메뉴 건너뛰기




Volumn 3, Issue FEB, 2016, Pages

Constraint based modeling going multicellular

Author keywords

Constraint based modeling; Metabolic modeling; Multi organism modeling; Multi scale modeling; Multi tissue modeling

Indexed keywords


EID: 85028077640     PISSN: None     EISSN: 2296889X     Source Type: Journal    
DOI: 10.3389/fmolb.2016.00003     Document Type: Review
Times cited : (32)

References (73)
  • 1
    • 84952637898 scopus 로고    scopus 로고
    • ischrunk-in silico approach to characterization and reduction of uncertainty in the kinetic models of genome-scale metabolic networks
    • Andreozzi, S., Miskovic, L., and Hatzimanikatis, V. (2015). ischrunk-in silico approach to characterization and reduction of uncertainty in the kinetic models of genome-scale metabolic networks. Metab. Eng. 33, 158-168. doi: 10.1016/j.ymben.2015.10.002
    • (2015) Metab. Eng , vol.33 , pp. 158-168
    • Andreozzi, S.1    Miskovic, L.2    Hatzimanikatis, V.3
  • 2
    • 2342627280 scopus 로고    scopus 로고
    • Thermodynamic constraints for biochemical networks
    • Beard, D. A., Babson, E., Curtis, E., and Qian, H. (2004). Thermodynamic constraints for biochemical networks. J. Theor. Biol. 228, 327-333. doi: 10.1016/j.jtbi.2004.01.008
    • (2004) J. Theor. Biol , vol.228 , pp. 327-333
    • Beard, D.A.1    Babson, E.2    Curtis, E.3    Qian, H.4
  • 3
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • Becker, S. A., and Palsson, B. Ø. (2008). Context-specific metabolic networks are consistent with experiments. PLoS Comput. Biol. 4:e1000082. doi: 10.1371/journal.pcbi.1000082
    • (2008) PLoS Comput. Biol , vol.4
    • Becker, S.A.1    Palsson, B.Ø.2
  • 4
    • 84888243694 scopus 로고    scopus 로고
    • Modeling integrated cellular machinery using hybrid petri-boolean networks
    • Berestovsky, N., Zhou, W., Nagrath, D., and Nakhleh, L. (2013). Modeling integrated cellular machinery using hybrid petri-boolean networks. PLoS Comput. Biol. 9:e1003306. doi: 10.1371/journal.pcbi.1003306
    • (2013) PLoS Comput. Biol , vol.9
    • Berestovsky, N.1    Zhou, W.2    Nagrath, D.3    Nakhleh, L.4
  • 5
    • 80054969621 scopus 로고    scopus 로고
    • A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
    • Bordbar, A., Feist, A. M., Usaite-Black, R., Woodcock, J., Palsson, B. Ø., and Famili, I. (2011). A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst. Biol. 5:180. doi: 10.1186/1752-0509-5-180
    • (2011) BMC Syst. Biol , vol.5 , pp. 180
    • Bordbar, A.1    Feist, A.M.2    Usaite-Black, R.3    Woodcock, J.4    Palsson, B.Ø.5    Famili, I.6
  • 6
    • 77958537509 scopus 로고    scopus 로고
    • Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions
    • Bordbar, A., Lewis, N. E., Schellenberger, J., Palsson, B. Ø., and Jamshidi, N. (2010). Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol. Syst. Biol. 6, 422. doi: 10.1038/msb.2010.68
    • (2010) Mol. Syst. Biol , vol.6 , pp. 422
    • Bordbar, A.1    Lewis, N.E.2    Schellenberger, J.3    Palsson, B.Ø.4    Jamshidi, N.5
  • 7
    • 84892788440 scopus 로고    scopus 로고
    • Constraint-based models predict metabolic and associated cellular functions
    • Bordbar, A., Monk, J. M., King, Z. A., and Palsson, B. Ø. (2014). Constraint-based models predict metabolic and associated cellular functions. Nat. Rev. Genet. 15, 107-120. doi: 10.1038/nrg3643
    • (2014) Nat. Rev. Genet , vol.15 , pp. 107-120
    • Bordbar, A.1    Monk, J.M.2    King, Z.A.3    Palsson, B.Ø.4
  • 8
    • 0242487787 scopus 로고    scopus 로고
    • OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • Burgard, A. P., Pharkya, P., and Maranas, C. D. (2003). OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84, 647-657. doi: 10.1002/bit.10803
    • (2003) Biotechnol. Bioeng , vol.84 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 9
    • 84901789998 scopus 로고    scopus 로고
    • A diel flux balance model captures interactions between light and dark metabolism during day-night cycles in C3 and crassulacean acid metabolism leaves
    • Cheung, C. Y. M., Poolman, M. G., Fell, D. A., Ratcliffe, R. G., and Sweetlove, L. J. (2014). A diel flux balance model captures interactions between light and dark metabolism during day-night cycles in C3 and crassulacean acid metabolism leaves. Plant Physiol. 165, 917-929. doi: 10.1104/pp.113.234468
    • (2014) Plant Physiol , vol.165 , pp. 917-929
    • Cheung, C.Y.M.1    Poolman, M.G.2    Fell, D.A.3    Ratcliffe, R.G.4    Sweetlove, L.J.5
  • 10
    • 70049110173 scopus 로고    scopus 로고
    • Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production
    • Colijn, C., Brandes, A., Zucker, J., Lun, D. S., Weiner, B., Farhat, M. R., et al. (2009). Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput. Biol. 5:e1000489. doi: 10.1371/journal.pcbi.1000489
    • (2009) PLoS Comput. Biol , vol.5
    • Colijn, C.1    Brandes, A.2    Zucker, J.3    Lun, D.S.4    Weiner, B.5    Farhat, M.R.6
  • 11
    • 0037008673 scopus 로고    scopus 로고
    • Transcriptional regulation in constraints-based metabolic models of Escherichia coli
    • Covert, M. W., and Palsson, B. Ø. (2002). Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 277, 28058-28064. doi: 10.1074/jbc. M201691200
    • (2002) J. Biol. Chem , vol.277 , pp. 28058-28064
    • Covert, M.W.1    Palsson, B.Ø.2
  • 12
    • 0035824029 scopus 로고    scopus 로고
    • Regulation of gene expression in flux balance models of metabolism
    • Covert, M. W., Schilling, C. H., and Palsson, B. Ø. (2001). Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213, 73-88. doi: 10.1006/jtbi.2001.2405
    • (2001) J. Theor. Biol , vol.213 , pp. 73-88
    • Covert, M.W.1    Schilling, C.H.2    Palsson, B.Ø.3
  • 13
    • 51749113592 scopus 로고    scopus 로고
    • Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
    • Covert, M. W., Xiao, N., Chen, T. J., and Karr, J. R. (2008). Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 24, 2044-2050. doi: 10.1093/bioinformatics/btn352
    • (2008) Bioinformatics , vol.24 , pp. 2044-2050
    • Covert, M.W.1    Xiao, N.2    Chen, T.J.3    Karr, J.R.4
  • 14
    • 16644395233 scopus 로고    scopus 로고
    • Multi-scale modelling and the IUPS physiome project
    • Crampin, E. J., Smith, N. P., and Hunter, P. J. (2004). Multi-scale modelling and the IUPS physiome project. J. Mol. Histol. 35, 707-714. doi: 10.1007/s10735-004-2676-6
    • (2004) J. Mol. Histol , vol.35 , pp. 707-714
    • Crampin, E.J.1    Smith, N.P.2    Hunter, P.J.3
  • 15
    • 75949088191 scopus 로고    scopus 로고
    • AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis
    • de Oliveira Dal'Molin, C. G., Quek, L.-E., Palfreyman, R. W., Brumbley, S. M., and Nielsen, L. K. (2010). AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol. 152, 579-589. doi: 10.1104/pp.109.148817
    • (2010) Plant Physiol , vol.152 , pp. 579-589
    • de Oliveira Dal'Molin, C.G.1    Quek, L.-E.2    Palfreyman, R.W.3    Brumbley, S.M.4    Nielsen, L.K.5
  • 16
    • 33846910173 scopus 로고    scopus 로고
    • Global reconstruction of the human metabolic network based on genomic and bibliomic data
    • Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., et al. (2007). Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. U.S.A. 104, 1777-1782. doi: 10.1073/pnas.0610772104
    • (2007) Proc. Natl. Acad. Sci. U.S.A , vol.104 , pp. 1777-1782
    • Duarte, N.C.1    Becker, S.A.2    Jamshidi, N.3    Thiele, I.4    Mo, M.L.5    Vo, T.D.6
  • 17
    • 0033580813 scopus 로고    scopus 로고
    • Systems properties of the Haemophilus influenzae Rd metabolic genotype
    • Edwards, J. S., and Palsson, B. Ø. (1999). Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem. 274, 17410-17416. doi: 10.1074/jbc.274.25.17410
    • (1999) J. Biol. Chem , vol.274 , pp. 17410-17416
    • Edwards, J.S.1    Palsson, B.Ø.2
  • 18
    • 77952886804 scopus 로고    scopus 로고
    • The biomass objective function
    • Feist, A. M., and Palsson, B. Ø. (2010). The biomass objective function. Curr. Opin. Microbiol. 13, 344-349. doi: 10.1016/j.mib.2010.03.003
    • (2010) Curr. Opin. Microbiol , vol.13 , pp. 344-349
    • Feist, A.M.1    Palsson, B.Ø.2
  • 19
    • 84895952176 scopus 로고    scopus 로고
    • QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells
    • Fisher, C. P., Plant, N. J., Moore, J. B., and Kierzek, A. M. (2013). QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. Bioinformatics 29, 3181-3190. doi: 10.1093/bioinformatics/btt552
    • (2013) Bioinformatics , vol.29 , pp. 3181-3190
    • Fisher, C.P.1    Plant, N.J.2    Moore, J.B.3    Kierzek, A.M.4
  • 20
    • 0042816453 scopus 로고    scopus 로고
    • Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae
    • Förster, J., Famili, I., Palsson, B. Ø., and Nielsen, J. (2003). Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS 7, 193-202. doi: 10.1089/153623103322246584
    • (2003) OMICS , vol.7 , pp. 193-202
    • Förster, J.1    Famili, I.2    Palsson, B.Ø.3    Nielsen, J.4
  • 21
    • 77956407882 scopus 로고    scopus 로고
    • HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology
    • Gille, C., Bölling, C., Hoppe, A., Bulik, S., Hoffmann, S., Hübner, K., et al. (2010). HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol. Syst. Biol. 6, 411. doi: 10.1038/msb.2010.62
    • (2010) Mol. Syst. Biol , vol.6 , pp. 411
    • Gille, C.1    Bölling, C.2    Hoppe, A.3    Bulik, S.4    Hoffmann, S.5    Hübner, K.6
  • 22
    • 84922335977 scopus 로고    scopus 로고
    • A multi-tissue genome-scale metabolic modelling framework for the analysis of whole plant systems
    • Gomes De Oliveira Dal'molin, C., Quek, L.-E., Saa, P. A., and Nielsen, L. K. (2015). A multi-tissue genome-scale metabolic modelling framework for the analysis of whole plant systems. Front. Plant. Sci. 6:4. doi: 10.3389/fpls.2015.00004
    • (2015) Front. Plant. Sci , vol.6 , pp. 4
    • Gomes De Oliveira Dal'molin, C.1    Quek, L.-E.2    Saa, P.A.3    Nielsen, L.K.4
  • 23
  • 24
    • 84871588520 scopus 로고    scopus 로고
    • Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
    • Heinken, A., Sahoo, S., Fleming, R. M. T., and Thiele, I. (2013). Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microb. 4, 28-40. doi: 10.4161/gmic.22370
    • (2013) Gut Microb , vol.4 , pp. 28-40
    • Heinken, A.1    Sahoo, S.2    Fleming, R.M.T.3    Thiele, I.4
  • 25
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
    • Jerby, L., Shlomi, T., and Ruppin, E. (2010). Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol. Syst. Biol. 6:401. doi: 10.1038/msb.2010.56
    • (2010) Mol. Syst. Biol , vol.6 , pp. 401
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 26
    • 84924359074 scopus 로고    scopus 로고
    • Multi-timescale modeling of activity-dependent metabolic coupling in the neuron-glia-vasculature ensemble
    • Jolivet, R., Coggan, J. S., Allaman, I., and Magistretti, P. J. (2015). Multi-timescale modeling of activity-dependent metabolic coupling in the neuron-glia-vasculature ensemble. PLoS Comput. Biol. 11:e1004036. doi: 10.1371/journal.pcbi.1004036
    • (2015) PLoS Comput. Biol , vol.11
    • Jolivet, R.1    Coggan, J.S.2    Allaman, I.3    Magistretti, P.J.4
  • 27
    • 84864258618 scopus 로고    scopus 로고
    • A whole-cell computational model predicts phenotype from genotype
    • Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., Bolival, B., et al. (2012). A whole-cell computational model predicts phenotype from genotype. Cell 150, 389-401. doi: 10.1016/j.cell.2012.05.044
    • (2012) Cell , vol.150 , pp. 389-401
    • Karr, J.R.1    Sanghvi, J.C.2    Macklin, D.N.3    Gutschow, M.V.4    Jacobs, J.M.5    Bolival, B.6
  • 28
  • 30
    • 84904361982 scopus 로고    scopus 로고
    • Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice
    • Kumar, A., Harrelson, T., Lewis, N. E., Gallagher, E. J., LeRoith, D., Shiloach, J., et al. (2014). Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PLoS ONE 9:e102319. doi: 10.1371/journal.pone.0102319
    • (2014) PLoS ONE , vol.9
    • Kumar, A.1    Harrelson, T.2    Lewis, N.E.3    Gallagher, E.J.4    LeRoith, D.5    Shiloach, J.6
  • 31
    • 84862301363 scopus 로고    scopus 로고
    • Improving metabolic flux predictions using absolute gene expression data
    • Lee, D., Smallbone, K., Dunn, W. B., Murabito, E., Winder, C. L., Kell, D. B., et al. (2012). Improving metabolic flux predictions using absolute gene expression data. BMC Syst. Biol. 6:73. doi: 10.1186/1752-0509-6-73
    • (2012) BMC Syst. Biol , vol.6 , pp. 73
    • Lee, D.1    Smallbone, K.2    Dunn, W.B.3    Murabito, E.4    Winder, C.L.5    Kell, D.B.6
  • 32
    • 44949247269 scopus 로고    scopus 로고
    • Dynamic analysis of integrated signaling, metabolic, and regulatory networks
    • Lee, J. M., Gianchandani, E. P., Eddy, J. A., and Papin, J. A. (2008). Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS Comput. Biol. 4:e1000086. doi: 10.1371/journal.pcbi.1000086
    • (2008) PLoS Comput. Biol , vol.4
    • Lee, J.M.1    Gianchandani, E.P.2    Eddy, J.A.3    Papin, J.A.4
  • 33
    • 84864843180 scopus 로고    scopus 로고
    • In silico method for modelling metabolism and gene product expression at genome scale
    • Lerman, J. A., Hyduke, D. R., Latif, H., Portnoy, V. A., Lewis, N. E., Orth, J. D., et al. (2012). In silico method for modelling metabolism and gene product expression at genome scale. Nat. Commun. 3, 929. doi: 10.1038/ncomms1928
    • (2012) Nat. Commun , vol.3 , pp. 929
    • Lerman, J.A.1    Hyduke, D.R.2    Latif, H.3    Portnoy, V.A.4    Lewis, N.E.5    Orth, J.D.6
  • 34
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    • Lewis, N. E., Nagarajan, H., and Palsson, B. Ø. (2012). Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat. Rev. Microbiol. 10, 291-305. doi: 10.1038/nrmicro2737
    • (2012) Nat. Rev. Microbiol , vol.10 , pp. 291-305
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.Ø.3
  • 35
    • 78650002545 scopus 로고    scopus 로고
    • Large-scale in silico modeling of metabolic interactions between cell types in the human brain
    • Lewis, N. E., Schramm, G., Bordbar, A., Schellenberger, J., Andersen, M. P., Cheng, J. K., et al. (2010). Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat. Biotechnol. 28, 1279-1285. doi: 10.1038/nbt.1711
    • (2010) Nat. Biotechnol , vol.28 , pp. 1279-1285
    • Lewis, N.E.1    Schramm, G.2    Bordbar, A.3    Schellenberger, J.4    Andersen, M.P.5    Cheng, J.K.6
  • 36
    • 39449095000 scopus 로고    scopus 로고
    • Stoichiometric modelling of cell metabolism
    • Llaneras, F., and Picó, J. (2008). Stoichiometric modelling of cell metabolism. J. Biosci. Bioeng. 105, 1-11. doi: 10.1263/jbb.105.1
    • (2008) J. Biosci. Bioeng , vol.105 , pp. 1-11
    • Llaneras, F.1    Picó, J.2
  • 37
    • 34548860112 scopus 로고    scopus 로고
    • The Edinburgh human metabolic network reconstruction and its functional analysis
    • Ma, H., Sorokin, A., Mazein, A., Selkov, A., Selkov, E., Demin, O., et al. (2007). The Edinburgh human metabolic network reconstruction and its functional analysis. Mol. Syst. Biol. 3, 135. doi: 10.1038/msb4100177
    • (2007) Mol. Syst. Biol , vol.3 , pp. 135
    • Ma, H.1    Sorokin, A.2    Mazein, A.3    Selkov, A.4    Selkov, E.5    Demin, O.6
  • 38
    • 84901306814 scopus 로고    scopus 로고
    • Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
    • Machado, D., and Herrgård, M. (2014). Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput. Biol. 10:e1003580. doi: 10.1371/journal.pcbi.1003580
    • (2014) PLoS Comput. Biol , vol.10
    • Machado, D.1    Herrgård, M.2
  • 39
    • 0036708443 scopus 로고    scopus 로고
    • Dynamic flux balance analysis of diauxic growth in Escherichia coli
    • Mahadevan, R., Edwards, J. S., and Doyle, 3rd, F. J. (2002). Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 83, 1331-1340. doi: 10.1016/S0006-3495(02)73903-9
    • (2002) Biophys. J , vol.83 , pp. 1331-1340
    • Mahadevan, R.1    Edwards, J.S.2    Doyle, F.J.3
  • 40
    • 84902144538 scopus 로고    scopus 로고
    • Genome-based modeling and design of metabolic interactions in microbial communities
    • Mahadevan, R., and Henson, M. A. (2012). Genome-based modeling and design of metabolic interactions in microbial communities. Comput. Struct. Biotechnol. J. 3:e201210008. doi: 10.5936/csbj.201210008
    • (2012) Comput. Struct. Biotechnol. J , vol.3
    • Mahadevan, R.1    Henson, M.A.2
  • 41
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • Mahadevan, R., and Schilling, C. (2003). The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5, 264-276. doi: 10.1016/j.ymben.2003.09.002
    • (2003) Metab. Eng , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.2
  • 42
    • 84898011025 scopus 로고    scopus 로고
    • Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease
    • Mardinoglu, A., Agren, R., Kampf, C., Asplund, A., Uhlen, M., and Nielsen, J. (2014). Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nat. Commun. 5, 3083. doi: 10.1038/ncomms4083
    • (2014) Nat. Commun , vol.5 , pp. 3083
    • Mardinoglu, A.1    Agren, R.2    Kampf, C.3    Asplund, A.4    Uhlen, M.5    Nielsen, J.6
  • 43
    • 34147122065 scopus 로고    scopus 로고
    • Mendelian Inheritance in Man and its online version, OMIM
    • McKusick, V. A. (2007). Mendelian Inheritance in Man and its online version, OMIM. Am. J. Hum. Genet. 80, 588-604. doi: 10.1086/514346
    • (2007) Am. J. Hum. Genet , vol.80 , pp. 588-604
    • McKusick, V.A.1
  • 45
    • 84879613996 scopus 로고    scopus 로고
    • 'ProNet-CN model: a dynamic and multi-scale process network combining photosynthesis, primary carbon metabolism and effects of leaf nitrogen status'
    • (PMA) 2012 IEEE Fourth International Symposium on (Shanghai)
    • Mueller, J., Eschenroeder, A., Christen, O., Junker, B. H., and Schreiber, F. (2012). "ProNet-CN model: a dynamic and multi-scale process network combining photosynthesis, primary carbon metabolism and effects of leaf nitrogen status". in Plant Growth Modeling, Simulation, Visualization and Applications (PMA), 2012 IEEE Fourth International Symposium on (Shanghai), 289-296. doi: 10.1109/PMA.2012.6524848
    • (2012) Plant Growth Modeling, Simulation, Visualization and Applications , pp. 289-296
    • Mueller, J.1    Eschenroeder, A.2    Christen, O.3    Junker, B.H.4    Schreiber, F.5
  • 46
    • 69149110444 scopus 로고    scopus 로고
    • Multiobjective flux balancing using the NISE method for metabolic network analysis
    • Oh, Y.-G., Lee, D.-Y., Lee, S. Y., and Park, S. (2009). Multiobjective flux balancing using the NISE method for metabolic network analysis. Biotechnol. Prog. 25, 999-1008. doi: 10.1002/btpr.193
    • (2009) Biotechnol. Prog , vol.25 , pp. 999-1008
    • Oh, Y.-G.1    Lee, D.-Y.2    Lee, S.Y.3    Park, S.4
  • 47
    • 78651335279 scopus 로고    scopus 로고
    • Systematizing the generation of missing metabolic knowledge
    • Orth, J. D., and Palsson, B. Ø. (2010). Systematizing the generation of missing metabolic knowledge. Biotechnol. Bioeng. 107, 403-412. doi: 10.1002/bit.22844
    • (2010) Biotechnol. Bioeng , vol.107 , pp. 403-412
    • Orth, J.D.1    Palsson, B.Ø.2
  • 48
    • 85009801543 scopus 로고    scopus 로고
    • Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond
    • [Epub ahead of print]
    • Pfau, T., Pacheco, M. P., and Sauter, T. (2015). Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. Brief. Bioinform. doi: 10.1093/bib/bbv100. [Epub ahead of print]
    • (2015) Brief. Bioinform
    • Pfau, T.1    Pacheco, M.P.2    Sauter, T.3
  • 49
    • 84866726930 scopus 로고    scopus 로고
    • Identifying the preferred subset of enzymatic profiles in nonlinear kinetic metabolic models via multiobjective global optimization and pareto filters
    • Pozo, C., Guillén-Gosálbez, G., Sorribas, A., and Jiménez, L. (2012). Identifying the preferred subset of enzymatic profiles in nonlinear kinetic metabolic models via multiobjective global optimization and pareto filters. PLoS ONE 7:e43487. doi: 10.1371/journal.pone.0043487
    • (2012) PLoS ONE , vol.7
    • Pozo, C.1    Guillén-Gosálbez, G.2    Sorribas, A.3    Jiménez, L.4
  • 50
    • 67449096729 scopus 로고    scopus 로고
    • Flux balance analysis of biological systems: applications and challenges
    • Raman, K., and Chandra, N. (2009). Flux balance analysis of biological systems: applications and challenges. Brief. Bioinform. 10, 435-449. doi: 10.1093/bib/bbp011
    • (2009) Brief. Bioinform , vol.10 , pp. 435-449
    • Raman, K.1    Chandra, N.2
  • 52
    • 84939950368 scopus 로고    scopus 로고
    • Modeling function-perfusion behavior in liver lobules including tissue, blood, glucose, lactate and glycogen by use of a coupled two-scale PDE-ODE approach
    • Ricken, T., Werner, D., Holzhütter, H., König, M., Dahmen, U., and Dirsch, O. (2015). Modeling function-perfusion behavior in liver lobules including tissue, blood, glucose, lactate and glycogen by use of a coupled two-scale PDE-ODE approach. Biomech. Model Mechanobiol. 14, 515-536. doi: 10.1007/s10237-014-0619-z
    • (2015) Biomech. Model Mechanobiol , vol.14 , pp. 515-536
    • Ricken, T.1    Werner, D.2    Holzhütter, H.3    König, M.4    Dahmen, U.5    Dirsch, O.6
  • 53
    • 84907288908 scopus 로고    scopus 로고
    • Generalized framework for context-specific metabolic model extraction methods
    • Robaina Estévez, S., and Nikoloski, Z. (2014). Generalized framework for context-specific metabolic model extraction methods. Front. Plant. Sci. 5:491. doi: 10.3389/fpls.2014.00491
    • (2014) Front. Plant. Sci , vol.5 , pp. 491
    • Robaina Estévez, S.1    Nikoloski, Z.2
  • 54
    • 77950960250 scopus 로고    scopus 로고
    • OptFlux: an open-source software platform for in silico metabolic engineering
    • Rocha, I., Maia, P., Evangelista, P., Vilaca, P., Soares, S., Pinto, J., et al. (2010). OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst. Biol. 4:45. doi: 10.1186/1752-0509-4-45
    • (2010) BMC Syst. Biol , vol.4 , pp. 45
    • Rocha, I.1    Maia, P.2    Evangelista, P.3    Vilaca, P.4    Soares, S.5    Pinto, J.6
  • 55
    • 84908190303 scopus 로고    scopus 로고
    • A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models
    • Ryll, A., Bucher, J., Bonin, A., Bongard, S., Gonalves, E., Saez-Rodriguez, J., et al. (2014). A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. Biosystems 124, 26-38. doi: 10.1016/j.biosystems.2014.07.002
    • (2014) Biosystems , vol.124 , pp. 26-38
    • Ryll, A.1    Bucher, J.2    Bonin, A.3    Bongard, S.4    Gonalves, E.5    Saez-Rodriguez, J.6
  • 56
    • 84938683599 scopus 로고    scopus 로고
    • Reconstruction of genome-scale human metabolic models using omics data
    • Ryu, J. Y., Kim, H. U., and Lee, S. Y. (2015). Reconstruction of genome-scale human metabolic models using omics data. Integr. Biol. 7, 859-868. doi: 10.1039/c5ib00002e
    • (2015) Integr. Biol , vol.7 , pp. 859-868
    • Ryu, J.Y.1    Kim, H.U.2    Lee, S.Y.3
  • 57
    • 0026594358 scopus 로고
    • Optimal selection of metabolic fluxes for in vivo measurement I. Development of mathematical methods
    • Savinell, J. M., and Palsson, B. Ø. (1992). Optimal selection of metabolic fluxes for in vivo measurement. I. Development of mathematical methods. J. Theor. Biol. 155, 201-214. doi: 10.1016/S0022-5193(05)80595-8
    • (1992) J. Theor. Biol , vol.155 , pp. 201-214
    • Savinell, J.M.1    Palsson, B.Ø.2
  • 58
    • 34447523907 scopus 로고    scopus 로고
    • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    • Schuetz, R., Kuepfer, L., and Sauer, U. (2007). Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol. Syst. Biol. 3, 119. doi: 10.1038/msb4100162
    • (2007) Mol. Syst. Biol , vol.3 , pp. 119
    • Schuetz, R.1    Kuepfer, L.2    Sauer, U.3
  • 59
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • Segrè, D., Vitkup, D., and Church, G. M. (2002). Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. U.S.A. 99, 15112-15117. doi: 10.1073/pnas.232349399
    • (2002) Proc. Natl. Acad. Sci. U.S.A , vol.99 , pp. 15112-15117
    • Segrè, D.1    Vitkup, D.2    Church, G.M.3
  • 60
    • 13544265458 scopus 로고    scopus 로고
    • Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus
    • Sheikh, K., Förster, J., and Nielsen, L. K. (2005). Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus. Biotechnol. Prog. 21, 112-121. doi: 10.1021/bp0498138
    • (2005) Biotechnol. Prog , vol.21 , pp. 112-121
    • Sheikh, K.1    Förster, J.2    Nielsen, L.K.3
  • 61
    • 19644386033 scopus 로고    scopus 로고
    • Regulatory on/offminimization of metabolic flux changes after genetic perturbations
    • Shlomi, T., Berkman, O., and Ruppin, E. (2005). Regulatory on/offminimization of metabolic flux changes after genetic perturbations. Proc. Natl. Acad. Sci. U.S.A. 102, 7695-7700. doi: 10.1073/pnas.0406346102
    • (2005) Proc. Natl. Acad. Sci. U.S.A , vol.102 , pp. 7695-7700
    • Shlomi, T.1    Berkman, O.2    Ruppin, E.3
  • 63
    • 84866975246 scopus 로고    scopus 로고
    • Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage
    • Thiele, I., Fleming, R. M. T., Que, R., Bordbar, A., Diep, D., and Palsson, B. Ø. (2012). Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS ONE 7:e45635. doi: 10.1371/journal.pone.0045635
    • (2012) PLoS ONE , vol.7
    • Thiele, I.1    Fleming, R.M.T.2    Que, R.3    Bordbar, A.4    Diep, D.5    Palsson, B.Ø.6
  • 65
    • 0028146781 scopus 로고
    • Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
    • Varma, A., and Palsson, B. Ø. (1994). Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl. Environ. Microbiol. 60, 3724-3731
    • (1994) Appl. Environ. Microbiol , vol.60 , pp. 3724-3731
    • Varma, A.1    Palsson, B.Ø.2
  • 66
    • 58149302231 scopus 로고    scopus 로고
    • The virtual physiological human - a european initiative for in silico human modelling
    • Viceconti, M., Clapworthy, G., and Jan, S. V. S. (2008). The virtual physiological human - a european initiative for in silico human modelling. J. Physiol. Sci. 58, 441-446. doi: 10.2170/physiolsci. RP009908
    • (2008) J. Physiol. Sci , vol.58 , pp. 441-446
    • Viceconti, M.1    Clapworthy, G.2    Jan, S.V.S.3
  • 67
    • 84896701551 scopus 로고    scopus 로고
    • Fast reconstruction of compact context-specific metabolic network models
    • Vlassis, N., Pires Pacheco, M., and Sauter, T. (2014). Fast reconstruction of compact context-specific metabolic network models. PLoS Comput. Biol. 10:e1003424. doi: 10.1371/journal.pcbi.1003424
    • (2014) PLoS Comput. Biol , vol.10
    • Vlassis, N.1    Pires Pacheco, M.2    Sauter, T.3
  • 68
    • 4544288672 scopus 로고    scopus 로고
    • Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data
    • Vo, T. D., Greenberg, H. J., and Palsson, B. Ø. (2004). Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J. Biol. Chem. 279, 39532-39540. doi: 10.1074/jbc. M403782200
    • (2004) J. Biol. Chem , vol.279 , pp. 39532-39540
    • Vo, T.D.1    Greenberg, H.J.2    Palsson, B.Ø.3
  • 69
    • 84896731390 scopus 로고    scopus 로고
    • Enumeration of smallest intervention strategies in genome-scale metabolic networks
    • von Kamp, A., and Klamt, S. (2014). Enumeration of smallest intervention strategies in genome-scale metabolic networks. PLoS Comput. Biol. 10:e1003378. doi: 10.1371/journal.pcbi.1003378
    • (2014) PLoS Comput. Biol , vol.10
    • von Kamp, A.1    Klamt, S.2
  • 70
    • 38549163285 scopus 로고    scopus 로고
    • The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
    • Yamasaki, C., Murakami, K., Fujii, Y., Sato, Y., Harada, E., Takeda, J.-I., et al. (2008). The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res. 36, D793-D799. doi: 10.1093/nar/gkm999
    • (2008) Nucleic Acids Res , vol.36 , pp. D793-D799
    • Yamasaki, C.1    Murakami, K.2    Fujii, Y.3    Sato, Y.4    Harada, E.5    Takeda, J.-I.6
  • 71
    • 84929269410 scopus 로고    scopus 로고
    • Regulation of liver metabolism by the endosomal (GTPase) rab5
    • Zeigerer, A., Bogorad, R., Sharma, K., Gilleron, J., Seifert, S., Sales, S., et al. (2015). Regulation of liver metabolism by the endosomal (GTPase) rab5. Cell Rep. 11, 884-892. doi: 10.1016/j.celrep.2015.04.018
    • (2015) Cell Rep , vol.11 , pp. 884-892
    • Zeigerer, A.1    Bogorad, R.2    Sharma, K.3    Gilleron, J.4    Seifert, S.5    Sales, S.6
  • 72
    • 84899012698 scopus 로고    scopus 로고
    • d-OptCom: dynamic multi-level and multi-objective metabolic modeling of microbial communities
    • Zomorrodi, A. R., Islam, M. M., and Maranas, C. D. (2014). d-OptCom: dynamic multi-level and multi-objective metabolic modeling of microbial communities. ACS Synth. Biol. 3, 247-257. doi: 10.1021/sb4001307
    • (2014) ACS Synth. Biol , vol.3 , pp. 247-257
    • Zomorrodi, A.R.1    Islam, M.M.2    Maranas, C.D.3
  • 73
    • 84861180223 scopus 로고    scopus 로고
    • OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities
    • Zomorrodi, A. R., and Maranas, C. D. (2012). OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput. Biol. 8:e1002363. doi: 10.1371/journal.pcbi.1002363
    • (2012) PLoS Comput. Biol , vol.8
    • Zomorrodi, A.R.1    Maranas, C.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.