-
1
-
-
0142037521
-
Model building and model checking for biochemical processes
-
Antoniotti,M. et al. (2003) Model building and model checking for biochemical processes. Cell Biochem. Biophys., 38, 271-286.
-
(2003)
Cell Biochem. Biophys
, vol.38
, pp. 271-286
-
-
Antoniotti, M.1
-
2
-
-
45849140560
-
The Parma Polyhedra Library: Toward a complete set of numerical abstractions for the analysis and verification of hardware and software systems
-
Bagnara,R. et al. (2008) The Parma Polyhedra Library: Toward a complete set of numerical abstractions for the analysis and verification of hardware and software systems. Sci. Comput. Program., 72, 3-21.
-
(2008)
Sci. Comput. Program
, vol.72
, pp. 3-21
-
-
Bagnara, R.1
-
3
-
-
0030797355
-
Robustness in simple biochemical networks
-
Barkai,N. and Leibler,S. (1997) Robustness in simple biochemical networks. Nature, 387, 913-916.
-
(1997)
Nature
, vol.387
, pp. 913-916
-
-
Barkai, N.1
Leibler, S.2
-
4
-
-
84860513120
-
Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli
-
Batt,G. et al. (2005) Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli. Bioinformatics, 21 (Suppl.1), i19-i28.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL.1
-
-
Batt, G.1
-
5
-
-
34548747486
-
Robustness analysis and tuning of synthetic gene networks
-
Batt,G. et al. (2007) Robustness analysis and tuning of synthetic gene networks. Bioinformatics, 23, 2415-2422.
-
(2007)
Bioinformatics
, vol.23
, pp. 2415-2422
-
-
Batt, G.1
-
6
-
-
3042693879
-
Application of formal methods to biological regulatory networks: Extending Thomas' asynchronous logical approach with temporal logic
-
Bernot,G. et al. (2004) Application of formal methods to biological regulatory networks: Extending Thomas' asynchronous logical approach with temporal logic. J. Theor. Biol., 229, 339-347.
-
(2004)
J. Theor. Biol
, vol.229
, pp. 339-347
-
-
Bernot, G.1
-
7
-
-
33747877324
-
BIOCHAM: An environment for modeling biological systems and formalizing experimental knowledge
-
Calzone,L. et al. (2006) BIOCHAM: An environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics, 22, 1805-1807.
-
(2006)
Bioinformatics
, vol.22
, pp. 1805-1807
-
-
Calzone, L.1
-
8
-
-
34547646131
-
Dynamical modeling of syncytial mitotic cycles in drosophila embryos
-
Calzone,L. et al. (2007) Dynamical modeling of syncytial mitotic cycles in drosophila embryos. Mol. Syst. Biol., 3, 131.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 131
-
-
Calzone, L.1
-
9
-
-
84958602011
-
Symbolic model checking of biochemical networks
-
C.Priami, ed, Proceedings of Computational Methods in Systems Biology CMSB'03, of, Springer, Berlin, pp
-
Chabrier,N. and Fages,F. (2003) Symbolic model checking of biochemical networks. In C.Priami, (ed.) Proceedings of Computational Methods in Systems Biology (CMSB'03). Vol. 2602 of Lecture Notes in Computer Science, Springer, Berlin, pp. 149-162.
-
(2003)
Lecture Notes in Computer Science
, vol.2602
, pp. 149-162
-
-
Chabrier, N.1
Fages, F.2
-
10
-
-
66349095597
-
Geometry and topology of parameter space: Investigating measures of robustness in regulatory networks
-
Chaves,M. et al. (2007) Geometry and topology of parameter space: investigating measures of robustness in regulatory networks. J. Math. Biol., 104, 13591-13596.
-
(2007)
J. Math. Biol
, vol.104
, pp. 13591-13596
-
-
Chaves, M.1
-
11
-
-
33646877664
-
Modular approaches to expanding the functions of living matter
-
Chin,J.W. (2006) Modular approaches to expanding the functions of living matter. Nat. Chem. Biol., 2, 304-311.
-
(2006)
Nat. Chem. Biol
, vol.2
, pp. 304-311
-
-
Chin, J.W.1
-
12
-
-
35348892535
-
Innovation and robustness in complex regulatory gene networks
-
Ciliberti,S. et al. (2007) Innovation and robustness in complex regulatory gene networks. Proc. Natl Acad. Sci. USA, 104, 13591-13596.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 13591-13596
-
-
Ciliberti, S.1
-
13
-
-
58149481232
-
Properties of developmental gene regulatory networks
-
Davidson,E.H. and Levine,M.S. (2008) Properties of developmental gene regulatory networks. Proc. Natl Acad. Sci. USA, 105, 20063-20066.
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 20063-20066
-
-
Davidson, E.H.1
Levine, M.S.2
-
14
-
-
0037452576
-
Reglatory gene networks and the properties of the developmental process
-
Davidson,E.H. et al. (2003) Reglatory gene networks and the properties of the developmental process. Proc. Natl Acad. Sci. USA 100, 1475-1480.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 1475-1480
-
-
Davidson, E.H.1
-
15
-
-
57049106843
-
A model checking approach to the parameter estimation of biochemical pathways
-
Heiner,M. and Uhrmacher,A, eds) Proceedings of the Fourth International Conference on Computational Methods in Systems Biology CMSB'08, of, Springer, Berlin, pp
-
Donaldson,R. and Gilbert,D. (2008) A model checking approach to the parameter estimation of biochemical pathways. In Heiner,M. and Uhrmacher,A. (eds) Proceedings of the Fourth International Conference on Computational Methods in Systems Biology (CMSB'08). Vol. 5307 of Lecture Notes in Computer Science, Springer, Berlin, pp. 269-287.
-
(2008)
Lecture Notes in Computer Science
, vol.5307
, pp. 269-287
-
-
Donaldson, R.1
Gilbert, D.2
-
16
-
-
35248878834
-
Reasoning with temporal logic on truncated paths
-
Proceedings of Fifteenth Computer-AidedVerification conference CAV'O3, of, Springer, pp
-
Eisner,C. et al. (2003) Reasoning with temporal logic on truncated paths. In Proceedings of Fifteenth Computer-AidedVerification conference (CAV'O3). Vol. 2725 of Lecture Notes in Computer Science, Springer, pp. 27-39.
-
(2003)
Lecture Notes in Computer Science
, vol.2725
, pp. 27-39
-
-
Eisner, C.1
-
17
-
-
14544280668
-
Surviving heat shock: Control strategies for robustness and performance
-
El-Samad,H. et al. (2005) Surviving heat shock: Control strategies for robustness and performance. Proc. Natl Acad. Sci. USA, 102 2736-2741.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 2736-2741
-
-
El-Samad, H.1
-
18
-
-
0001449325
-
Temporal and modal logic
-
ed, Formal Models and Sematics, MIT Press, Cambridge, pp
-
Emerson,E.A. (1990) Temporal and modal logic. In van Leeuwen,J. ed. Handbook of Theoretical Computer Science. Vol. B: Formal Models and Sematics, MIT Press, Cambridge, pp. 995-1072.
-
(1990)
Handbook of Theoretical Computer Science
, vol.B
, pp. 995-1072
-
-
Emerson, E.A.1
-
19
-
-
54449099185
-
On temporal logic constraint solving for the analysis of numerical data time series
-
Fages,F. and Rizk,A. (2008) On temporal logic constraint solving for the analysis of numerical data time series. Theor. Comput. Sci., 408, 55-65.
-
(2008)
Theor. Comput. Sci
, vol.408
, pp. 55-65
-
-
Fages, F.1
Rizk, A.2
-
20
-
-
38049156042
-
Robustness of temporal logic specifications
-
Havelund,K. et al, eds Proceedings of International the Workshop on Formal Approaches to Software Testing and Runtime Verification, FATES/RV'06, of, Springer, Berlin, pp
-
Fainekos,G.E. and Pappas,G.J. (2006) Robustness of temporal logic specifications. In Havelund,K. et al. (eds) Proceedings of International the Workshop on Formal Approaches to Software Testing and Runtime Verification, (FATES/RV'06). Vol. 4262 of Lecture Notes in Computer Science, Springer, Berlin, pp. 178-192.
-
(2006)
Lecture Notes in Computer Science
, vol.4262
, pp. 178-192
-
-
Fainekos, G.E.1
Pappas, G.J.2
-
21
-
-
38149116993
-
Robust sampling for MITL specifications
-
Raskin,J.-F. and Thiagarajan,P, eds Proceedings of the Fifth International Conference on Formal Modeling and Analysis of Timed Systems, FORMATS'07, of, Springer, Berlin, pp
-
Fainekos,G.E. and Pappas,G.J. (2007) Robust sampling for MITL specifications. In Raskin,J.-F. and Thiagarajan,P. (eds) Proceedings of the Fifth International Conference on Formal Modeling and Analysis of Timed Systems, (FORMATS'07). Vol. 4763 of Lecture Notes in Computer Science, Springer, Berlin, pp. 147-162.
-
(2007)
Lecture Notes in Computer Science
, vol.4763
, pp. 147-162
-
-
Fainekos, G.E.1
Pappas, G.J.2
-
22
-
-
38549096995
-
Robustness and evolution: Concepts, insights and challenges from a developmental model system
-
Felix,M.-A. and Wagner,A. (2008) Robustness and evolution: Concepts, insights and challenges from a developmental model system. Heredity 100, 132-140.
-
(2008)
Heredity
, vol.100
, pp. 132-140
-
-
Felix, M.-A.1
Wagner, A.2
-
23
-
-
14844364430
-
Optimizing genetic circuits by global sensitivity analysis
-
Feng,X.-J. et al. (2004) Optimizing genetic circuits by global sensitivity analysis. Biophys. J., 87, 2195-2202.
-
(2004)
Biophys. J
, vol.87
, pp. 2195-2202
-
-
Feng, X.-J.1
-
24
-
-
0037154231
-
Robustness of circadian rhythms with respect to molecular noise
-
Gonze,D. et al. (2002) Robustness of circadian rhythms with respect to molecular noise. Proc. Natl Acad. Sci. USA, 99, 673-678.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 673-678
-
-
Gonze, D.1
-
25
-
-
0035377566
-
Completely derandomized self-adaptation in evolution strategies
-
Hansen,N. and Ostermeier,A. (2001) Completely derandomized self-adaptation in evolution strategies. Evol. Comput., 9, 159-195.
-
(2001)
Evol. Comput
, vol.9
, pp. 159-195
-
-
Hansen, N.1
Ostermeier, A.2
-
26
-
-
14844358192
-
Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
-
Hooshangi,S. et al. (2005) Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl Acad. Sci. USA, 102, 3581-3586.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 3581-3586
-
-
Hooshangi, S.1
-
27
-
-
3142517462
-
Topology and robustness in the drosophila segment polarity network
-
Ingolia,N.T. (2004) Topology and robustness in the drosophila segment polarity network. PLoS Biol., 2, e123.
-
(2004)
PLoS Biol
, vol.2
-
-
Ingolia, N.T.1
-
28
-
-
7644238181
-
Biological robustness
-
Kitano,H. (2004) Biological robustness. Nat. Rev. Genet., 11 826-837.
-
(2004)
Nat. Rev. Genet
, vol.11
, pp. 826-837
-
-
Kitano, H.1
-
29
-
-
34548825690
-
Towards a theory of biological robustness
-
Kitano,H. (2007) Towards a theory of biological robustness. Mol. Syst. Biol., 3, 137.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 137
-
-
Kitano, H.1
-
30
-
-
33846106739
-
Robustness and modular design of the drosophila segment polarity network
-
Ma,W. et al. (2006) Robustness and modular design of the drosophila segment polarity network. Mol. Syst. Biol., 2, 70.
-
(2006)
Mol. Syst. Biol
, vol.2
, pp. 70
-
-
Ma, W.1
-
31
-
-
50049096161
-
Checking temporal properties of discrete, timed and continuous behaviors
-
Avron,A. et al, eds Pillars of Computer Science, Essays Dedicated to B. Trakhtenbrot. of, Springer, pp
-
Maler,O. et al. (2008) Checking temporal properties of discrete, timed and continuous behaviors. In Avron,A. et al. (eds) Pillars of Computer Science, Essays Dedicated to B. Trakhtenbrot. Vol. 4800 of Lecture Notes in Computer Science, Springer, pp. 475-505.
-
(2008)
Lecture Notes in Computer Science
, vol.4800
, pp. 475-505
-
-
Maler, O.1
-
32
-
-
33746373126
-
Developing Itô stochastic differential equation models for neuronal signal transduction pathways
-
Manninen,T. et al. (2006) Developing Itô stochastic differential equation models for neuronal signal transduction pathways. Comp. Biol. Chem., 30, 280-291.
-
(2006)
Comp. Biol. Chem
, vol.30
, pp. 280-291
-
-
Manninen, T.1
-
33
-
-
23444461901
-
Advances in synthetic biology: On the path from prototypes to applications
-
McDaniel,R. and Weiss,R. (2005) Advances in synthetic biology: On the path from prototypes to applications. Curr. Opin. Biotechnol., 16, 476-483.
-
(2005)
Curr. Opin. Biotechnol
, vol.16
, pp. 476-483
-
-
McDaniel, R.1
Weiss, R.2
-
34
-
-
38149086757
-
AMT: A property-based monitoring tool for analog systems
-
Raskin,J.-F. and Thiagarajan,P.S, eds) Proceedings of conference on Formal Modeling and Analysis of Timed Systems FORMAT'07, of, Springer, Berlin, pp
-
Nickovic,D. and Maler,O. (2007) AMT: A property-based monitoring tool for analog systems. In Raskin,J.-F. and Thiagarajan,P.S. (eds) Proceedings of conference on Formal Modeling and Analysis of Timed Systems (FORMAT'07). Vol. 4763 of Lecture Notes in Computer Sciences, Springer, Berlin, pp. 304-319.
-
(2007)
Lecture Notes in Computer Sciences
, vol.4763
, pp. 304-319
-
-
Nickovic, D.1
Maler, O.2
-
35
-
-
57049127120
-
On a continuous degree of satisfaction of temporal logic formulae with applications to systems biology
-
Heiner,M. and Uhrmacher,A, eds) Proceedings of the Fourth International Conference on Computational Methods in Systems Biology CMSB'08, of, Springer, Berlin, pp
-
Rizk,A. et al. (2008) On a continuous degree of satisfaction of temporal logic formulae with applications to systems biology. In Heiner,M. and Uhrmacher,A. (eds) Proceedings of the Fourth International Conference on Computational Methods in Systems Biology (CMSB'08). Vol. 5307 of Lecture Notes in Computer Science, Springer, Berlin, pp. 251-268.
-
(2008)
Lecture Notes in Computer Science
, vol.5307
, pp. 251-268
-
-
Rizk, A.1
-
37
-
-
49649109935
-
Architecture and inherent robustness of a bacterial cell-cycle control system
-
Shen,X. et al. (2008) Architecture and inherent robustness of a bacterial cell-cycle control system. Proc. Natl Acad. Sci. USA, 105, 11340-11345.
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 11340-11345
-
-
Shen, X.1
-
38
-
-
36749094352
-
Input-output robustness in simple bacterial signaling systems
-
Shinar,G. et al. (2007) Input-output robustness in simple bacterial signaling systems. Proc. Natl Acad. Sci. USA, 104, 19931-19935.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 19931-19935
-
-
Shinar, G.1
-
39
-
-
4544346660
-
Robustness of cellular functions
-
Stelling,J. et al. (2004a) Robustness of cellular functions. Cell, 118, 675-685.
-
(2004)
Cell
, vol.118
, pp. 675-685
-
-
Stelling, J.1
-
40
-
-
4444322221
-
Robustness properties of circadian clock architectures
-
Stelling,J. et al. (2004b) Robustness properties of circadian clock architectures. Proc. Natl Acad. Sci. USA, 101, 13210-13215.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 13210-13215
-
-
Stelling, J.1
-
41
-
-
39149113411
-
Modular cell biology: Retroactivity and insulation
-
Vecchio,D.D. et al. (2008) Modular cell biology: Retroactivity and insulation. Mol. Syst. Biol., 4, 161.
-
(2008)
Mol. Syst. Biol
, vol.4
, pp. 161
-
-
Vecchio, D.D.1
-
42
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
von Dassow,G. et al. (2000) The segment polarity network is a robust developmental module. Nature, 406, 188-192.
-
(2000)
Nature
, vol.406
, pp. 188-192
-
-
von Dassow, G.1
-
43
-
-
0034712843
-
Robust perfect adaptation in bacterial chemotaxis through integral feedback control
-
Yi,T. et al. (2000) Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc. Natl Acad. Sci. USA, 97, 4649-4653.
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 4649-4653
-
-
Yi, T.1
|