메뉴 건너뛰기




Volumn 24, Issue 2, 2013, Pages 271-277

Plant genome-scale metabolic reconstruction and modelling

Author keywords

[No Author keywords available]

Indexed keywords

COMPARTMENTATION; COMPLEX PHENOTYPE; GENOME-SCALE METABOLIC MODELS; INCOMPLETE KNOWLEDGE; INDUSTRIAL STRAIN; METABOLIC RECONSTRUCTION; MICROBIAL METABOLISM; POTENTIAL VALUES;

EID: 84874976941     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2012.08.007     Document Type: Review
Times cited : (61)

References (51)
  • 1
    • 0033580813 scopus 로고    scopus 로고
    • Systems properties of the Haemophilus influenzae Rd metabolic genotype
    • Edwards J.S., Palsson B.O. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem 1999, 274:17410-17416.
    • (1999) J Biol Chem , vol.274 , pp. 17410-17416
    • Edwards, J.S.1    Palsson, B.O.2
  • 2
    • 57549102595 scopus 로고    scopus 로고
    • Genome-scale models of bacterial metabolism: reconstruction and applications
    • Durot M., Bourguignon P.Y., Schachter V. Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev 2009, 33:164-190.
    • (2009) FEMS Microbiol Rev , vol.33 , pp. 164-190
    • Durot, M.1    Bourguignon, P.Y.2    Schachter, V.3
  • 4
    • 84863012205 scopus 로고    scopus 로고
    • Butanol production from renewable biomass: rediscovery of metabolic pathways and metabolic engineering
    • Jang Y.S., Lee J., Malaviya A., Seung do Y., Cho J.H., Lee S.Y. Butanol production from renewable biomass: rediscovery of metabolic pathways and metabolic engineering. Biotechnol J 2012, 7:186-198.
    • (2012) Biotechnol J , vol.7 , pp. 186-198
    • Jang, Y.S.1    Lee, J.2    Malaviya, A.3    Seung do, Y.4    Cho, J.H.5    Lee, S.Y.6
  • 5
    • 79959610473 scopus 로고    scopus 로고
    • Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production
    • Park J.M., Kim T.Y., Lee S.Y. Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production. BMC Syst Biol 2011, 5:101.
    • (2011) BMC Syst Biol , vol.5 , pp. 101
    • Park, J.M.1    Kim, T.Y.2    Lee, S.Y.3
  • 6
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • Edwards J.S., Ibarra R.U., Palsson B.O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 2001, 19:125-130.
    • (2001) Nat Biotechnol , vol.19 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.O.3
  • 7
    • 67650220754 scopus 로고    scopus 로고
    • Systems biology: properties of reconstructed networks
    • Werner E. Systems biology: properties of reconstructed networks. Nature 2007, 446:493-494.
    • (2007) Nature , vol.446 , pp. 493-494
    • Werner, E.1
  • 8
    • 70350676551 scopus 로고    scopus 로고
    • A genome-scale metabolic model of Arabidopsis and some of its properties
    • Poolman M.G., Miguet L., Sweetlove L.J., Fell D.A. A genome-scale metabolic model of Arabidopsis and some of its properties. Plant Physiol 2009, 151:1570-1581.
    • (2009) Plant Physiol , vol.151 , pp. 1570-1581
    • Poolman, M.G.1    Miguet, L.2    Sweetlove, L.J.3    Fell, D.A.4
  • 10
    • 84856015478 scopus 로고    scopus 로고
    • Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity
    • Mintz-Oron S., Meir S., Malitsky S., Ruppin E., Aharoni A., Shlomi T. Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity. Proc Natl Acad Sci USA 2012, 109:339-344.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 339-344
    • Mintz-Oron, S.1    Meir, S.2    Malitsky, S.3    Ruppin, E.4    Aharoni, A.5    Shlomi, T.6
  • 12
    • 79959946634 scopus 로고    scopus 로고
    • Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism
    • Saha R., Suthers P.F., Maranas C.D. Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. PLoS ONE 2011, 6:e21784.
    • (2011) PLoS ONE , vol.6
    • Saha, R.1    Suthers, P.F.2    Maranas, C.D.3
  • 13
    • 84859367668 scopus 로고    scopus 로고
    • Frontiers in metabolic reconstruction and modeling of plant genomes
    • Seaver S.M., Henry C.S., Hanson A.D. Frontiers in metabolic reconstruction and modeling of plant genomes. J Exp Bot 2012, 63:2247-2258.
    • (2012) J Exp Bot , vol.63 , pp. 2247-2258
    • Seaver, S.M.1    Henry, C.S.2    Hanson, A.D.3
  • 14
    • 73149122136 scopus 로고    scopus 로고
    • Applications of genome-scale metabolic reconstructions
    • Oberhardt M.A., Palsson B.O., Papin J.A. Applications of genome-scale metabolic reconstructions. Mol Syst Biol 2009, 5:320.
    • (2009) Mol Syst Biol , vol.5 , pp. 320
    • Oberhardt, M.A.1    Palsson, B.O.2    Papin, J.A.3
  • 15
    • 0033971754 scopus 로고    scopus 로고
    • EcoGene: a genome sequence database for Escherichia coli K-12
    • Rudd K.E. EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 2000, 28:60-64.
    • (2000) Nucleic Acids Res , vol.28 , pp. 60-64
    • Rudd, K.E.1
  • 16
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • Forster J., Famili I., Fu P., Palsson B.O., Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003, 13:244-253.
    • (2003) Genome Res , vol.13 , pp. 244-253
    • Forster, J.1    Famili, I.2    Fu, P.3    Palsson, B.O.4    Nielsen, J.5
  • 17
    • 77951122415 scopus 로고    scopus 로고
    • Reconstruction annotation jamborees: a community approach to systems biology
    • Thiele I., Palsson B.O. Reconstruction annotation jamborees: a community approach to systems biology. Mol Syst Biol 2010, 6:361.
    • (2010) Mol Syst Biol , vol.6 , pp. 361
    • Thiele, I.1    Palsson, B.O.2
  • 18
    • 67651209209 scopus 로고    scopus 로고
    • On the reconstruction of the Mus musculus genome-scale metabolic network model
    • Quek L., Nielsen L.K. On the reconstruction of the Mus musculus genome-scale metabolic network model. Genome Inform 2008, 21:89-100.
    • (2008) Genome Inform , vol.21 , pp. 89-100
    • Quek, L.1    Nielsen, L.K.2
  • 20
  • 21
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I., Palsson B.O. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 2010, 5:93-121.
    • (2010) Nat Protoc , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 23
    • 84861372886 scopus 로고    scopus 로고
    • Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth
    • Sohn S.B., Kim T.Y., Lee J.H., Lee S.Y. Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth. BMC Syst Biol 2012, 6:49.
    • (2012) BMC Syst Biol , vol.6 , pp. 49
    • Sohn, S.B.1    Kim, T.Y.2    Lee, J.H.3    Lee, S.Y.4
  • 24
    • 84859199206 scopus 로고    scopus 로고
    • Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials
    • Caspeta L., Shoaie S., Agren R., Nookaew I., Nielsen J. Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC Syst Biol 2012, 6:24.
    • (2012) BMC Syst Biol , vol.6 , pp. 24
    • Caspeta, L.1    Shoaie, S.2    Agren, R.3    Nookaew, I.4    Nielsen, J.5
  • 25
    • 41149105489 scopus 로고    scopus 로고
    • Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger
    • Andersen M.R., Nielsen M.L., Nielsen J. Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol 2008, 4:178.
    • (2008) Mol Syst Biol , vol.4 , pp. 178
    • Andersen, M.R.1    Nielsen, M.L.2    Nielsen, J.3
  • 27
    • 77956456621 scopus 로고    scopus 로고
    • Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis
    • Huthmacher C., Huthmacher C., Hoppe A., Bulik S., Holzhütter H.G. Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. BMC Syst Biol 2010, 4:120.
    • (2010) BMC Syst Biol , vol.4 , pp. 120
    • Huthmacher, C.1    Huthmacher, C.2    Hoppe, A.3    Bulik, S.4    Holzhütter, H.G.5
  • 29
    • 84255195408 scopus 로고    scopus 로고
    • AlgaGEM - a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome
    • de Oliveira Dal'Molin C.G.D., Quek L.E., Palfreyman R.W., Nielsen L.K. AlgaGEM - a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome. BMC Genomics 2011, 12(Suppl 4):S5.
    • (2011) BMC Genomics , vol.12 , Issue.SUPPL. 4
    • de Oliveira Dal'Molin, C.G.D.1    Quek, L.E.2    Palfreyman, R.W.3    Nielsen, L.K.4
  • 32
    • 84857081283 scopus 로고    scopus 로고
    • The pathway tools pathway prediction algorithm
    • Karp P.D., Latendresse M., Caspi R. The pathway tools pathway prediction algorithm. Stand Genomic Sci 2011, 5:424-429.
    • (2011) Stand Genomic Sci , vol.5 , pp. 424-429
    • Karp, P.D.1    Latendresse, M.2    Caspi, R.3
  • 33
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • Arabidopsis G.I. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
    • (2000) Nature , vol.408 , pp. 796-815
    • Arabidopsis, G.I.1
  • 34
    • 84861165967 scopus 로고    scopus 로고
    • Are we ready for genome-scale modeling in plants?
    • Collakova E., Yen J.Y., Senger R.S. Are we ready for genome-scale modeling in plants?. Plant Sci 2012, 191-132:53-70.
    • (2012) Plant Sci , pp. 53-70
    • Collakova, E.1    Yen, J.Y.2    Senger, R.S.3
  • 35
    • 66349097905 scopus 로고    scopus 로고
    • Network-based prediction of metabolic enzymes' subcellular localization
    • Mintz-Oron S., Aharoni A., Ruppin E., Shlomi T. Network-based prediction of metabolic enzymes' subcellular localization. Bioinformatics 2009, 25:i247-i252.
    • (2009) Bioinformatics , vol.25
    • Mintz-Oron, S.1    Aharoni, A.2    Ruppin, E.3    Shlomi, T.4
  • 40
    • 34547888003 scopus 로고    scopus 로고
    • A genome-scale, constraint-based approach to systems biology of human metabolism
    • Mo M.L., Jamshidi N., Palsson B.O. A genome-scale, constraint-based approach to systems biology of human metabolism. Mol Biosyst 2007, 3:598-603.
    • (2007) Mol Biosyst , vol.3 , pp. 598-603
    • Mo, M.L.1    Jamshidi, N.2    Palsson, B.O.3
  • 41
    • 67449096729 scopus 로고    scopus 로고
    • Flux balance analysis of biological systems: applications and challenges
    • Raman K., Chandra N Flux balance analysis of biological systems: applications and challenges. Brief Bioinform 2009, 10:435-449.
    • (2009) Brief Bioinform , vol.10 , pp. 435-449
    • Raman, K.1    Chandra, N.2
  • 42
    • 34247256814 scopus 로고    scopus 로고
    • Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains
    • Cakir T., Efe C., Dikicioglu D., Hortaçsu A., Kirdar B., Oliver S.G. Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains. Biotechnol Progr 2007, 23:320-326.
    • (2007) Biotechnol Progr , vol.23 , pp. 320-326
    • Cakir, T.1    Efe, C.2    Dikicioglu, D.3    Hortaçsu, A.4    Kirdar, B.5    Oliver, S.G.6
  • 43
    • 33748464202 scopus 로고    scopus 로고
    • Flux balance analysis in the era of metabolomics
    • Lee J.M., Gianchandani E.P., Papin J.A. Flux balance analysis in the era of metabolomics. Brief Bioinform 2006, 7:140-150.
    • (2006) Brief Bioinform , vol.7 , pp. 140-150
    • Lee, J.M.1    Gianchandani, E.P.2    Papin, J.A.3
  • 45
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • Mahadevan R., Schilling C.H. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 2003, 5:264-276.
    • (2003) Metab Eng , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 46
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • Segre D., Vitkup D., Church G.M. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 2002, 99:15112-15117.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 15112-15117
    • Segre, D.1    Vitkup, D.2    Church, G.M.3
  • 47
    • 19644386033 scopus 로고    scopus 로고
    • Regulatory on/off minimization of metabolic flux changes after genetic perturbations
    • Shlomi T., Berkman O., Ruppin E. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 2005, 102:7695-7700.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 7695-7700
    • Shlomi, T.1    Berkman, O.2    Ruppin, E.3
  • 48
    • 70350645014 scopus 로고    scopus 로고
    • Analysis of metabolic flux phenotypes for two Arabidopsis mutants with severe impairment in seed storage lipid synthesis
    • Lonien J., Schwender J. Analysis of metabolic flux phenotypes for two Arabidopsis mutants with severe impairment in seed storage lipid synthesis. Plant Physiol 2009, 151:1617-1634.
    • (2009) Plant Physiol , vol.151 , pp. 1617-1634
    • Lonien, J.1    Schwender, J.2
  • 49
    • 33645960112 scopus 로고    scopus 로고
    • Functional differentiation of bundle sheath and mesophyll maize chloroplasts determined by comparative proteomics
    • Majeran W., Majeran W., Cai Y., Sun Q., van Wijk K.J. Functional differentiation of bundle sheath and mesophyll maize chloroplasts determined by comparative proteomics. Plant Cell 2005, 17:3111-3140.
    • (2005) Plant Cell , vol.17 , pp. 3111-3140
    • Majeran, W.1    Majeran, W.2    Cai, Y.3    Sun, Q.4    van Wijk, K.J.5
  • 50
    • 52649096494 scopus 로고    scopus 로고
    • Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells
    • Majeran W., Majeran W., Zybailov B., Ytterberg A.J., Dunsmore J., Sun Q., van Wijk K.J. Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells. Mol Cell Proteomics 2008, 7:1609-1638.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 1609-1638
    • Majeran, W.1    Majeran, W.2    Zybailov, B.3    Ytterberg, A.J.4    Dunsmore, J.5    Sun, Q.6    van Wijk, K.J.7
  • 51
    • 77949565231 scopus 로고    scopus 로고
    • Reconstruction of metabolic pathways, protein expression, and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts: large-scale quantitative proteomics using the first maize genome assembly
    • Friso G., Majeran W., Huang M., Sun Q., van Wijk K.J. Reconstruction of metabolic pathways, protein expression, and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts: large-scale quantitative proteomics using the first maize genome assembly. Plant Physiol 2010, 152:1219-1250.
    • (2010) Plant Physiol , vol.152 , pp. 1219-1250
    • Friso, G.1    Majeran, W.2    Huang, M.3    Sun, Q.4    van Wijk, K.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.