-
1
-
-
33750314698
-
Collecting and organizing systematic sets of protein data
-
Albeck, J. G., MacBeath, G., White, F. M., Sorger, P. K., Lauffenburger, D. A. and Gaudet, S. (2006). Collecting and organizing systematic sets of protein data. Nat. Rev. Mol. Cell Biol. 7, 803-812.
-
(2006)
Nat. Rev. Mol. Cell Biol
, vol.7
, pp. 803-812
-
-
Albeck, J.G.1
MacBeath, G.2
White, F.M.3
Sorger, P.K.4
Lauffenburger, D.A.5
Gaudet, S.6
-
2
-
-
33845200552
-
Stronger computational modelling of signalling pathways using both continuous and discrete-state methods
-
Computational Methods in Systems Biology , ed. C. Priami, pp, Berlin: Springer
-
Calder, M., Duguid, A., Gilmore, S. and Hillston, J. (2006a). Stronger computational modelling of signalling pathways using both continuous and discrete-state methods. In Computational Methods in Systems Biology (Lecture Notes in Computer Science, Vol. 4210) (ed. C. Priami), pp. 63-77. Berlin: Springer.
-
(2006)
Lecture Notes in Computer Science
, vol.4210
, pp. 63-77
-
-
Calder, M.1
Duguid, A.2
Gilmore, S.3
Hillston, J.4
-
3
-
-
38549120134
-
Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA
-
VII 4230, 1-23
-
Calder, M., Gilmore, S. and Hillston, J. (2006b). Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA. Trans. Comput. Syst. Biol. VII 4230, 1-23.
-
(2006)
Trans. Comput. Syst. Biol
-
-
Calder, M.1
Gilmore, S.2
Hillston, J.3
-
4
-
-
43049179364
-
Bio-PEPA: An extension of the process algebra PEPA for biochemical networks
-
Ciocchetta, F. and Hillston, J. (2008). Bio-PEPA: an extension of the process algebra PEPA for biochemical networks. Electr. Notes Theor. Comput. Sci. 194, 103-117.
-
(2008)
Electr. Notes Theor. Comput. Sci
, vol.194
, pp. 103-117
-
-
Ciocchetta, F.1
Hillston, J.2
-
5
-
-
38949133783
-
An automatic translation of SBML into beta-binders
-
Ciocchetta, F., Priami, C. and Quaglia, P. (2008). An automatic translation of SBML into beta-binders. IEEE/ACM Trans. Comput. Biol. Bioinform. 5, 80-90.
-
(2008)
IEEE/ACM Trans. Comput. Biol. Bioinform
, vol.5
, pp. 80-90
-
-
Ciocchetta, F.1
Priami, C.2
Quaglia, P.3
-
7
-
-
34047105227
-
Explaining a complex living system: Dynamics, multiscaling and emergence
-
Cohen, I. R. and Harel, D. (2007). Explaining a complex living system: dynamics, multiscaling and emergence. J. R. Soc. Interface 4, 175-182.
-
(2007)
J. R. Soc. Interface
, vol.4
, pp. 175-182
-
-
Cohen, I.R.1
Harel, D.2
-
8
-
-
38149083357
-
Rule-based modelling of cellular signalling
-
Concur 2007, Berlin: Springer
-
Danos, V., Feret, J., Fontana, W., Harmer, R. and Krivine, J. (2007). Rule-based modelling of cellular signalling. In Concur 2007 (Lecture Notes in Computer Science, Vol. 4703), pp. 17-41. Berlin: Springer.
-
(2007)
Lecture Notes in Computer Science
, vol.4703
, pp. 17-41
-
-
Danos, V.1
Feret, J.2
Fontana, W.3
Harmer, R.4
Krivine, J.5
-
9
-
-
49949112078
-
The Beta Workbench: A tool to study the dynamics of biological systems
-
Dematte, L., Priami, C. and Romanel, A. (2008). The Beta Workbench: a tool to study the dynamics of biological systems. Brief. Bioinformatics 9, 437-449.
-
(2008)
Brief. Bioinformatics
, vol.9
, pp. 437-449
-
-
Dematte, L.1
Priami, C.2
Romanel, A.3
-
10
-
-
48249142459
-
-
Deutscher, D., Meilijson, I., Schuster, S. and Ruppin, E. (2008). Can single knockouts accurately single out gene functions? BMC Syst. Biol. 2, 50.
-
Deutscher, D., Meilijson, I., Schuster, S. and Ruppin, E. (2008). Can single knockouts accurately single out gene functions? BMC Syst. Biol. 2, 50.
-
-
-
-
12
-
-
13844309568
-
Computational insights into Caenorhabditis elegans vulval development
-
Fisher, J., Piterman, N., Hubbard, E. J., Stern, M. J. and Harel, D. (2005). Computational insights into Caenorhabditis elegans vulval development. Proc. Natl. Acad. Sci. USA 102, 1951-1956.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 1951-1956
-
-
Fisher, J.1
Piterman, N.2
Hubbard, E.J.3
Stern, M.J.4
Harel, D.5
-
13
-
-
34249725570
-
Predictive modeling of signaling crosstalk during C. elegans vulval development
-
Fisher, J., Piterman, N., Hajnal, A. and Henzinger, T. A. (2007). Predictive modeling of signaling crosstalk during C. elegans vulval development. PLoS Comput. Biol. 3, e92.
-
(2007)
PLoS Comput. Biol
, vol.3
-
-
Fisher, J.1
Piterman, N.2
Hajnal, A.3
Henzinger, T.A.4
-
14
-
-
55349146959
-
A mass action model of a fibroblast growth factor signaling pathway and its simplification
-
Gaffney, E., Heath, J. K. and Kwiatkowska, M. Z. (2008). A mass action model of a fibroblast growth factor signaling pathway and its simplification. Bull. Math. Biol. 70, 2229-2263.
-
(2008)
Bull. Math. Biol
, vol.70
, pp. 2229-2263
-
-
Gaffney, E.1
Heath, J.K.2
Kwiatkowska, M.Z.3
-
15
-
-
34547402660
-
The theory of facilitated variation
-
Gerhart, J. and Kirschner, M. (2007). The theory of facilitated variation. Proc. Natl. Acad. Sci. USA 104 Suppl. 1, 8582-8589.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, Issue.SUPPL. 1
, pp. 8582-8589
-
-
Gerhart, J.1
Kirschner, M.2
-
16
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361.
-
(1977)
J. Phys. Chem
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
17
-
-
38049169080
-
An automated translation from a narrative language for biological modeling into process algebra
-
Computational Methods in Systems Biology , ed. M. Calder and S. Gilmore, pp, Berlin: Springer
-
Guerriero, M. L., Heath, J. K. and Priami, C. (2007). An automated translation from a narrative language for biological modeling into process algebra. In Computational Methods in Systems Biology (Lecture Notes in Computer Science, Vol. 4695) (ed. M. Calder and S. Gilmore), pp. 136-151. Berlin: Springer.
-
(2007)
Lecture Notes in Computer Science
, vol.4695
, pp. 136-151
-
-
Guerriero, M.L.1
Heath, J.K.2
Priami, C.3
-
18
-
-
65549137015
-
-
Guerriero, M. L., Dudka, A., Underhill-Day, N., Heath, J. K. and Priami, C. (2009). Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway. BMC Syst. Biol. 3, 40.
-
Guerriero, M. L., Dudka, A., Underhill-Day, N., Heath, J. K. and Priami, C. (2009). Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway. BMC Syst. Biol. 3, 40.
-
-
-
-
19
-
-
67249124193
-
Approximate parameter synthesis for probabilistic time-bounded reachability
-
RTSS, pp, Piscataway, NJ: IEEE
-
Han, T., Katoen, J. P. and Mereacre, A. (2008). Approximate parameter synthesis for probabilistic time-bounded reachability. In Proceedings of the Real-Time Systems Symposium (RTSS), pp. 173-182. Piscataway, NJ: IEEE.
-
(2008)
Proceedings of the Real-Time Systems Symposium
, pp. 173-182
-
-
Han, T.1
Katoen, J.P.2
Mereacre, A.3
-
20
-
-
2542433976
-
Shp2, an SH2-containing protein-tyrosine phosphatase, positively regulates receptor tyrosine kinase signaling by dephosphorylating and inactivating the inhibitor Sprouty
-
Hanafusa, H., Torii, S., Yasunaga, T., Matsumoto, K. and Nishida, E. (2004). Shp2, an SH2-containing protein-tyrosine phosphatase, positively regulates receptor tyrosine kinase signaling by dephosphorylating and inactivating the inhibitor Sprouty. J. Biol. Chem. 279, 22992-22995.
-
(2004)
J. Biol. Chem
, vol.279
, pp. 22992-22995
-
-
Hanafusa, H.1
Torii, S.2
Yasunaga, T.3
Matsumoto, K.4
Nishida, E.5
-
21
-
-
0023365727
-
Statecharts: A visual formalism for complex systems
-
Harel, D. (1987). Statecharts: a visual formalism for complex systems. Sci. Comput. Program 8, 231-274.
-
(1987)
Sci. Comput. Program
, vol.8
, pp. 231-274
-
-
Harel, D.1
-
22
-
-
23644440995
-
A Turing-like test for biological modeling
-
Harel, D. (2005). A Turing-like test for biological modeling. Nat. Biotechnol. 23, 495-496.
-
(2005)
Nat. Biotechnol
, vol.23
, pp. 495-496
-
-
Harel, D.1
-
23
-
-
38649122071
-
Probabilistic model checking of complex biological pathways
-
Heath, J., Kwiatkowska, M., Norman, G., Parker, D. and Tymchyshyn, O. (2007). Probabilistic model checking of complex biological pathways. Theor. Comput. Sci. 391, 239-257.
-
(2007)
Theor. Comput. Sci
, vol.391
, pp. 239-257
-
-
Heath, J.1
Kwiatkowska, M.2
Norman, G.3
Parker, D.4
Tymchyshyn, O.5
-
25
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A. et al. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
-
26
-
-
46949111947
-
Dichotomies between computational and mathematical models
-
Hunt, C. A., Ropella, G. E., Park, S. and Engeleberg, J. (2008). Dichotomies between computational and mathematical models. Nat. Biotechnol. 26, 737-738.
-
(2008)
Nat. Biotechnol
, vol.26
, pp. 737-738
-
-
Hunt, C.A.1
Ropella, G.E.2
Park, S.3
Engeleberg, J.4
-
27
-
-
38049154228
-
Simulation and verification for computational modelling of signalling pathways
-
Piscataway, NJ: IEEE
-
Kwiatkowska, M., Norman, G., Parker, D., Tymchyshyn, O., Heath, J. and Gaffney, E. (2006). Simulation and verification for computational modelling of signalling pathways. In Proceedings of the Winter Simulation Symposium on Modelling and Simulation in Systems Biology, pp. 1666-1674. Piscataway, NJ: IEEE.
-
(2006)
Proceedings of the Winter Simulation Symposium on Modelling and Simulation in Systems Biology
, pp. 1666-1674
-
-
Kwiatkowska, M.1
Norman, G.2
Parker, D.3
Tymchyshyn, O.4
Heath, J.5
Gaffney, E.6
-
28
-
-
34548060449
-
Stochastic model checking
-
Formal Methods for Performance Evaluation: 7th International School on Formal Methods for the Design of Computer, Communication and Software Systems , ed. M. Bernardo and J. Hillston, pp, Berlin: Springer
-
Kwiatkowska, M., Norman, G. and Parker, D. (2007). Stochastic model checking. In Formal Methods for Performance Evaluation: 7th International School on Formal Methods for the Design of Computer, Communication and Software Systems (SFM 2007 Advanced Lecture Notes in Computer Science, Vol. 4486) (ed. M. Bernardo and J. Hillston), pp. 220-270. Berlin: Springer.
-
(2007)
SFM 2007 Advanced Lecture Notes in Computer Science
, vol.4486
, pp. 220-270
-
-
Kwiatkowska, M.1
Norman, G.2
Parker, D.3
-
29
-
-
40449107017
-
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes
-
McGary, K. L., Lee, I. and Marcotte, E. M. (2007). Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biol. 8, R258.
-
(2007)
Genome Biol
, vol.8
-
-
McGary, K.L.1
Lee, I.2
Marcotte, E.M.3
-
31
-
-
44049113210
-
A calculus of mobile processes, Pts 1 and 2
-
Milner, R., Parrow, J. and Walker, D. (1992). A calculus of mobile processes, Pts 1 and 2. Inf. Comput. 100, 1-40.
-
(1992)
Inf. Comput
, vol.100
, pp. 1-40
-
-
Milner, R.1
Parrow, J.2
Walker, D.3
-
32
-
-
48349105261
-
WikiPathways: Pathway editing for the people
-
Pico, A. R., Kelder, T., van Iersel, M. P., Hanspers, K., Conklin, B. R. and Evelo, C. (2008). WikiPathways: pathway editing for the people. PLoS Biol. 6, 1403-1407.
-
(2008)
PLoS Biol
, vol.6
, pp. 1403-1407
-
-
Pico, A.R.1
Kelder, T.2
van Iersel, M.P.3
Hanspers, K.4
Conklin, B.R.5
Evelo, C.6
-
33
-
-
67049143968
-
Algorithmic systems biology: An opportunity for computer science
-
Priami, C. (2009). Algorithmic systems biology: an opportunity for computer science. Commun. ACM 52, 80-88.
-
(2009)
Commun. ACM
, vol.52
, pp. 80-88
-
-
Priami, C.1
-
34
-
-
26444448026
-
Beta binders for biological interactions
-
Computational Methods in Systems Biology , ed. D. Vincent and S. Vincent, pp, Berlin: Springer
-
Priami, C. and Quaglia, P. (2005). Beta binders for biological interactions. In Computational Methods in Systems Biology (Lecture Notes in Computer Science, Vol. 3082) (ed. D. Vincent and S. Vincent), pp. 20-33. Berlin: Springer.
-
(2005)
Lecture Notes in Computer Science
, vol.3082
, pp. 20-33
-
-
Priami, C.1
Quaglia, P.2
-
35
-
-
0035888407
-
Application of a stochastic name-passing calculus to representation and simulation of molecular processes
-
Priami, C., Regev, A., Shapiro, E. and Silverman, W. (2001). Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inf. Process. Letters 80, 25-31.
-
(2001)
Inf. Process. Letters
, vol.80
, pp. 25-31
-
-
Priami, C.1
Regev, A.2
Shapiro, E.3
Silverman, W.4
-
36
-
-
0037179670
-
Cells as computation
-
Regev, A. and Shapiro, E. (2002). Cells as computation. Nature 419, 343.
-
(2002)
Nature
, vol.419
, pp. 343
-
-
Regev, A.1
Shapiro, E.2
-
37
-
-
0035235039
-
Representation and simulation of biochemical processes using the pi-calculus process algebra
-
Regev, A., Silverman, W. and Shapiro, E. (2001). Representation and simulation of biochemical processes using the pi-calculus process algebra. Pac. Symp. Biocomput. 2001, 459-470.
-
(2001)
Pac. Symp. Biocomput
, vol.2001
, pp. 459-470
-
-
Regev, A.1
Silverman, W.2
Shapiro, E.3
-
38
-
-
4444383325
-
Bioambients: An abstraction for biological compartments
-
Regev, A., Panina, E. M., Silverman, W., Cardelli, L. and Shapiro, E. (2004). Bioambients: an abstraction for biological compartments. Theor. Comput. Sci. 2004, 141-167.
-
(2004)
Theor. Comput. Sci
, vol.2004
, pp. 141-167
-
-
Regev, A.1
Panina, E.M.2
Silverman, W.3
Cardelli, L.4
Shapiro, E.5
-
39
-
-
36748999354
-
Src kinase modulates the activation, transport and signalling dynamics of fibroblast growth factor receptors
-
Sandilands, E., Akbarzadeh, S., Vecchione, A., McEwan, D. G., Frame, M. C. and Heath, J. K. (2007). Src kinase modulates the activation, transport and signalling dynamics of fibroblast growth factor receptors. EMBO Rep. 8, 1162-1169.
-
(2007)
EMBO Rep
, vol.8
, pp. 1162-1169
-
-
Sandilands, E.1
Akbarzadeh, S.2
Vecchione, A.3
McEwan, D.G.4
Frame, M.C.5
Heath, J.K.6
-
40
-
-
0024309272
-
The combined action of two intercellular signaling pathways specifies three cell fates during vulval induction in C. elegans
-
Sternberg, P. W. and Horvitz, H. R. (1989). The combined action of two intercellular signaling pathways specifies three cell fates during vulval induction in C. elegans. Cell 58, 679-693.
-
(1989)
Cell
, vol.58
, pp. 679-693
-
-
Sternberg, P.W.1
Horvitz, H.R.2
-
42
-
-
34347329333
-
In search of the biological significance of modular structures in protein networks
-
Wang, Z. and Zhang, J. (2007). In search of the biological significance of modular structures in protein networks. PLoS Comput. Biol. 3, 1011-1021.
-
(2007)
PLoS Comput. Biol
, vol.3
, pp. 1011-1021
-
-
Wang, Z.1
Zhang, J.2
|