-
1
-
-
0026802334
-
Metabolic control analysis: A survey of its theoretical and experimental development
-
Fell D: Metabolic control analysis: a survey of its theoretical and experimental development. Biochem. J. 286, 313-330 (1992).
-
(1992)
Biochem. J.
, vol.286
, pp. 313-330
-
-
Fell, D.1
-
2
-
-
33751356224
-
Systems biology, metabolic modelling and metabolomics in drug discovery and development
-
Kell D: Systems biology, metabolic modelling and metabolomics in drug discovery and development. Drug Discov. Today 11, 1085-1092 (2006).
-
(2006)
Drug Discov. Today
, vol.11
, pp. 1085-1092
-
-
Kell, D.1
-
3
-
-
1542680576
-
A computer model of the gene network of the cholesterol biosynthesis regulation in the cell: Analysis of the effect of mutations
-
Ratushnyi A, Likhoshvai V, Ignat'eva E et al.: A computer model of the gene network of the cholesterol biosynthesis regulation in the cell: analysis of the effect of mutations. Doklady Biochem. Biophys. 389, 90-93 (2003).
-
(2003)
Doklady Biochem. Biophys.
, vol.389
, pp. 90-93
-
-
Ratushnyi, A.1
Likhoshvai, V.2
Ignat'Eva, E.3
-
4
-
-
34548860112
-
The Edinburgh human metabolic network reconstruction and its functional analysis
-
Ma A, Sorokin A, Mazein A et al.: The Edinburgh human metabolic network reconstruction and its functional analysis. Mol. Sys. Biol. 3, 135 (2007).
-
(2007)
Mol. Sys. Biol.
, vol.3
, pp. 135
-
-
Ma, A.1
Sorokin, A.2
Mazein, A.3
-
5
-
-
0031029852
-
Stochastic mechanisms in gene expression
-
McAdams H, Arkin A: Stochastic mechanisms in gene expression. Proc. Natl Acad. Sci. USA 94, 814-819 (1997).
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 814-819
-
-
McAdams, H.1
Arkin, A.2
-
6
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage l-infected Escherichia coli cells
-
Arkin A, Ross J, McAdams H: Stochastic kinetic analysis of developmental pathway bifurcation in phage l-infected Escherichia coli cells. Genetics 149, 1633-1648 (1998).
-
(1998)
Genetics
, vol.149
, pp. 1633-1648
-
-
Arkin, A.1
Ross, J.2
McAdams, H.3
-
7
-
-
0032229446
-
Quantitative modelling of biochemical networks
-
Hofestadt R, Thelen S: Quantitative modelling of biochemical networks. In Silico Biol. 1, 39-53 (1998).
-
(1998)
Silico Biol
, vol.1
, pp. 39-53
-
-
Hofestadt, R.1
Thelen, S.2
-
8
-
-
0033670135
-
Pathway analysis in metabolic databases via differential metabolic display (DMD)
-
Küffner R, Zimmer R, Lengauer T: Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics 16, 825-836 (2000).
-
(2000)
Bioinformatics
, vol.16
, pp. 825-836
-
-
Küffner, R.1
Zimmer, R.2
Lengauer, T.3
-
9
-
-
0032499741
-
Quantitative modelling of stochastic systems in molecular biology by using stochastic Petri Nets
-
Goss P, Peccoud J: Quantitative modelling of stochastic systems in molecular biology by using stochastic Petri Nets. Proc. Natl Acad. Sci. USA 95, 6750-6755 (1998).
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 6750-6755
-
-
Goss, P.1
Peccoud, J.2
-
10
-
-
38549120134
-
Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA
-
Istrail S, Pevzner P, Waterman M (Eds). Springer Berlin/ Heidelberg, Germany
-
Calder M, Gilmore S, Hillston J: Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA. In: Transactions on Computational Systems Biology VII. Istrail S, Pevzner P, Waterman M (Eds). Springer Berlin/ Heidelberg, Germany, 1-23 (2006).
-
(2006)
Transactions on Computational Systems Biology
, vol.7
, pp. 1-23
-
-
Calder, M.1
Gilmore, S.2
Hillston, J.3
-
11
-
-
0035235039
-
Representation and simulation of biochemical processes using the p-calculus process algebra
-
Regev A, Silverman W, Shapiro E: Representation and simulation of biochemical processes using the p-calculus process algebra. Pac. Symp. Biocomput. 459-470 (2001).
-
(2001)
Pac. Symp. Biocomput.
, pp. 459-470
-
-
Regev, A.1
Silverman, W.2
Shapiro, E.3
-
12
-
-
71549155391
-
Rule-based modelling of cellular signaling
-
Presented at: Caires L Vasconcelos V (Eds), Lecture Notes in Computer Science
-
Danos V, Feret J, Fontana W, Harmer R, Krivine J: Rule-based modelling of cellular signalling. Presented at: Proceedings of the 18th International Conference on Concurrency Theory (CONCUR'07). Caires L, Vasconcelos, V (Eds), Lecture Notes in Computer Science (2007).
-
(2007)
Proceedings of the 18th International Conference on Concurrency Theory (CONCUR'07)
-
-
Danos, V.1
Feret, J.2
Fontana, W.3
Harmer, R.4
Krivine, J.5
-
16
-
-
84932847893
-
A symbolic analysis of relay and switching circuits
-
Shannon C: A symbolic analysis of relay and switching circuits. Trans. AIEE 57, 713-722 (1938).
-
(1938)
Trans. AIEE
, vol.57
, pp. 713-722
-
-
Shannon, C.1
-
17
-
-
0014671878
-
Homeostasis and differentiation in random genetic control networks
-
Kauffman S: Homeostasis and differentiation in random genetic control networks. Nature 224(5215), 177-178 (1969).
-
(1969)
Nature
, vol.224
, Issue.5215
, pp. 177-178
-
-
Kauffman, S.1
-
18
-
-
0033616563
-
A logical analysis of T cell activation and anergy
-
Kaufman M, Andris F, Leo O: A logical analysis of T cell activation and anergy. Proc. Natl Acad. Sci. USA 96(7), 3894-3899 (1999).
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, Issue.7
, pp. 3894-3899
-
-
Kaufman, M.1
Andris, F.2
Leo, O.3
-
19
-
-
3042799574
-
A computational algebra approach to the reverse engineering of gene regulatory networks
-
Laubenbacher R, Stigler B: A computational algebra approach to the reverse engineering of gene regulatory networks. J. Theor. Biol. 229(4), 523-537 (2004).
-
(2004)
J. Theor. Biol.
, vol.229
, Issue.4
, pp. 523-537
-
-
Laubenbacher, R.1
Stigler, B.2
-
20
-
-
0036184629
-
Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks
-
Shmulevich I, Dougherty E, Kim S, Zhang W: Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18(2), 261-274 (2002). (Pubitemid 34183104)
-
(2002)
Bioinformatics
, vol.18
, Issue.2
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
Zhang, W.4
-
22
-
-
70049105859
-
The logic of EGFR/ErbB signaling: Theoretical properties and analysis of high-throughput data
-
Samaga R, Saez-Rodriguez J, Alexopoulos L, Sorger P, Klamt S: The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comp. Biol. 5(8), E1000438 (2009).
-
(2009)
PLoS Comp. Biol.
, vol.5
, Issue.8
-
-
Samaga, R.1
Saez-Rodriguez, J.2
Alexopoulos, L.3
Sorger, P.4
Klamt, S.5
-
23
-
-
74549172058
-
ON/OFF and beyond - A Boolean model of apoptosis
-
Schlatter R, Schmich K, Vizcarra I et al.: ON/OFF and beyond - a Boolean model of apoptosis. PLoS Comp. Biol. 5(12), E1000595 (2009).
-
(2009)
PLoS Comp. Biol.
, vol.5
, Issue.12
-
-
Schlatter, R.1
Schmich, K.2
Vizcarra, I.3
-
24
-
-
55849100058
-
Network model of survival signaling in large granular lymphocyte leukemia
-
Zhang B, Shah M, Yang J et al.: Network model of survival signaling in large granular lymphocyte leukemia. Proc. Natl Acad. Sci. USA105(42), 16308-16313 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, Issue.42
, pp. 16308-16313
-
-
Zhang, B.1
Shah, M.2
Yang, J.3
-
25
-
-
0345983657
-
From Boolean to probabilistic Boolean networks as models of genetic regulatory networks
-
Shmulevich I, Dougherty E, Zhang W: From Boolean to probabilistic Boolean networks as models of genetic regulatory networks. Proc. IEEE 90(11), 1778-1792 (2002).
-
(2002)
Proc. IEEE
, vol.90
, Issue.11
, pp. 1778-1792
-
-
Shmulevich, I.1
Dougherty, E.2
Zhang, W.3
-
27
-
-
33747867029
-
PDQ Wizard: Automated prioritization and characterization of gene and protein lists using biomedical literature
-
Grimes G, Wen T, Mewissen M et al.: PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature. Bioinformatics 22, 2055-2057 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 2055-2057
-
-
Grimes, G.1
Wen, T.2
Mewissen, M.3
-
28
-
-
33751340584
-
The pathway editor: A tool for managing complex biological networks
-
Sorokin A, Paliy K, Selkov A et al.: The pathway editor: a tool for managing complex biological networks. IBM J. Res. Dev. 50, 561-573 (2006).
-
(2006)
IBM J. Res. Dev.
, vol.50
, pp. 561-573
-
-
Sorokin, A.1
Paliy, K.2
Selkov, A.3
-
29
-
-
9444266171
-
Cell designer: A process diagram editor for gene-regulatory and biochemical networks
-
Funahashi A, Tanimura N, Morohashi M, Kitano H: Cell designer: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 1, 159-162 (2003).
-
(2003)
BIOSILICO
, vol.1
, pp. 159-162
-
-
Funahashi, A.1
Tanimura, N.2
Morohashi, M.3
Kitano, H.4
-
30
-
-
33845368513
-
COPASI - A complex pathway simulator
-
Hoops S, Sahle S, Gauges R et al.: COPASI - a complex pathway simulator. Bioinformatics 22, 3067-3074 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
-
31
-
-
68449103579
-
The systems biology graphical notation
-
Le Novere N, Hucka M, Mi H: The systems biology graphical notation. Nat. Biotechnol. 27, 735-741 (2009).
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 735-741
-
-
Le Novere, N.1
Hucka, M.2
Mi, H.3
-
32
-
-
23444439817
-
Using process diagrams for the graphical representation of biological networks
-
Kitano H, Funahashi A, Matsuoka Y, Oda K: Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol. 23(8), 961-966 (2005).
-
(2005)
Nat. Biotechnol.
, vol.23
, Issue.8
, pp. 961-966
-
-
Kitano, H.1
Funahashi, A.2
Matsuoka, Y.3
Oda, K.4
-
33
-
-
0032776303
-
Molecular interaction map of the mammalian cell cycle control and DNA repair systems
-
Kohn K: Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol. Biol. Cell 10(8), 2703-2734 (1999).
-
(1999)
Mol. Biol. Cell
, vol.10
, Issue.8
, pp. 2703-2734
-
-
Kohn, K.1
-
34
-
-
44049087861
-
A logic-based diagram of signalling pathways central to macrophage activation
-
Raza S, Robertson K, Lacaze P et al.: A logic-based diagram of signalling pathways central to macrophage activation. BMC Syst. Biol. 2, 36 (2008).
-
(2008)
BMC Syst. Biol.
, vol.2
, pp. 36
-
-
Raza, S.1
Robertson, K.2
Lacaze, P.3
-
35
-
-
0035171884
-
BIND - The biomolecular interaction network database
-
Bader G, Donaldson I, Wolting C: BIND - the biomolecular interaction network database. Nucleic Acids Res. 29(1), 242-245 (2001).
-
(2001)
Nucleic Acids Res
, vol.29
, Issue.1
, pp. 242-245
-
-
Bader, G.1
Donaldson, I.2
Wolting, C.3
-
36
-
-
0742323374
-
The HUPO PSI's molecular interaction format - A community standard for the representation of protein interaction data
-
Hermjakob H, Montecchi-Palazzi L, Bader G et al.: The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat. Biotechnol. 22, 177-183 (2004).
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 177-183
-
-
Hermjakob, H.1
Montecchi-Palazzi, L.2
Bader, G.3
-
38
-
-
48349105261
-
WikiPathways: Pathway editing for the people
-
Pico A, Kelder T, van Iersel M: WikiPathways: pathway editing for the people. PLoS Biol. 6(7), E184 (2008).
-
(2008)
PLoS Biol
, vol.6
, Issue.7
-
-
Pico, A.1
Kelder, T.2
Van Iersel, M.3
-
39
-
-
27544448014
-
Molecular interaction map of macrophage
-
DA
-
Oda K, Kimura T, Matsuoka Y, Muramatsu M, Kitano H: Molecular interaction map of macrophage. AfCS Res. Rep. 2(14), DA (2004).
-
(2004)
AfCS Res. Rep.
, vol.2
, Issue.14
-
-
Oda, K.1
Kimura, T.2
Matsuoka, Y.3
Muramatsu, M.4
Kitano, H.5
-
40
-
-
34147189208
-
A graphical notation to describe the logical interactions of biological pathways
-
Moodie S, Sorokin A, Ghazal P: A graphical notation to describe the logical interactions of biological pathways. J. Integr. Bioinform. 3(2), 36 (2006).
-
(2006)
J. Integr. Bioinform.
, vol.3
, Issue.2
, pp. 36
-
-
Moodie, S.1
Sorokin, A.2
Ghazal, P.3
-
41
-
-
10644250404
-
Evolving a lingua franca and associated software infrastructure for computational systems biology: The systems biology markup language (SBML) project
-
Hucka M, Finney A, Bornstein B et al.: Evolving a lingua franca and associated software infrastructure for computational systems biology: the systems biology markup language (SBML) project. IEE Syst. Biol. 1(1), 41-53 (2004).
-
(2004)
IEE Syst. Biol.
, vol.1
, Issue.1
, pp. 41-53
-
-
Hucka, M.1
Finney, A.2
Bornstein, B.3
-
43
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie D: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81(25), 2340-2361 (1977).
-
(1977)
J. Phys. Chem.
, vol.81
, Issue.25
, pp. 2340-2361
-
-
Gillespie, D.1
-
44
-
-
0033838720
-
Principles of homeostasis in governing virus activation and latency
-
Ghazal P, Garcia-Ramirez J, Gonzales-Armas JC, Kurz S, Angulo A: Principles of homeostasis in governing virus activation and latency. Immunol. Res. 21(2-3), 219-223 (2000).
-
(2000)
Immunol. Res.
, vol.21
, Issue.2-3
, pp. 219-223
-
-
Ghazal, P.1
Garcia-Ramirez, J.2
Gonzales-Armas, J.C.3
Kurz, S.4
Angulo, A.5
-
45
-
-
0034734807
-
Viruses: Hostages to the cell
-
Ghazal P, Gonzalez-Armas JC, Garcia-Ramirez JJ, Kurz S, Angulo A: Viruses: hostages to the cell. Virology 275(2), 233-237 (2000).
-
(2000)
Virology
, vol.275
, Issue.2
, pp. 233-237
-
-
Ghazal, P.1
Gonzalez-Armas, J.C.2
Garcia-Ramirez, J.J.3
Kurz, S.4
Angulo, A.5
-
46
-
-
67649660551
-
Redefining chronic viral infection
-
Virgin HW, Wherry EJ, Ahmed R: Redefining chronic viral infection. Cell 138(1), 30-50 (2009).
-
(2009)
Cell
, vol.138
, Issue.1
, pp. 30-50
-
-
Virgin, H.W.1
Wherry, E.J.2
Ahmed, R.3
-
47
-
-
18144408736
-
Cell fates as high-dimensional attractor states of a complex gene regulatory network
-
Huang S, Eichler G, Bar-Yam Y, Ingber D: Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys. Rev. Lett. 94, 128701 (2005).
-
(2005)
Phys. Rev. Lett.
, vol.94
, pp. 128701
-
-
Huang, S.1
Eichler, G.2
Bar-Yam, Y.3
Ingber, D.4
-
48
-
-
0017834347
-
Prediction of limit cycles in mathematical models of biological oscillations
-
Glass L, Pasternack J: Predictions of limit cycles in mathematical models of biological oscillations. Bull. Math. Biol. 40(1), 27-44 (1978). (Pubitemid 8292021)
-
(1978)
Bulletin of Mathematical Biology
, vol.40
, Issue.1
, pp. 27-44
-
-
Glass, L.1
Pasternack, J.S.2
-
49
-
-
0003588118
-
-
Gould SH, Hale JK (Eds). American Mathematical Society, RI, USA
-
Yan-Qian Y, Chi Y: Theory of Limit Cycles. Gould SH, Hale JK (Eds). American Mathematical Society, RI, USA (2009).
-
(2009)
Theory of Limit Cycles
-
-
Yan-Qian, Y.1
Chi, Y.2
-
50
-
-
84960561455
-
On computable numbers with an application to the Entscheidungs problem
-
Turing A: On computable numbers with an application to the Entscheidungs problem. Proc. Lond. Math. Soc. 2(42), 230-265 (1937).
-
(1937)
Proc. Lond. Math. Soc.
, vol.2
, Issue.42
, pp. 230-265
-
-
Turing, A.1
-
51
-
-
26444603940
-
The Church-Turing thesis: Breaking the myth
-
Springer Berlin/Hamberg, Germany
-
Goldin D, Wegner P: The Church-Turing thesis: breaking the myth. Lecture notes in computer science. Springer Berlin/Hamberg, Germany, 3526 (2005).
-
(2005)
Lecture Notes in Computer Science
, pp. 3526
-
-
Goldin, D.1
Wegner, P.2
-
52
-
-
52749092289
-
Inferring Boolean networks with perturbation from sparse gene expression data: A general model applied to the interferon regulatory network
-
Yu L, Watterson S, Marshall S, Ghazal P: Inferring Boolean networks with perturbation from sparse gene expression data: a general model applied to the interferon regulatory network. Mol. Biosyst. 4, 1024-1030 (2008).
-
(2008)
Mol. Biosyst.
, vol.4
, pp. 1024-1030
-
-
Yu, L.1
Watterson, S.2
Marshall, S.3
Ghazal, P.4
|