-
2
-
-
34548302044
-
Petri net modelling of biological networks
-
Chaouiya C. Petri net modelling of biological networks. Brief Bioinform 2007;8:210-19.
-
(2007)
Brief Bioinform
, vol.8
, pp. 210-219
-
-
Chaouiya, C.1
-
4
-
-
0027370376
-
GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems
-
Mendes P. GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput Applic Biosci 1993;9:563-71.
-
(1993)
Comput Applic Biosci
, vol.9
, pp. 563-571
-
-
Mendes, P.1
-
5
-
-
33746061326
-
From Petri nets to differential equations - an integrative approach for biochemical network analysis
-
Proceedings of the 27th ICATPN 2006, Heidelberg, Germany: Springer
-
Gilbert D, Heiner M. From Petri nets to differential equations - an integrative approach for biochemical network analysis. In: Proceedings of the 27th ICATPN 2006, LNCS 4024. Heidelberg, Germany: Springer, 2006;181-200.
-
(2006)
LNCS
, vol.4024
, pp. 181-200
-
-
Gilbert, D.1
Heiner, M.2
-
6
-
-
84958662607
-
Mathematical modeling of the influence of RKIP on the ERK signaling pathway
-
Cho K-H, Shin S-Y, Kim H-W, et al. Mathematical modeling of the influence of RKIP on the ERK signaling pathway. Lect Notes Comput Sci 2003;2602:127-41.
-
(2003)
Lect Notes Comput Sci
, vol.2602
, pp. 127-141
-
-
Cho, K.-H.1
Shin, S.-Y.2
Kim, H.-W.3
-
7
-
-
29144435996
-
Computational modelling of the tyrosine receptor kinase activated MAPK pathway
-
Orton R, Sturm O, Vyshemirsky V, et al. Computational modelling of the tyrosine receptor kinase activated MAPK pathway. Biochem J 2005;392:249-61.
-
(2005)
Biochem J
, vol.392
, pp. 249-261
-
-
Orton, R.1
Sturm, O.2
Vyshemirsky, V.3
-
8
-
-
0036212767
-
Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors
-
Schoeberl B, Eichler-Jonsson C, Gilles E, et al. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol 2002;20:370-5.
-
(2002)
Nat Biotechnol
, vol.20
, pp. 370-375
-
-
Schoeberl, B.1
Eichler-Jonsson, C.2
Gilles, E.3
-
9
-
-
14844318077
-
When kinases meet mathematics: The systems biology of MAPK signalling
-
Kolch W, Calder M, Gilbert D. When kinases meet mathematics: The systems biology of MAPK signalling. FEBS Lett 2005;579:1891-5.
-
(2005)
FEBS Lett
, vol.579
, pp. 1891-1895
-
-
Kolch, W.1
Calder, M.2
Gilbert, D.3
-
10
-
-
27744486991
-
Current challenges in quantitative modeling of epidermal growth factor signaling
-
Breitling R, Hoeller D. Current challenges in quantitative modeling of epidermal growth factor signaling. FEBS Lett 2005;579 6289-94.
-
(2005)
FEBS Lett
, vol.579
, pp. 6289-6294
-
-
Breitling, R.1
Hoeller, D.2
-
11
-
-
0037213006
-
Computational modeling of the EGF-receptor system: A paradigm for systems biology
-
Wiley H.S, Shvartsman SY, Lauffenburger DA. Computational modeling of the EGF-receptor system: A paradigm for systems biology. Trends Cell Biol 2003;13: 43-50.
-
(2003)
Trends Cell Biol
, vol.13
, pp. 43-50
-
-
Wiley, H.S.1
Shvartsman, S.Y.2
Lauffenburger, D.A.3
-
12
-
-
0029790351
-
-
Huang C. Ferrell J. Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci USA 996;93: 10078-83.
-
Huang C. Ferrell J. Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci USA 996;93: 10078-83.
-
-
-
-
13
-
-
0030972112
-
The activating dual phosphorylation of MAPK by MEK is nonprocessive
-
Burack W, Sturgill T. The activating dual phosphorylation of MAPK by MEK is nonprocessive. Biochemistry 1997;36: 5929-33.
-
(1997)
Biochemistry
, vol.36
, pp. 5929-5933
-
-
Burack, W.1
Sturgill, T.2
-
14
-
-
0033570090
-
Quantification of short term signaling by the epidermal growth factor receptor
-
Kholodenko B, Demin O, Moehren G, Hoek J. Quantification of short term signaling by the epidermal growth factor receptor. J Biol Chem 1999;274:30169-81.
-
(1999)
J Biol Chem
, vol.274
, pp. 30169-30181
-
-
Kholodenko, B.1
Demin, O.2
Moehren, G.3
Hoek, J.4
-
15
-
-
0034613112
-
Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells
-
Brightman F, Fell D. Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells. FEBS Lett 2003; 482:169-74.
-
(2003)
FEBS Lett
, vol.482
, pp. 169-174
-
-
Brightman, F.1
Fell, D.2
-
16
-
-
17644427530
-
Sensitivity analysis of parameters controlling oscillatory signalling in the NF-kappaB pathway: The roles of IKK and IkappaBalpha
-
Ihekwaba A, Broomhead D, Grimley R, et al. Sensitivity analysis of parameters controlling oscillatory signalling in the NF-kappaB pathway: the roles of IKK and IkappaBalpha. Syst Biol (Stevenage) 2004;1 93-103.
-
(2004)
Syst Biol (Stevenage)
, vol.1
, pp. 93-103
-
-
Ihekwaba, A.1
Broomhead, D.2
Grimley, R.3
-
17
-
-
0034705227
-
Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties
-
Levchenko A, Bruck J, Sternberg P. Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc Natl Acad Sci USA 2000;97 5818-23.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 5818-5823
-
-
Levchenko, A.1
Bruck, J.2
Sternberg, P.3
-
18
-
-
0034019315
-
Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades
-
Kholodenko B. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur J Biochem 2000;267:1583-88.
-
(2000)
Eur J Biochem
, vol.267
, pp. 1583-1588
-
-
Kholodenko, B.1
-
19
-
-
33748557777
-
The statistical mechanics of complex signaling networks: Nerve growth factor signaling
-
Brown K, Hill C, Calero G, et al. The statistical mechanics of complex signaling networks: Nerve growth factor signaling. Phys Biol 2004;1:184-95.
-
(2004)
Phys Biol
, vol.1
, pp. 184-195
-
-
Brown, K.1
Hill, C.2
Calero, G.3
-
20
-
-
0942300661
-
Model analysis of difference between EGF pathway and FGF pathway
-
Yamada S, Taketomi T, Yoshimura A. Model analysis of difference between EGF pathway and FGF pathway. Biochem Biophys Res Commun 2003; 314:1113-20.
-
(2003)
Biochem Biophys Res Commun
, vol.314
, pp. 1113-1120
-
-
Yamada, S.1
Taketomi, T.2
Yoshimura, A.3
-
21
-
-
85016942990
-
Model checking
-
Clarke E, Grumberg O, Peled D. Model checking. Cambridge, MA: MIT Press 1999, third printing, 2001.
-
(2001)
Cambridge, MA: MIT Press 1999, third printing
-
-
Clarke, E.1
Grumberg, O.2
Peled, D.3
-
22
-
-
33746052350
-
The model checking kit
-
Proceeding of ICATPN 2007, Heidelberg, Germany: Springer
-
Schröter C, Schwoon S, Esparza J. The model checking kit. In: Proceeding of ICATPN 2007, LNCS 2679. Heidelberg, Germany: Springer, 2003;463-72.
-
(2003)
LNCS
, vol.2679
, pp. 463-472
-
-
Schröter, C.1
Schwoon, S.2
Esparza, J.3
-
23
-
-
0003953265
-
Ina - The Intergrated Net Analyzer
-
Technical report. Berlin, Germany: Humboldt University Berlin, May 2008, date last accessed
-
Starke P, Roch S. Ina - The Intergrated Net Analyzer. Technical report. Berlin, Germany: Humboldt University Berlin. http://www.informatik.hu-berlin.de/~starke/ina.html (May 2008, date last accessed).
-
-
-
Starke, P.1
Roch, S.2
-
24
-
-
49949102984
-
-
Charlie Website. A Tool for the Analysis of Place/Transition Nets. BTU Cottbus. http://www-dssz.informatik.tu-cottbus.de/software/charlie/ charlie.html (May 2008, date last accessed).
-
Charlie Website. A Tool for the Analysis of Place/Transition Nets. BTU Cottbus. http://www-dssz.informatik.tu-cottbus.de/software/charlie/ charlie.html (May 2008, date last accessed).
-
-
-
-
25
-
-
38049136584
-
A unifying framework for modelling and analysing biochemical pathways using Petri nets
-
Heidelberg, Germany: Springer
-
Gilbert D, Heiner M, Lehrack S. A unifying framework for modelling and analysing biochemical pathways using Petri nets. In: Proceeding of CMSB 2007, LNCS/LNBI 4695. Heidelberg, Germany: Springer, 2007;200-16.
-
(2007)
Proceeding of CMSB 2007, LNCS/LNBI 4695
, pp. 200-216
-
-
Gilbert, D.1
Heiner, M.2
Lehrack, S.3
-
26
-
-
0024645936
-
Petri nets: Properties, analysis and applications
-
Murata T. Petri nets: Properties, analysis and applications. In: Proceeding of IEEE 1989;77:541-80.
-
(1989)
Proceeding of IEEE
, vol.77
, pp. 541-580
-
-
Murata, T.1
-
28
-
-
34547845212
-
A Petri net approach to persistence analysis in chemical reaction networks
-
Queinnec I, Tarbouriech S, Garcia G, Niculescu S-I, eds, Heidelberg, Germany: Springer
-
Angeli D, De Leenheer P, Sontag E. A Petri net approach to persistence analysis in chemical reaction networks. In: Queinnec I, Tarbouriech S, Garcia G, Niculescu S-I, (eds). Biology and Control Theory: Current Challenges, Lecture Notes in Control and Information Sciences. Heidelberg, Germany: Springer, 2007;181-216.
-
(2007)
Biology and Control Theory: Current Challenges, Lecture Notes in Control and Information Sciences
, pp. 181-216
-
-
Angeli, D.1
De Leenheer, P.2
Sontag, E.3
-
29
-
-
38049142307
-
Machine learning biochemical networks from temporal logic properties
-
Transaction on Compuatational System Biology VI, Heidelberg, Germany: Springer
-
Calzone L, Chabrier-Rivier N, Fages F, et al. Machine learning biochemical networks from temporal logic properties. In: Transaction on Compuatational System Biology VI, LNCS 4220. Heidelberg, Germany: Springer, 2006.
-
(2006)
LNCS
, vol.4220
-
-
Calzone, L.1
Chabrier-Rivier, N.2
Fages, F.3
-
30
-
-
49949113858
-
-
MC2 Website. MC2 - PLTL Model Checker. University of Glasgow. http://www.brc.dcs.gla.ac.uk/software/mc2/2008 (May 2008, date last accessed).
-
MC2 Website. MC2 - PLTL Model Checker. University of Glasgow. http://www.brc.dcs.gla.ac.uk/software/mc2/2008 (May 2008, date last accessed).
-
-
-
-
33
-
-
33745075591
-
Tools for kinetic modeling of biochemical networks
-
Alves R, Antunes F, Salvador S. Tools for kinetic modeling of biochemical networks. Nat Biotechnol 2006;24: 667-72.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 667-672
-
-
Alves, R.1
Antunes, F.2
Salvador, S.3
-
34
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka M, Finney A, Sauro HM, et al. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 2003;19:524-31.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
-
35
-
-
49949097377
-
-
BioNessie, University of Glasgow, May, date last accessed
-
BioNessie. A biochemical pathway simulation and analysis tool. University of Glasgow. www.bionessie.org (May 2008, date last accessed).
-
(2008)
A biochemical pathway simulation and analysis tool
-
-
-
36
-
-
33845368513
-
COPASI - a complex pathway simulator
-
Hoops S, Sahle S, Gauges R, et al. COPASI - a complex pathway simulator. Bioinformatics 2006;22:3067-74.
-
(2006)
Bioinformatics
, vol.22
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
-
38
-
-
38549124182
-
SBW - a modular framework for systems biology
-
eds
-
Bergmann FT, Sauro HM. SBW - a modular framework for systems biology. In: Perrone LF, Lawson B, Liu J, Wieland FP, (eds). In: Proceedings of the Winter Simulation Conference WSC 2006, Monterey, California, USA, 2006. WSC, 2006; 1637-1645.
-
(2006)
Proceedings of the Winter Simulation Conference WSC 2006, Monterey, California, USA, 2006. WSC
, pp. 1637-1645
-
-
Bergmann, F.T.1
Sauro, H.M.2
-
39
-
-
35748973241
-
Cyto-Sim: A formal language model and stochastic simulator of membrane-enclosed biochemical processes
-
Sedwards S, Mazza T. Cyto-Sim: A formal language model and stochastic simulator of membrane-enclosed biochemical processes. Bioinformatics 2007;23:2800-2.
-
(2007)
Bioinformatics
, vol.23
, pp. 2800-2802
-
-
Sedwards, S.1
Mazza, T.2
-
40
-
-
0003945142
-
-
Philadelphia, PA: SIAM
-
Ermentrout B. Simulating, Analyzing, and Animating Dynamical Systems: a Guide to Xppaut for Researchers and Students (Software, Environments, Tools). Philadelphia, PA: SIAM, 2002.
-
(2002)
Simulating, Analyzing, and Animating Dynamical Systems: A Guide to Xppaut for Researchers and Students (Software, Environments, Tools)
-
-
Ermentrout, B.1
-
41
-
-
49949110422
-
-
Snoopy, BTU Cottbus, CS Dep, May, date last accessed
-
Snoopy. A Tool to Design and Animate Hierarchical Graphs. BTU Cottbus, CS Dep. www-dssz.informatik.tu-cottbus.de (May 2008, date last accessed).
-
(2008)
A Tool to Design and Animate Hierarchical Graphs
-
-
|