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For: Lee DY, Yun C, Cho A, Hou BK, Park S, Lee SY. WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks. Bioinformatics 2006;22:1150-1. [PMID: 16543278 DOI: 10.1093/bioinformatics/btl091] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Sriyudthsak K, Mejia RF, Arita M, Hirai MY. PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems. Nucleic Acids Res 2016;44:W205-11. [PMID: 27174940 PMCID: PMC4987946 DOI: 10.1093/nar/gkw415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/01/2016] [Indexed: 12/29/2022]  Open
2
Costa RS, Hartmann A, Vinga S. Kinetic modeling of cell metabolism for microbial production. J Biotechnol 2015;219:126-41. [PMID: 26724578 DOI: 10.1016/j.jbiotec.2015.12.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/25/2015] [Accepted: 12/15/2015] [Indexed: 12/20/2022]
3
Wu Z, Pang W, Coghill GM. An Integrated Qualitative and Quantitative Biochemical Model Learning Framework Using Evolutionary Strategy and Simulated Annealing. Cognit Comput 2015;7:637-651. [PMID: 26693255 PMCID: PMC4675806 DOI: 10.1007/s12559-015-9328-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 04/20/2015] [Indexed: 12/01/2022]
4
Eom MH, Kim W, Lee J, Cho JH, Seung D, Park S, Lee JH. Modeling of a Biobutanol Adsorption Process for Designing an Extractive Fermentor. Ind Eng Chem Res 2013. [DOI: 10.1021/ie301249z] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
5
Dandekar T, Fieselmann A, Majeed S, Ahmed Z. Software applications toward quantitative metabolic flux analysis and modeling. Brief Bioinform 2012;15:91-107. [PMID: 23142828 DOI: 10.1093/bib/bbs065] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
6
Khazaei T, McGuigan A, Mahadevan R. Ensemble modeling of cancer metabolism. Front Physiol 2012;3:135. [PMID: 22623918 PMCID: PMC3353412 DOI: 10.3389/fphys.2012.00135] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 04/22/2012] [Indexed: 11/28/2022]  Open
7
Gerdtzen ZP. Modeling metabolic networks for mammalian cell systems: general considerations, modeling strategies, and available tools. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012;127:71-108. [PMID: 21984615 DOI: 10.1007/10_2011_120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
8
Systems biology and inflammation. Methods Mol Biol 2010;662:181-201. [PMID: 20824472 DOI: 10.1007/978-1-60761-800-3_9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
9
Ensemble modeling and related mathematical modeling of metabolic networks. J Taiwan Inst Chem Eng 2009. [DOI: 10.1016/j.jtice.2009.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
10
Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C, Le Novère N. Designing and encoding models for synthetic biology. J R Soc Interface 2009;6 Suppl 4:S405-17. [PMID: 19364720 PMCID: PMC2843962 DOI: 10.1098/rsif.2009.0035.focus] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 03/09/2009] [Indexed: 11/12/2022]  Open
11
Systems biology model databases and resources. Essays Biochem 2008;45:223-36. [PMID: 18793135 DOI: 10.1042/bse0450223] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
12
Ensemble modeling of metabolic networks. Biophys J 2008;95:5606-17. [PMID: 18820235 DOI: 10.1529/biophysj.108.135442] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
13
Lee DY, Saha R, Yusufi FNK, Park W, Karimi IA. Web-based applications for building, managing and analysing kinetic models of biological systems. Brief Bioinform 2008;10:65-74. [PMID: 18805901 DOI: 10.1093/bib/bbn039] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
14
Weidemann A, Richter S, Stein M, Sahle S, Gauges R, Gabdoulline R, Surovtsova I, Semmelrock N, Besson B, Rojas I, Wade R, Kummer U. SYCAMORE--a systems biology computational analysis and modeling research environment. Bioinformatics 2008;24:1463-4. [PMID: 18463116 DOI: 10.1093/bioinformatics/btn207] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
15
Rios-Estepa R, Lange BM. Experimental and mathematical approaches to modeling plant metabolic networks. PHYTOCHEMISTRY 2007;68:2351-74. [PMID: 17561179 DOI: 10.1016/j.phytochem.2007.04.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 04/16/2007] [Accepted: 04/17/2007] [Indexed: 05/15/2023]
16
Mandel JJ, Fuß H, Palfreyman NM, Dubitzky W. Modeling biochemical transformation processes and information processing with Narrator. BMC Bioinformatics 2007;8:103. [PMID: 17389034 PMCID: PMC1847530 DOI: 10.1186/1471-2105-8-103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Accepted: 03/27/2007] [Indexed: 11/10/2022]  Open
17
Our Senior Editors. Biotechnol J 2007. [DOI: 10.1002/biot.200790000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
18
Barrett CL, Kim TY, Kim HU, Palsson BØ, Lee SY. Systems biology as a foundation for genome-scale synthetic biology. Curr Opin Biotechnol 2006;17:488-92. [PMID: 16934450 DOI: 10.1016/j.copbio.2006.08.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 07/28/2006] [Accepted: 08/14/2006] [Indexed: 12/29/2022]
19
Heinemann M, Panke S. Synthetic biology--putting engineering into biology. Bioinformatics 2006;22:2790-9. [PMID: 16954140 DOI: 10.1093/bioinformatics/btl469] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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