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For: Poolman MG, Bonde BK, Gevorgyan A, Patel HH, Fell DA. Challenges to be faced in the reconstruction of metabolic networks from public databases. ACTA ACUST UNITED AC 2006;153:379-84. [PMID: 16986322 DOI: 10.1049/ip-syb:20060012] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Number Cited by Other Article(s)
1
Jin H, Moseley HNB. md_harmonize: A Python Package for Atom-Level Harmonization of Public Metabolic Databases. Metabolites 2023;13:1199. [PMID: 38132881 PMCID: PMC10744849 DOI: 10.3390/metabo13121199] [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: 11/14/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]  Open
2
Jin H, Moseley HNB. Hierarchical Harmonization of Atom-Resolved Metabolic Reactions across Metabolic Databases. Metabolites 2021;11:metabo11070431. [PMID: 34209357 PMCID: PMC8307411 DOI: 10.3390/metabo11070431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022]  Open
3
Gholizadeh M, Fayazi J, Asgari Y, Zali H, Kaderali L. Reconstruction and Analysis of Cattle Metabolic Networks in Normal and Acidosis Rumen Tissue. Animals (Basel) 2020;10:ani10030469. [PMID: 32168900 PMCID: PMC7142512 DOI: 10.3390/ani10030469] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 12/29/2022]  Open
4
Mancini A, Eyassu F, Conway M, Occhipinti A, Liò P, Angione C, Pucciarelli S. CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design. BMC Bioinformatics 2018;19:442. [PMID: 30497359 PMCID: PMC6266953 DOI: 10.1186/s12859-018-2422-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
5
Shaw R, Cheung CYM. A Dynamic Multi-Tissue Flux Balance Model Captures Carbon and Nitrogen Metabolism and Optimal Resource Partitioning During Arabidopsis Growth. FRONTIERS IN PLANT SCIENCE 2018;9:884. [PMID: 29997643 PMCID: PMC6028781 DOI: 10.3389/fpls.2018.00884] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 06/06/2018] [Indexed: 05/19/2023]
6
Chatterjee A, Huma B, Shaw R, Kundu S. Reconstruction of Oryza sativa indica Genome Scale Metabolic Model and Its Responses to Varying RuBisCO Activity, Light Intensity, and Enzymatic Cost Conditions. FRONTIERS IN PLANT SCIENCE 2017;8:2060. [PMID: 29250098 PMCID: PMC5715477 DOI: 10.3389/fpls.2017.02060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 11/17/2017] [Indexed: 05/12/2023]
7
Ahmad A, Hartman HB, Krishnakumar S, Fell DA, Poolman MG, Srivastava S. A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate. J Biotechnol 2017;251:30-37. [DOI: 10.1016/j.jbiotec.2017.03.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 01/29/2023]
8
Flux balance analysis of genome-scale metabolic model of rice (Oryza sativa): aiming to increase biomass. J Biosci 2016;40:819-28. [PMID: 26564982 DOI: 10.1007/s12038-015-9563-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
9
Kim W, Park H, Seo S. Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome. PLoS One 2016;11:e0150974. [PMID: 26992093 PMCID: PMC4798299 DOI: 10.1371/journal.pone.0150974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/22/2016] [Indexed: 11/23/2022]  Open
10
Salehzadeh-Yazdi A, Asgari Y, Saboury AA, Masoudi-Nejad A. Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach. PLoS One 2014;9:e111686. [PMID: 25365344 PMCID: PMC4218804 DOI: 10.1371/journal.pone.0111686] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 10/07/2014] [Indexed: 12/13/2022]  Open
11
Najafi A, Bidkhori G, Bozorgmehr JH, Koch I, Masoudi-Nejad A. Genome scale modeling in systems biology: algorithms and resources. Curr Genomics 2014;15:130-59. [PMID: 24822031 PMCID: PMC4009841 DOI: 10.2174/1389202915666140319002221] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 02/16/2014] [Accepted: 03/17/2014] [Indexed: 12/18/2022]  Open
12
Liberal R, Pinney JW. Simple topological properties predict functional misannotations in a metabolic network. Bioinformatics 2013;29:i154-61. [PMID: 23812979 PMCID: PMC3694667 DOI: 10.1093/bioinformatics/btt236] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
13
Poolman MG, Kundu S, Shaw R, Fell DA. Responses to light intensity in a genome-scale model of rice metabolism. PLANT PHYSIOLOGY 2013;162:1060-72. [PMID: 23640755 PMCID: PMC3668040 DOI: 10.1104/pp.113.216762] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/30/2013] [Indexed: 05/08/2023]
14
Evaluating Sphingolipid Biochemistry in the Consensus Reconstruction of Yeast Metabolism. Ind Biotechnol (New Rochelle N Y) 2012. [DOI: 10.1089/ind.2012.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
15
Alcántara R, Axelsen KB, Morgat A, Belda E, Coudert E, Bridge A, Cao H, de Matos P, Ennis M, Turner S, Owen G, Bougueleret L, Xenarios I, Steinbeck C. Rhea--a manually curated resource of biochemical reactions. Nucleic Acids Res 2011;40:D754-60. [PMID: 22135291 PMCID: PMC3245052 DOI: 10.1093/nar/gkr1126] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
16
LEE LW, YIN L, ZHU XM, AO P. GENERIC ENZYMATIC RATE EQUATION UNDER LIVING CONDITIONS. J BIOL SYST 2011. [DOI: 10.1142/s0218339007002295] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
17
XU MJ, ZHU XM, LIN PH, AO P. Generic Enzymatic Rate Equation*. PROG BIOCHEM BIOPHYS 2011. [DOI: 10.3724/sp.j.1206.2010.00500] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
18
Kaleta C, de Figueiredo LF, Heiland I, Klamt S, Schuster S. Special issue: integration of OMICs datasets into metabolic pathway analysis. Biosystems 2011;105:107-8. [PMID: 21619911 DOI: 10.1016/j.biosystems.2011.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
19
Zhou W, Nakhleh L. The strength of chemical linkage as a criterion for pruning metabolic graphs. Bioinformatics 2011;27:1957-63. [PMID: 21551141 DOI: 10.1093/bioinformatics/btr271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
20
Teusink B, Westerhoff HV, Bruggeman FJ. Comparative systems biology: from bacteria to man. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011;2:518-532. [PMID: 20836045 DOI: 10.1002/wsbm.74] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
21
Gevorgyan A, Bushell ME, Avignone-Rossa C, Kierzek AM. SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks. Bioinformatics 2010;27:433-4. [PMID: 21148545 DOI: 10.1093/bioinformatics/btq679] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
22
Building and analysing genome-scale metabolic models. Biochem Soc Trans 2010;38:1197-201. [DOI: 10.1042/bst0381197] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
23
Radrich K, Tsuruoka Y, Dobson P, Gevorgyan A, Swainston N, Baart G, Schwartz JM. Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. BMC SYSTEMS BIOLOGY 2010;4:114. [PMID: 20712863 PMCID: PMC2930596 DOI: 10.1186/1752-0509-4-114] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 08/16/2010] [Indexed: 01/13/2023]
24
Ruppin E, Papin JA, de Figueiredo LF, Schuster S. Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Curr Opin Biotechnol 2010;21:502-10. [DOI: 10.1016/j.copbio.2010.07.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 07/05/2010] [Indexed: 11/27/2022]
25
Smith GR, Shanley DP. Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways. PLoS One 2010;5:e11092. [PMID: 20567500 PMCID: PMC2886341 DOI: 10.1371/journal.pone.0011092] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 05/01/2010] [Indexed: 01/10/2023]  Open
26
Schellenberger J, Park JO, Conrad TM, Palsson BØ. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 2010;11:213. [PMID: 20426874 PMCID: PMC2874806 DOI: 10.1186/1471-2105-11-213] [Citation(s) in RCA: 356] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 04/29/2010] [Indexed: 12/28/2022]  Open
27
Bourguignon PY, Samal A, Képès F, Jost J, Martin OC. Challenges in experimental data integration within genome-scale metabolic models. Algorithms Mol Biol 2010;5:20. [PMID: 20412574 PMCID: PMC2865480 DOI: 10.1186/1748-7188-5-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2010] [Accepted: 04/22/2010] [Indexed: 11/10/2022]  Open
28
Poolman MG, Miguet L, Sweetlove LJ, Fell DA. A genome-scale metabolic model of Arabidopsis and some of its properties. PLANT PHYSIOLOGY 2009;151:1570-81. [PMID: 19755544 PMCID: PMC2773075 DOI: 10.1104/pp.109.141267] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 09/11/2009] [Indexed: 05/17/2023]
29
Figueiredo LFD, Schuster S, Kaleta C, Fell DA. Response to comment on 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'. Bioinformatics 2009;25:3330-1. [DOI: 10.1093/bioinformatics/btp591] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
30
Christian N, May P, Kempa S, Handorf T, Ebenhöh O. An integrative approach towards completing genome-scale metabolic networks. MOLECULAR BIOSYSTEMS 2009;5:1889-903. [PMID: 19763335 DOI: 10.1039/b915913b] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
31
Seo S, Lewin HA. Reconstruction of metabolic pathways for the cattle genome. BMC SYSTEMS BIOLOGY 2009;3:33. [PMID: 19284618 PMCID: PMC2669051 DOI: 10.1186/1752-0509-3-33] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Accepted: 03/12/2009] [Indexed: 01/21/2023]
32
Faust K, Croes D, van Helden J. Metabolic pathfinding using RPAIR annotation. J Mol Biol 2009;388:390-414. [PMID: 19281817 DOI: 10.1016/j.jmb.2009.03.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2008] [Revised: 02/25/2009] [Accepted: 03/03/2009] [Indexed: 12/21/2022]
33
Kotera M, McDonald AG, Boyce S, Tipton KF. Eliciting possible reaction equations and metabolic pathways involving orphan metabolites. J Chem Inf Model 2009;48:2335-49. [PMID: 19053521 DOI: 10.1021/ci800213g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
34
de Figueiredo LF, Schuster S, Kaleta C, Fell DA. Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics 2009;25:152-8. [PMID: 19117076 DOI: 10.1093/bioinformatics/btn621] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
35
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 2008;26:1155-60. [PMID: 18846089 DOI: 10.1038/nbt1492] [Citation(s) in RCA: 405] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
36
Nishikawa T, Gulbahce N, Motter AE. Spontaneous reaction silencing in metabolic optimization. PLoS Comput Biol 2008;4:e1000236. [PMID: 19057639 PMCID: PMC2582435 DOI: 10.1371/journal.pcbi.1000236] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 10/20/2008] [Indexed: 11/18/2022]  Open
37
Metabolic networks are NP-hard to reconstruct. J Theor Biol 2008;254:807-16. [DOI: 10.1016/j.jtbi.2008.07.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 07/14/2008] [Accepted: 07/14/2008] [Indexed: 11/22/2022]
38
de Figueiredo LF, Schuster S, Kaleta C, Fell DA. Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics 2008;24:2615-21. [DOI: 10.1093/bioinformatics/btn500] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
39
Gevorgyan A, Poolman MG, Fell DA. Detection of stoichiometric inconsistencies in biomolecular models. Bioinformatics 2008;24:2245-51. [DOI: 10.1093/bioinformatics/btn425] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
40
Kotera M, McDonald AG, Boyce S, Tipton KF. Functional group and substructure searching as a tool in metabolomics. PLoS One 2008;3:e1537. [PMID: 18253485 PMCID: PMC2212108 DOI: 10.1371/journal.pone.0001537] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 01/06/2008] [Indexed: 01/31/2023]  Open
41
Getting to grips with the plant metabolic network. Biochem J 2008;409:27-41. [PMID: 18062772 DOI: 10.1042/bj20071115] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
42
Modular decomposition of metabolic systems via null-space analysis. J Theor Biol 2007;249:691-705. [PMID: 17949756 DOI: 10.1016/j.jtbi.2007.08.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Revised: 07/02/2007] [Accepted: 08/03/2007] [Indexed: 11/23/2022]
43
Hoppe A, Hoffmann S, Holzhütter HG. Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks. BMC SYSTEMS BIOLOGY 2007;1:23. [PMID: 17543097 PMCID: PMC1903363 DOI: 10.1186/1752-0509-1-23] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 06/01/2007] [Indexed: 01/04/2023]
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