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Volumn 7, Issue , 2013, Pages

Bridging the gap between gene expression and metabolic phenotype via kinetic models

Author keywords

Fluxomics; Gene expression; Kinetic models; Metabolic networks; Metabolomics; S. cerevisiae; Transcriptomics

Indexed keywords

SACCHAROMYCES CEREVISIAE;

EID: 84880335117     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-63     Document Type: Article
Times cited : (18)

References (39)
  • 2
    • 80051708188 scopus 로고    scopus 로고
    • Modeling synergistic drug inhibition of Mycobacterium tuberculosis growth in murine macrophages
    • 10.1039/c1mb05106g, 21713281
    • Fang X, Wallqvist A, Reifman J. Modeling synergistic drug inhibition of Mycobacterium tuberculosis growth in murine macrophages. Mol Biosyst 2011, 7:2622-2636. 10.1039/c1mb05106g, 21713281.
    • (2011) Mol Biosyst , vol.7 , pp. 2622-2636
    • Fang, X.1    Wallqvist, A.2    Reifman, J.3
  • 3
    • 34347258175 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
    • 10.1038/nprot.2007.99, 17406635
    • Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2007, 2:727-738. 10.1038/nprot.2007.99, 17406635.
    • (2007) Nat Protoc , vol.2 , pp. 727-738
    • Becker, S.A.1    Feist, A.M.2    Mo, M.L.3    Hannum, G.4    Palsson, B.O.5    Herrgard, M.J.6
  • 4
    • 8744224466 scopus 로고    scopus 로고
    • OptStrain: a computational framework for redesign of microbial production systems
    • 10.1101/gr.2872004, 525696, 15520298
    • Pharkya P, Burgard AP, Maranas CD. OptStrain: a computational framework for redesign of microbial production systems. Genome Res 2004, 14:2367-2376. 10.1101/gr.2872004, 525696, 15520298.
    • (2004) Genome Res , vol.14 , pp. 2367-2376
    • Pharkya, P.1    Burgard, A.P.2    Maranas, C.D.3
  • 5
    • 77953128693 scopus 로고    scopus 로고
    • Use of genome-scale metabolic models for understanding microbial physiology
    • 10.1016/j.febslet.2010.04.052, 20420838
    • Liu L, Agren R, Bordel S, Nielsen J. Use of genome-scale metabolic models for understanding microbial physiology. FEBS Lett 2010, 584:2556-2564. 10.1016/j.febslet.2010.04.052, 20420838.
    • (2010) FEBS Lett , vol.584 , pp. 2556-2564
    • Liu, L.1    Agren, R.2    Bordel, S.3    Nielsen, J.4
  • 6
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering
    • 10.1016/S0167-7799(98)01290-6, 10087604
    • Schuster S, Dandekar T, Fell DA. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol 1999, 17:53-60. 10.1016/S0167-7799(98)01290-6, 10087604.
    • (1999) Trends Biotechnol , vol.17 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.A.3
  • 7
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • 10.1371/journal.pcbi.1000082, 2366062, 18483554
    • Becker SA, Palsson BO. Context-specific metabolic networks are consistent with experiments. PLOS Comput Biol 2008, 4:e1000082. 10.1371/journal.pcbi.1000082, 2366062, 18483554.
    • (2008) PLOS Comput Biol , vol.4
    • Becker, S.A.1    Palsson, B.O.2
  • 8
    • 77957837882 scopus 로고    scopus 로고
    • Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection
    • 10.1128/JB.00900-10, 2950489, 20709898
    • Oberhardt MA, Goldberg JB, Hogardt M, Papin JA. Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection. J Bacteriol 2010, 192:5534-5548. 10.1128/JB.00900-10, 2950489, 20709898.
    • (2010) J Bacteriol , vol.192 , pp. 5534-5548
    • Oberhardt, M.A.1    Goldberg, J.B.2    Hogardt, M.3    Papin, J.A.4
  • 9
    • 51349092391 scopus 로고    scopus 로고
    • Network-based prediction of human tissue-specific metabolism
    • 10.1038/nbt.1487, 18711341
    • Shlomi T, Cabili MN, Herrgard MJ, Palsson BO, Ruppin E. Network-based prediction of human tissue-specific metabolism. Nat Biotechnol 2008, 26:1003-1010. 10.1038/nbt.1487, 18711341.
    • (2008) Nat Biotechnol , vol.26 , pp. 1003-1010
    • Shlomi, T.1    Cabili, M.N.2    Herrgard, M.J.3    Palsson, B.O.4    Ruppin, E.5
  • 10
    • 84866925914 scopus 로고    scopus 로고
    • Modeling phenotypic metabolic adaptations of Mycobacterium tuberculosis H37Rv under hypoxia
    • 10.1371/journal.pcbi.1002688, 3441462, 23028286
    • Fang X, Wallqvist A, Reifman J. Modeling phenotypic metabolic adaptations of Mycobacterium tuberculosis H37Rv under hypoxia. PLOS Comput Biol 2012, 8:e1002688. 10.1371/journal.pcbi.1002688, 3441462, 23028286.
    • (2012) PLOS Comput Biol , vol.8
    • Fang, X.1    Wallqvist, A.2    Reifman, J.3
  • 11
    • 78650773077 scopus 로고    scopus 로고
    • A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks
    • 3132400, 20951196
    • Narendra V, Lytkin NI, Aliferis CF, Statnikov A. A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks. Genomics 2010, 97:7-18. 3132400, 20951196.
    • (2010) Genomics , vol.97 , pp. 7-18
    • Narendra, V.1    Lytkin, N.I.2    Aliferis, C.F.3    Statnikov, A.4
  • 12
    • 34247183123 scopus 로고    scopus 로고
    • A genome-scale computational study of the interplay between transcriptional regulation and metabolism
    • 1865583, 17437026
    • Shlomi T, Eisenberg Y, Sharan R, Ruppin E. A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol 2007, 3:101. 1865583, 17437026.
    • (2007) Mol Syst Biol , vol.3 , pp. 101
    • Shlomi, T.1    Eisenberg, Y.2    Sharan, R.3    Ruppin, E.4
  • 13
    • 51749113592 scopus 로고    scopus 로고
    • Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
    • 10.1093/bioinformatics/btn352, 18621757
    • Covert MW, Xiao N, Chen TJ, Karr JR. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 2008, 24:2044-2050. 10.1093/bioinformatics/btn352, 18621757.
    • (2008) Bioinformatics , vol.24 , pp. 2044-2050
    • Covert, M.W.1    Xiao, N.2    Chen, T.J.3    Karr, J.R.4
  • 14
    • 77951552860 scopus 로고    scopus 로고
    • OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains
    • 10.1186/1752-0509-4-53, 2887412, 20426856
    • Kim J, Reed JL. OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst Biol 2010, 4:53. 10.1186/1752-0509-4-53, 2887412, 20426856.
    • (2010) BMC Syst Biol , vol.4 , pp. 53
    • Kim, J.1    Reed, J.L.2
  • 15
    • 44949247269 scopus 로고    scopus 로고
    • Dynamic analysis of integrated signaling, metabolic, and regulatory networks
    • 10.1371/journal.pcbi.1000086, 2377155, 18483615
    • Lee JM, Min Lee J, Gianchandani EP, Eddy JA, Papin JA. Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLOS Comput Biol 2008, 4:e1000086. 10.1371/journal.pcbi.1000086, 2377155, 18483615.
    • (2008) PLOS Comput Biol , vol.4
    • Lee, J.M.1    Min Lee, J.2    Gianchandani, E.P.3    Eddy, J.A.4    Papin, J.A.5
  • 16
    • 60149094488 scopus 로고    scopus 로고
    • A divide-and-conquer approach to analyze underdetermined biochemical models
    • 10.1093/bioinformatics/btp004, 19126574
    • Kotte O, Heinemann M. A divide-and-conquer approach to analyze underdetermined biochemical models. Bioinformatics 2009, 25:519-525. 10.1093/bioinformatics/btp004, 19126574.
    • (2009) Bioinformatics , vol.25 , pp. 519-525
    • Kotte, O.1    Heinemann, M.2
  • 17
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: evaluating the consequences of constraints
    • 10.1038/nrmicro1023, 15494745
    • Price ND, Reed JL, Palsson BO. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2004, 2:886-897. 10.1038/nrmicro1023, 15494745.
    • (2004) Nat Rev Microbiol , vol.2 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 19
    • 33846617808 scopus 로고    scopus 로고
    • Bringing metabolic networks to life: convenience rate law and thermodynamic constraints
    • 10.1186/1742-4682-3-41, 1781438, 17173669
    • Liebermeister W, Klipp E. Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor Biol Med Model 2006, 3:41. 10.1186/1742-4682-3-41, 1781438, 17173669.
    • (2006) Theor Biol Med Model , vol.3 , pp. 41
    • Liebermeister, W.1    Klipp, E.2
  • 20
    • 58749106454 scopus 로고    scopus 로고
    • Ensemble modeling of metabolic networks
    • 10.1529/biophysj.108.135442, 2599852, 18820235
    • Tran LM, Rizk ML, Liao JC. Ensemble modeling of metabolic networks. Biophys J 2008, 95:5606-5617. 10.1529/biophysj.108.135442, 2599852, 18820235.
    • (2008) Biophys J , vol.95 , pp. 5606-5617
    • Tran, L.M.1    Rizk, M.L.2    Liao, J.C.3
  • 21
    • 77049084742 scopus 로고    scopus 로고
    • Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models
    • 10.1016/j.bpj.2009.09.064, 2808481, 20338839
    • Jamshidi N, Palsson BO. Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. Biophys J 2010, 98:175-185. 10.1016/j.bpj.2009.09.064, 2808481, 20338839.
    • (2010) Biophys J , vol.98 , pp. 175-185
    • Jamshidi, N.1    Palsson, B.O.2
  • 22
    • 77649176477 scopus 로고    scopus 로고
    • Towards a genome-scale kinetic model of cellular metabolism
    • 10.1186/1752-0509-4-6, 2829494, 20109182
    • Smallbone K, Simeonidis E, Swainston N, Mendes P. Towards a genome-scale kinetic model of cellular metabolism. BMC Syst Biol 2010, 4:6. 10.1186/1752-0509-4-6, 2829494, 20109182.
    • (2010) BMC Syst Biol , vol.4 , pp. 6
    • Smallbone, K.1    Simeonidis, E.2    Swainston, N.3    Mendes, P.4
  • 23
    • 20444478968 scopus 로고    scopus 로고
    • Computation and analysis of time-dependent sensitivities in Generalized Mass Action systems
    • 10.1016/j.jtbi.2005.02.013, 15967181
    • Schwacke JH, Voit EO. Computation and analysis of time-dependent sensitivities in Generalized Mass Action systems. J Theor Biol 2005, 236:21-38. 10.1016/j.jtbi.2005.02.013, 15967181.
    • (2005) J Theor Biol , vol.236 , pp. 21-38
    • Schwacke, J.H.1    Voit, E.O.2
  • 24
    • 34547868108 scopus 로고    scopus 로고
    • Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae
    • 10.1111/j.1567-1364.2007.00242.x, 17484738
    • Abbott DA, Knijnenburg TA, de-Poorter LM, Reinders MJ, Pronk JT, van-Maris AJ. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res 2007, 7:819-833. 10.1111/j.1567-1364.2007.00242.x, 17484738.
    • (2007) FEMS Yeast Res , vol.7 , pp. 819-833
    • Abbott, D.A.1    Knijnenburg, T.A.2    de-Poorter, L.M.3    Reinders, M.J.4    Pronk, J.T.5    van-Maris, A.J.6
  • 26
    • 76649110552 scopus 로고    scopus 로고
    • Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin
    • 10.1074/mcp.M900415-MCP200, 2830839, 19955083
    • Fournier ML, Paulson A, Pavelka N, Mosley AL, Gaudenz K, Bradford WD, Glynn E, Li H, Sardiu ME, Fleharty B, et al. Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin. Mol Cell Proteomics 2010, 9:271-284. 10.1074/mcp.M900415-MCP200, 2830839, 19955083.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 271-284
    • Fournier, M.L.1    Paulson, A.2    Pavelka, N.3    Mosley, A.L.4    Gaudenz, K.5    Bradford, W.D.6    Glynn, E.7    Li, H.8    Sardiu, M.E.9    Fleharty, B.10
  • 27
    • 79960581086 scopus 로고    scopus 로고
    • A dynamic model of proteome changes reveals new roles for transcript alteration in yeast
    • 3159980, 21772262
    • Lee MV, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP. A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol Syst Biol 2011, 7:514. 3159980, 21772262.
    • (2011) Mol Syst Biol , vol.7 , pp. 514
    • Lee, M.V.1    Topper, S.E.2    Hubler, S.L.3    Hose, J.4    Wenger, C.D.5    Coon, J.J.6    Gasch, A.P.7
  • 28
    • 84936916896 scopus 로고
    • Robust locally weighted regression and smoothing scatterplots
    • Cleveland WS. Robust locally weighted regression and smoothing scatterplots. J Am Stat Assoc 1979, 74:829-836.
    • (1979) J Am Stat Assoc , vol.74 , pp. 829-836
    • Cleveland, W.S.1
  • 29
    • 27144510561 scopus 로고    scopus 로고
    • Translational regulation of GCN4 and the general amino acid control of yeast
    • 10.1146/annurev.micro.59.031805.133833, 16153175
    • Hinnebusch AG. Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol 2005, 59:407-450. 10.1146/annurev.micro.59.031805.133833, 16153175.
    • (2005) Annu Rev Microbiol , vol.59 , pp. 407-450
    • Hinnebusch, A.G.1
  • 30
    • 84863399669 scopus 로고    scopus 로고
    • Exploring polypharmacology using a ROCS-based target fishing approach
    • 10.1021/ci2003544, 22196353
    • AbdulHameed MD, Chaudhury S, Singh N, Sun H, Wallqvist A, Tawa GJ. Exploring polypharmacology using a ROCS-based target fishing approach. J Chem Inf Model 2012, 52:492-505. 10.1021/ci2003544, 22196353.
    • (2012) J Chem Inf Model , vol.52 , pp. 492-505
    • AbdulHameed, M.D.1    Chaudhury, S.2    Singh, N.3    Sun, H.4    Wallqvist, A.5    Tawa, G.J.6
  • 31
    • 0032479995 scopus 로고    scopus 로고
    • The pdr12 ABC transporter is required for the development of weak organic acid resistance in yeast
    • 10.1093/emboj/17.15.4257, 1170759, 9687494
    • Piper P, Mahe Y, Thompson S, Pandjaitan R, Holyoak C, Egner R, Muhlbauer M, Coote P, Kuchler K. The pdr12 ABC transporter is required for the development of weak organic acid resistance in yeast. EMBO J 1998, 17:4257-4265. 10.1093/emboj/17.15.4257, 1170759, 9687494.
    • (1998) EMBO J , vol.17 , pp. 4257-4265
    • Piper, P.1    Mahe, Y.2    Thompson, S.3    Pandjaitan, R.4    Holyoak, C.5    Egner, R.6    Muhlbauer, M.7    Coote, P.8    Kuchler, K.9
  • 32
    • 0030574106 scopus 로고    scopus 로고
    • MCA has more to say
    • 10.1006/jtbi.1996.0160, 8944154
    • Hatzimanikatis V, Bailey JE. MCA has more to say. J Theor Biol 1996, 182:233-242. 10.1006/jtbi.1996.0160, 8944154.
    • (1996) J Theor Biol , vol.182 , pp. 233-242
    • Hatzimanikatis, V.1    Bailey, J.E.2
  • 33
    • 77952797285 scopus 로고    scopus 로고
    • Streamlining the construction of large-scale dynamic models using generic kinetic equations
    • 10.1093/bioinformatics/btq136, 20363732
    • Adiamah DA, Handl J, Schwartz JM. Streamlining the construction of large-scale dynamic models using generic kinetic equations. Bioinformatics 2010, 26:1324-1331. 10.1093/bioinformatics/btq136, 20363732.
    • (2010) Bioinformatics , vol.26 , pp. 1324-1331
    • Adiamah, D.A.1    Handl, J.2    Schwartz, J.M.3
  • 34
    • 67649997281 scopus 로고    scopus 로고
    • Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis
    • Bruck J, Liebermeister W, Klipp E. Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis. Genome Inform 2008, 20:1-14.
    • (2008) Genome Inform , vol.20 , pp. 1-14
    • Bruck, J.1    Liebermeister, W.2    Klipp, E.3
  • 36
    • 33745433792 scopus 로고    scopus 로고
    • Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data
    • 1681506, 16788595
    • Kummel A, Panke S, Heinemann M. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol 2006, 2:2006.0034. 1681506, 16788595.
    • (2006) Mol Syst Biol , vol.2
    • Kummel, A.1    Panke, S.2    Heinemann, M.3
  • 37
    • 0015989446 scopus 로고
    • A linear steady-state treatment of enzymatic chains. General properties, control and effector strength
    • 10.1111/j.1432-1033.1974.tb03318.x, 4830198
    • Heinrich R, Rapoport TA. A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur J Biochem 1974, 42:89-95. 10.1111/j.1432-1033.1974.tb03318.x, 4830198.
    • (1974) Eur J Biochem , vol.42 , pp. 89-95
    • Heinrich, R.1    Rapoport, T.A.2


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