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Items: 1 to 20 of 171

1.

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.

Liebermeister W, Uhlendorf J, Klipp E.

Bioinformatics. 2010 Jun 15;26(12):1528-34. doi: 10.1093/bioinformatics/btq141. Epub 2010 Apr 12.

PMID:
20385728
2.

SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks.

Dräger A, Hassis N, Supper J, Schröder A, Zell A.

BMC Syst Biol. 2008 Apr 30;2:39. doi: 10.1186/1752-0509-2-39.

3.
4.

Annotation and merging of SBML models with semanticSBML.

Krause F, Uhlendorf J, Lubitz T, Schulz M, Klipp E, Liebermeister W.

Bioinformatics. 2010 Feb 1;26(3):421-2. doi: 10.1093/bioinformatics/btp642. Epub 2009 Nov 17.

PMID:
19933161
5.

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints.

Liebermeister W, Klipp E.

Theor Biol Med Model. 2006 Dec 15;3:41.

6.

Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells.

Selivanov VA, Meshalkina LE, Solovjeva ON, Kuchel PW, Ramos-Montoya A, Kochetov GA, Lee PW, Cascante M.

Bioinformatics. 2005 Sep 1;21(17):3558-64. Epub 2005 Jul 7.

PMID:
16002431
7.

Parameter balancing in kinetic models of cell metabolism.

Lubitz T, Schulz M, Klipp E, Liebermeister W.

J Phys Chem B. 2010 Dec 16;114(49):16298-303. doi: 10.1021/jp108764b. Epub 2010 Nov 1.

8.

Accuracy of alternative representations for integrated biochemical systems.

Voit EO, Savageau MA.

Biochemistry. 1987 Oct 20;26(21):6869-80.

PMID:
3427048
9.

Enzymatic reaction rate limits with constraints on equilibrium constants and experimental parameters.

Bish DR, Mavrovouniotis ML.

Biosystems. 1998 Jun-Jul;47(1-2):37-60.

PMID:
9715750
10.

WinBEST-KIT: Windows-based biochemical reaction simulator for metabolic pathways.

Sekiguchi T, Okamoto M.

J Bioinform Comput Biol. 2006 Jun;4(3):621-38.

PMID:
16960966
11.

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson BO.

BMC Syst Biol. 2016 Jun 6;10(1):40. doi: 10.1186/s12918-016-0283-2.

12.

A general framework for thermodynamically consistent parameterization and efficient sampling of enzymatic reactions.

Saa P, Nielsen LK.

PLoS Comput Biol. 2015 Apr 14;11(4):e1004195. doi: 10.1371/journal.pcbi.1004195. eCollection 2015 Apr.

13.

Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules.

Saez-Rodriguez J, Gayer S, Ginkel M, Gilles ED.

Bioinformatics. 2008 Aug 15;24(16):i213-9. doi: 10.1093/bioinformatics/btn289.

PMID:
18689828
14.

Kinetic and thermodynamic aspects of enzyme control and regulation.

Rohwer JM, Hofmeyr JH.

J Phys Chem B. 2010 Dec 16;114(49):16280-9. doi: 10.1021/jp108412s. Epub 2010 Oct 28.

PMID:
21028763
15.

A note on the kinetics of enzyme action: a decomposition that highlights thermodynamic effects.

Noor E, Flamholz A, Liebermeister W, Bar-Even A, Milo R.

FEBS Lett. 2013 Sep 2;587(17):2772-7. doi: 10.1016/j.febslet.2013.07.028. Epub 2013 Jul 23. Review.

16.

Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations.

Costa RS, Machado D, Rocha I, Ferreira EC.

Biosystems. 2010 May;100(2):150-7. doi: 10.1016/j.biosystems.2010.03.001. Epub 2010 Mar 10.

PMID:
20226228
17.

Renormalization group approach to power-law modeling of complex metabolic networks.

Hernández-Bermejo B.

J Theor Biol. 2010 Aug 7;265(3):422-32. doi: 10.1016/j.jtbi.2010.04.024. Epub 2010 May 4.

PMID:
20447410
18.

Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium.

Qian H, Beard DA.

Biophys Chem. 2005 Apr 22;114(2-3):213-20. Epub 2004 Dec 22. Review.

PMID:
15829355
19.

A general model of reaction kinetics in biological systems.

Haag JE, Vande Wouwer A, Remy M.

Bioprocess Biosyst Eng. 2005 Aug;27(5):303-9. Epub 2005 Jun 29.

PMID:
15986214
20.

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

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