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Items: 1 to 20 of 97

1.

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
2.

Simulation of large-scale rule-based models.

Colvin J, Monine MI, Faeder JR, Hlavacek WS, Von Hoff DD, Posner RG.

Bioinformatics. 2009 Apr 1;25(7):910-7. doi: 10.1093/bioinformatics/btp066.

3.

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.

Blinov ML, Faeder JR, Goldstein B, Hlavacek WS.

Bioinformatics. 2004 Nov 22;20(17):3289-91.

PMID:
15217809
4.

RuleMonkey: software for stochastic simulation of rule-based models.

Colvin J, Monine MI, Gutenkunst RN, Hlavacek WS, Von Hoff DD, Posner RG.

BMC Bioinformatics. 2010 Jul 30;11:404. doi: 10.1186/1471-2105-11-404.

5.

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. Review.

6.

Rule-based modeling of biochemical systems with BioNetGen.

Faeder JR, Blinov ML, Hlavacek WS.

Methods Mol Biol. 2009;500:113-67. doi: 10.1007/978-1-59745-525-1_5.

PMID:
19399430
7.

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
8.

Leveraging modeling approaches: reaction networks and rules.

Blinov ML, Moraru II.

Adv Exp Med Biol. 2012;736:517-30. doi: 10.1007/978-1-4419-7210-1_30.

9.

Reduced modeling of signal transduction - a modular approach.

Koschorreck M, Conzelmann H, Ebert S, Ederer M, Gilles ED.

BMC Bioinformatics. 2007 Sep 13;8:336.

10.

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling.

Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, Berens ME, Han H, Bussey KJ, Von Hoff DD, Hlavacek WS, Posner RG.

BMC Syst Biol. 2012 Aug 22;6:107. doi: 10.1186/1752-0509-6-107.

11.

Intrinsic information carriers in combinatorial dynamical systems.

Harmer R, Danos V, Feret J, Krivine J, Fontana W.

Chaos. 2010 Sep;20(3):037108. doi: 10.1063/1.3491100.

PMID:
20887074
12.

ProtNet: a tool for stochastic simulations of protein interaction networks dynamics.

Bernaschi M, Castiglione F, Ferranti A, Gavrila C, Tinti M, Cesareni G.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S4.

13.

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.

14.

Engineering Aspects of Olfaction.

Persaud KC.

In: Persaud KC, Marco S, Gutiérrez-Gálvez A, editors. Neuromorphic Olfaction. Boca Raton (FL): CRC Press/Taylor & Francis; 2013. Chapter 1.

15.

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
16.

COPASI--a COmplex PAthway SImulator.

Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U.

Bioinformatics. 2006 Dec 15;22(24):3067-74.

PMID:
17032683
17.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

Ueno Y, Ito S, Konagaya A.

J Bioinform Comput Biol. 2014 Dec;12(6):1442003. doi: 10.1142/S0219720014420037.

PMID:
25385079
18.

A rule-based detection of functional modules in protein-protein interaction networks.

Park J, Choi J, Yang J, Park SJ.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:5810-3.

PMID:
17946335
19.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.

Bortfeldt RH, Schuster S, Koch I.

In Silico Biol. 2010;10(1):89-123. doi: 10.3233/ISB-2010-0419.

PMID:
22430224
20.

NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules.

Cheng HC, Angermann BR, Zhang F, Meier-Schellersheim M.

BMC Syst Biol. 2014 Jun 16;8:70. doi: 10.1186/1752-0509-8-70.

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