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Items: 1 to 20 of 112

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. Epub 2009 Feb 11.

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. Epub 2004 Jun 24.

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. Epub 2013 Sep 30. 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.

Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules.

Suderman R, Fricke GM, Hlavacek WS.

Methods Mol Biol. 2019;1945:33-42. doi: 10.1007/978-1-4939-9102-0_2.

PMID:
30945241
11.

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.

12.

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
13.

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.

14.

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
15.

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. Epub 2006 Oct 10.

PMID:
17032683
16.

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
17.

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
18.

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.

19.

Encoding the states of interacting proteins to facilitate biological pathways reconstruction.

Termanini A, Tieri P, Franceschi C.

Biol Direct. 2010 Aug 13;5:52; discussion 52. doi: 10.1186/1745-6150-5-52.

20.

Bioinformatics, multiscale modeling and the IUPS Physiome Project.

Hunter PJ, Crampin EJ, Nielsen PM.

Brief Bioinform. 2008 Jul;9(4):333-43. doi: 10.1093/bib/bbn024. Epub 2008 May 13.

PMID:
18477639

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