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Priming nonlinear searches for pathway identification.

Veflingstad SR, Almeida J, Voit EO.

Theor Biol Med Model. 2004 Sep 14;1:8.PMID: 15367330 [PubMed - indexed for MEDLINE]Related articlesFree article

Recent developments in parameter estimation and structure identification of biochemical and genomic systems.

Chou IC, Voit EO.

Math Biosci. 2009 Jun;219(2):57-83. Epub 2009 Mar 25. Review.PMID: 19327372 [PubMed - indexed for MEDLINE]Related articles

Challenges for the identification of biological systems from in vivo time series data.

Voit EO, Marino S, Lall R.

In Silico Biol. 2005;5(2):83-92.PMID: 15972008 [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

Parameter estimation in biochemical systems models with alternating regression.

Chou IC, Martens H, Voit EO.

Theor Biol Med Model. 2006 Jul 19;3:25.PMID: 16854227 [PubMed - indexed for MEDLINE]Related articlesFree article

An automated procedure for the extraction of metabolic network information from time series data.

Marino S, Voit EO.

J Bioinform Comput Biol. 2006 Jun;4(3):665-91.PMID: 16960969 [PubMed - indexed for MEDLINE]Related articles

Decoupling dynamical systems for pathway identification from metabolic profiles.

Voit EO, Almeida J.

Bioinformatics. 2004 Jul 22;20(11):1670-81. Epub 2004 Feb 26.PMID: 14988125 [PubMed - indexed for MEDLINE]Related articlesFree article

Estimating parameters for generalized mass action models with connectivity information.

Ko CL, Voit EO, Wang FS.

BMC Bioinformatics. 2009 May 11;10:140.PMID: 19432964 [PubMed - indexed for MEDLINE]Related articlesFree article

Parameter estimation in modulated, unbranched reaction chains within biochemical systems.

Lall R, Voit EO.

Comput Biol Chem. 2005 Oct;29(5):309-18. Epub 2005 Oct 6.PMID: 16213792 [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

Efficient, sparse biological network determination.

August E, Papachristodoulou A.

BMC Syst Biol. 2009 Feb 23;3:25.PMID: 19236711 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of neutral biochemical network models from time series data.

Vilela M, Vinga S, Maia MA, Voit EO, Almeida JS.

BMC Syst Biol. 2009 May 5;3:47.PMID: 19416537 [PubMed - indexed for MEDLINE]Related articlesFree article

Spectral embedding finds meaningful (relevant) structure in image and microarray data.

Higgs BW, Weller J, Solka JL.

BMC Bioinformatics. 2006 Feb 16;7:74.PMID: 16483359 [PubMed - indexed for MEDLINE]Related articlesFree article

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

Mixed-integer nonlinear optimisation approach to coarse-graining biochemical networks.

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

IET Syst Biol. 2009 Jan;3(1):24-39.PMID: 19154082 [PubMed - indexed for MEDLINE]Related articlesFree article

Hybrid optimization method with general switching strategy for parameter estimation.

Balsa-Canto E, Peifer M, Banga JR, Timmer J, Fleck C.

BMC Syst Biol. 2008 Mar 24;2:26.PMID: 18366722 [PubMed - indexed for MEDLINE]Related articlesFree article

Reverse engineering module networks by PSO-RNN hybrid modeling.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S15.PMID: 19594874 [PubMed - indexed for MEDLINE]Related articlesFree article

Parameter optimization in S-system models.

Vilela M, Chou IC, Vinga S, Vasconcelos AT, Voit EO, Almeida JS.

BMC Syst Biol. 2008 Apr 16;2:35.PMID: 18416837 [PubMed - indexed for MEDLINE]Related articlesFree article

Accelerated search for biomolecular network models to interpret high-throughput experimental data.

Datta S, Sokhansanj BA.

BMC Bioinformatics. 2007 Jul 18;8:258.PMID: 17640351 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of functional modules using network topology and high-throughput data.

Ulitsky I, Shamir R.

BMC Syst Biol. 2007 Jan 26;1:8.PMID: 17408515 [PubMed - indexed for MEDLINE]Related articlesFree article