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Items: 1 to 20 of 30

1.

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
2.

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
3.

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.

4.

Computational modeling of the EGF-receptor system: a paradigm for systems biology.

Wiley HS, Shvartsman SY, Lauffenburger DA.

Trends Cell Biol. 2003 Jan;13(1):43-50. Review.

PMID:
12480339
5.

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
6.

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
7.

Computational modeling of signal transduction networks: a pedagogical exposition.

Prasad A.

Methods Mol Biol. 2012;880:219-41. doi: 10.1007/978-1-61779-833-7_10. Review.

PMID:
23361987
8.

Detecting structural invariants in biological reaction networks.

Behre J, de Figueiredo LF, Schuster S, Kaleta C.

Methods Mol Biol. 2012;804:377-407. doi: 10.1007/978-1-61779-361-5_20. Review.

PMID:
22144164
9.

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.

PMID:
17107967
10.

SBMLmerge, a system for combining biochemical network models.

Schulz M, Uhlendorf J, Klipp E, Liebermeister W.

Genome Inform. 2006;17(1):62-71. Review.

PMID:
17503356
11.

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
12.

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways.

Breitling R, Gilbert D, Heiner M, Orton R.

Brief Bioinform. 2008 Sep;9(5):404-21. doi: 10.1093/bib/bbn026. Epub 2008 Jun 23. Review.

PMID:
18573813
13.

Toward large-scale modeling of the microbial cell for computer simulation.

Ishii N, Robert M, Nakayama Y, Kanai A, Tomita M.

J Biotechnol. 2004 Sep 30;113(1-3):281-94. Review.

PMID:
15380661
14.

Computational methodologies for modelling, analysis and simulation of signalling networks.

Gilbert D, Fuss H, Gu X, Orton R, Robinson S, Vyshemirsky V, Kurth MJ, Downes CS, Dubitzky W.

Brief Bioinform. 2006 Dec;7(4):339-53. Epub 2006 Nov 20. Review.

PMID:
17116646
15.

Current challenges in quantitative modeling of epidermal growth factor signaling.

Breitling R, Hoeller D.

FEBS Lett. 2005 Nov 21;579(28):6289-94. Epub 2005 Nov 2. Review.

16.

The executable pathway to biological networks.

Fisher J, Piterman N.

Brief Funct Genomics. 2010 Jan;9(1):79-92. doi: 10.1093/bfgp/elp054. Review.

17.

Modeling metabolic networks for mammalian cell systems: general considerations, modeling strategies, and available tools.

Gerdtzen ZP.

Adv Biochem Eng Biotechnol. 2012;127:71-108. doi: 10.1007/10_2011_120. Review.

PMID:
21984615
18.

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
19.

Multiscale modeling for biologists.

Meier-Schellersheim M, Fraser ID, Klauschen F.

Wiley Interdiscip Rev Syst Biol Med. 2009 Jul-Aug;1(1):4-14. doi: 10.1002/wsbm.33. Review.

20.

Challenges in structural approaches to cell modeling.

Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA.

J Mol Biol. 2016 Jul 31;428(15):2943-64. doi: 10.1016/j.jmb.2016.05.024. Epub 2016 May 30. Review.

PMID:
27255863

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