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Hybrid dynamic/static method for large-scale simulation of metabolism.

Yugi K, Nakayama Y, Kinoshita A, Tomita M.

Theor Biol Med Model. 2005 Oct 4;2:42.PMID: 16202166 [PubMed - indexed for MEDLINE]Related articlesFree article

Distinguishing enzymes using metabolome data for the hybrid dynamic/static method.

Ishii N, Nakayama Y, Tomita M.

Theor Biol Med Model. 2007 May 20;4:19.PMID: 17511884 [PubMed - indexed for MEDLINE]Related articlesFree article

Extraction of elementary rate constants from global network analysis of E. coli central metabolism.

Zhao J, Ridgway D, Broderick G, Kovalenko A, Ellison M.

BMC Syst Biol. 2008 May 7;2:41.PMID: 18462493 [PubMed - indexed for MEDLINE]Related articlesFree article

A hybrid model of anaerobic E. coli GJT001: combination of elementary flux modes and cybernetic variables.

Kim JI, Varner JD, Ramkrishna D.

Biotechnol Prog. 2008 Sep-Oct;24(5):993-1006.PMID: 19194908 [PubMed - indexed for MEDLINE]Related articles

A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles.

Kitayama T, Kinoshita A, Sugimoto M, Nakayama Y, Tomita M.

Theor Biol Med Model. 2006 Jul 17;3:24.PMID: 16846504 [PubMed - indexed for MEDLINE]Related articlesFree article

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks.

Hoppe A, Hoffmann S, Holzhütter HG.

BMC Syst Biol. 2007 Jun 1;1:23.PMID: 17543097 [PubMed - indexed for MEDLINE]Related articlesFree article

Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws--a promising method for speeding up the kinetic modelling of complex metabolic networks.

Bulik S, Grimbs S, Huthmacher C, Selbig J, Holzhütter HG.

FEBS J. 2009 Jan;276(2):410-24.PMID: 19137631 [PubMed - indexed for MEDLINE]Related articles

Large-scale prediction of phenotype: concept.

Varner JD.

Biotechnol Bioeng. 2000 Sep 20;69(6):664-78.PMID: 10918142 [PubMed - indexed for MEDLINE]Related articles

Steady state analysis of metabolic pathways using Petri nets.

Voss K, Heiner M, Koch I.

In Silico Biol. 2003;3(3):367-87.PMID: 14700469 [PubMed - indexed for MEDLINE]Related articlesFree article

Hybrid simulation of cellular behavior.

Kiehl TR, Mattheyses RM, Simmons MK.

Bioinformatics. 2004 Feb 12;20(3):316-22.PMID: 14960457 [PubMed - indexed for MEDLINE]Related articlesFree article

MetaFluxNet, a program package for metabolic pathway construction and analysis, and its use in large-scale metabolic flux analysis of Escherichia coli.

Lee SY, Lee DY, Hong SH, Kim TY, Yun H, Oh YG, Park S.

Genome Inform. 2003;14:23-33.PMID: 15706517 [PubMed - indexed for MEDLINE]Related articles

Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

Salis H, Sotiropoulos V, Kaznessis YN.

BMC Bioinformatics. 2006 Feb 24;7:93.PMID: 16504125 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparison of biochemical simulations using integrators derived from "Adomian" decomposition with traditional numerical methods.

Bulliman BT, Kuchel PW.

Biomed Biochim Acta. 1990;49(8-9):661-70.PMID: 2082915 [PubMed - indexed for MEDLINE]Related articles

A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics.

Nikerel IE, van Winden WA, van Gulik WM, Heijnen JJ.

BMC Bioinformatics. 2006 Dec 21;7:540.PMID: 17184531 [PubMed - indexed for MEDLINE]Related articlesFree article

Estimation of metabolic fluxes, expression levels and metabolite dynamics of a secondary metabolic pathway in potato using label pulse-feeding experiments combined with kinetic network modelling and simulation.

Heinzle E, Matsuda F, Miyagawa H, Wakasa K, Nishioka T.

Plant J. 2007 Apr;50(1):176-87. Epub 2007 Mar 12.PMID: 17355439 [PubMed - indexed for MEDLINE]Related articles

Dynamic simulation of the human red blood cell metabolic network.

Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO.

Bioinformatics. 2001 Mar;17(3):286-7.PMID: 11294796 [PubMed - indexed for MEDLINE]Related articlesFree article

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 [PubMed - indexed for MEDLINE]Related articles

Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data.

Liebermeister W, Klipp E.

Theor Biol Med Model. 2006 Dec 15;3:42.PMID: 17173670 [PubMed - indexed for MEDLINE]Related articlesFree article

Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia.

Cakir T, Alsan S, Saybaşili H, Akin A, Ulgen KO.

Theor Biol Med Model. 2007 Dec 10;4:48. Review.PMID: 18070347 [PubMed - indexed for MEDLINE]Related articlesFree article

Use of randomized sampling for analysis of metabolic networks.

Schellenberger J, Palsson BØ.

J Biol Chem. 2009 Feb 27;284(9):5457-61. Epub 2008 Oct 20. Review.PMID: 18940807 [PubMed - indexed for MEDLINE]Related articlesFree article