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Items: 1 to 20 of 75

1.

In silico generation of alternative hypotheses using causal mapping (CMAP).

Weinreb GE, Kapustina MT, Jacobson K, Elston TC.

PLoS One. 2009;4(4):e5378. doi: 10.1371/journal.pone.0005378. Epub 2009 Apr 29.

2.
3.

A system biology approach to understand functional activity of cell communication systems.

Vera J, Wolkenhauer O.

Methods Cell Biol. 2008;90:399-415. doi: 10.1016/S0091-679X(08)00817-0.

PMID:
19195559
4.

Boolean modeling in systems biology: an overview of methodology and applications.

Wang RS, Saadatpour A, Albert R.

Phys Biol. 2012 Oct;9(5):055001. doi: 10.1088/1478-3975/9/5/055001. Epub 2012 Sep 25. Review.

PMID:
23011283
5.

Qualitative networks: a symbolic approach to analyze biological signaling networks.

Schaub MA, Henzinger TA, Fisher J.

BMC Syst Biol. 2007 Jan 8;1:4.

6.

Dynamic simulation of regulatory networks using SQUAD.

Di Cara A, Garg A, De Micheli G, Xenarios I, Mendoza L.

BMC Bioinformatics. 2007 Nov 26;8:462.

7.
8.

Discrete dynamic modeling of cellular signaling networks.

Albert R, Wang RS.

Methods Enzymol. 2009;467:281-306. doi: 10.1016/S0076-6879(09)67011-7.

PMID:
19897097
9.

Visinets: a web-based pathway modeling and dynamic visualization tool.

Spychala J, Spychala P, Gomez S, Weinreb GE.

PLoS One. 2015 May 28;10(5):e0123773. doi: 10.1371/journal.pone.0123773. eCollection 2015.

10.

Network modeling of signal transduction: establishing the global view.

Kestler HA, Wawra C, Kracher B, Kühl M.

Bioessays. 2008 Nov;30(11-12):1110-25. doi: 10.1002/bies.20834. Review.

PMID:
18937364
11.

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling.

Wittmann DM, Krumsiek J, Saez-Rodriguez J, Lauffenburger DA, Klamt S, Theis FJ.

BMC Syst Biol. 2009 Sep 28;3:98. doi: 10.1186/1752-0509-3-98.

12.

Proteomic and computational methods in systems modeling of cellular signaling.

Kleppe R, Kjarland E, Selheim F.

Curr Pharm Biotechnol. 2006 Jun;7(3):135-45. Review.

PMID:
16789899
13.

DEEP--a tool for differential expression effector prediction.

Degenhardt J, Haubrock M, Dönitz J, Wingender E, Crass T.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W619-24. Epub 2007 Jun 21.

14.

A computational tool for Monte Carlo simulations of biomolecular reaction networks modeled on physical principles.

Li IT, Mills E, Truong K.

IEEE Trans Nanobioscience. 2010 Mar;9(1):24-30. doi: 10.1109/TNB.2009.2035114. Epub 2009 Nov 3.

PMID:
19887331
15.

Computational modeling of biological pathways by executable biology.

Guerriero ML, Heath JK.

Methods Enzymol. 2011;487:217-51. doi: 10.1016/B978-0-12-381270-4.00008-1.

PMID:
21187227
16.

Use of randomized sampling for analysis of metabolic networks.

Schellenberger J, Palsson BØ.

J Biol Chem. 2009 Feb 27;284(9):5457-61. doi: 10.1074/jbc.R800048200. Epub 2008 Oct 20. Review.

17.
18.

From reaction networks to information flow--using modular response analysis to track information in signaling networks.

Schulthess P, Blüthgen N.

Methods Enzymol. 2011;500:397-409. doi: 10.1016/B978-0-12-385118-5.00020-7.

PMID:
21943908
19.

Bioinformatics analyses for signal transduction networks.

Liu W, Li D, Zhu Y, He F.

Sci China C Life Sci. 2008 Nov;51(11):994-1002. doi: 10.1007/s11427-008-0134-5. Epub 2008 Nov 7.

PMID:
18989642
20.

Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments.

van Riel NA.

Brief Bioinform. 2006 Dec;7(4):364-74. Epub 2006 Nov 14. Review.

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