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Items: 1 to 20 of 23

1.

The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail.

Kolczyk K, Samaga R, Conzelmann H, Mirschel S, Conradi C.

BMC Bioinformatics. 2012 Sep 28;13:251. doi: 10.1186/1471-2105-13-251.

2.

Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways.

Alves R, Vilaprinyo E, Hernádez-Bermejo B, Sorribas A.

Biotechnol Genet Eng Rev. 2008;25:1-40. Review.

PMID:
21412348
3.

Rule-based modeling of signal transduction: a primer.

Sekar JA, Faeder JR.

Methods Mol Biol. 2012;880:139-218. doi: 10.1007/978-1-61779-833-7_9. Review.

PMID:
23361986
4.

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.

Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS.

Wiley Interdiscip Rev Syst Biol Med. 2014 Jan-Feb;6(1):13-36. doi: 10.1002/wsbm.1245. Epub 2013 Sep 30. Review.

5.

State-time spectrum of signal transduction logic models.

MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J.

Phys Biol. 2012 Aug;9(4):045003. doi: 10.1088/1478-3975/9/4/045003. Epub 2012 Aug 7. Review.

PMID:
22871648
6.

Discrete dynamic modeling of signal transduction networks.

Saadatpour A, Albert R.

Methods Mol Biol. 2012;880:255-72. doi: 10.1007/978-1-61779-833-7_12. Review.

PMID:
23361989
7.

Discrete, qualitative models of interaction networks.

Ballerstein K, Haus UU, Lindquist JA, Beyer T, Schraven B, Weismantel R.

Front Biosci (Schol Ed). 2013 Jan 1;5:149-66. Review.

PMID:
23277042
8.

Metabolic networks: a signal-oriented approach to cellular models.

Lengeler JW.

Biol Chem. 2000 Sep-Oct;381(9-10):911-20. Review.

PMID:
11076022
9.

Understanding complex signaling networks through models and metaphors.

Bhalla US.

Prog Biophys Mol Biol. 2003 Jan;81(1):45-65. Review.

PMID:
12475569
10.

Rules for modeling signal-transduction systems.

Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W.

Sci STKE. 2006 Jul 18;2006(344):re6. Review.

PMID:
16849649
11.

Representation, simulation, and hypothesis generation in graph and logical models of biological networks.

Whelan K, Ray O, King RD.

Methods Mol Biol. 2011;759:465-82. doi: 10.1007/978-1-61779-173-4_26. Review.

PMID:
21863503
12.

A tutorial on mathematical modeling of biological signaling pathways.

Zi Z.

Methods Mol Biol. 2012;880:41-51. doi: 10.1007/978-1-61779-833-7_3. Review.

PMID:
23361980
13.

Computational modeling of the main signaling pathways involved in mast cell activation.

Niarakis A, Bounab Y, Grieco L, Roncagalli R, Hesse AM, Garin J, Malissen B, Daëron M, Thieffry D.

Curr Top Microbiol Immunol. 2014;382:69-93. doi: 10.1007/978-3-319-07911-0_4. Review.

PMID:
25116096
14.

Bioengineering models of cell signaling.

Asthagiri AR, Lauffenburger DA.

Annu Rev Biomed Eng. 2000;2:31-53. Review.

PMID:
11701506
15.

Logic-based models for the analysis of cell signaling networks.

Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA.

Biochemistry. 2010 Apr 20;49(15):3216-24. doi: 10.1021/bi902202q. Review.

16.

Logical Modeling and Dynamical Analysis of Cellular Networks.

Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C.

Front Genet. 2016 May 31;7:94. doi: 10.3389/fgene.2016.00094. eCollection 2016. Review.

17.

Modeling for (physical) biologists: an introduction to the rule-based approach.

Chylek LA, Harris LA, Faeder JR, Hlavacek WS.

Phys Biol. 2015 Jul 16;12(4):045007. doi: 10.1088/1478-3975/12/4/045007. Review.

18.

Design of experiments to investigate dynamic cell signaling models.

Bandara S, Meyer T.

Methods Mol Biol. 2012;880:109-18. doi: 10.1007/978-1-61779-833-7_7. Review.

PMID:
23361984
19.

Toward a comprehensive language for biological systems.

Faeder JR.

BMC Biol. 2011 Oct 17;9:68. doi: 10.1186/1741-7007-9-68. Review.

20.

The (Mathematical) Modeling Process in Biosciences.

Torres NV, Santos G.

Front Genet. 2015 Dec 22;6:354. doi: 10.3389/fgene.2015.00354. eCollection 2015. Review.

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