html
-
The Idd-CSL
-
-
-
37
-
-
45749112203
-
-
Heiner, M., Gilbert, D., Donaldson, R.: Petri Nets for Systems and Synthetic Biology. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, 5016, pp. 215-264. Springer, Heidelberg (2008)
-
Heiner, M., Gilbert, D., Donaldson, R.: Petri Nets for Systems and Synthetic Biology. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 215-264. Springer, Heidelberg (2008)
-
-
-
-
38
-
-
70450151398
-
-
Home Page
-
The BIOCHAM Home Page: http://contraintes.inria.fr/BIOCHAM/
-
The BIOCHAM
-
-
-
39
-
-
20144377930
-
Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM
-
Fages, F., Soliman, S., Chabrier-Rivier, N.: Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM. Journal of Biological Physics and Chemistry 4(2), 64-73 (2004)
-
(2004)
Journal of Biological Physics and Chemistry
, vol.4
, Issue.2
, pp. 64-73
-
-
Fages, F.1
Soliman, S.2
Chabrier-Rivier, N.3
-
40
-
-
70450151399
-
-
Home Page
-
NuSMV Home Page: http://nusmv.irst.itc.it/
-
NuSMV
-
-
|