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Improved methods for the mathematically controlled comparison of biochemical systems.

Schwacke JH, Voit EO.

Theor Biol Med Model. 2004 Jun 4;1:1.PMID: 15285792 [PubMed - indexed for MEDLINE]Related articlesFree article

Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

Papin JA, Reed JL, Palsson BO.

Trends Biochem Sci. 2004 Dec;29(12):641-7. Review.PMID: 15544950 [PubMed - indexed for MEDLINE]Related articles

Extending the method of mathematically controlled comparison to include numerical comparisons.

Alves R, Savageau MA.

Bioinformatics. 2000 Sep;16(9):786-98.PMID: 11108701 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2008 Jun 23. Review.PMID: 18573813 [PubMed - indexed for MEDLINE]Related articles

Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB.

Ullah M, Schmidt H, Cho KH, Wolkenhauer O.

Syst Biol (Stevenage). 2006 Mar;153(2):53-60.PMID: 16986253 [PubMed - indexed for MEDLINE]Related articles

Modularization of biochemical networks based on classification of Petri net t-invariants.

Grafahrend-Belau E, Schreiber F, Heiner M, Sackmann A, Junker BH, Grunwald S, Speer A, Winder K, Koch I.

BMC Bioinformatics. 2008 Feb 8;9:90.PMID: 18257938 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational methods for diffusion-influenced biochemical reactions.

Dobrzynski M, Rodríguez JV, Kaandorp JA, Blom JG.

Bioinformatics. 2007 Aug 1;23(15):1969-77. Epub 2007 May 30.PMID: 17537752 [PubMed - indexed for MEDLINE]Related articlesFree article

A hybrid approach for efficient and robust parameter estimation in biochemical pathways.

Rodriguez-Fernandez M, Mendes P, Banga JR.

Biosystems. 2006 Feb-Mar;83(2-3):248-65. Epub 2005 Oct 19.PMID: 16236429 [PubMed - indexed for MEDLINE]Related articles

Sampling rare switching events in biochemical networks.

Allen RJ, Warren PB, Ten Wolde PR.

Phys Rev Lett. 2005 Jan 14;94(1):018104. Epub 2005 Jan 6.PMID: 15698138 [PubMed - indexed for MEDLINE]Related articles

Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module.

Maurya MR, Bornheimer SJ, Venkatasubramanian V, Subramaniam S.

Syst Biol (Stevenage). 2005 Dec;152(4):229-42.PMID: 16986265 [PubMed - indexed for MEDLINE]Related articles

Reverse engineering of biochemical equations from time-course data by means of genetic programming.

Sugimoto M, Kikuchi S, Tomita M.

Biosystems. 2005 May;80(2):155-64. Epub 2004 Dec 15.PMID: 15823414 [PubMed - indexed for MEDLINE]Related articles

Behavioral interventions to reduce risk for sexual transmission of HIV among men who have sex with men.

Johnson WD, Diaz RM, Flanders WD, Goodman M, Hill AN, Holtgrave D, Malow R, McClellan WM.

Cochrane Database Syst Rev. 2008 Jul 16;(3):CD001230. Review.PMID: 18646068 [PubMed - indexed for MEDLINE]Related articles

Highly optimised global organisation of metabolic networks.

Tanaka R, Csete M, Doyle J.

Syst Biol (Stevenage). 2005 Dec;152(4):179-84. Review.PMID: 16986258 [PubMed - indexed for MEDLINE]Related articles

Cell++--simulating biochemical pathways.

Sanford C, Yip ML, White C, Parkinson J.

Bioinformatics. 2006 Dec 1;22(23):2918-25. Epub 2006 Oct 11.PMID: 17038347 [PubMed - indexed for MEDLINE]Related articlesFree article

Linear systems approach to analysis of complex dynamic behaviours in biochemical networks.

Schmidt H, Jacobsen EW.

Syst Biol (Stevenage). 2004 Jun;1(1):149-58.PMID: 17052125 [PubMed - indexed for MEDLINE]Related articles

In silico evolution of functional modules in biochemical networks.

Paladugu SR, Chickarmane V, Deckard A, Frumkin JP, McCormack M, Sauro HM.

Syst Biol (Stevenage). 2006 Jul;153(4):223-35.PMID: 16986624 [PubMed - indexed for MEDLINE]Related articles

Extended kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks.

Sun X, Jin L, Xiong M.

PLoS One. 2008;3(11):e3758. Epub 2008 Nov 19.PMID: 19018286 [PubMed - indexed for MEDLINE]Related articlesFree article

Biochemical networks with uncertain parameters.

Liebermeister W, Klipp E.

Syst Biol (Stevenage). 2005 Sep;152(3):97-107.PMID: 16986274 [PubMed - indexed for MEDLINE]Related articles

Structural robustness of biochemical network models-with application to the oscillatory metabolism of activated neutrophils.

Jacobsen EW, Cedersund G.

IET Syst Biol. 2008 Jan;2(1):39-47.PMID: 18248085 [PubMed - indexed for MEDLINE]Related articles

Least-squares methods for identifying biochemical regulatory networks from noisy measurements.

Kim J, Bates DG, Postlethwaite I, Heslop-Harrison P, Cho KH.

BMC Bioinformatics. 2007 Jan 10;8:8.PMID: 17212835 [PubMed - indexed for MEDLINE]Related articlesFree article