-
1
-
-
0003880161
-
-
4th ed. Garland Science
-
Alberts, B., A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. 2002. Molecular biology of the cell. 4th ed. Garland Science.
-
(2002)
Molecular Biology of the Cell
-
-
Alberts, B.1
Johnson, A.2
Lewis, J.3
Raff, M.4
Roberts, K.5
Walter, P.6
-
2
-
-
57849158644
-
Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning
-
An, G. C., and J. R. Faeder. 2009. Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. Math. Biosci. 217 (1): 53-63.
-
(2009)
Math. Biosci.
, vol.217
, Issue.1
, pp. 53-63
-
-
An, G.C.1
Faeder, J.R.2
-
3
-
-
66249114051
-
A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases
-
Barua, D., J. R. Faeder, and J. M. Haugh. 2009. A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases. PLoS Comput. Biol. 5 (4): e1000364.
-
(2009)
PLoS Comput. Biol.
, vol.5
, Issue.4
-
-
Barua, D.1
Faeder, J.R.2
Haugh, J.M.3
-
4
-
-
54049090016
-
Complexity and modularity of intracellular networks: A systematic approach for modelling and simulation
-
Blinov, M. L., O. Ruebenacker, and I. I. Moraru. 2008. Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation. IET Syst. Biol. 2 (5): 363-368.
-
(2008)
IET Syst. Biol.
, vol.2
, Issue.5
, pp. 363-368
-
-
Blinov, M.L.1
Ruebenacker, O.2
Moraru, I.I.3
-
5
-
-
36549008035
-
Graph theory for rule-based modeling of biochemical networks
-
Blinov, M. L., J. Yang, J. R. Faeder, and W. S. Hlavacek. 2006. Graph theory for rule-based modeling of biochemical networks. Lect. Notes Comput. Sci. 4230:89-106.
-
(2006)
Lect. Notes Comput. Sci.
, vol.4230
, pp. 89-106
-
-
Blinov, M.L.1
Yang, J.2
Faeder, J.R.3
Hlavacek, W.S.4
-
6
-
-
54049108116
-
Domain-oriented reduction of rule-based network models
-
Borisov, N. M., A. S. Chistopolsky, J. R. Faeder, and B. N. Kholodenko. 2008. Domain-oriented reduction of rule-based network models. IET Syst. Biol. 2 (5): 342-351.
-
(2008)
IET Syst. Biol.
, vol.2
, Issue.5
, pp. 342-351
-
-
Borisov, N.M.1
Chistopolsky, A.S.2
Faeder, J.R.3
Kholodenko, B.N.4
-
7
-
-
33747877324
-
BIOCHAM: An environment for modeling biological systems and formalizing experimental knowledge
-
DOI 10.1093/bioinformatics/btl172
-
Calzone, L., F. Fages, and S. Soliman. 2006. BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22 (14): 1805-1807. (Pubitemid 44288351)
-
(2006)
Bioinformatics
, vol.22
, Issue.14
, pp. 1805-1807
-
-
Calzone, L.1
Fages, F.2
Soliman, S.3
-
8
-
-
26444592298
-
Brane calculi - Interactions of biological membranes
-
Cardelli, L. 2005. Brane calculi - Interactions of biological membranes. Lect. Notes Comput. Sci. 3082:257-278.
-
(2005)
Lect. Notes Comput. Sci.
, vol.3082
, pp. 257-278
-
-
Cardelli, L.1
-
9
-
-
49249126766
-
Bitonal membrane systems
-
Cardelli, L. 2008. Bitonal membrane systems. Theor. Comput. Sci. 404 (1-2): 5-18.
-
(2008)
Theor. Comput. Sci.
, vol.404
, Issue.1-2
, pp. 5-18
-
-
Cardelli, L.1
-
10
-
-
63549099634
-
Simulation of large-scale rule-based models
-
Colvin, J., M. I. Monine, J. R. Faeder, W. S. Hlavacek, D. D. Von Hoff, and R. G. Posner. 2009. Simulation of large-scale rule-based models. Bioinformatics 25 (7): 910-917.
-
(2009)
Bioinformatics
, vol.25
, Issue.7
, pp. 910-917
-
-
Colvin, J.1
Monine, M.I.2
Faeder, J.R.3
Hlavacek, W.S.4
Von Hoff, D.D.5
Posner, R.G.6
-
11
-
-
77951592923
-
-
Technical Report TR-2008-2116, IT University of Copenhagen, Rued Langgaards Vej 7, DK-2300 Copenhagen V
-
Damgaard, T. C., V. Danos, and J. Krivine. 2008. A language for the cell. Technical Report TR-2008-2116, IT University of Copenhagen, Rued Langgaards Vej 7, DK-2300 Copenhagen V.
-
(2008)
A Language for the Cell
-
-
Damgaard, T.C.1
Danos, V.2
Krivine, J.3
-
12
-
-
38149083357
-
Rule-based modelling of cellular signalling
-
Danos, V., J. Feret, W. Fontana, R. Harmer, and J. Krivine. 2007. Rule-based modelling of cellular signalling. Lect. Notes Comput. Sci 4703:17-41.
-
(2007)
Lect. Notes Comput. Sci
, vol.4703
, pp. 17-41
-
-
Danos, V.1
Feret, J.2
Fontana, W.3
Harmer, R.4
Krivine, J.5
-
13
-
-
49949112078
-
The Beta Workbench: A computational tool to study the dynamics of biological systems
-
Dematte, L., C. Priami, and A. Romanel. 2008. The Beta Workbench: a computational tool to study the dynamics of biological systems. Brief. Bioinform. 9 (5): 437-449.
-
(2008)
Brief. Bioinform.
, vol.9
, Issue.5
, pp. 437-449
-
-
Dematte, L.1
Priami, C.2
Romanel, A.3
-
14
-
-
65649154507
-
Rule-based modeling of biochemical systems with BioNetGen
-
ed. I. V. Maly, p. Humana Press
-
Faeder, J. R., M. L. Blinov, and W. S. Hlavacek. 2009. Rule-based modeling of biochemical systems with BioNetGen. In Methods in Molecular Biology: Systems Biology, ed. I. V. Maly, p. 113-168. Humana Press.
-
(2009)
Methods in Molecular Biology: Systems Biology
, pp. 113-168
-
-
Faeder, J.R.1
Blinov, M.L.2
Hlavacek, W.S.3
-
15
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
Gillespie, D. T. 1976. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22 (4): 403-434.
-
(1976)
J. Comput. Phys.
, vol.22
, Issue.4
, pp. 403-434
-
-
Gillespie, D.T.1
-
16
-
-
0030998039
-
Physical modulation of intracellular signaling processes by locational regulation
-
Haugh, J. M., and D. A. Lauffenburger. 1997. Physical modulation of intracellular signaling processes by locational regulation. Biophys. J. 72 (5): 2014-2031.
-
(1997)
Biophys. J.
, vol.72
, Issue.5
, pp. 2014-2031
-
-
Haugh, J.M.1
Lauffenburger, D.A.2
-
17
-
-
0346502078
-
The complexity of complexes in signal transduction
-
Hlavacek, W. S., J. R. Faeder, M. L. Blinov, A. S. Perelson, and B. Goldstein. 2003. The complexity of complexes in signal transduction. Biotechnol. Bioeng. 84 (7): 783-794.
-
(2003)
Biotechnol. Bioeng.
, vol.84
, Issue.7
, pp. 783-794
-
-
Hlavacek, W.S.1
Faeder, J.R.2
Blinov, M.L.3
Perelson, A.S.4
Goldstein, B.5
-
18
-
-
33747366698
-
Rules for modeling signal-transduction systems
-
2006:re6
-
Hlavacek, W. S., J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka, and W. Fontana. 2006. Rules for modeling signal-transduction systems. Science STKE 2006:re6.
-
(2006)
Science STKE
-
-
Hlavacek, W.S.1
Faeder, J.R.2
Blinov, M.L.3
Posner, R.G.4
Hucka, M.5
Fontana, W.6
-
19
-
-
65649104062
-
GetBonNie for building, analyzing and sharing rule-based models
-
Hu, B., G. M. Fricke, J. R. Faeder, R. G. Posner, and W. S. Hlavacek. 2009. GetBonNie for building, analyzing and sharing rule-based models. Bioinformatics 25 (11): 1457-1460.
-
(2009)
Bioinformatics
, vol.25
, Issue.11
, pp. 1457-1460
-
-
Hu, B.1
Fricke, G.M.2
Faeder, J.R.3
Posner, R.G.4
Hlavacek, W.S.5
-
20
-
-
77951618514
-
Systems Biology Markup Language (SBML) Level 2: Structures and facilities for model definitions
-
Hucka, M., S. Hoops, S. M. Keating, N. Le Novère, S. Sahle, and D. Wilkinson. 2008. Systems Biology Markup Language (SBML) Level 2: Structures and facilities for model definitions. Nature Precedings. http://dx.doi.org/10.1038/ npre.2008.2715.1.
-
(2008)
Nature Precedings
-
-
Hucka, M.1
Hoops, S.2
Keating, S.M.3
Le Novère, N.4
Sahle, S.5
Wilkinson, D.6
-
21
-
-
0034194467
-
Why cytoplasmic signalling proteins should be recruited to cell membranes
-
Kholodenko, B. N., J. B. Hoek, and H. V. Westerhoff. 2000. Why cytoplasmic signalling proteins should be recruited to cell membranes. Trends Cell Biol. 10 (5): 173-178.
-
(2000)
Trends Cell Biol.
, vol.10
, Issue.5
, pp. 173-178
-
-
Kholodenko, B.N.1
Hoek, J.B.2
Westerhoff, H.V.3
-
22
-
-
49249114177
-
A simple calculus for proteins and cells
-
Laneve, C., and F. Tarissan. 2008. A simple calculus for proteins and cells. Theor. Comput. Sci. 404 (1-2): 127-141.
-
(2008)
Theor. Comput. Sci.
, vol.404
, Issue.1-2
, pp. 127-141
-
-
Laneve, C.1
Tarissan, F.2
-
23
-
-
69949127857
-
Efficient stochastic simulation of reaction-diffusion processes via direct compilation
-
in press; doi:10.1093/bioinformatics/btp387
-
Lis, M., M. N. Artyomov, S. Devadas, and A. K. Chakraborty. 2009. Efficient stochastic simulation of reaction-diffusion processes via direct compilation. Bioinformatics. in press; doi:10.1093/bioinformatics/btp387.
-
(2009)
Bioinformatics
-
-
Lis, M.1
Artyomov, M.N.2
Devadas, S.3
Chakraborty, A.K.4
-
24
-
-
64549144670
-
Programming with models: Modularity and abstraction provide powerful capabilities for systems biology
-
Mallavarapu, A., M. Thomson, B. Ullian, and J. Gunawardena. 2009. Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J. R. Soc. Interface 6 (32): 257-270.
-
(2009)
J. R. Soc. Interface
, vol.6
, Issue.32
, pp. 257-270
-
-
Mallavarapu, A.1
Thomson, M.2
Ullian, B.3
Gunawardena, J.4
-
25
-
-
33746595848
-
Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method
-
Meier-Schellersheim, M., X. Xu, B. Angermann, E. J. Kunkel, T. Jin, and R. N. Germain. 2006. Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method. PLOS Comput. Biol. 2 (7): 710-724.
-
(2006)
PLOS Comput. Biol.
, vol.2
, Issue.7
, pp. 710-724
-
-
Meier-Schellersheim, M.1
Xu, X.2
Angermann, B.3
Kunkel, E.J.4
Jin, T.5
Germain, R.N.6
-
26
-
-
0032492834
-
Predicting temporal fluctuations in an intracellular signalling pathway
-
Morton-Firth, C. J., and D. Bray. 1998. Predicting temporal fluctuations in an intracellular signalling pathway. J. Theor. Biol. 192 (1): 117.
-
(1998)
J. Theor. Biol.
, vol.192
, Issue.1
, pp. 117
-
-
Morton-Firth, C.J.1
Bray, D.2
-
27
-
-
67649383566
-
Aggregation of membrane proteins by cytosolic cross-linkers: Theory and simulation of the LAT-Grb2-SOS1 system
-
Nag, A., M. I. Monine, J. R. Faeder, and B. Goldstein. 2009. Aggregation of membrane proteins by cytosolic cross-linkers: Theory and simulation of the LAT-Grb2-SOS1 system. Biophys. J. 96 (7): 2604-2623.
-
(2009)
Biophys. J.
, vol.96
, Issue.7
, pp. 2604-2623
-
-
Nag, A.1
Monine, M.I.2
Faeder, J.R.3
Goldstein, B.4
-
28
-
-
0037453510
-
Assembly of cell regulatory systems through protein interaction domains
-
DOI 10.1126/science.1083653
-
Pawson, T., and P. Nash. 2003. Assembly of cell regulatory systems through protein interaction domains. Science 300 (5618): 445-452. (Pubitemid 36444318)
-
(2003)
Science
, vol.300
, Issue.5618
, pp. 445-452
-
-
Pawson, T.1
Nash, P.2
-
29
-
-
4444383325
-
BioAmbients: An abstraction for biological compartments
-
Regev, A., E. M. Panina, W. Silverman, L. Cardelli, and E. Shapiro. 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
-
-
Regev, A.1
Panina, E.M.2
Silverman, W.3
Cardelli, L.4
Shapiro, E.5
-
30
-
-
35748973241
-
Cyto-Sim: A formal language model and stochastic simulator of membrane-enclosed biochemical processes
-
DOI 10.1093/bioinformatics/btm416
-
Sedwards, S., and T. Mazza. 2007. Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes. Bioinformatics 23 (20): 2800-2802. (Pubitemid 350048349)
-
(2007)
Bioinformatics
, vol.23
, Issue.20
, pp. 2800-2802
-
-
Sedwards, S.1
Mazza, T.2
-
31
-
-
77951554539
-
-
Sneddon, M., J. R. Faeder, and T. Emonet. 2009. In preparation
-
Sneddon, M., J. R. Faeder, and T. Emonet. 2009. In preparation.
-
-
-
-
32
-
-
51849129931
-
Kinetic Monte Carlo method for rule-based modeling of biochemical networks
-
Yang, J., M. I. Monine, J. R. Faeder, and W. S. Hlavacek. 2008. Kinetic Monte Carlo method for rule-based modeling of biochemical networks. Phys. Rev. E 78 (3): 031910.
-
(2008)
Phys. Rev. E
, vol.78
, Issue.3
, pp. 031910
-
-
Yang, J.1
Monine, M.I.2
Faeder, J.R.3
Hlavacek, W.S.4
|