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Items: 1 to 20 of 46

1.

The markup is the model: reasoning about systems biology models in the Semantic Web era.

Kell DB, Mendes P.

J Theor Biol. 2008 Jun 7;252(3):538-43. Epub 2007 Dec 3. Review.

PMID:
18054049
2.

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

Hucka M, Finney A, Bornstein BJ, Keating SM, Shapiro BE, Matthews J, Kovitz BL, Schilstra MJ, Funahashi A, Doyle JC, Kitano H.

Syst Biol (Stevenage). 2004 Jun;1(1):41-53. Review.

PMID:
17052114
3.

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
4.

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
5.

Representing, storing and accessing molecular interaction data: a review of models and tools.

Strömbäck L, Jakoniene V, Tan H, Lambrix P.

Brief Bioinform. 2006 Dec;7(4):331-8. Review.

6.

Automation of in-silico data analysis processes through workflow management systems.

Romano P.

Brief Bioinform. 2008 Jan;9(1):57-68. Epub 2007 Dec 2. Review.

PMID:
18056132
7.

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
8.

Use of genome-scale metabolic models in evolutionary systems biology.

Papp B, Szappanos B, Notebaart RA.

Methods Mol Biol. 2011;759:483-97. doi: 10.1007/978-1-61779-173-4_27. Review.

PMID:
21863504
9.

Systems biology approaches and pathway tools for investigating cardiovascular disease.

Wheelock CE, Wheelock AM, Kawashima S, Diez D, Kanehisa M, van Erk M, Kleemann R, Haeggström JZ, Goto S.

Mol Biosyst. 2009 Jun;5(6):588-602. doi: 10.1039/b902356a. Epub 2009 Apr 27. Review.

PMID:
19462016
10.

Systems biology model databases and resources.

van Gend C, Snoep JL.

Essays Biochem. 2008;45:223-36. doi: 10.1042/BSE0450223. Review.

PMID:
18793135
11.

Standards, tools, and databases for the analysis of yeast 'omics data.

Kowald A, Wierling C.

Methods Mol Biol. 2011;759:345-65. doi: 10.1007/978-1-61779-173-4_20. Review.

PMID:
21863497
12.

Designing and encoding models for synthetic biology.

Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C, Le Novère N.

J R Soc Interface. 2009 Aug 6;6 Suppl 4:S405-17. doi: 10.1098/rsif.2009.0035.focus. Epub 2009 Apr 1. Review.

13.

Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery.

Hohman M, Gregory K, Chibale K, Smith PJ, Ekins S, Bunin B.

Drug Discov Today. 2009 Mar;14(5-6):261-70. doi: 10.1016/j.drudis.2008.11.015. Epub 2009 Feb 11. Review.

14.

Systems approaches to modelling pathways and networks.

Pfau T, Christian N, Ebenhöh O.

Brief Funct Genomics. 2011 Sep;10(5):266-79. doi: 10.1093/bfgp/elr022. Epub 2011 Sep 8. Review.

PMID:
21903724
15.

Toward integration of systems biology formalism: the gene regulatory networks case.

Gentilini R.

Genome Inform. 2005;16(2):215-24. Review.

PMID:
16901104
16.

Knowledge-making distinctions in synthetic biology.

O'Malley MA, Powell A, Davies JF, Calvert J.

Bioessays. 2008 Jan;30(1):57-65. Review.

PMID:
18081015
17.

From metabolic reactions to networks and pathways.

Arita M.

Methods Mol Biol. 2012;804:93-106. doi: 10.1007/978-1-61779-361-5_6. Review.

PMID:
22144150
18.

Systems biology--an engineering perspective.

Kremling A, Saez-Rodriguez J.

J Biotechnol. 2007 Apr 30;129(2):329-51. Epub 2007 Feb 24. Review.

PMID:
17400319
19.

Stoichiometric analysis of self-maintaining metabolisms.

Montero F, Nuño JC, Meléndez-Hevia E, Olasagasti F, Vázquez S, Morán F.

J Theor Biol. 2008 Jun 7;252(3):427-32. doi: 10.1016/j.jtbi.2007.11.025. Epub 2007 Nov 28. Review.

PMID:
18222485
20.

Sensitivity analysis approaches applied to systems biology models.

Zi Z.

IET Syst Biol. 2011 Nov;5(6):336-6. doi: 10.1049/iet-syb.2011.0015. Review.

PMID:
22129029

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