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Items: 1 to 20 of 76

1.

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.

Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K, Klamt S, Rocha M, Saez-Rodriguez J.

Mol Biosyst. 2013 Jul;9(7):1576-83. doi: 10.1039/c3mb25489e. Epub 2013 Mar 25. Review.

PMID:
23525368
2.

Integrative modelling of gene expression and cell metabolism.

de la Fuente A, Mendes P.

Appl Bioinformatics. 2003;2(2):79-90. Review.

PMID:
15130824
3.

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.

Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S.

Biosystems. 2014 Oct;124:26-38. doi: 10.1016/j.biosystems.2014.07.002. Epub 2014 Jul 23.

PMID:
25063553
4.

Mathematical optimization applications in metabolic networks.

Zomorrodi AR, Suthers PF, Ranganathan S, Maranas CD.

Metab Eng. 2012 Nov;14(6):672-86. doi: 10.1016/j.ymben.2012.09.005. Epub 2012 Sep 28. Review.

PMID:
23026121
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.

Flux balance analysis of biological systems: applications and challenges.

Raman K, Chandra N.

Brief Bioinform. 2009 Jul;10(4):435-49. doi: 10.1093/bib/bbp011. Epub 2009 Mar 15.

PMID:
19287049
7.

SysBioMed report: advancing systems biology for medical applications.

Wolkenhauer O, Fell D, De Meyts P, Blüthgen N, Herzel H, Le Novère N, Höfer T, Schürrle K, van Leeuwen I.

IET Syst Biol. 2009 May;3(3):131-6. doi: 10.1049/iet-syb.2009.0005.

PMID:
19449974
8.

Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.coli.

Simão E, Remy E, Thieffry D, Chaouiya C.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii190-6.

PMID:
16204102
9.

Modelling cyanobacteria: from metabolism to integrative models of phototrophic growth.

Steuer R, Knoop H, Machné R.

J Exp Bot. 2012 Mar;63(6):2259-74. doi: 10.1093/jxb/ers018. Review.

PMID:
22450165
10.

Integration of Boolean models exemplified on hepatocyte signal transduction.

Schlatter R, Philippi N, Wangorsch G, Pick R, Sawodny O, Borner C, Timmer J, Ederer M, Dandekar T.

Brief Bioinform. 2012 May;13(3):365-76. doi: 10.1093/bib/bbr065. Epub 2011 Oct 20.

PMID:
22016404
11.

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
12.

From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways.

Bauer-Mehren A, Furlong LI, Rautschka M, Sanz F.

BMC Bioinformatics. 2009 Aug 27;10 Suppl 8:S6. doi: 10.1186/1471-2105-10-S8-S6.

13.

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
14.

Integration of metabolic reactions and gene regulation.

Yeang CH.

Mol Biotechnol. 2011 Jan;47(1):70-82. doi: 10.1007/s12033-010-9325-y. Review.

PMID:
20737299
15.

Gene regulatory network inference: data integration in dynamic models-a review.

Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R.

Biosystems. 2009 Apr;96(1):86-103. doi: 10.1016/j.biosystems.2008.12.004. Epub 2008 Dec 27. Review.

PMID:
19150482
16.

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach.

Steggles LJ, Banks R, Shaw O, Wipat A.

Bioinformatics. 2007 Feb 1;23(3):336-43. Epub 2006 Nov 22.

PMID:
17121774
17.

Engineered gene circuits.

Hasty J, McMillen D, Collins JJ.

Nature. 2002 Nov 14;420(6912):224-30. Review.

PMID:
12432407
18.

Metabolomics technology and bioinformatics.

Shulaev V.

Brief Bioinform. 2006 Jun;7(2):128-39. Epub 2006 May 18. Review.

PMID:
16772266
19.

Systems biology approaches and tools for analysis of interactomes and multi-target drugs.

Schrattenholz A, Groebe K, Soskic V.

Methods Mol Biol. 2010;662:29-58. doi: 10.1007/978-1-60761-800-3_2. Review.

PMID:
20824465
20.

Modelling spatio-temporal interactions within the cell.

Rangamani P, Iyengar R.

J Biosci. 2007 Jan;32(1):157-67. Review. Erratum in: J Biosci. 2007 Jun;32(4):805.

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