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Volumn 10, Issue 7, 2015, Pages

Context-specific metabolic model extraction based on regularized least squares optimization

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ARTICLE; AUTOMATION; COMPARATIVE STUDY; CONTROLLED STUDY; GENE EXPRESSION PROFILING; HUMAN; HUMAN TISSUE; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; PERFORMANCE; PROTEIN EXPRESSION; REGRESSION ANALYSIS; REGULARIZED CONTEXT SPECIFIC MODEL EXTRACTION METHOD; RNA SEQUENCE; BIOLOGICAL MODEL; LEAST SQUARE ANALYSIS; METABOLISM; SEQUENCE ANALYSIS;

EID: 84941312579     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0131875     Document Type: Article
Times cited : (46)

References (46)
  • 1
    • 77951612556 scopus 로고    scopus 로고
    • BiGG: A biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions
    • 20426874
    • 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. doi: 10. 1186/1471-2105-11-213 PMID: 20426874
    • (2010) BMC Bioinformatics. , vol.11 , pp. 213
    • Schellenberger, J.1    Park, J.O.2    Conrad, T.M.3    Palsson BØ4
  • 2
    • 84859346785 scopus 로고    scopus 로고
    • Strategies for investigating the plant metabolic network with steady-state metabolic flux analysis: Lessons from an Arabidopsis cell culture and other systems
    • 22140245
    • Kruger NJ, Masakapalli SK, Ratcliffe RG. Strategies for investigating the plant metabolic network with steady-state metabolic flux analysis: Lessons from an Arabidopsis cell culture and other systems. Journal of Experimental Botany. 2012. pp. 2309-2323. doi: 10.1093/jxb/err382 PMID: 22140245
    • (2012) Journal of Experimental Botany , pp. 2309-2323
    • Kruger, N.J.1    Masakapalli, S.K.2    Ratcliffe, R.G.3
  • 3
    • 79954459893 scopus 로고    scopus 로고
    • Construction of an E. Coli genome-scale atom mapping model for MFA calculations
    • 21328316
    • Ravikirthi P, Suthers PF, Maranas CD. Construction of an E. Coli genome-scale atom mapping model for MFA calculations. Biotechnol Bioeng. 2011;108:1372-1382. doi: 10.1002/bit.23070 PMID: 21328316
    • (2011) Biotechnol Bioeng. , vol.108 , pp. 1372-1382
    • Ravikirthi, P.1    Suthers, P.F.2    Maranas, C.D.3
  • 4
    • 80555122963 scopus 로고    scopus 로고
    • Mapping photoautotrophic metabolism with isotopically nonstationary (13) C flux analysis
    • 21907300
    • Young JD, Shastri AA, Stephanopoulos G, Morgan JA. Mapping photoautotrophic metabolism with isotopically nonstationary (13) C flux analysis. Metab Eng. 2011;13:656-65. doi: 10.1016/j.ymben. 2011. 08.002 PMID: 21907300
    • (2011) Metab Eng. , vol.13 , pp. 656-665
    • Young, J.D.1    Shastri, A.A.2    Stephanopoulos, G.3    Morgan, J.A.4
  • 5
    • 84872093417 scopus 로고    scopus 로고
    • Analysis of omics data with genome-scale models of metabolism
    • 23247105
    • Hyduke DR, Lewis NE, Palsson BØ. Analysis of omics data with genome-scale models of metabolism. Mol Biosyst. 2013;9:167-74. doi: 10.1039/c2mb25453k PMID: 23247105
    • (2013) Mol Biosyst. , vol.9 , pp. 167-174
    • Hyduke, D.R.1    Lewis, N.E.2    Palsson BØ3
  • 6
    • 84866487453 scopus 로고    scopus 로고
    • Integration of expression data in genome-scale metabolic network reconstructions
    • Blazier AS, Papin JA. Integration of expression data in genome-scale metabolic network reconstructions. Frontiers in Physiology. 2012. doi: 10.3389/fphys.2012.00299
    • (2012) Frontiers in Physiology
    • Blazier, A.S.1    Papin, J.A.2
  • 7
  • 9
    • 84901306814 scopus 로고    scopus 로고
    • Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
    • 24762745
    • 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. Available: http://www.ncbi.nlm.nih.gov/pubmed/24762745. doi: 10.1371/journal.pcbi.1003580 PMID: 24762745
    • (2014) PLoS Comput Biol. , vol.10 , pp. e1003580
    • Machado, D.1    Herrgård, M.2
  • 10
    • 84907288908 scopus 로고    scopus 로고
    • Generalized framework for context-specific metabolic model extraction methods
    • Robaina Estévez S, Nikoloski Z. Generalized framework for context-specific metabolic model extraction methods. Front Plant Sci. 2014;5. doi: 10.3389/fpls.2014.00491
    • (2014) Front Plant Sci. , pp. 5
    • Robaina Estévez, S.1    Nikoloski, Z.2
  • 11
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • Becker SA, Palsson BO. Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol. 2008;4.
    • (2008) PLoS Comput Biol. , pp. 4
    • Becker, S.A.1    Palsson, B.O.2
  • 12
    • 84890092837 scopus 로고    scopus 로고
    • GIM3E: Condition-specific models of cellular metabolism developed from metabolomics and expression data
    • 23975765
    • Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson B, Hyduke DR. GIM3E: Condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics. 2013;29:2900-2908. doi: 10.1093/bioinformatics/btt493 PMID: 23975765
    • (2013) Bioinformatics. , vol.29 , pp. 2900-2908
    • Schmidt, B.J.1    Ebrahim, A.2    Metz, T.O.3    Adkins, J.N.4    Palsson, B.5    Hyduke, D.R.6
  • 13
    • 77749320898 scopus 로고    scopus 로고
    • What is flux balance analysis?
    • 20212490
    • Orth JD, Thiele I, Palsson BØ. What is flux balance analysis? Nat Biotechnol. 2010;28:245-248. doi: 10.1038/nbt.1614 PMID: 20212490
    • (2010) Nat Biotechnol. , vol.28 , pp. 245-248
    • Orth, J.D.1    Thiele, I.2    Palsson BØ3
  • 14
    • 51349092391 scopus 로고    scopus 로고
    • Network-based prediction of human tissuespecific metabolism
    • 18711341
    • Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. Network-based prediction of human tissuespecific metabolism. Nat Biotechnol. 2008;26:1003-1010. doi: 10.1038/nbt.1487 PMID: 18711341
    • (2008) Nat Biotechnol. , vol.26 , pp. 1003-1010
    • Shlomi, T.1    Cabili, M.N.2    Herrgård, M.J.3    Palsson B.Ø.4    Ruppin, E.5
  • 15
  • 16
    • 84898663879 scopus 로고    scopus 로고
    • Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling
    • 24646661
    • 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. doi: 10.1002/msb.145122 PMID: 24646661
    • (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
  • 17
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: Application to human liver metabolism
    • 20823844
    • Jerby L, Shlomi T, Ruppin E. Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol. 2010;6:401. doi: 10.1038/msb.2010.56 PMID: 20823844
    • (2010) Mol Syst Biol. , vol.6 , pp. 401
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 18
    • 84870933131 scopus 로고    scopus 로고
    • Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
    • 23234303
    • Wang Y, Eddy J A, Price ND. Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst Biol. 2012;6:153. doi: 10.1186/1752-0509-6-153 PMID: 23234303
    • (2012) BMC Syst Biol. , vol.6 , pp. 153
    • Wang, Y.1    Eddy, J.A.2    Price, N.D.3
  • 19
    • 84896701551 scopus 로고    scopus 로고
    • Fast reconstruction of compact context-specific metabolic network models
    • Vlassis N, Pacheco MP, Sauter T. Fast Reconstruction of Compact Context-Specific Metabolic Network Models. PLoS Comput Biol. 2014;10.
    • (2014) PLoS Comput Biol. , pp. 10
    • Vlassis, N.1    Pacheco, M.P.2    Sauter, T.3
  • 20
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    • Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nature Reviews Microbiology. 2012. doi: 10.1038/nrmicro2737
    • (2012) Nature Reviews Microbiology
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.O.3
  • 21
    • 34548275795 scopus 로고    scopus 로고
    • The Dantzig selector: Statistical estimation when p is much larger than n
    • Candes E, Tao T. The Dantzig selector: Statistical estimation when p is much larger than n. Ann Stat. 2007;35:2313-2351. doi: 10.1214/009053606000001523
    • (2007) Ann Stat. , vol.35 , pp. 2313-2351
    • Candes, E.1    Tao, T.2
  • 23
    • 16244401458 scopus 로고    scopus 로고
    • Regularization and variable selection via the elastic net
    • Zou H, Hastie T. Regularization and variable selection via the elastic net. J R Stat Soc Ser B Stat Methodol. 2005;67:301-320. doi: 10.1111/j.1467-9868.2005.00503.x
    • (2005) J R Stat Soc Ser B Stat Methodol. , vol.67 , pp. 301-320
    • Zou, H.1    Hastie, T.2
  • 24
    • 85194972808 scopus 로고
    • Regression Selection and Shrinkage via the Lasso
    • Tibshirani R. Regression Selection and Shrinkage via the Lasso. J R Stat Soc B. 1994;58:267-288.
    • (1994) J R Stat Soc B , vol.58 , pp. 267-288
    • Tibshirani, R.1
  • 26
    • 58349104057 scopus 로고    scopus 로고
    • Least angle and L1 penalized regression: A review
    • Hesterberg T, Choi NH, Meier L, Fraley C. Least Angle and L1 Penalized Regression: A Review. Stat Surv. 2008;2:61-93. doi: 10.1214/08-SS035
    • (2008) Stat Surv. , vol.2 , pp. 61-93
    • Hesterberg, T.1    Choi, N.H.2    Meier, L.3    Fraley, C.4
  • 27
    • 84941305055 scopus 로고    scopus 로고
    • Reconstruction of arbitrary biochemical reaction networks: A compressive sensing approach
    • abs/1205.1:1-15
    • Pan W, Yuan Y, Stan G. Reconstruction of arbitrary biochemical reaction networks: a compressive sensing approach. CoRR. 2012; abs/1205.1:1-15. Available: http://arxiv.org/abs/1205.1720.
    • (2012) CoRR.
    • Pan, W.1    Yuan, Y.2    Stan, G.3
  • 29
    • 80053175304 scopus 로고    scopus 로고
    • TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks
    • 21943338
    • Jensen PA, Lutz KA, Papin JA. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. BMC Systems Biology. 2011. p. 147. doi: 10. 1186/1752-0509-5-147 PMID: 21943338
    • (2011) BMC Systems Biology , pp. 147
    • Jensen, P.A.1    Lutz, K.A.2    Papin, J.A.3
  • 32
    • 33846910173 scopus 로고    scopus 로고
    • Global reconstruction of the human metabolic network based on genomic and bibliomic data
    • 17267599
    • Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A. 2007;104:1777-1782. doi: 10.1073/pnas.0610772104 PMID: 17267599
    • (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
  • 33
    • 79951745716 scopus 로고    scopus 로고
    • IMAT: An integrative metabolic analysis tool
    • 21081510
    • Zur H, Ruppin E, Shlomi T. iMAT: An integrative metabolic analysis tool. Bioinformatics. 2010;26:3140-3142. doi: 10.1093/bioinformatics/btq602 PMID: 21081510
    • (2010) Bioinformatics. , vol.26 , pp. 3140-3142
    • Zur, H.1    Ruppin, E.2    Shlomi, T.3
  • 35
    • 84859740873 scopus 로고    scopus 로고
    • RNA-Seq Atlas -A reference database for gene expression profiling in normal tissue by next-generation sequencing
    • 22345621
    • Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A. RNA-Seq Atlas-a reference database for gene expression profiling in normal tissue by next-generation sequencing. Bioinformatics. 2012;28:1184-1185. doi: 10.1093/bioinformatics/bts084 PMID: 22345621
    • (2012) Bioinformatics. , vol.28 , pp. 1184-1185
    • Krupp, M.1    Marquardt, J.U.2    Sahin, U.3    Galle, P.R.4    Castle, J.5    Teufel, A.6
  • 38
    • 84920269464 scopus 로고    scopus 로고
    • Tissue-based map of the human proteome
    • Uhlén M et al. Tissue-based map of the human proteome. Science (80-). 2015;347. doi: 10.1126/science.1260419
    • (2015) Science , Issue.80 , pp. 347
    • Uhlén, M.1
  • 39
    • 84941305058 scopus 로고    scopus 로고
    • BioMart (Ensembl) [Internet]. Available: http://www.ensembl.org/biomart/martview/2a3c1aa45a4126aa9947f83d577eee2b.
    • BioMart (Ensembl) [Internet]1
  • 40
    • 33144474263 scopus 로고    scopus 로고
    • Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae
    • 16467155
    • Rossell S, Van Der Weijden CC, Lindenbergh A, Van Tuijl A, Francke C, Bakker BM, et al. Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2006;103:2166-2171. doi: 10.1073/pnas.0509831103 PMID: 16467155
    • (2006) Proc Natl Acad Sci U S A. , vol.103 , pp. 2166-2171
    • Rossell, S.1    Van Der Weijden, C.C.2    Lindenbergh, A.3    Van Tuijl, A.4    Francke, C.5    Bakker, B.M.6
  • 41
    • 66149122278 scopus 로고    scopus 로고
    • Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p
    • 19346491
    • Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, et al. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A. 2009;106:6477-6482. doi: 10.1073/pnas.0811091106 PMID: 19346491
    • (2009) Proc Natl Acad Sci U S A. , vol.106 , pp. 6477-6482
    • Moxley, J.F.1    Jewett, M.C.2    Antoniewicz, M.R.3    Villas-Boas, S.G.4    Alper, H.5    Wheeler, R.T.6
  • 42
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genomescale metabolic models
    • 14642354
    • Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genomescale metabolic models. Metab Eng. 2003;5:264-276. PMID: 14642354
    • (2003) Metab Eng. , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 43
    • 34250616386 scopus 로고    scopus 로고
    • Fatty acid metabolism in adipose tissue, muscle and liver in health and disease
    • 17144882
    • Frayn KN, Arner P, Yki-Järvinen H. Fatty acid metabolism in adipose tissue, muscle and liver in health and disease. Essays Biochem. 2006;42:89-103. doi: 10.1042/bse0420089 PMID: 17144882
    • (2006) Essays Biochem. , vol.42 , pp. 89-103
    • Frayn, K.N.1    Arner, P.2    Yki-Järvinen, H.3
  • 44
    • 17444419341 scopus 로고    scopus 로고
    • Role of glutathione transport processes in kidney function
    • Lash LH. Role of glutathione transport processes in kidney function. Toxicology and Applied Pharmacology. 2005. pp. 329-342. doi: 10.1016/j.taap. 2004.10.004
    • (2005) Toxicology and Applied Pharmacology , pp. 329-342
    • Lash, L.H.1


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