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For: Wiback SJ, Mahadevan R, Palsson BØ. Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum. J Theor Biol 2003;224:313-24. [PMID: 12941590 DOI: 10.1016/s0022-5193(03)00168-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Number Cited by Other Article(s)
1
Walton JR, Lindahl PA. Basic pathway decomposition of biochemical reaction networks within growing cells. iScience 2024;27:108506. [PMID: 38161422 PMCID: PMC10757263 DOI: 10.1016/j.isci.2023.108506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/01/2023] [Accepted: 11/18/2023] [Indexed: 01/03/2024]  Open
2
Chitpin JG, Perkins TJ. A Markov constraint to uniquely identify elementary flux mode weights in unimolecular metabolic networks. J Theor Biol 2023;575:111632. [PMID: 37804942 DOI: 10.1016/j.jtbi.2023.111632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/21/2023] [Accepted: 10/01/2023] [Indexed: 10/09/2023]
3
Mattei G, Gan Z, Ramazzotti M, Palsson BO, Zielinski DC. Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways. Metabolites 2023;13:1127. [PMID: 37999223 PMCID: PMC10672963 DOI: 10.3390/metabo13111127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 10/19/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]  Open
4
Understanding FBA Solutions under Multiple Nutrient Limitations. Metabolites 2021;11:metabo11050257. [PMID: 33919383 PMCID: PMC8143296 DOI: 10.3390/metabo11050257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 11/27/2022]  Open
5
Röhl A, Bockmayr A. Finding MEMo: minimum sets of elementary flux modes. J Math Biol 2019;79:1749-1777. [PMID: 31388689 DOI: 10.1007/s00285-019-01409-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/15/2019] [Indexed: 10/26/2022]
6
Xi Y, Wang F. Extreme pathway analysis reveals the organizing rules of metabolic regulation. PLoS One 2019;14:e0210539. [PMID: 30721240 PMCID: PMC6363282 DOI: 10.1371/journal.pone.0210539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/27/2018] [Indexed: 11/18/2022]  Open
7
Ataman M, Hernandez Gardiol DF, Fengos G, Hatzimanikatis V. redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models. PLoS Comput Biol 2017;13:e1005444. [PMID: 28727725 PMCID: PMC5519011 DOI: 10.1371/journal.pcbi.1005444] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 03/01/2017] [Indexed: 11/18/2022]  Open
8
Vilkhovoy M, Minot M, Varner JD. Effective Dynamic Models of Metabolic Networks. ACTA ACUST UNITED AC 2016. [DOI: 10.1109/lls.2016.2644649] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
9
Eanes WF. New views on the selection acting on genetic polymorphism in central metabolic genes. Ann N Y Acad Sci 2016;1389:108-123. [PMID: 27859384 DOI: 10.1111/nyas.13285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/20/2016] [Accepted: 09/29/2016] [Indexed: 12/14/2022]
10
Richelle A, Gziri KM, Bogaerts P. A methodology for building a macroscopic FBA-based dynamical simulator of cell cultures through flux variability analysis. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.06.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
11
von Stosch M, Rodrigues de Azevedo C, Luis M, Feyo de Azevedo S, Oliveira R. A principal components method constrained by elementary flux modes: analysis of flux data sets. BMC Bioinformatics 2016;17:200. [PMID: 27146133 PMCID: PMC4855838 DOI: 10.1186/s12859-016-1063-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/26/2016] [Indexed: 12/21/2022]  Open
12
Folch-Fortuny A, Marques R, Isidro IA, Oliveira R, Ferrer A. Principal elementary mode analysis (PEMA). MOLECULAR BIOSYSTEMS 2016;12:737-46. [PMID: 26905301 DOI: 10.1039/c5mb00828j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
13
Horvat P, Koller M, Braunegg G. Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies. World J Microbiol Biotechnol 2015;31:1315-28. [DOI: 10.1007/s11274-015-1887-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/05/2015] [Indexed: 11/25/2022]
14
Chan SHJ, Solem C, Jensen PR, Ji P. Estimating biological elementary flux modes that decompose a flux distribution by the minimal branching property. ACTA ACUST UNITED AC 2014;30:3232-9. [PMID: 25100687 DOI: 10.1093/bioinformatics/btu529] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
15
Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol Syst Biol 2014;10:737. [PMID: 24987116 PMCID: PMC4299494 DOI: 10.15252/msb.20145243] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]  Open
16
A novel methodology to estimate metabolic flux distributions in constraint-based models. Metabolites 2013;3:838-52. [PMID: 24958152 PMCID: PMC3901294 DOI: 10.3390/metabo3030838] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/10/2013] [Accepted: 09/10/2013] [Indexed: 11/25/2022]  Open
17
Colombo M, Laayouni H, Invergo BM, Bertranpetit J, Montanucci L. Metabolic flux is a determinant of the evolutionary rates of enzyme-encoding genes. Evolution 2013;68:605-13. [PMID: 24102646 DOI: 10.1111/evo.12262] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 08/15/2013] [Indexed: 01/25/2023]
18
Zomorrodi AR, Lafontaine Rivera JG, Liao JC, Maranas CD. Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks. Biotechnol J 2013;8:1090-104. [DOI: 10.1002/biot.201200270] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 01/22/2013] [Accepted: 02/28/2013] [Indexed: 11/08/2022]
19
Qin T, Tsoi LC, Sims KJ, Lu X, Zheng WJ. Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network. BMC SYSTEMS BIOLOGY 2012;6 Suppl 3:S3. [PMID: 23282239 PMCID: PMC3524013 DOI: 10.1186/1752-0509-6-s3-s3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
20
Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks. Sci Rep 2012;2:580. [PMID: 22896812 PMCID: PMC3419370 DOI: 10.1038/srep00580] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 07/30/2012] [Indexed: 12/27/2022]  Open
21
Orman MA, Berthiaume F, Androulakis IP, Ierapetritou MG. Advanced stoichiometric analysis of metabolic networks of mammalian systems. Crit Rev Biomed Eng 2012;39:511-34. [PMID: 22196224 DOI: 10.1615/critrevbiomedeng.v39.i6.30] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
22
Network reduction in metabolic pathway analysis: elucidation of the key pathways involved in the photoautotrophic growth of the green alga Chlamydomonas reinhardtii. Metab Eng 2012;14:458-67. [PMID: 22342232 DOI: 10.1016/j.ymben.2012.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/13/2012] [Accepted: 01/31/2012] [Indexed: 11/21/2022]
23
Trinh CT, Thompson RA. Elementary mode analysis: a useful metabolic pathway analysis tool for reprograming microbial metabolic pathways. Subcell Biochem 2012;64:21-42. [PMID: 23080244 DOI: 10.1007/978-94-007-5055-5_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
24
Isidro IA, Ferreira AR, Clemente JJ, Cunha AE, Dias JML, Oliveira R. Design of Pathway-Level Bioprocess Monitoring and Control Strategies Supported by Metabolic Networks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012;132:193-215. [DOI: 10.1007/10_2012_168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
25
Orman MA, Ierapetritou MG, Androulakis IP, Berthiaume F. Metabolic response of perfused livers to various oxygenation conditions. Biotechnol Bioeng 2011;108:2947-57. [PMID: 21755498 PMCID: PMC3193557 DOI: 10.1002/bit.23261] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/21/2011] [Accepted: 06/24/2011] [Indexed: 01/06/2023]
26
Ferreira AR, Dias JML, Teixeira AP, Carinhas N, Portela RMC, Isidro IA, von Stosch M, Oliveira R. Projection to latent pathways (PLP): a constrained projection to latent variables (PLS) method for elementary flux modes discrimination. BMC SYSTEMS BIOLOGY 2011;5:181. [PMID: 22044634 PMCID: PMC3750108 DOI: 10.1186/1752-0509-5-181] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 11/01/2011] [Indexed: 11/22/2022]
27
Orman MA, Androulakis IP, Berthiaume F, Ierapetritou MG. Metabolic network analysis of perfused livers under fed and fasted states: incorporating thermodynamic and futile-cycle-associated regulatory constraints. J Theor Biol 2011;293:101-10. [PMID: 22037644 DOI: 10.1016/j.jtbi.2011.10.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/28/2011] [Accepted: 10/14/2011] [Indexed: 10/16/2022]
28
Do elementary flux modes combine linearly at the “atomic” level? Integrating tracer-based metabolomics data and elementary flux modes. Biosystems 2011;105:140-6. [DOI: 10.1016/j.biosystems.2011.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 02/14/2011] [Accepted: 04/17/2011] [Indexed: 11/20/2022]
29
Chan SHJ, Ji P. Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks. ACTA ACUST UNITED AC 2011;27:2256-62. [PMID: 21685054 DOI: 10.1093/bioinformatics/btr367] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
30
Teixeira AP, Dias JM, Carinhas N, Sousa M, Clemente JJ, Cunha AE, von Stosch M, Alves PM, Carrondo MJ, Oliveira R. Cell functional enviromics: unravelling the function of environmental factors. BMC SYSTEMS BIOLOGY 2011;5:92. [PMID: 21645360 PMCID: PMC3118353 DOI: 10.1186/1752-0509-5-92] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 06/06/2011] [Indexed: 11/20/2022]
31
Orman MA, Berthiaume F, Androulakis IP, Ierapetritou MG. Pathway analysis of liver metabolism under stressed condition. J Theor Biol 2011;272:131-40. [PMID: 21163266 PMCID: PMC3038651 DOI: 10.1016/j.jtbi.2010.11.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 11/17/2010] [Accepted: 11/24/2010] [Indexed: 11/28/2022]
32
Terzer M, Maynard ND, Covert MW, Stelling J. Genome-scale metabolic networks. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011;1:285-297. [PMID: 20835998 DOI: 10.1002/wsbm.37] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
33
Gudmundsson S, Thiele I. Computationally efficient flux variability analysis. BMC Bioinformatics 2010;11:489. [PMID: 20920235 PMCID: PMC2963619 DOI: 10.1186/1471-2105-11-489] [Citation(s) in RCA: 214] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 09/29/2010] [Indexed: 01/23/2023]  Open
34
A Statistical Thermodynamical Interpretation of Metabolism. ENTROPY 2010. [DOI: 10.3390/e12081921] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
35
Which metabolic pathways generate and characterize the flux space? A comparison among elementary modes, extreme pathways and minimal generators. J Biomed Biotechnol 2010;2010:753904. [PMID: 20467567 PMCID: PMC2868190 DOI: 10.1155/2010/753904] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 12/29/2009] [Accepted: 02/11/2010] [Indexed: 01/05/2023]  Open
36
Hughey JJ, Lee TK, Covert MW. Computational modeling of mammalian signaling networks. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2010;2:194-209. [PMID: 20836022 PMCID: PMC3105527 DOI: 10.1002/wsbm.52] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
37
Xi Y, Chen YPP, Qian C, Wang F. Comparative study of computational methods to detect the correlated reaction sets in biochemical networks. Brief Bioinform 2010;12:132-50. [DOI: 10.1093/bib/bbp068] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
38
Mo ML, Palsson BØ. Understanding human metabolic physiology: a genome-to-systems approach. Trends Biotechnol 2009;27:37-44. [DOI: 10.1016/j.tibtech.2008.09.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 09/25/2008] [Accepted: 09/26/2008] [Indexed: 01/27/2023]
39
Trinh CT, Wlaschin A, Srienc F. Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl Microbiol Biotechnol 2009;81:813-26. [PMID: 19015845 PMCID: PMC2909134 DOI: 10.1007/s00253-008-1770-1] [Citation(s) in RCA: 184] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Revised: 10/23/2008] [Accepted: 10/25/2008] [Indexed: 12/19/2022]
40
Carlson RP. Decomposition of complex microbial behaviors into resource-based stress responses. ACTA ACUST UNITED AC 2008;25:90-7. [PMID: 19008248 DOI: 10.1093/bioinformatics/btn589] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
41
A bilevel optimization algorithm to identify enzymatic capacity constraints in metabolic networks. Comput Chem Eng 2008. [DOI: 10.1016/j.compchemeng.2007.10.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
42
Young JD, Henne KL, Morgan JA, Konopka AE, Ramkrishna D. Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control. Biotechnol Bioeng 2008;100:542-59. [DOI: 10.1002/bit.21780] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
43
Llaneras F, Picó J. Stoichiometric modelling of cell metabolism. J Biosci Bioeng 2008;105:1-11. [DOI: 10.1263/jbb.105.1] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Accepted: 10/25/2007] [Indexed: 10/22/2022]
44
Matsubara Y, Kikuchi S, Sugimoto M, Oka K, Tomita M. Algebraic method for the analysis of signaling crosstalk. ARTIFICIAL LIFE 2008;14:81-94. [PMID: 18171132 DOI: 10.1162/artl.2008.14.1.81] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
45
Nookaew I, Meechai A, Thammarongtham C, Laoteng K, Ruanglek V, Cheevadhanarak S, Nielsen J, Bhumiratana S. Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks. Biotechnol Bioeng 2007;97:1535-49. [PMID: 17238207 DOI: 10.1002/bit.21339] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
46
Heino J, Tunyan K, Calvetti D, Somersalo E. Bayesian flux balance analysis applied to a skeletal muscle metabolic model. J Theor Biol 2007;248:91-110. [PMID: 17568615 PMCID: PMC2065751 DOI: 10.1016/j.jtbi.2007.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Revised: 03/06/2007] [Accepted: 04/04/2007] [Indexed: 10/23/2022]
47
Kurata H, Zhao Q, Okuda R, Shimizu K. Integration of enzyme activities into metabolic flux distributions by elementary mode analysis. BMC SYSTEMS BIOLOGY 2007;1:31. [PMID: 17640350 PMCID: PMC1973080 DOI: 10.1186/1752-0509-1-31] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 07/18/2007] [Indexed: 11/16/2022]
48
Wang Q, Yang Y, Ma H, Zhao X. Metabolic network properties help assign weights to elementary modes to understand physiological flux distributions. Bioinformatics 2007;23:1049-52. [PMID: 17341495 DOI: 10.1093/bioinformatics/btm074] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
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Llaneras F, Picó J. An interval approach for dealing with flux distributions and elementary modes activity patterns. J Theor Biol 2007;246:290-308. [PMID: 17292923 DOI: 10.1016/j.jtbi.2006.12.029] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Revised: 12/21/2006] [Accepted: 12/22/2006] [Indexed: 11/22/2022]
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Metabolic Engineering. CELL ENGINEERING 2007. [DOI: 10.1007/1-4020-5252-9_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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