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Items: 1 to 20 of 63

1.

Parameter optimization and sensitivity analysis for large kinetic models using a real-coded genetic algorithm.

Tohsato Y, Ikuta K, Shionoya A, Mazaki Y, Ito M.

Gene. 2013 Apr 10;518(1):84-90. doi: 10.1016/j.gene.2012.11.080. Epub 2012 Dec 27.

PMID:
23274652
2.

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data.

Khodayari A, Zomorrodi AR, Liao JC, Maranas CD.

Metab Eng. 2014 Sep;25:50-62. doi: 10.1016/j.ymben.2014.05.014. Epub 2014 Jun 10.

PMID:
24928774
3.
4.

Parameter optimization by using differential elimination: a general approach for introducing constraints into objective functions.

Nakatsui M, Horimoto K, Okamoto M, Tokumoto Y, Miyake J.

BMC Syst Biol. 2010 Sep 13;4 Suppl 2:S9. doi: 10.1186/1752-0509-4-S2-S9.

5.

Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux.

Tan Y, Rivera JG, Contador CA, Asenjo JA, Liao JC.

Metab Eng. 2011 Jan;13(1):60-75. doi: 10.1016/j.ymben.2010.11.001. Epub 2010 Nov 12.

PMID:
21075211
6.

Comparison of different algorithms for simultaneous estimation of multiple parameters in kinetic metabolic models.

Baker SM, Schallau K, Junker BH.

J Integr Bioinform. 2010 Mar 25;7(3). doi: 10.2390/biecoll-jib-2010-133.

PMID:
20375457
7.
8.

Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites.

Meinicke P, Tech M, Morgenstern B, Merkl R.

BMC Bioinformatics. 2004 Oct 28;5:169.

9.

An improved differential evolution algorithm for enhancing biochemical pathways simulation and production.

Chong CK, Mohamad MS, Deris S, Shamsir MS, Abdullah A.

Int J Data Min Bioinform. 2014;10(4):424-39.

PMID:
25946887
10.

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
11.

Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization.

Guillén-Gosálbez G, Miró A, Alves R, Sorribas A, Jiménez L.

BMC Syst Biol. 2013 Oct 31;7:113. doi: 10.1186/1752-0509-7-113.

12.

Towards kinetic modeling of global metabolic networks: Methylobacterium extorquens AM1 growth as validation.

Ao P, Lee LW, Lidstrom ME, Yin L, Zhu X.

Sheng Wu Gong Cheng Xue Bao. 2008 Jun;24(6):980-94.

PMID:
18807980
14.

Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis.

Bruck J, Liebermeister W, Klipp E.

Genome Inform. 2008;20:1-14.

PMID:
19425118
15.
16.

The recognition and prediction of sigma70 promoters in Escherichia coli K-12.

Li QZ, Lin H.

J Theor Biol. 2006 Sep 7;242(1):135-41. Epub 2006 Apr 17.

PMID:
16603195
17.
18.

The dynamics of hybrid metabolic-genetic oscillators.

Reznik E, Kaper TJ, Segrè D.

Chaos. 2013 Mar;23(1):013132. doi: 10.1063/1.4793573.

PMID:
23556969
19.

Modeling cellular metabolism and energetics in skeletal muscle: large-scale parameter estimation and sensitivity analysis.

Dash RK, Li Y, Kim J, Saidel GM, Cabrera ME.

IEEE Trans Biomed Eng. 2008 Apr;55(4):1298-318. doi: 10.1109/TBME.2007.913422.

PMID:
18390321
20.

Simultaneous versus sequential optimal experiment design for the identification of multi-parameter microbial growth kinetics as a function of temperature.

Van Derlinden E, Bernaerts K, Van Impe JF.

J Theor Biol. 2010 May 21;264(2):347-55. doi: 10.1016/j.jtbi.2010.01.003. Epub 2010 Jan 11.

PMID:
20064532

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