메뉴 건너뛰기




Volumn 2, Issue , 2017, Pages 29-38

In silico analysis of human metabolism: Reconstruction, contextualization and application of genome-scale models

Author keywords

Constraint based analysis; Drug development; Genome scale metabolic model; Human metabolism; Topological analysis

Indexed keywords

BIBLIOMETRICS; CELL INTERACTION; CIRCULATION; CLINICAL FEATURE; COMPUTER MODEL; CONCEPTUAL FRAMEWORK; DATA ANALYSIS; DATA BASE; DRUG MANUFACTURE; GENETIC MODEL; GENOME SCALE METABOLIC MODEL; GENOTYPE; HUMAN; HUMAN GENOME; INFORMATION PROCESSING; LIVER CELL CARCINOMA; METABOLISM; METABOLITE; METABOLOMICS; NONALCOHOLIC FATTY LIVER; PHENOTYPE; REVIEW; STOICHIOMETRY; TISSUE INTERACTION; TRANSCRIPTOMICS;

EID: 85041388327     PISSN: None     EISSN: 24523100     Source Type: Journal    
DOI: 10.1016/j.coisb.2017.01.001     Document Type: Review
Times cited : (17)

References (79)
  • 2
    • 84878930738 scopus 로고    scopus 로고
    • Progression of NAFLD to diabetes mellitus, cardiovascular disease or cirrhosis
    • Anstee Q.M., Targher G., Day C.P. Progression of NAFLD to diabetes mellitus, cardiovascular disease or cirrhosis. Nat Rev Gastroenterol Hepatol 2013, 10:330-344.
    • (2013) Nat Rev Gastroenterol Hepatol , vol.10 , pp. 330-344
    • Anstee, Q.M.1    Targher, G.2    Day, C.P.3
  • 3
    • 84879435168 scopus 로고    scopus 로고
    • Metabolic syndrome and insulin resistance: underlying causes and modification by exercise training
    • Roberts C.K., Hevener A.L., Barnard R.J. Metabolic syndrome and insulin resistance: underlying causes and modification by exercise training. Compr Physiol 2013, 3:1-58.
    • (2013) Compr Physiol , vol.3 , pp. 1-58
    • Roberts, C.K.1    Hevener, A.L.2    Barnard, R.J.3
  • 6
    • 84999971472 scopus 로고    scopus 로고
    • Systems medicine: the application of systems biology approaches for modern medical research and drug development
    • Ayers D., Day P.J. Systems medicine: the application of systems biology approaches for modern medical research and drug development. Mol Biol Int 2015, 2015:8.
    • (2015) Mol Biol Int , vol.2015 , pp. 8
    • Ayers, D.1    Day, P.J.2
  • 8
    • 84855929956 scopus 로고    scopus 로고
    • Using the reconstructed genome-scale human metabolic network to study physiology and pathology
    • Bordbar A., Palsson B.O. Using the reconstructed genome-scale human metabolic network to study physiology and pathology. J Intern Med 2012, 271:131-141.
    • (2012) J Intern Med , vol.271 , pp. 131-141
    • Bordbar, A.1    Palsson, B.O.2
  • 9
    • 84855955467 scopus 로고    scopus 로고
    • Systems medicine and metabolic modelling
    • Mardinoglu A., Nielsen J. Systems medicine and metabolic modelling. J Intern Med 2012, 271:142-154.
    • (2012) J Intern Med , vol.271 , pp. 142-154
    • Mardinoglu, A.1    Nielsen, J.2
  • 10
    • 84930227327 scopus 로고    scopus 로고
    • Using genome-scale models to predict biological capabilities
    • O'Brien Edward J., Monk Jonathan M., Palsson Bernhard O. Using genome-scale models to predict biological capabilities. Cell 2015, 161:971-987.
    • (2015) Cell , vol.161 , pp. 971-987
    • O'Brien Edward, J.1    Monk Jonathan, M.2    Palsson Bernhard, O.3
  • 11
    • 84938683599 scopus 로고    scopus 로고
    • Reconstruction of genome-scale human metabolic models using omics data
    • Ryu J.Y., Kim H.U., Lee S.Y. Reconstruction of genome-scale human metabolic models using omics data. Integr Biol 2015, 7:859-868.
    • (2015) Integr Biol , vol.7 , pp. 859-868
    • Ryu, J.Y.1    Kim, H.U.2    Lee, S.Y.3
  • 14
    • 84863662483 scopus 로고    scopus 로고
    • Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
    • Agren R., Bordel S., Mardinoglu A., Pornputtapong N., Nookaew I., Nielsen J. Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput Biol 2012, 8:e1002518.
    • (2012) PLoS Comput Biol , vol.8
    • Agren, R.1    Bordel, S.2    Mardinoglu, A.3    Pornputtapong, N.4    Nookaew, I.5    Nielsen, J.6
  • 15
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa M., Goto S., Furumichi M., Tanabe M., Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010, 38:D355-D360.
    • (2010) Nucleic Acids Res , vol.38 , pp. D355-D360
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 16
    • 14844326483 scopus 로고    scopus 로고
    • Computational prediction of human metabolic pathways from the complete human genome
    • Romero P., Wagg J., Green M.L., Kaiser D., Krummenacker M., Karp P.D. Computational prediction of human metabolic pathways from the complete human genome. Genome Biol 2005, 6:R2.
    • (2005) Genome Biol , vol.6 , pp. R2
    • Romero, P.1    Wagg, J.2    Green, M.L.3    Kaiser, D.4    Krummenacker, M.5    Karp, P.D.6
  • 17
    • 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., Nielsen J. Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nat Commun 2014, 5.
    • (2014) Nat Commun , vol.5
    • Mardinoglu, A.1    Agren, R.2    Kampf, C.3    Asplund, A.4    Uhlen, M.5    Nielsen, J.6
  • 22
    • 84878949529 scopus 로고    scopus 로고
    • Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells
    • Sahoo S., Thiele I. Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells. Hum Mol Genet 2013, 22:2705-2722.
    • (2013) Hum Mol Genet , vol.22 , pp. 2705-2722
    • Sahoo, S.1    Thiele, I.2
  • 25
    • 66249132328 scopus 로고    scopus 로고
    • Predicting metabolic biomarkers of human inborn errors of metabolism
    • Shlomi T., Cabili M.N., Ruppin E. Predicting metabolic biomarkers of human inborn errors of metabolism. Mol Syst Biol 2009, 5:263.
    • (2009) Mol Syst Biol , vol.5 , pp. 263
    • Shlomi, T.1    Cabili, M.N.2    Ruppin, E.3
  • 26
    • 84941268169 scopus 로고    scopus 로고
    • The genotype-tissue expression (GTEx) project: linking clinical data with molecular analysis to advance personalized medicine
    • Keen J.C., Moore H.M. The genotype-tissue expression (GTEx) project: linking clinical data with molecular analysis to advance personalized medicine. J Pers Med 2015, 5:22-29.
    • (2015) J Pers Med , vol.5 , pp. 22-29
    • Keen, J.C.1    Moore, H.M.2
  • 30
    • 84901306814 scopus 로고    scopus 로고
    • Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
    • Machado D., Herrgård M. Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput Biol 2014, 10:e1003580.
    • (2014) PLoS Comput Biol , vol.10
    • Machado, D.1    Herrgård, M.2
  • 31
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • Becker S.A., Palsson B.O. Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol 2008, 4:e1000082.
    • (2008) PLoS Comput Biol , vol.4
    • Becker, S.A.1    Palsson, B.O.2
  • 32
    • 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., Jamshidi N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol Syst Biol 2010, 6:422.
    • (2010) Mol Syst Biol , vol.6 , pp. 422
    • Bordbar, A.1    Lewis, N.E.2    Schellenberger, J.3    Palsson, B.O.4    Jamshidi, N.5
  • 33
    • 78049445175 scopus 로고    scopus 로고
    • Drug off-target effects predicted using structural analysis in the context of a metabolic network model
    • Chang R.L., Xie L., Xie L., Bourne P.E., Palsson B.Ø. Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol 2010, 6:e1000938.
    • (2010) PLoS Comput Biol , vol.6
    • Chang, R.L.1    Xie, L.2    Xie, L.3    Bourne, P.E.4    Palsson, B.O.5
  • 34
    • 79951745716 scopus 로고    scopus 로고
    • IMAT: an integrative metabolic analysis tool
    • Zur H., Ruppin E., Shlomi T. iMAT: an integrative metabolic analysis tool. Bioinformatics 2010, 26:3140-3142.
    • (2010) Bioinformatics , vol.26 , pp. 3140-3142
    • Zur, H.1    Ruppin, E.2    Shlomi, T.3
  • 35
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
    • Jerby L., Shlomi T., Ruppin E. Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol 2010, 6:401.
    • (2010) Mol Syst Biol , vol.6 , pp. 401
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 36
    • 82355175105 scopus 로고    scopus 로고
    • Reconstruction and analysis of human heart-specific metabolic network based on transcriptome and proteome data
    • Zhao Y., Huang J. Reconstruction and analysis of human heart-specific metabolic network based on transcriptome and proteome data. Biochem Biophys Res Commun 2011, 415:450-454.
    • (2011) Biochem Biophys Res Commun , vol.415 , pp. 450-454
    • Zhao, Y.1    Huang, J.2
  • 37
    • 84870933131 scopus 로고    scopus 로고
    • Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
    • Wang Y., Eddy J.A., Price N.D. Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst Biol 2012, 6:1-16.
    • (2012) BMC Syst Biol , vol.6 , pp. 1-16
    • Wang, Y.1    Eddy, J.A.2    Price, N.D.3
  • 38
    • 84896701551 scopus 로고    scopus 로고
    • Fast reconstruction of compact context-specific metabolic network models
    • Vlassis N., Pacheco M.P., Sauter T. Fast reconstruction of compact context-specific metabolic network models. PLoS Comput Biol 2014, 10:e1003424.
    • (2014) PLoS Comput Biol , vol.10
    • Vlassis, N.1    Pacheco, M.P.2    Sauter, T.3
  • 40
    • 84898663879 scopus 로고    scopus 로고
    • Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling
    • Agren R., Mardinoglu A., Asplund A., Kampf C., Uhlen M., Nielsen J. Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling. Mol Syst Biol 2014, 10:721.
    • (2014) Mol Syst Biol , vol.10 , pp. 721
    • Agren, R.1    Mardinoglu, A.2    Asplund, A.3    Kampf, C.4    Uhlen, M.5    Nielsen, J.6
  • 43
    • 84962059544 scopus 로고    scopus 로고
    • Reconstruction of tissue-specific metabolic networks using CORDA
    • Schultz A., Qutub A.A. Reconstruction of tissue-specific metabolic networks using CORDA. PLoS Comput Biol 2016, 12:e1004808.
    • (2016) PLoS Comput Biol , vol.12
    • Schultz, A.1    Qutub, A.A.2
  • 44
    • 34547676311 scopus 로고    scopus 로고
    • Optimization based automated curation of metabolic reconstructions
    • Satish Kumar V., Dasika M.S., Maranas C.D. Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 2007, 8:212.
    • (2007) BMC Bioinformatics , vol.8 , pp. 212
    • Satish Kumar, V.1    Dasika, M.S.2    Maranas, C.D.3
  • 45
    • 84907026934 scopus 로고    scopus 로고
    • FastGapFill: efficient gap filling in metabolic networks
    • Thiele I., Vlassis N., Fleming R.M.T. fastGapFill: efficient gap filling in metabolic networks. Bioinformatics 2014, 30:2529-2531.
    • (2014) Bioinformatics , vol.30 , pp. 2529-2531
    • Thiele, I.1    Vlassis, N.2    Fleming, R.M.T.3
  • 47
    • 33746218840 scopus 로고    scopus 로고
    • Prediction of protein subcellular localization
    • Yu C.-S., Chen Y.-C., Lu C.-H., Hwang J.-K. Prediction of protein subcellular localization. Proteins 2006, 64:643-651.
    • (2006) Proteins , vol.64 , pp. 643-651
    • Yu, C.-S.1    Chen, Y.-C.2    Lu, C.-H.3    Hwang, J.-K.4
  • 48
    • 65349131424 scopus 로고    scopus 로고
    • Reconstruction of metabolic pathways for the cattle genome
    • Seo S., Lewin H.A. Reconstruction of metabolic pathways for the cattle genome. BMC Syst Biol 2009, 3:33.
    • (2009) BMC Syst Biol , vol.3 , pp. 33
    • Seo, S.1    Lewin, H.A.2
  • 49
    • 72949118860 scopus 로고    scopus 로고
    • Genome-scale modeling and in silico analysis of mouse cell metabolic network
    • Selvarasu S., Karimi I.A., Ghim G.-H., Lee D.-Y. Genome-scale modeling and in silico analysis of mouse cell metabolic network. Mol Biosyst 2009, 6:152-161.
    • (2009) Mol Biosyst , vol.6 , pp. 152-161
    • Selvarasu, S.1    Karimi, I.A.2    Ghim, G.-H.3    Lee, D.-Y.4
  • 52
    • 84867527044 scopus 로고    scopus 로고
    • Metabolic associations of reduced proliferation and oxidative stress in advanced breast cancer
    • Jerby L., Wolf L., Denkert C., Stein G.Y., Hilvo M., Oresic M., Geiger T., Ruppin E. Metabolic associations of reduced proliferation and oxidative stress in advanced breast cancer. Cancer Res 2012, 72:5712-5720.
    • (2012) Cancer Res , vol.72 , pp. 5712-5720
    • Jerby, L.1    Wolf, L.2    Denkert, C.3    Stein, G.Y.4    Hilvo, M.5    Oresic, M.6    Geiger, T.7    Ruppin, E.8
  • 53
    • 84898857127 scopus 로고    scopus 로고
    • Prediction of therapeutic microRNA based on the human metabolic network
    • Wu M., Chan C. Prediction of therapeutic microRNA based on the human metabolic network. Bioinformatics 2014, 30:1163-1171.
    • (2014) Bioinformatics , vol.30 , pp. 1163-1171
    • Wu, M.1    Chan, C.2
  • 54
    • 84894266778 scopus 로고    scopus 로고
    • Controllability in cancer metabolic networks according to drug targets as driver nodes
    • Asgari Y., Salehzadeh-Yazdi A., Schreiber F., Masoudi-Nejad A. Controllability in cancer metabolic networks according to drug targets as driver nodes. PLoS One 2013, 8:e79397.
    • (2013) PLoS One , vol.8
    • Asgari, Y.1    Salehzadeh-Yazdi, A.2    Schreiber, F.3    Masoudi-Nejad, A.4
  • 57
    • 75549083303 scopus 로고    scopus 로고
    • Tumor heterogeneity: causes and consequences
    • Marusyk A., Polyak K. Tumor heterogeneity: causes and consequences. Biochim Biophys Acta 2010, 1805:105.
    • (2010) Biochim Biophys Acta , vol.1805 , pp. 105
    • Marusyk, A.1    Polyak, K.2
  • 60
    • 14544268137 scopus 로고    scopus 로고
    • Uncovering transcriptional regulation of metabolism by using metabolic network topology
    • Patil K.R., Nielsen J. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci U S A 2005, 102:2685-2689.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 2685-2689
    • Patil, K.R.1    Nielsen, J.2
  • 61
    • 0029127584 scopus 로고
    • Inhibition of mitochondrial beta-oxidation as a mechanism of hepatotoxicity
    • Fromenty B., Pessayre D. Inhibition of mitochondrial beta-oxidation as a mechanism of hepatotoxicity. Pharmacol Ther 1995, 67:101-154.
    • (1995) Pharmacol Ther , vol.67 , pp. 101-154
    • Fromenty, B.1    Pessayre, D.2
  • 62
    • 0035742829 scopus 로고    scopus 로고
    • Hepatic steatosis and very low density lipoprotein secretion: the involvement of apolipoprotein E
    • Mensenkamp A.R., Havekes L.M., Romijn J.A., Kuipers F. Hepatic steatosis and very low density lipoprotein secretion: the involvement of apolipoprotein E. J Hepatol 2001, 35:816-822.
    • (2001) J Hepatol , vol.35 , pp. 816-822
    • Mensenkamp, A.R.1    Havekes, L.M.2    Romijn, J.A.3    Kuipers, F.4
  • 66
    • 77952674482 scopus 로고    scopus 로고
    • Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes
    • Zelezniak A., Pers T.H., Soares S., Patti M.E., Patil K.R. Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes. PLoS Comput Biol 2010, 6:e1000729.
    • (2010) PLoS Comput Biol , vol.6
    • Zelezniak, A.1    Pers, T.H.2    Soares, S.3    Patti, M.E.4    Patil, K.R.5
  • 68
    • 79953661070 scopus 로고    scopus 로고
    • Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the warburg effect
    • Shlomi T., Benyamini T., Gottlieb E., Sharan R., Ruppin E. Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the warburg effect. PLoS Comput Biol 2011, 7:e1002018.
    • (2011) PLoS Comput Biol , vol.7
    • Shlomi, T.1    Benyamini, T.2    Gottlieb, E.3    Sharan, R.4    Ruppin, E.5
  • 69
    • 78049304837 scopus 로고    scopus 로고
    • Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes
    • Bordel S., Agren R., Nielsen J. Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes. PLoS Comput Biol 2010, 6:e1000859.
    • (2010) PLoS Comput Biol , vol.6
    • Bordel, S.1    Agren, R.2    Nielsen, J.3
  • 70
    • 84930662704 scopus 로고    scopus 로고
    • Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism
    • Gatto F., Miess H., Schulze A., Nielsen J. Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism. Sci Rep 2015, 5:10738.
    • (2015) Sci Rep , vol.5 , pp. 10738
    • Gatto, F.1    Miess, H.2    Schulze, A.3    Nielsen, J.4
  • 71
    • 84942693276 scopus 로고    scopus 로고
    • Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival
    • Megchelenbrink W., Katzir R., Lu X., Ruppin E., Notebaart R.A. Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival. Proc Natl Acad Sci U S A 2015, 112:12217-12222.
    • (2015) Proc Natl Acad Sci U S A , vol.112 , pp. 12217-12222
    • Megchelenbrink, W.1    Katzir, R.2    Lu, X.3    Ruppin, E.4    Notebaart, R.A.5
  • 74
    • 84980047670 scopus 로고    scopus 로고
    • A multi-scale computational platform to mechanistically assess the effect of genetic variation on drug responses in human erythrocyte metabolism
    • Mih N., Brunk E., Bordbar A., Palsson B.O. A multi-scale computational platform to mechanistically assess the effect of genetic variation on drug responses in human erythrocyte metabolism. PLoS Comput Biol 2016, 12:e1005039.
    • (2016) PLoS Comput Biol , vol.12
    • Mih, N.1    Brunk, E.2    Bordbar, A.3    Palsson, B.O.4
  • 75
    • 63549148162 scopus 로고    scopus 로고
    • Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization
    • Thiele I., Jamshidi N., Fleming R.M.T., Palsson B.Ø. Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol 2009, 5:e1000312.
    • (2009) PLoS Comput Biol , vol.5
    • Thiele, I.1    Jamshidi, N.2    Fleming, R.M.T.3    Palsson, B.O.4
  • 76
    • 84885367114 scopus 로고    scopus 로고
    • Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
    • O'Brien E.J., Lerman J.A., Chang R.L., Hyduke D.R., Palsson B.Ø. Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol Syst Biol 2013, 9:693.
    • (2013) Mol Syst Biol , vol.9 , pp. 693
    • O'Brien, E.J.1    Lerman, J.A.2    Chang, R.L.3    Hyduke, D.R.4    Palsson, B.O.5
  • 78
    • 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.O., Famili I. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst Biol 2011, 5:1-17.
    • (2011) BMC Syst Biol , vol.5 , pp. 1-17
    • Bordbar, A.1    Feist, A.M.2    Usaite-Black, R.3    Woodcock, J.4    Palsson, B.O.5    Famili, I.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.